go-perl-0.15/000755 000765 000024 00000000000 12156117750 012725 5ustar00cjmstaff000000 000000 go-perl-0.15/Changes000644 000765 000024 00000014367 11615622160 014226 0ustar00cjmstaff000000 000000 2005-01-31 - [cjm] Inititation of Changes file 2005-01-31 - [cjm] changed dependencies in Makefile.PL Data::Stag 0.07 is the only dependency (and as of 0.08, no dependencies for Data::Stag) - [cjm] XML::LibXML now used in place of xsltproc hack - [cjm] Added acc2name_h to base_parser - index can be used for fast ID checking during parsing - [cjm] fixed litemode to report namespace (map2slim no longer complains) - [cjm] fixed prob with go_ont_parser files with '*' as a type code 2005-02-01 - [cjm] map2slim now uses no_duplicates option 2005-02-08 - [cjm] new scripts: go-dag-summary.pl go-filter-subset.pl go-show-paths-to-root.pl 2005-03-14 - [cjm] new parser/handler: obj_storable added caching to parser new script option: -use_cache 2005-03-28 - [cjm] added go-apply-xslt to go-perl/scripts 2005-04-02 - [cjm] obo_text output date is now oboedit compatible 2005-04-16 - [cjm] fixed subtle obo_text_parser bug is_root was not being set if the root term was immediately followed by a Typedef stanza 2005-05-20 - [cjm] allowed unsetting of $term->synonym_list - [cjm] new scripts go-show-assocs-by-node.pl go-apply-xslt 2005-05-25 - [cjm] xslt processing: behaviour unchanged for when GO_ROOT is set; if GO_ROOT is not set, then the install directory (eg %INC{GO/..}) is checked for the xsl directory. This makes things easier for users who wish to use go-perl and the xslts without downloading and installing all of go-dev This affects: go-apply-xslt GO::Parsers::base_parser 2005-06-29 - [cjm] now accepts obo1.2 format synonyms accepts obo1.2 xref tag (maps to xref_analog in xml) VERSION 0.04 ============ 2005-08-18 - [cjm] made no_duplicates(1) default in exporting an ontology to deprecated go_ont format (this was causing problems with cycles) 2005-09-06 - [cjm] incorporate changes to xsl for chadoxml when converting to chadoxml, only use relationship as cv.name if no namespace specified 2005-10-05 - [cjm] obo_text_parser - no longer warns of missing namespace, if it is a header-only obo file owl2obo fixed VERSION 0.05 ============ 2005-12-01 - [cjm] more docs for map2slim. made -b option safe' new convenience methods in Graph and GeneProduct added create_handler to Parser improved POD docs new test t140 2006-02-12 - [cjm] added methods for new obo Typedef tag is_transitive, transitive_over etc 2006-03-29 - [cjm] added GO::Model::LogicalDefinition 2006-04-19 - [cjm] added new test for chadoxml 2006-07-14 - [cjm] support for idspace tag 2006-07-24 - [cjm] support for synonymtypedef tag [cjm] more synonym info from ncbi_taxonomy_parser 2006-08-25 - [cjm] added checks to dbxref parsing 2006-09-11 - [cjm] exports subsetdefs in obo format fixed definition dbxref parsing (was only getting 1 dbxref) 2006-10-18 - [cjm] finalised code for GO::Model::LogicalDefinition added Relationship->complete - [cjm] removed some cruft VERSION 0.06 ============ No code changes in this release; the 0.05 CPAN release erroneously contained out of date copies of the XSL files VERSION 0.07 ============ 2006-11-28 - [cjm] fixed obo export to properly escape {}s 2006-12-06 - [cjm] fixed boolean tags in obo format export ncbi_taxonomy_parser - has_rank is now metadata property 2006-12-12 - [cjm] handles unquoted trailing modifier correctly in obof1.2 2006-12-12 - [cjm] added GO::Model::DB 2007-03-02 - [cjm] Fixed GO::Parsers::go_xref_parser - now handles >1 xref per line 2007-05-13 - [cjm] object model now handles consider and replaced_by tags - [cjm] disjointness and union_of support in object model - [cjm] fixed definition xref parsing with escape characters 2007-07-05 - [cjm] parses secondary taxon IDs (multi-species terms) 2007-07-10 - [cjm] GO::Parsers::obo_text_parser - handles term expresssions (obof1.3) 2007-07-10 - [cjm] GO::Parsers::go_assoc_parser - handles new properties column(16) 2007-08-02 - [cjm] object parser now catches species & assocdate 2007-09-09 - [cjm] GO::Parsers::obo_text_parser - synonymtypedef now uses ID and NAME as sub-elements VERSION 0.08 ============ 2007-01-06 - [cjm] includes modified xslt xref handling for OBO_REL xrefs 2007-01-06 - [cjm] added test for handling of xrefs in OBO_REL 2007-01-17 - [cjm] support for instances 2007-01-22 - [cjm] fixed bug in exporting synonymtypedefs - was not quoting description/name VERSION 0.09 ============ 2007-02-14 - [cjm] add test for disjoint_from 2007-03-14 - [cjm] imports tag followed 2007-06-10 - [cjm] chadoxml only: xref handling of OBO_REL : relationship namespace is used 2007-06-10 - [cjm] shownames option in map2slim VERSION 0.10 ============ VERSION 0.11 ============ 2010-05-18 - [cjm] macro expansion in OWL VERSION 0.12 ============ 2010-05-31 - [hsk] fix: 17 cols for GAF2.0. https://rt.cpan.org/Public/Bug/Display.html?id=57994 2010-05-31 - [hsk] no refs to undefs. https://rt.cpan.org/Ticket/Display.html?id=57997 2010-06-25 - [cjm] latest owl xslt fixes: URI treatment fixed. allow * idspace option. expansion tags VERSION 0.13 ============ 2010-10-10 - [cjm] latest owl xslt fixes for annotation propertiesgo-perl-0.15/create-manifest.sh000755 000765 000024 00000000321 11615622160 016322 0ustar00cjmstaff000000 000000 svn list -R | egrep -v "/$" | sort -u > MANIFEST #cvs status | perl -ne 'print "$1\n" if m@Repository revision.*/cvsroot/geneontology/go\-dev/go\-perl/(.*),v@' > MANIFEST find GO/xsl -name "*.xsl" >> MANIFEST go-perl-0.15/doc/000755 000765 000024 00000000000 12156117750 013472 5ustar00cjmstaff000000 000000 go-perl-0.15/GO/000755 000765 000024 00000000000 12156117750 013232 5ustar00cjmstaff000000 000000 go-perl-0.15/go-perl.pod000644 000765 000024 00000017130 12156117523 014776 0ustar00cjmstaff000000 000000 # $Id: go-perl.pod,v 1.21 2009/08/17 00:46:42 cmungall Exp $ # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself =head1 NAME go-perl - perl modules for GO and other OBO ontologies =head1 SYNOPSIS # ** FETCHING GRAPH OBJECTS FROM AN ONTOLOGY FILE ** use GO::Parser; my $parser = new GO::Parser({handler=>'obj'}); # create parser object $parser->parse("gene_ontology.obo"); # parse file -> objects my $graph = $parser->handler->graph; # get L object my $term = $graph->get_term("GO:0001303"); # fetch a term by ID printf "Got term: %s %s\n", $term->acc, $term->name; my $ancestor_terms = $graph->get_recursive_parent_terms($term->acc); foreach my $anc_term (@$ancestor_terms) { printf " Ancestor term: %s %s\n", $anc_term->acc, $anc_term->name; } # ** FROM THE COMMAND LINE ** (requires go-dev/xml) go2xml gene_ontology.obo | xsltproc $GO_ROOT/xml/xsl/my-transform.xsl - =head1 DESCRIPTION go-perl is part of the go-dev code distribution. It is also available as a seperate library in its own right. go-perl is a collection of perl modules for working with ontologies and data, in particular the Gene Ontology and other Open Bio-Ontologies. For background on these projects, see http://www.geneontology.org http://obo.sourceforge.net go-perl provides the following functionality: =over =item parsers Biological ontologies and associated data come in assorted formats. See: L =item handlers/writers All parsers are XML event based - they emit Obo-XML, which can be caught by different handlers. Some of these handlers effectively transform the parsed file into a different format or summary. If you are not interested in generating XML, you can use an object handler, which will give you objects for traversing an ontology; see below =item a graph-based object model Biological ontologies typically have graph-based structures (DAGs). go-perl provides a perl object model representing ontologies and associations to ontologies. Classes include: L -- a node/term within an ontology L -- collection of terms and the relationships between them L -- a typed relationship between two terms L -- a database xref, for a term or any other object L -- an association between a term and a gene product L -- a gene or product of a gene or similar annotated entity L -- supporting evidence for an association L -- a biological sequence of residues for a gene product =begin html =end html =back =head2 SIMPLE PROGRAMMERS INTERFACE L simple procedural access to GO files =head1 SCRIPTS These scripts come as part of the go-perl distribution =over =item map2slim Given a GO slim file, and a current ontology (in one or more files), this script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim. The script can be used to either create a new gene association file, containing the most pertinent GO slim accessions, or in count-mode, in which case it will give distinct gene product counts for each slim term. for full instructions, see L =item go-dag-summary.pl Generates a summary of the DAG structure of an ontology file A row will be generated for every ontology in the file, with the following data columns: input filename total no of terms total no of relationships total no of paths avg no of paths per term (p/t) maximum no of paths for any term ID of term with maximum no of paths for full instructions, see L =item go-show-paths-to-root.pl Will show all possible paths from a term to the root/top in the ontology for full instructions, see L =item go-apply-xslt Will apply a GO XSL transform (by name) on an OBO-XML file For a full list of XSLs available, see L =item go-export-graph.pl Writes an obo file out as an ascii-tree, a graphviz PNG or other format for full instructions, see L =item go-show-assocs-by-node.pl given a GO ontology file and an association file and a term ID, will list all products associated to that ID for full instructions, see L =item go-filter-subset.pl Exports a subset of an ontology from a file. The subset can be based on a specified set of IDs, a preset "subset" filter in the ontology file (eg a GO "slim" or subset), or a user-defined filter. The subset can be exported in any format, including a graphical image for full instructions, see L =item go2fmt.pl generic file converter. This will convert any go/obo formatted file such as ontology files and association files and write output in some other format or report. See the full list of convenience scripts below. for full instructions, see L =item go2chadoxml converts a file in any valid go/obo format to chadoxml. See also L =item go2godb_prestore converts a file in any valid go/obo format to an xml format that is isomorphic to the GO MySQL Db schema, and can be loaded with L. See also L =item go2error_report converts a file in any valid go/obo format to error_report. See also L =item go2obo_test (alias: go2obo) converts a file in any valid go/obo format to obo. See also L =item go2obo_html converts a file in any valid go/obo format to obo_html. See also L =item go2obo_xml (alias: go2xml) converts a file in any valid go/obo format to obo_xml. See also L =item go2owl converts a file in any valid go/obo format to owl. See also L =item go2pathlist converts a file in any valid go/obo format to pathlist. See also L =item go2prolog converts a file in any valid go/obo format to prolog. See also L =item go2rdfxml converts a file in any valid go/obo format to rdfxml. See also L =item go2summary converts a file in any valid go/obo format to summary. See also L =item go2sxpr converts a file in any valid go/obo format to sxpr. See also L =item go2tbl converts a file in any valid go/obo format to tbl. See also L =item go2text_html converts a file in any valid go/obo format to text_html. See also L =back =head1 RELATED PACKAGES Download the full go-dev distribution for access to more functionality. go-perl is a subset of go-dev go-dev includes the following: =over =item go-perl This package http://www.godatabase.org/dev/go-perl/doc/go-perl-doc.html =item go-db-perl Database API for use in conjunction with go-perl Allows for loading of GO databases and fetching graph objects from the database http://www.godatabase.org/dev/go-db-perl/doc/go-db-perl-doc.html L =item amigo Ontology browser, written in perl Requires installation of both go-perl and go-db-perl =item java The DAG-Edit curation tool http://www.godatabase.org/dev =item xml DTDs for the Obo-XML format, and XSL stylesheets for converting to and from Obo-XML format http://www.godatabase.org/dev/xml/doc/xml-doc.html =item sql Schema and SQL code for the GO database http://www.godatabase.org/dev/sql/doc/godb-sql-doc.html =back =head1 AUTHORS (C) Chris Mungall 2000-2006 This module is free software. You may distribute under the same terms as perl itself. =cut package go-perl; $VERSION='0.15'; 1; go-perl-0.15/INSTALL000644 000765 000024 00000023623 11615622160 013757 0ustar00cjmstaff000000 000000 INSTALL ======= If you have never installed a perl module before, you may want to seek help from a friendly nearby perl programmer or sys admin. The instructions below aren't guaranteed to work on all systems. These instructions are for Linux/Unix and Mac OS X. Other users have installed successfully on PCs before; we are unable to provide installation instruction, but the protocols below may work. You will of course need perl in order to run this; perl5.8 is required (version 5.6.x should also work, but go-perl is no longer tested with this setup) There's a lot of instructions here. There are a number of different ways to set up go-perl; the best way for you depends on your experience of perl and how your system is set up. These ways are described as different protocols below. Hopefully you should only need to follow one protocol to get going! Protocol I - set up via CPAN installer -------------------------------------- If you are already familiar with installing CPAN modules, go-perl is no different from any other. If you aren't, you may wish to experiment now. Try typing the following: ---------- perl -MCPAN -e shell install GO::Parser ---------- The following may also work: ---------- cpan GO::Parser ---------- If this is the first time using the CPAN installer, you will be asked a barrage of questions. You are best to answer with the defaults - you can always change this later. If you do NOT have access to the system-wide perl directories on your system (these will typically be in /Library or /usr/local), then you should either get some help setting up CPAN for use with your system, OR you should follow an alternate protocol below. (You may wish to modify the value of PREFIX to ~ in the CPAN setup, as detailed in protocol III) If you are on OS X you may need to do this: ---------- sudo cpan GO::Parser ---------- Providing you do have write-access to these directories, the above commands should hopefully go smoothly. When installing go-perl, you may be asked if you wish to also install Data::Stag and IO::String - you should answer 'yes' After this, you should be ready to use go-perl! The scripts should be in your path and the libraries should be in the standard place. You may wish to start by trying "map2slim" or "go2obo_xml" There are certain applications that require additional third-party modules. All these are available from CPAN, and can be installed in the above manner. For example, if you try and use the go-filter-subset.pl script to generate a PNG image of an ontology subgraph, the system will complain you do not have the module "GraphViz" installed. To install this, simply type: ---------- perl -MCPAN -e shell install GraphViz ---------- Depending on what you use go-perl for, you may not ever need to install other CPAN modules Protocol II - Manual installation --------------------------------- these are step-by-step manual installation instructions. These should be followed if protocol I does not work for you Installing required modules ~~~~~~~~~~~~~~~~~~~~~~~~~~~ go-perl requires the Data::Stag module in order to run. You can download this module from here: http://search.cpan.org/~cmungall/Data-Stag/ (version 0.07 or higher is required; these docs assume you have downloaded 0.08) Data::Stag in turn requires the following module: http://search.cpan.org/~gaas/IO-String/ After downloading, type the following instructions to install IO-String: ---------- cd ~ tar -zxvf IO-String-1.06 cd IO-String-1.06 perl Makefile.PL make test ---------- If you have permission to install system-wide, you should then type: ---------- make install ---------- On Mac OS X, you may need to type ---------- sudo make install ---------- If you do not have permission to install perl modules in the default directory on your system, you need to follow protocol III Once you have installed IO::String, you can install Data::Stag - the directions are the same: ---------- cd ~ tar -zxvf Data-Stag-0.08.tar.gz cd Data-Stag-0.08 perl Makefile.PL make test make install ---------- Once you have installed Data::Stag, you are now ready to install go-perl NOTE: There are certain applications that require additional third-party modules (all available from CPAN); if you run into problems running any of these applications, see the section "Additional Modules" below Installing go-perl ~~~~~~~~~~~~~~~~~~ If you are reading this, then presumably you have unpacked the distribution - either the go-perl distribution, or the go-dev distribution that contains go-perl. To install the modules system wide, type this: ---------------- cd go-perl-0.02 perl Makefile.PL make test make install ---------------- The first command may tell you that you have certain optional modules missing - these may not be required. If you do require them, see "Additional Modules" below If the system complains when you type "make install" you may not have sufficient permissions. In this case you need to use the modules from your home directory Additional Modules ~~~~~~~~~~~~~~~~~~ You may need additional modules for running certain scripts in certain modes. You can obtain all these from this website: http://www.cpan.org/ Protocol III - installing modules in your home directory ------------------------------------------------------- If you do not have sufficient permission to install system-wide, there is a third method you can try, which is to install IO::String, Data::Stag and go-perl in your home directory. To do this, you need to set the PREFIX variable when installing. First download Data::Stag and IO::String from CPAN, as detailed in protocol II. Then try this: ---------- setenv PERL5LIB "${PERL5LIB}:$HOME/lib/perl5/site_perl/5.8.0/ cd ~ tar -zxvf IO-String-1.06 cd IO-String-1.06 perl Makefile.PL PREFIX=~ make test make install cd ~ tar -zxvf Data-Stag-0.08.tar.gz cd Data-Stag-0.08 perl Makefile.PL PREFIX=~ make test make install make install cd cd go-perl-0.02 perl Makefile.PL PREFIX=~ make test make install ---------- If this works, then place this in your startup file: ---------- setenv PERL5LIB "${PERL5LIB}:$HOME/lib/perl5/site_perl/5.8.0/ setenv PATH "${PATH}:$HOME/bin" ---------- You may need to modify the above, depending on your setup. Instructions for this are outwith the scope of this document. Try consulting online sources, such as: http://www.perl.com/pub/a/2002/04/10/mod_perl.html Additional Modules ------------------ Certain applications (for example, those involving XML parsing) will require additional modules from CPAN. If you are going on to install go-db-perl and/or AmiGO you will probably need a few extra modules. If this is the case, you are strongly advised to use the CPAN auto-installer. Once you have set this up, installing perl modules will be *much* easier. To use this, type: -------------------- perl -MCPAN -e shell -------------------- Then follow the setup instructions Then type: -------------------- install <> quit -------------------- You can use the CPAN installer to install go-perl itself; just type -------------------- perl -MCPAN -e shell install go-perl -------------------- This is the easiest way of keeping up to date with go-perl releases Using go-perl as part of go-dev ------------------------------- go-perl is part of the wider go-dev distribution, although it can be used independently. go-dev also includes go-db-perl (for GO MySQL DB access) and an xml library (for converting to other XML based formats such as OWL), the AmiGO web application and the schema for the GO MySQL db If you are using all of go-dev, you may need to alter the instructions above (for example, your go-perl library may be unpacked in ~/go-dev/go-perl). You may also need to set GO_ROOT: The GO_ROOT environment variable ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ If you are using go-perl as part of the wider go-dev distribution, there are some applications that require you to specify the location of go-dev using the GO_ROOT env var bash shells: ---------- export GO_ROOT=$HOME/go-dev ---------- other shells: ---------- setenv GO_ROOT $HOME/go-dev ---------- It is a good idea to put this in your startup file Installing from CVS ------------------- You can get the latest bleeding-edge version of go-perl from the go-dev cvs tree. See http://www.godatabase.org/dev for details Once you have checked out go-dev/go-perl, do the usual thing (if you're installing from cvs it's assumed you're a bleeding edge user and know how to do this): cd ~/cvs/go-dev/go-perl perl Makefile.PL make test setenv GO_ROOT ~/cvs/go-dev setenv PERL5LIB "$PERL5LIB:~/cvs/go-dev/go-perl" The assumption is that if you are using cvs you want to use the working copy; if you want to install from cvs, instead do the following steps: cd go-dev/go-perl perl Makefile.PL make GO/xsl make test make install The "make GO/xsl" stage is not strictly necessary; if you omit it you will get warnings. You can ignore these, but if you ever want to use the XSL you will need to check out go-dev/xml and set the GO_ROOT environment variaable as above. Note that none of this is necessary if you install from CPAN - the installation of the XSL is taken care of automatically Documentation ------------- For full documentation, see the doc/ directory, or look online http://www.godatabase.org/dev Mailing List ------------ http://lists.sourceforge.net/lists/listinfo/gmod-ontol-sw-dev Installing Documentation Locally -------------------------------- it's unlikely you'll need to do this: you can always browse the pod documentation online at: http://www.godatabase.org/dev/pod The documentation can be installed in a web-viewable directory; this is best done in a directory that is visible as $BASE_URL/dev/pod Just type ---------- cd go-perl perl Makefile.PL make pod cp -pR pod/* $HTTP_DOCUMENT_ROOT/dev/pod ---------- substituting HTTP_DOCUMENT_ROOT with the root path of the WWW documents on your webserver You can now browse the documentation: http://www.yourhost.com/dev/pod (You may also wish to copy the whole go-dev distribution under the /dev/ directory) go-perl-0.15/INSTALL.html000644 000765 000024 00000041440 11615622160 014717 0ustar00cjmstaff000000 000000 INSTALL

If you have never installed a perl module before, you may want to seek help from a friendly nearby perl programmer or sys admin. The instructions below aren't guaranteed to work on all systems. These instructions are for Linux/Unix and Mac OS X. Other users have installed successfully on PCs before; we are unable to provide installation instruction, but the protocols below may work.

You will of course need perl in order to run this; perl5.8 is required (version 5.6.x should also work, but go-perl is no longer tested with this setup)

There's a lot of instructions here. There are a number of different ways to set up go-perl; the best way for you depends on your experience of perl and how your system is set up. These ways are described as different protocols below. Hopefully you should only need to follow one protocol to get going!

Protocol I - set up via CPAN installer

If you are already familiar with installing CPAN modules, go-perl is no different from any other. If you aren't, you may wish to experiment now.

Try typing the following:

perl -MCPAN -e shell
install GO::Parser

The following may also work:

cpan GO::Parser

If this is the first time using the CPAN installer, you will be asked a barrage of questions. You are best to answer with the defaults - you can always change this later.

If you do NOT have access to the system-wide perl directories on your system (these will typically be in /Library or /usr/local), then you should either get some help setting up CPAN for use with your system, OR you should follow an alternate protocol below. (You may wish to modify the value of PREFIX to ~ in the CPAN setup, as detailed in protocol III)

If you are on OS X you may need to do this:

sudo cpan GO::Parser

Providing you do have write-access to these directories, the above commands should hopefully go smoothly. When installing go-perl, you may be asked if you wish to also install Data::Stag and IO::String - you should answer yes

After this, you should be ready to use go-perl! The scripts should be in your path and the libraries should be in the standard place. You may wish to start by trying "map2slim" or "go2obo_xml"

There are certain applications that require additional third-party modules. All these are available from CPAN, and can be installed in the above manner. For example, if you try and use the go-filter-subset.pl script to generate a PNG image of an ontology subgraph, the system will complain you do not have the module "GraphViz" installed. To install this, simply type:

perl -MCPAN -e shell
install GraphViz

Depending on what you use go-perl for, you may not ever need to install other CPAN modules

Protocol II - Manual installation

these are step-by-step manual installation instructions. These should be followed if protocol I does not work for you

Installing required modules

go-perl requires the Data::Stag module in order to run. You can download this module from here:

http://search.cpan.org/~cmungall/Data-Stag/

(version 0.07 or higher is required; these docs assume you have downloaded 0.08)

Data::Stag in turn requires the following module:

http://search.cpan.org/~gaas/IO-String/

After downloading, type the following instructions to install IO-String:

cd ~
tar -zxvf IO-String-1.06
cd IO-String-1.06
perl Makefile.PL
make test

If you have permission to install system-wide, you should then type:

make install

On Mac OS X, you may need to type

sudo make install

If you do not have permission to install perl modules in the default directory on your system, you need to follow protocol III

Once you have installed IO::String, you can install Data::Stag - the directions are the same:

cd ~
tar -zxvf Data-Stag-0.08.tar.gz
cd Data-Stag-0.08
perl Makefile.PL
make test
make install

Once you have installed Data::Stag, you are now ready to install go-perl

Note
 There are certain applications that require additional third-party modules (all available from CPAN); if you run into problems running any of these applications, see the section "Additional Modules" below

Installing go-perl

If you are reading this, then presumably you have unpacked the distribution - either the go-perl distribution, or the go-dev distribution that contains go-perl.

To install the modules system wide, type this:

cd go-perl-0.02
perl Makefile.PL
make test
make install

The first command may tell you that you have certain optional modules missing - these may not be required. If you do require them, see "Additional Modules" below

If the system complains when you type "make install" you may not have sufficient permissions. In this case you need to use the modules from your home directory

Additional Modules

You may need additional modules for running certain scripts in certain modes. You can obtain all these from this website:

http://www.cpan.org/

Protocol III - installing modules in your home directory

If you do not have sufficient permission to install system-wide, there is a third method you can try, which is to install IO::String, Data::Stag and go-perl in your home directory. To do this, you need to set the PREFIX variable when installing.

First download Data::Stag and IO::String from CPAN, as detailed in protocol II.

Then try this:

setenv PERL5LIB "${PERL5LIB}:$HOME/lib/perl5/site_perl/5.8.0/
cd ~
tar -zxvf IO-String-1.06
cd IO-String-1.06
perl Makefile.PL PREFIX=~
make test
make install
cd ~
tar -zxvf Data-Stag-0.08.tar.gz
cd Data-Stag-0.08
perl Makefile.PL PREFIX=~
make test
make install
make install
cd
cd go-perl-0.02
perl Makefile.PL PREFIX=~
make test
make install

If this works, then place this in your startup file:

setenv PERL5LIB "${PERL5LIB}:$HOME/lib/perl5/site_perl/5.8.0/
setenv PATH "${PATH}:$HOME/bin"

You may need to modify the above, depending on your setup. Instructions for this are outwith the scope of this document. Try consulting online sources, such as:

http://www.perl.com/pub/a/2002/04/10/mod_perl.html

Additional Modules

Certain applications (for example, those involving XML parsing) will require additional modules from CPAN. If you are going on to install go-db-perl and/or AmiGO you will probably need a few extra modules.

If this is the case, you are strongly advised to use the CPAN auto-installer. Once you have set this up, installing perl modules will be much easier.

To use this, type:

perl -MCPAN -e shell

Then follow the setup instructions

Then type:

install <<Module name here>>
quit

You can use the CPAN installer to install go-perl itself; just type

perl -MCPAN -e shell
install go-perl

This is the easiest way of keeping up to date with go-perl releases

Using go-perl as part of go-dev

go-perl is part of the wider go-dev distribution, although it can be used independently. go-dev also includes go-db-perl (for GO MySQL DB access) and an xml library (for converting to other XML based formats such as OWL), the AmiGO web application and the schema for the GO MySQL db

If you are using all of go-dev, you may need to alter the instructions above (for example, your go-perl library may be unpacked in ~/go-dev/go-perl). You may also need to set GO_ROOT:

The GO_ROOT environment variable

If you are using go-perl as part of the wider go-dev distribution, there are some applications that require you to specify the location of go-dev using the GO_ROOT env var

bash shells:

export GO_ROOT=$HOME/go-dev

other shells:

setenv GO_ROOT $HOME/go-dev

It is a good idea to put this in your startup file

Installing from CVS

You can get the latest bleeding-edge version of go-perl from the go-dev cvs tree. See http://www.godatabase.org/dev for details

Once you have checked out go-dev/go-perl, do the usual thing (if you're installing from cvs it's assumed you're a bleeding edge user and know how to do this):

cd /cvs/go-dev/go-perl perl Makefile.PL make test setenv GO_ROOT /cvs/go-dev setenv PERL5LIB "$PERL5LIB:~/cvs/go-dev/go-perl"

The assumption is that if you are using cvs you want to use the working copy; if you want to install from cvs, instead do the following steps:

cd go-dev/go-perl perl Makefile.PL make GO/xsl make test make install

The "make GO/xsl" stage is not strictly necessary; if you omit it you will get warnings. You can ignore these, but if you ever want to use the XSL you will need to check out go-dev/xml and set the GO_ROOT environment variaable as above.

Note that none of this is necessary if you install from CPAN - the installation of the XSL is taken care of automatically

Documentation

For full documentation, see the doc/ directory, or look online

http://www.godatabase.org/dev

Mailing List

http://lists.sourceforge.net/lists/listinfo/gmod-ontol-sw-dev

Installing Documentation Locally

it's unlikely you'll need to do this: you can always browse the pod documentation online at:

http://www.godatabase.org/dev/pod

The documentation can be installed in a web-viewable directory; this is best done in a directory that is visible as $BASE_URL/dev/pod

Just type

cd go-perl
perl Makefile.PL
make pod
cp -pR pod/* $HTTP_DOCUMENT_ROOT/dev/pod

substituting HTTP_DOCUMENT_ROOT with the root path of the WWW documents on your webserver

You can now browse the documentation: http://www.yourhost.com/dev/pod

(You may also wish to copy the whole go-dev distribution under the /dev/ directory)

go-perl-0.15/Makefile.PL000644 000765 000024 00000012144 12156117444 014701 0ustar00cjmstaff000000 000000 # $id$ use ExtUtils::MakeMaker; require 5.6.0; #use Config; if (system("which xsltproc > /dev/null")) { print < "GO", 'DISTNAME' => "go-perl", 'ABSTRACT' => 'GO Perl', 'AUTHOR' => 'Chris Mungall ', 'VERSION_FROM' => "go-perl.pod", 'PREREQ_PM' => { 'Data::Stag' => "0.07", 'Data::Dumper' => 0, }, # PL_FILES => { 'doc/makedoc.PL' => ['bioscripts.pod','biodatabases.pod','biodesign.pod','bioperl.pod'] }, 'EXE_FILES' => [ qw( scripts/go-apply-xslt scripts/go-dag-summary.pl scripts/go-show-assocs-by-node.pl scripts/go-show-paths-to-root.pl scripts/go-filter-subset.pl scripts/go-export-graph.pl scripts/go-export-prolog.pl scripts/go2chadoxml scripts/go2error_report scripts/go2fmt.pl scripts/go2godb_prestore scripts/go2obo scripts/go2obo_html scripts/go2obo_text scripts/go2obo_xml scripts/go2owl scripts/go2pathlist scripts/go2prolog scripts/go2rdf scripts/go2rdfxml scripts/go2summary scripts/go2sxpr scripts/go2tbl scripts/go2text_html scripts/go2xml scripts/map2slim ) ], 'dist' => { 'SUFFIX' => ".gz", 'DIST_DEFAULT' => 'all tardist', 'COMPRESS' => "gzip -9f" }, clean => { FILES => 'go-perl-$(VERSION).tar.gz', }, ); sub MY::postamble { qq{ pod :: \ go-perl-make-pod-html.pl < MANIFEST pod.tar.gz :: pod\ tar cvf pod.tar pod && gzip pod.tar # INSTALL .xsl FILES AS PERL MODULES # this is only required by the go-perl developer to make # a go-perl dist that includes the XSLs # directory for source XSLs; this only makes sense if go-perl # is a subdir of go-dev #XSL_SRC_DIR = ../xml/xsl XSL_SRC_DIR = xsl # xsls which go-perl can use XSL = chadoxml_to_oboxml oboxml_filter oboxml_to_chadoxml oboxml_to_dig oboxml_to_godb_prestore oboxml_to_obotext oboxml_to_owl oboxml_to_simple_owl oboxml_to_racer owl_to_oboxml oboxml_to_summary_table ipr_to_oboxml oboxml_to_obd_prestore text_html XSL_FILES = \$(patsubst %,\$(XSL_SRC_DIR)/%.xsl,\$(XSL)) # this dir should always be made before a distribution; the end-user # installer never needs to build this, their distribution will come # with these files. When a 'make install' is performed, the xsls will # go in the location where perl modules usually go. # we re-run 'make' at the end of this to rebuild TO_INST_PM in Makefile GO/xsl :: \$(XSL_FILES) (test -d GO/xsl || mkdir GO/xsl) && cp \$(XSL_FILES) GO/xsl && make }; } go-perl-0.15/MANIFEST000644 000765 000024 00000011125 12156117750 014056 0ustar00cjmstaff000000 000000 Changes GO/Basic.pm GO/Handlers/abstract_prolog_writer.pm GO/Handlers/abstract_sql_writer.pm GO/Handlers/base.pm GO/Handlers/go_def.pm GO/Handlers/go_ont.pm GO/Handlers/go_xref.pm GO/Handlers/godb_prestore.pm GO/Handlers/lexanalysis.pm GO/Handlers/lexanalysis2sql.pm GO/Handlers/obj.pm GO/Handlers/obj_storable.pm GO/Handlers/obj_yaml.pm GO/Handlers/obo.pm GO/Handlers/obo_godb_flat.pm GO/Handlers/obo_html.pm GO/Handlers/obo_sxpr.pm GO/Handlers/obo_text.pm GO/Handlers/obo_xml.pm GO/Handlers/owl.pm GO/Handlers/owl_to_obo_text.pm GO/Handlers/pathlist.pm GO/Handlers/prolog.pm GO/Handlers/rdf.pm GO/Handlers/summary.pm GO/Handlers/sxpr.pm GO/Handlers/tbl.pm GO/Handlers/text_html.pm GO/Handlers/xml.pm GO/Handlers/xsl_base.pm GO/IO/Analysis.pm GO/IO/Blast.pm GO/IO/Dotty.pm GO/IO/OBDXML.pm GO/IO/ObanOwl.pm GO/IO/RDFXML.pm GO/IO/XML.pm GO/IO/go_assoc.pm GO/Metadata/Panther.pm GO/Model/Association.pm GO/Model/CrossProduct.pm GO/Model/DB.pm GO/Model/Evidence.pm GO/Model/GeneProduct.pm GO/Model/Graph.pm GO/Model/GraphIterator.pm GO/Model/GraphNodeInstance.pm GO/Model/LogicalDefinition.pm GO/Model/Modification.pm GO/Model/Ontology.pm GO/Model/Path.pm GO/Model/Property.pm GO/Model/Relationship.pm GO/Model/Restriction.pm GO/Model/Root.pm GO/Model/Seq.pm GO/Model/Species.pm GO/Model/Term.pm GO/Model/TreeIterator.pm GO/Model/Xref.pm GO/ObjCache.pm GO/ObjFactory.pm GO/Parser.pm GO/Parsers/ParserEventNames.pm GO/Parsers/base_parser.pm GO/Parsers/generic_tagval_parser.pm GO/Parsers/go_assoc_parser.pm GO/Parsers/go_def_parser.pm GO/Parsers/go_ids_parser.pm GO/Parsers/go_ont_parser.pm GO/Parsers/go_xref_parser.pm GO/Parsers/locuslink_parser.pm GO/Parsers/mesh_parser.pm GO/Parsers/mgi_assoc_parser.pm GO/Parsers/ncbi_taxon_names_parser.pm GO/Parsers/ncbi_taxonomy_parser.pm GO/Parsers/obj_emitter.pm GO/Parsers/obj_storable_parser.pm GO/Parsers/obj_yaml_parser.pm GO/Parsers/obo_parser.pm GO/Parsers/obo_text_parser.pm GO/Parsers/obo_xml_parser.pm GO/Parsers/owl_parser.pm GO/Parsers/references_parser.pm GO/Parsers/refgenomes_parser.pm GO/Parsers/unknown_format_parser.pm GO/Parsers/xrf_abbs_parser.pm GO/Utils.pm INSTALL INSTALL.html MANIFEST Makefile.PL README create-manifest.sh doc/go-perl-doc.html doc/go-perl-event-handling.html doc/gomodel.dia doc/gomodel.png doc/map2slim.gif doc/stylesheet.css go-perl.pod scripts/go-apply-xslt scripts/go-dag-summary.pl scripts/go-export-graph.pl scripts/go-export-prolog.pl scripts/go-filter-subset.pl scripts/go-make-slim.pl scripts/go-perl-make-pod-html.pl scripts/go-show-assocs-by-node.pl scripts/go-show-paths-to-root.pl scripts/go-validate-xml scripts/go2chadoxml scripts/go2error_report scripts/go2fmt.pl scripts/go2godb_prestore scripts/go2obo scripts/go2obo_html scripts/go2obo_text scripts/go2obo_xml scripts/go2owl scripts/go2owl_simple scripts/go2pathlist scripts/go2prolog scripts/go2racer scripts/go2rdf scripts/go2rdfxml scripts/go2summary scripts/go2sxpr scripts/go2tbl scripts/go2text_html scripts/go2xml scripts/ipr2obo scripts/ipr2obo_xml scripts/map2slim t/data/GO.defs t/data/bad-dbxref.obo t/data/gene_association.test_properties t/data/generic.0208 t/data/go-truncated.obo t/data/go-with-local-id-mapping.obo t/data/impliedlinks.obo t/data/llm.obo t/data/llm2.obo t/data/mged.obo t/data/process.ontology t/data/regulation_of_somitogenesis.obo t/data/regulation_test.obo t/data/relationship.obo t/data/sample.ncbi_taxonomy t/data/spkw2go t/data/systematic_synonym_test.obo t/data/test-enrichment-genes.txt t/data/test-function.dat t/data/test-gene_association.fb t/data/test-go.obo t/data/test-nucleolar.obo t/data/test2.ontology t/data/test_bad_function.dat t/data/xref_encoding_test.obo t/t010build.t t/t020paths.t t/t030detecterror.t t/t050oboformat.t t/t060oboformat2.t t/t070parseannot2obj.t t/t080gofmt2.t t/t100roundtrip.t t/t110basic.t t/t120rt.sh t/t130relations.t t/t140subgraph.t t/t150xref.t t/t160logicaldef.t t/t170chadoxml.t t/t175chadoxml_oborel.t t/t180ncbi_taxonomy.t t/t200impliedlinks.t t/t210cache.t t/t220xref_esc.t t/t230term_expression.t t/t240ga2obj.t t/t260oborel_in_chado.t t/t270oborel_in_owl.t t/t290disjoint.t t/validate_all.x GO/xsl/chadoxml_to_oboxml.xsl GO/xsl/ipr_to_oboxml.xsl GO/xsl/oboxml_filter.xsl GO/xsl/oboxml_to_chadoxml.xsl GO/xsl/oboxml_to_dig.xsl GO/xsl/oboxml_to_godb_prestore.xsl GO/xsl/oboxml_to_obd_prestore.xsl GO/xsl/oboxml_to_obotext.xsl GO/xsl/oboxml_to_owl.xsl GO/xsl/oboxml_to_racer.xsl GO/xsl/oboxml_to_simple_owl.xsl GO/xsl/oboxml_to_summary_table.xsl GO/xsl/owl_to_oboxml.xsl GO/xsl/text_html.xsl META.yml Module YAML meta-data (added by MakeMaker) META.json Module JSON meta-data (added by MakeMaker) go-perl-0.15/META.json000644 000765 000024 00000001570 12156117750 014351 0ustar00cjmstaff000000 000000 { "abstract" : "GO Perl", "author" : [ "Chris Mungall " ], "dynamic_config" : 1, "generated_by" : "ExtUtils::MakeMaker version 6.62, CPAN::Meta::Converter version 2.120921", "license" : [ "unknown" ], "meta-spec" : { "url" : "http://search.cpan.org/perldoc?CPAN::Meta::Spec", "version" : "2" }, "name" : "go-perl", "no_index" : { "directory" : [ "t", "inc" ] }, "prereqs" : { "build" : { "requires" : { "ExtUtils::MakeMaker" : "0" } }, "configure" : { "requires" : { "ExtUtils::MakeMaker" : "0" } }, "runtime" : { "requires" : { "Data::Dumper" : "0", "Data::Stag" : "0.07" } } }, "release_status" : "stable", "version" : "0.15" } go-perl-0.15/META.yml000644 000765 000024 00000000746 12156117750 014205 0ustar00cjmstaff000000 000000 --- abstract: 'GO Perl' author: - 'Chris Mungall ' build_requires: ExtUtils::MakeMaker: 0 configure_requires: ExtUtils::MakeMaker: 0 dynamic_config: 1 generated_by: 'ExtUtils::MakeMaker version 6.62, CPAN::Meta::Converter version 2.120921' license: unknown meta-spec: url: http://module-build.sourceforge.net/META-spec-v1.4.html version: 1.4 name: go-perl no_index: directory: - t - inc requires: Data::Dumper: 0 Data::Stag: 0.07 version: 0.15 go-perl-0.15/README000644 000765 000024 00000001000 11615622160 013567 0ustar00cjmstaff000000 000000 go-perl modules =============== This is a collection of perl code for dealing with GO and OBO style ontologies. It is part of the go-dev distribution, but can be used independently. The code contains both scripts (which can be used with no knowledge of perl), and libraries which will be of use to perl programmers using GO or OBO. See the doc/ directory for more documentation See also perldoc go-perl.pod Or look online http://www.godatabase.org/dev see the file INSTALL for installation instructions go-perl-0.15/scripts/000755 000765 000024 00000000000 12156117750 014414 5ustar00cjmstaff000000 000000 go-perl-0.15/t/000755 000765 000024 00000000000 12156117750 013170 5ustar00cjmstaff000000 000000 go-perl-0.15/t/data/000755 000765 000024 00000000000 12156117750 014101 5ustar00cjmstaff000000 000000 go-perl-0.15/t/t010build.t000644 000765 000024 00000002045 11615622157 015063 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; BEGIN { eval { require Test; }; use Test; plan tests => 6; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; use GO::ObjCache; # ----- REQUIREMENTS ----- # This test script tests the following requirements:/x # GO::Model::Graph must implement the GO::Builder interface; ie # it should be possible to pass in a graph to a parser and have it build # up a graph object # ------------------------ my $parser = new GO::Parser ({format=>'go_ont', handler=>'obj'}); my $graph = $parser->handler->g; ok(1); $parser->parse ("./t/data/test-function.dat"); ok($parser->acc2name_h->{'GO:0003677'} = 'DNA binding'); # lets check we got stuff #print $graph->dump; my $t = $graph->get_term("GO:0003677"); ok($t); ok(1); $t->add_synonym_by_type(foo=>"abc"); $t->add_synonym_by_type(foo=>"def"); $t->add_synonym_by_type(goo=>"xyz"); ok(scalar(@{$t->synonym_list}),3); $t->synonym_list([]); ok(scalar(@{$t->synonym_list}),0); go-perl-0.15/t/t020paths.t000644 000765 000024 00000003261 11615622157 015105 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w # All tests must be run from the software directory; # make sure we are getting the modules from here: use lib '.'; BEGIN { eval { require Test; }; use Test; plan tests => 7; } use strict; use GO::Model::Graph; # ----- REQUIREMENTS ----- # A graph object must be able to trace multiple paths to the root, if # there exists > 1path # Graphs should deal with redundant info gracefully # It should be possible to iterate from a root of the graph to the leaf nodes, # tracing multiple paths if required # ------------------------ my $graph = GO::Model::Graph->new; ok(1); map { $graph->add_term({acc=>$_}); } qw (1 2 3 4 5 6); $graph->add_relationship(1, 2); $graph->add_relationship(1, 3); #$graph->add_relationship(2, 4); # add_relationship can be used in two ways with identical reuslts; # let's checkboth $graph->add_relationship({acc1=>2, acc2=>4}); $graph->add_relationship(3, 4); $graph->add_relationship(4, 5); # lets check we got stuff my $pl; $pl = $graph->paths_to_top(5); #map {stmt_note("path length = ".$_->length."\n")} @$pl; ok(@$pl == 2); # $graph->add_relationship(4, 5); $pl = $graph->paths_to_top(5); #map {stmt_note("path length = ".$_->length."\n")} @$pl; ok(@$pl == 2); # my $tl; $tl = $graph->get_parent_terms(4); ok(@$tl == 2); $tl = $graph->get_child_terms(1); ok(@$tl == 2); # traverse my $n = 0; my @nodes = (1); while (@nodes) { $n++; my $node = shift @nodes; my @children= map {$_->{acc}} @{$graph->get_child_terms($node)}; # stmt_note("node:$node has ".join(";",@children)." children\n"); push(@nodes, map {$_->{acc}} @{$graph->get_child_terms($node)}); } # some paths should have been traversed twice ok($n == 7); ok(1); go-perl-0.15/t/t030detecterror.t000644 000765 000024 00000001422 11615622157 016306 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w # All tests must be run from the software directory; # make sure we are getting the modules from here: use lib '.'; BEGIN { eval { require Test; }; use Test; plan tests => 4; } use strict; use GO::Parser; # ----- REQUIREMENTS ----- # This test script tests the following requirements: # mistakes in the GO files must be passed to the # errhandler # ------------------------ ok(1); my $parser = new GO::Parser ({format=>'go_ont'}); ok(1); $parser->cache_errors; $parser->parse ("./t/data/test_bad_function.dat"); my @errs = $parser->errlist; print $_->sxpr foreach @errs; ok(@errs == 2); $parser->parse ("./t/data/test_bad_function.dat"); @errs = $parser->errlist; print $_->sxpr foreach @errs; # lets check we got stuff ok(@errs == 2); go-perl-0.15/t/t050oboformat.t000644 000765 000024 00000002453 11615622157 015763 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; BEGIN { eval { require Test; }; use Test; plan tests => 6; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; # ----- REQUIREMENTS ----- # This test script tests the following requirements:/x # GO::Model::Graph must implement the GO::Builder interface; ie # it should be possible to pass in a graph to a parser and have it build # up a graph object # ------------------------ my $parser = new GO::Parser ({format=>'obo_text', handler=>'obj'}); ok(1); $parser->parse (shift @ARGV || "./t/data/test-go.obo"); ok(1); my $graph = $parser->handler->g; my $terms = $graph->find_roots; foreach my $term (@$terms) { printf "ROOT: %s\n", $term->name; } ok(@$terms == 3); $terms = $graph->get_all_nodes; my $t = 0; my $t2 = 0; ok(@$terms == 97); foreach my $term (@$terms) { my $rels = $graph->get_relationships($term->acc); $t2 += @$rels; $t+= @{$graph->get_parent_relationships($term->acc)}; foreach my $rel (@$rels) { printf "EDGE|%s|%s|%s\n", $rel->subject_acc, $rel->object_acc, $rel->type; } } printf "total parent rels:%s\n", $t; printf "total (both ways):%s\n", $t2; ok($t == 118); ok($t2 == 218); # trailing rels counted only once go-perl-0.15/t/t060oboformat2.t000644 000765 000024 00000007310 11615622157 016043 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; use constant NUMTESTS => 12*3; BEGIN { eval { require Test; }; use Test; plan tests => NUMTESTS; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; eval { require "XML/Parser/PerlSAX.pm"; }; if ($@) { for (1..NUMTESTS) { skip("XML::Parser::PerlSAX not installed",1); } exit 0; } # ----- REQUIREMENTS ----- # make sure synonums etc are parsed # ------------------------ my $f = shift @ARGV || "./t/data/go-truncated.obo"; check_file($f); $f = cvt($f, 'obo_text', 'obo_xml'); check_file($f); $f = cvt($f, 'obo_xml', 'obo_text'); check_file($f); exit 0; sub check_file { my $f = shift; my $parser = new GO::Parser ({ # format=>'obo_text', handler=>'obj'}); $parser->handler->add_root; ok(1); print "Parsing: $f\n"; $parser->parse ($f); ok(1); my $graph = $parser->handler->g; my $terms = $graph->find_roots; foreach my $term (@$terms) { printf "ROOT: %s\n", $term->name; } $terms = $graph->get_all_nodes; my $t = 0; my $t2 = 0; my $n_obs = 0; my $n_syns = 0; my $n_exact_syns = 0; my $n_alt_ids = 0; my $n_xrefs = 0; my $n_def_xrefs = 0; my $n_defs = 0; my $n_comments = 0; printf "TERMS: %d\n", scalar(@$terms); #ok(@$terms == 97); foreach my $term (@$terms) { my $syns = $term->synonym_list || []; if (@$syns) { printf "SYNS:%s\n", join('|',@$syns); $n_syns += @$syns; } my $exact_syns = $term->synonyms_by_type('exact') || []; if (@$exact_syns) { printf "EXACT SYNS:%s\n", join('|',@$exact_syns); $n_exact_syns += @$exact_syns; } $n_alt_ids += @{$term->alt_id_list}; my $xrefs = $term->dbxref_list || []; if (@$xrefs) { printf "XREFS:%s\n", join('|',map {$_->as_str} @$xrefs); $n_xrefs += @$xrefs; } my $comment = $term->comment; if ($comment) { printf "COMMENT:%s\n", $comment; $n_comments++; } my $def = $term->definition; if ($def) { my $xrefs = $term->definition_dbxref_list; printf "DEFXREFS:%s\n", join('|', map {$_->as_str} @$xrefs); $n_def_xrefs += @$xrefs; $n_defs++; } $n_obs ++ if $term->is_obsolete; my $rels = $graph->get_relationships($term->acc); $t2 += @$rels; $t+= @{$graph->get_parent_relationships($term->acc)}; foreach my $rel (@$rels) { printf "EDGE|%s|%s|%s\n", $rel->subject_acc, $rel->object_acc, $rel->type; } } printf "total defs:%s\n", $n_defs; printf "total def xrefs:%s\n", $n_def_xrefs; printf "total xrefs:%s\n", $n_xrefs; printf "total comments:%s\n", $n_comments; printf "total syns:%s\n", $n_syns; printf "total EXACT syns:%s\n", $n_exact_syns; printf "total obs:%s\n", $n_obs; printf "total parent rels:%s\n", $t; printf "total (both ways):%s\n", $t2; ok($n_defs, 27); ok($n_xrefs, 2); ok($n_def_xrefs, 42); ok($n_comments, 2); ok($n_syns, 12); ok($n_exact_syns, 1); ok($n_obs, 1); ok($n_alt_ids, 1); ok($t, 37); ok($t2, 64); # trailing rels counted only once } sub cvt { my $f = shift; my ($from, $to) = @_; print "$f from:$from to:$to\n"; my $parser = new GO::Parser ({format=>$from, handler=>$to}); my $outf = "$f.$to"; unlink $outf if -f $outf; $parser->handler->file($outf); $parser->parse($f); return $outf; } go-perl-0.15/t/t070parseannot2obj.t000644 000765 000024 00000004520 11615622157 016721 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; BEGIN { eval { require Test; }; use Test; plan tests => 5; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; # ----- REQUIREMENTS ----- # ------------------------ my $parser = new GO::Parser ({format=>'go_ont', handler=>'obj'}); #$parser->handler->add_root; ok(1); $parser->parse (shift @ARGV || "./t/data/generic.0208"); my $a2n = $parser->acc2name_h; #$parser->parse (shift @ARGV || "./t/data/go-truncated.obo"); $parser = new GO::Parser ({format=>'go_assoc', handler=>$parser->handler}); $parser->acc2name_h($a2n); $parser->cache_errors; $parser->parse (shift @ARGV || "./t/data/test-gene_association.fb"); # we expect one error because of the deliberately bogus last line # refering to a non-existent GO ID my @errs = $parser->errlist; #print $_->sxpr foreach @errs; ok(@errs == 1); # bogus last line my $graph = $parser->handler->graph; my $it = $graph->create_iterator; while(my $node = $it->next_node_instance){ my $term = $node->term; #use Data::Dumper; #print Dumper $graph; printf "TERM: %s %s\n", $term->acc, $term->name; die $term->acc unless $term->namespace || $term->is_relationship_type; my $aspect = $term->get_code_from_namespace; die $term->acc unless ($term->is_relationship_type || $term->namespace =~ /Gene/ || $aspect eq 'F' || $aspect eq 'C' || $aspect eq 'P'); my $assocs = $term->association_list; foreach my $assoc (@$assocs) { my $prod = $assoc->gene_product; printf " PROD: %s\n", $prod->symbol; die unless $assoc->assigned_by eq 'FB'; die unless $assoc->assocdate eq '20040228'; die unless $prod->species->ncbi_taxa_id eq '7227'; } #this causes an error my $deep_assocs = $graph->deep_association_list($term->public_acc); printf " *DEEP: %d\n", scalar(@$deep_assocs); } my $term = $graph->get_term('GO:0003673'); ok(!@{$term->association_list || []}); printf "annots: %d\n", scalar @{$graph->deep_association_list('GO:0003673')}; ok(@{$graph->deep_association_list('GO:0003673')} == 86); #ok(@{$term->deep_association_list} == 86); my $prods = $graph->deep_product_list($term->acc); ok((grep {printf "Type:%s\n", $_->type;$_->type eq 'gene'} @$prods) == 16); go-perl-0.15/t/t080gofmt2.t000644 000765 000024 00000001570 11615622157 015173 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; use constant NUMTESTS => 3; BEGIN { eval { require Test; }; use Test; plan tests => NUMTESTS; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; # ----- REQUIREMENTS ----- # goflat format files using !type: headers should be parsed # types may be odd characters # ------------------------ if (1) { my $f = './t/data/test2.ontology'; my $parser = new GO::Parser; $parser->parse($f); my $obo = $parser->handler->stag; my @typedefs = $obo->get_typedef; my %th = map {$_->sget_id => 1} @typedefs; ok(scalar (@typedefs),5); my @terms = $obo->get_term; ok(scalar (@terms),7); print $_->sxpr foreach @terms; my @rels = $obo->find_relationship; my @bad = grep {!$th{$_->sget_type}} @rels; ok(!@bad); } go-perl-0.15/t/t100roundtrip.t000644 000765 000024 00000003434 11615622157 016015 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; use constant NUMTESTS => 2; BEGIN { eval { require Test; }; use Test; plan tests => NUMTESTS; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; eval { require "XML/Parser/PerlSAX.pm"; }; if ($@) { for (1..NUMTESTS) { skip("XML::Parser::PerlSAX not installed",1); } exit 0; } eval { require "XML/Writer.pm"; }; if ($@) { for (1..NUMTESTS) { skip("XML::Writer not installed",1); } exit 0; } # ----- REQUIREMENTS ----- # This test script tests the following requirements:/x # GO::Model::Graph must implement the GO::Builder interface; ie # it should be possible to pass in a graph to a parser and have it build # up a graph object # ------------------------ if (1) { my $f = './t/data/test-function.dat'; my $of; $of = cvt($f, qw(go_ont prolog)); cvt($f, qw(go_ont obo_xml)); cvt($f, qw(go_ont rdf)); #cvt($f, qw(go_ont godb_prestore)); cvt($f, qw(go_ont pathlist)); cvt($f, qw(go_ont summary)); $of = cvt($f, qw(go_ont obo_text)); cvt($of, qw(obo_text prolog)); cvt($of, qw(obo_text rdf)); cvt($of, qw(obo_text pathlist)); cvt($of, qw(obo_text summary)); $of = cvt($of, qw(obo_text obo_xml)); $of = cvt($of, qw(obo_xml go_ont)); ok(1); $f = './t/data/GO.defs'; $of = cvt($f, qw(go_def obo_xml)); $of = cvt($of, qw(obo_xml go_def)); ok(2); } sub cvt { my $f = shift; my ($from, $to) = @_; print "$f from:$from to:$to\n"; my $parser = new GO::Parser ({format=>$from, handler=>$to}); my $outf = "$f.$to"; unlink $outf if -f $outf; $parser->handler->file($outf); $parser->parse($f); return $outf; } go-perl-0.15/t/t110basic.t000644 000765 000024 00000002463 11615622157 015052 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; BEGIN { eval { require Test; }; use Test; plan tests => 4; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; # ----- REQUIREMENTS ----- # This test script tests the following requirements:/x # GO::Model::Graph must implement the GO::Builder interface; ie # it should be possible to pass in a graph to a parser and have it build # up a graph object # ------------------------ use GO::Basic; parse_obo("t/data/test-nucleolar.obo"); find_term(name=>"nuclear body"); print term->acc,"\n"; # OO usage print acc(),"\n"; # procedural usage ok(acc eq 'GO:0016604'); print "PARENTS\n"; get_parents; print names, "\n"; ok(names == 1); get_rparents; my @names = sort {$a cmp $b} names(); print "@names\n"; ok ("@names" eq "Gene_Ontology cell cellular_component intracellular nucleoplasm nucleus"); find_term("nucleoplasm"); print acc(),"\n"; # procedural usage get_rchildren; @names = sort {$a cmp $b} names(); print "@names\n"; ok ("@names" eq "RENT complex chromatin remodeling complex chromatin silencing complex nuclear body nuclear speck"); find_term(name=>"nuclear organisation and biogenesis"); print term->acc,"\n"; # OO usage go-perl-0.15/t/t120rt.sh000755 000765 000024 00000000210 11615622157 014555 0ustar00cjmstaff000000 000000 #!/bin/sh go2oboxml ~/cvs/go/ontology/gene_ontology.obo | go2obo -p obo_xml - > go.obo diff ~/cvs/go/ontology/gene_ontology.obo go.obo go-perl-0.15/t/t130relations.t000644 000765 000024 00000002137 11615622157 015771 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; BEGIN { eval { require Test; }; use Test; plan tests => 7; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; use GO::ObjCache; # ----- REQUIREMENTS ----- # This test script tests the following requirements:/x # GO::Model::Graph must implement the GO::Builder interface; ie # it should be possible to pass in a graph to a parser and have it build # up a graph object # also tests id-mapping tag # ------------------------ my $parser = new GO::Parser ({handler=>'obj'}); my $graph = $parser->handler->g; ok(1); $parser->parse ("./t/data/relationship.obo"); $parser->parse ("./t/data/test-nucleolar.obo"); my $t = $graph->get_term("GO:0007569"); ok($t->name, 'cell aging'); my $parents = $graph->get_parent_terms_by_type($t->acc,'OBO_REL:part_of'); ok(@$parents == 1); my $t2 = shift @$parents; ok($t2->name eq 'cell death'); ok(1); my $rel = $graph->get_term('OBO_REL:derives_from'); ok($rel); print $rel->transitive_over, "\n"; ok($rel->transitive_over eq 'OBO_REL:part_of'); go-perl-0.15/t/t140subgraph.t000644 000765 000024 00000001026 11615622157 015601 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; BEGIN { eval { require Test; }; use Test; plan tests => 1; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; # ----- REQUIREMENTS ----- # ------------------------ my $parser = new GO::Parser ({format=>'go_ont'}); my $graph = $parser->parse_to_graph("./t/data/test-function.dat"); my $subgraph = $graph->subgraph({acc=>'GO:0003700'}); $subgraph->to_text_output; ok($subgraph->term_count == 5); go-perl-0.15/t/t150xref.t000644 000765 000024 00000001267 11615622157 014742 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; BEGIN { eval { require Test; }; use Test; plan tests => 2; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; use GO::ObjCache; # ----- REQUIREMENTS ----- # This test script tests the following requirements:/x # GO::Model::Graph must implement the GO::Builder interface; ie # it should be possible to pass in a graph to a parser and have it build # up a graph object # ------------------------ my $parser = new GO::Parser ({format=>'go_xref', handler=>'obj'}); my $graph = $parser->handler->g; ok(1); $parser->parse ("./t/data/spkw2go"); ok(2); go-perl-0.15/t/t160logicaldef.t000644 000765 000024 00000001727 11615622157 016071 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; BEGIN { eval { require Test; }; use Test; plan tests => 5; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; use GO::ObjCache; # ----- REQUIREMENTS ----- # This test script tests the GO::Model::LogicalDefinition # ------------------------ my $parser = new GO::Parser ({handler=>'obj'}); my $graph = $parser->handler->g; ok(1); $parser->parse ("./t/data/llm.obo"); my $t = $graph->get_term_by_name("larval locomotory behavior"); printf "ns: %s\n", $t->namespace; ok ($t->namespace eq 'biological_process'); my $ldef = $t->logical_definition; printf "ldef ns: %s\n", $ldef->namespace; ok ($ldef->namespace eq 'foo'); foreach (@{$ldef->intersection_list}) { print "@$_\n"; } my $gacc = $ldef->generic_term_acc; print "$gacc\n"; ok($gacc eq 'GO:0007626'); my $diff = $ldef->differentia->[0]; ok("@$diff" eq "OBOL:during FBdv:00005336"); go-perl-0.15/t/t170chadoxml.t000644 000765 000024 00000003644 11615622157 015600 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; use constant NUMTESTS => 9; BEGIN { eval { require Test; }; use Test; plan tests => NUMTESTS; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; eval { require "XML/Parser/PerlSAX.pm"; }; if ($@) { for (1..NUMTESTS) { skip("XML::Parser::PerlSAX not installed",1); } exit 0; } eval { require "XML/Writer.pm"; }; if ($@) { for (1..NUMTESTS) { skip("XML::Writer not installed",1); } exit 0; } # ----- REQUIREMENTS ----- # ------------------------ my $f = './t/data/llm.obo'; my $parser = new GO::Parser ({format=>'obo' }); # handler=>'xml'}); $parser->xslt("oboxml_to_chadoxml"); $parser->parse($f); my $chado = $parser->handler->stag; my @cvterms = $chado->get_cvterm; my %relh = (); foreach my $cvterm (@cvterms) { $relh{$cvterm->sget('@/id')} = $cvterm; } my %cv_h = (); $cv_h{$_->sget('@/id')} = $_->sget('name') foreach $chado->get_cv; # builtin # intersection_of tags are parsed #ok($relh{intersection_of}->sget_cv_id eq 'cvterm_property_type'); ok(1); # explicitly listed relation, declared to be in relationship my $cv_id = $relh{'OBO_REL:part_of'}->sget('cv_id'); ok($cv_h{$cv_id} eq 'relationship'); # only mentioned in header - not listed so we presume loaded ok(!$relh{'OBOL:during'}->sget('cv_id')); # by default, place unqualified rel in default-namespace cv ok($cv_h{$relh{bzz}->sget_cv_id} eq 'gene_ontology'); ok($relh{bzz}->sget('dbxref_id/dbxref/db_id') eq '_default_idspace'); ok($cv_h{$relh{foo}->sget_cv_id} eq 'gene_ontology'); ok($relh{foo}->sget('dbxref_id/dbxref/db_id') eq '_default_idspace'); # genuine ID and no namespace explicitly provided, use default ok($cv_h{$relh{'X:Y'}->sget('cv_id')} eq 'gene_ontology'); ok($cv_h{$relh{'Y:Z'}->sget('cv_id')} eq 'yz'); go-perl-0.15/t/t175chadoxml_oborel.t000644 000765 000024 00000003623 11615622157 017144 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; use constant NUMTESTS => 9; BEGIN { eval { require Test; }; use Test; plan tests => NUMTESTS; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; eval { require "XML/Parser/PerlSAX.pm"; }; if ($@) { for (1..NUMTESTS) { skip("XML::Parser::PerlSAX not installed",1); } exit 0; } eval { require "XML/Writer.pm"; }; if ($@) { for (1..NUMTESTS) { skip("XML::Writer not installed",1); } exit 0; } # ----- REQUIREMENTS ----- # ------------------------ my $f = './t/data/llm2.obo'; my $parser = new GO::Parser ({format=>'obo' }); # handler=>'xml'}); $parser->xslt("oboxml_to_chadoxml"); $parser->parse($f); my $chado = $parser->handler->stag; my @cvterms = $chado->get_cvterm; my %relh = (); foreach my $cvterm (@cvterms) { $relh{$cvterm->sget('@/id')} = $cvterm; } my %cv_h = (); $cv_h{$_->sget('@/id')} = $_->sget('name') foreach $chado->get_cv; # builtin # intersection_of tags are parsed #ok($relh{intersection_of}->sget_cv_id eq 'cvterm_property_type'); ok(1); # explicitly listed relation, declared to be in relationship my $cv_id = $relh{'part_of'}->sget('cv_id'); ok($cv_h{$cv_id} eq 'relationship'); # only mentioned in header - not listed so we presume loaded ok(!$relh{'OBOL:during'}->sget('cv_id')); # by default, place unqualified rel in default-namespace cv ok($cv_h{$relh{bzz}->sget_cv_id} eq 'gene_ontology'); ok($relh{bzz}->sget('dbxref_id/dbxref/db_id') eq '_default_idspace'); ok($cv_h{$relh{foo}->sget_cv_id} eq 'relationship'); ok($relh{foo}->sget('dbxref_id/dbxref/db_id') eq 'OBO_REL'); # genuine ID and no namespace explicitly provided, use default ok($cv_h{$relh{'X:Y'}->sget('cv_id')} eq 'gene_ontology'); ok($cv_h{$relh{'Y:Z'}->sget('cv_id')} eq 'yz'); go-perl-0.15/t/t180ncbi_taxonomy.t000644 000765 000024 00000002774 11615622157 016656 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; use constant NUMTESTS => 4; BEGIN { eval { require Test; }; use Test; plan tests => NUMTESTS; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; # ----- REQUIREMENTS ----- # ncbi_taxonomy roundtrips # this test involves class properties # ------------------------ if (1) { my $f = './t/data/sample.ncbi_taxonomy'; my $f2 = cvt($f,'ncbi_taxonomy','obo'); # some taxon terms contain {} - test that escaping of these works open(F,$f2) || die; my $matched; while () { # ID 21 has a fake {...} entry if (/\\\{test\\\}/) { $matched=1; last; } } ok($matched); my $parser = new GO::Parser; $parser->parse($f2); my $obo = $parser->handler->stag; ok($obo->get('header/synonymtypedef')); ok($obo->get('term/synonym/@/synonym_type')); my @terms = $obo->get_term; my ($t) = grep {$_->sget_id eq 'NCBITaxon:21'} @terms; # some taxon terms contain {} - test that escaping of these works print $t->get_name,"\n"; ok($t->get_name eq 'Phenylobacterium immobile {test}'); } exit 0; sub cvt { my $f = shift; my ($from, $to) = @_; print "$f from:$from to:$to\n"; my $parser = new GO::Parser ({format=>$from, handler=>$to}); my $outf = "$f.$to"; unlink $outf if -f $outf; $parser->handler->file($outf); $parser->parse($f); return $outf; } go-perl-0.15/t/t200impliedlinks.t000644 000765 000024 00000001161 11615622157 016447 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; BEGIN { eval { require Test; }; use Test; plan tests => 2; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; use GO::ObjCache; # ----- REQUIREMENTS ----- # This test script tests the GO::Model::LogicalDefinition # ------------------------ my $parser = new GO::Parser ({handler=>'obj'}); my $graph = $parser->handler->g; ok(1); $parser->parse ("./t/data/impliedlinks.obo"); my $g = $parser->handler->graph; my $t = $g->get_term("A"); my $ps = $g->get_parent_terms($t); ok (@$ps==4); go-perl-0.15/t/t210cache.t000644 000765 000024 00000002044 11615622157 015030 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; BEGIN { eval { require Test; }; use Test; plan tests => 6; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; use GO::ObjCache; # ----- REQUIREMENTS ----- # This test script tests the following requirements:/x # GO::Model::Graph must implement the GO::Builder interface; ie # it should be possible to pass in a graph to a parser and have it build # up a graph object # ------------------------ my $parser = new GO::Parser ({format=>'obo', handler=>'obj'}); my $graph = $parser->handler->g; ok(1); $parser->parse ("./t/data/test-nucleolar.obo"); ok($parser->acc2name_h->{'GO:0003723'} = 'RNA binding'); # lets check we got stuff #print $graph->dump; my $t = $graph->get_term("GO:0003723"); ok($t); ok(1); $t->add_synonym_by_type(foo=>"abc"); $t->add_synonym_by_type(foo=>"def"); $t->add_synonym_by_type(goo=>"xyz"); ok(scalar(@{$t->synonym_list}),3); $t->synonym_list([]); ok(scalar(@{$t->synonym_list}),0); go-perl-0.15/t/t220xref_esc.t000644 000765 000024 00000002206 11615622157 015564 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; BEGIN { eval { require Test; }; use Test; plan tests => 6; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; use GO::ObjCache; # ----- REQUIREMENTS ----- # This test script tests the following requirements:/x # GO::Model::Graph must implement the GO::Builder interface; ie # it should be possible to pass in a graph to a parser and have it build # up a graph object # ------------------------ my $parser = new GO::Parser ({format=>'obo', handler=>'obj'}); my $graph = $parser->handler->g; ok(1); $parser->parse ("./t/data/xref_encoding_test.obo"); my $terms = $graph->term_query({name=>"2,4,5-trichlorophenoxyacetic acid metabolic process"}); my $t = shift @$terms; ok($t); ok(1); my @xrefs = (); foreach my $xref (@{$t->dbxref_list}) { print $xref->as_str,"\n"; push(@xrefs, $xref->as_str); } foreach my $xref (@{$t->definition_dbxref_list}) { print $xref->as_str,"\n"; push(@xrefs, $xref->as_str); } ok(@xrefs==2); ok($xrefs[0] eq $xrefs[1]); ok($xrefs[0] eq 'UM-BBD_pathwayID:2,4,5-t'); go-perl-0.15/t/t230term_expression.t000644 000765 000024 00000001413 11615622157 017214 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; BEGIN { eval { require Test; }; use Test; plan tests => 1; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; use Data::Stag; my $parser = GO::Parser->new({format=>'obo_text'}); my $te = $parser->parse_term_expression("GO:1234^part_of(CL:abc)"); print $te->xml; $te = $parser->parse_term_expression("GO:1234^part_of(CL:abc^part_of(AO:999))"); print $te->xml; $te = $parser->parse_term_expression("GO:1234^part_of(CL:abc^part_of(AO:999)^has_coordinate(x:left))"); print $te->xml; $te = $parser->parse_term_expression("(GO:1234^results_in_output_of(CHEBI:765))^part_of(CL:abc^part_of(AO:999)^has_coordinate(x:left))"); print $te->xml; ok(1); go-perl-0.15/t/t240ga2obj.t000644 000765 000024 00000001575 11615622157 015144 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; use constant NUMTESTS => 3; BEGIN { eval { require Test; }; use Test; plan tests => NUMTESTS; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; # ----- REQUIREMENTS ----- # The gene association file must be isomorphic to the GO model # ------------------------ if (1) { ## Setup my $f = './t/data/test-gene_association.fb'; my $p = GO::Parser->new({format=>'go_assoc', handler=>'obj'}); $p->parse($f); my $g = $p->handler->graph; my $term_l = $g->get_all_nodes; ## Get all the nodes? ok(scalar(@{$g->get_all_nodes}), 40); ## Examine one node in detail. my $t = $g->get_term("GO:0000003"); ## Acc right? ok($t->acc,'GO:0000003'); ## Aspect right? ok($t->get_code_from_namespace,'P'); } go-perl-0.15/t/t260oborel_in_chado.t000644 000765 000024 00000002743 11615622157 017106 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; use constant NUMTESTS => 6; BEGIN { eval { require Test; }; use Test; plan tests => NUMTESTS; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; eval { require "XML/Parser/PerlSAX.pm"; }; if ($@) { for (1..NUMTESTS) { skip("XML::Parser::PerlSAX not installed",1); } exit 0; } eval { require "XML/Writer.pm"; }; if ($@) { for (1..NUMTESTS) { skip("XML::Writer not installed",1); } exit 0; } # ----- REQUIREMENTS ----- # ------------------------ my $f = './t/data/go-with-local-id-mapping.obo'; my $parser = new GO::Parser ({format=>'obo' }); # handler=>'xml'}); $parser->xslt("oboxml_to_chadoxml"); $parser->parse($f); my $chado = $parser->handler->stag; my @cvterms = $chado->get_cvterm; my %relh = (); foreach my $cvterm (@cvterms) { $relh{$cvterm->sget('@/id')} = $cvterm; } my %cv_h = (); $cv_h{$_->sget('@/id')} = $_->sget('name') foreach $chado->get_cv; # explicitly listed relation, declared to be in relationship my $part_of = $relh{'part_of'}; print $part_of->xml; ok($part_of); my $cv_id = $part_of->sget('cv_id'); print($cv_h{$cv_id},"\n"); ok($cv_h{$cv_id} eq 'relationship'); ok($part_of->sget('dbxref_id/dbxref/db_id') eq 'OBO_REL'); ok($relh{foo}); ok($relh{foo}->sget('dbxref_id/dbxref/db_id') eq '_default_idspace'); ok($relh{bar}); go-perl-0.15/t/t270oborel_in_owl.t000644 000765 000024 00000003033 11615622157 016623 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; use constant NUMTESTS => 4; BEGIN { eval { require Test; }; use Test; plan tests => NUMTESTS; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; eval { require "XML/Parser/PerlSAX.pm"; }; if ($@) { for (1..NUMTESTS) { skip("XML::Parser::PerlSAX not installed",1); } exit 0; } eval { require "XML/Writer.pm"; }; if ($@) { for (1..NUMTESTS) { skip("XML::Writer not installed",1); } exit 0; } # ----- REQUIREMENTS ----- # ------------------------ my $f = './t/data/go-with-local-id-mapping.obo'; my $parser = new GO::Parser ({format=>'obo' }); # handler=>'xml'}); $parser->xslt("oboxml_to_owl"); $parser->parse($f); my $owl = $parser->handler->stag; # explicitly listed relation, declared to be in relationship my $part_of = $owl->get('owl:TransitiveProperty'); print $part_of->sxpr; ok($part_of); print $part_of->sget('@/rdf:about'). "\n"; ok($part_of->sget('@/rdf:about') eq 'http://purl.org/obo/owl/OBO_REL#part_of'); my ($foo) = $owl->qmatch('owl:ObjectProperty','@/rdf:about','http://purl.org/obo/owl/obo#foo'); print $foo->sxpr; ok($foo->sget('@/rdf:about') eq 'http://purl.org/obo/owl/obo#foo'); my ($bar) = $owl->where('owl:AnnotationProperty',sub {shift->sget('@/rdf:about') eq 'http://purl.org/obo/owl/obo#bar'}); print $bar->sxpr; ok($bar->sget('@/rdf:about') eq 'http://purl.org/obo/owl/obo#bar'); go-perl-0.15/t/t290disjoint.t000644 000765 000024 00000001326 11615622157 015622 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; BEGIN { eval { require Test; }; use Test; plan tests => 2; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; # ----- REQUIREMENTS ----- # parser and model must handle disjoint_from # ------------------------ my $parser = new GO::Parser ({format=>'obo', handler=>'obj'}); my $graph = $parser->handler->g; ok(1); $parser->parse ("./t/data/regulation_of_somitogenesis.obo"); my $terms = $graph->get_all_nodes; my $term = $graph->get_term("GO:0032501"); my $ok; foreach (@{$term->disjoint_from_term_list}) { printf "%s\n", $_; $ok = 1 if $_ eq 'GO:0009987'; } ok($ok); go-perl-0.15/t/validate_all.x000644 000765 000024 00000004023 11615622157 016002 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use lib '.'; BEGIN { eval { require Test; }; use Test; plan tests => 1; } # All tests must be run from the software directory; # make sure we are getting the modules from here: use strict; use GO::Parser; use GO::ObjCache; use Data::Stag; # ----- REQUIREMENTS ----- # ------------------------ # you may need to set your classpath to msv.jar # sun multi schema validator my @bad = (); foreach my $file ((glob "$ENV{GODATA_ROOT}/ontology/*.{ontology,defs,obo}"), "$ENV{GODATA_ROOT}/external2go/ec2go", (glob "$ENV{GODATA_ROOT}/gene-associations/gene_associaton.fb*") ) { parse_and_validate($file, 'obo_xml', "tmp.obo-xml"); parse_and_validate("tmp.obo-xml", 'godb_prestore', 'tmp.godb_prestore.xml'); } ok (!@bad); sub parse_and_validate { my $file = shift; my $htype = shift; my $outfile = shift; my $parser = new GO::Parser ({handler=>$htype}); print STDERR "PARSING:$file => $outfile [$htype]\n"; if ($parser->handler->can("is_transform") && $parser->handler->is_transform) { my $inner_handler = $parser->handler; my $w = Data::Stag->getformathandler('xml'); $w->file($outfile); my $handler = Data::Stag->chainhandlers([$parser->handler->CONSUMES], $inner_handler, $w); $parser->handler($handler); } else { $parser->handler->file($outfile); } $parser->parse($file); my $dtd = $parser->parser->dtd; if ($htype eq 'godb_prestore') { $dtd = 'godb_prestore-events.dtd'; } $dtd || die "no dtd for $parser"; print STDERR "VALIDATING:$outfile with $dtd\n"; my $err = system("java -jar ~/msv/msv.jar $ENV{GO_ROOT}/xml/dtd/$dtd $outfile >& tmp.err"); if ($err) { system("cat tmp.err"); print STDERR "PROBLEM VALIDATING $file VIA $dtd\n"; push(@bad, $file); } else { print STDERR "Validates OK!\n"; } } go-perl-0.15/t/data/bad-dbxref.obo000644 000765 000024 00000001260 11615622157 016600 0ustar00cjmstaff000000 000000 [Term] id: MP:0000554 name: abnormal carpal bone morphology def: "any structural anomaly of the nine nodular bones of the joint between the forelimb bones and the front paws/hands consisting of the scapholunar, triangular, greater multiangular, lesser multiangular, capitate, hamate, centrale and the sesamoids" [Anatomy of the Rat:Greene EC_Hafner Publishing Co_1935, Stedman's Medical Dictionary_27th edition:ISBN 0-683-40008-8] comment: Note that the bony structure of the human and rodent carpals are different. synonym: "abnormal carpal bone" EXACT [] synonym: "abnormal carpus" EXACT [] synonym: "abnormal wrist" EXACT [] is_a: MP:0002115 ! abnormal skeleton extremities morphology go-perl-0.15/t/data/gene_association.test_properties000644 000765 000024 00002237450 11615622157 022606 0ustar00cjmstaff000000 000000 MGI MGI:1914306 2610024G14Rik GO:0005743 MGI:MGI:3615096|PMID:16380119 IDA C RIKEN cDNA 2610024G14 gene AtNOS1|mAtNOS1 gene taxon:10090 20060501 MGI relationship(CL:0000002) MGI MGI:1922169 4930471M23Rik GO:0005764 MGI:MGI:3692368|PMID:16367739 IDA C RIKEN cDNA 4930471M23 gene p40 gene taxon:10090 20070209 MGI relationship(CL:0000002) MGI MGI:1915003 4930579C15Rik GO:0005634 MGI:MGI:3653981|PMID:16831425 IDA C RIKEN cDNA 4930579C15 gene Afaf gene taxon:10090 20061102 MGI relationship(CL:0000002) MGI MGI:1915003 4930579C15Rik GO:0005737 MGI:MGI:3653981|PMID:16831425 IDA C RIKEN cDNA 4930579C15 gene Afaf gene taxon:10090 20061102 MGI relationship(CL:0000002) MGI MGI:1915003 4930579C15Rik GO:0005769 MGI:MGI:3653981|PMID:16831425 IDA C RIKEN cDNA 4930579C15 gene Afaf gene taxon:10090 20061102 MGI relationship(CL:0000002) MGI MGI:1915003 4930579C15Rik GO:0005886 MGI:MGI:3653981|PMID:16831425 IDA C RIKEN cDNA 4930579C15 gene Afaf gene taxon:10090 20061102 MGI relationship(CL:0000002) MGI MGI:99607 Abca1 GO:0045332 MGI:MGI:1860694|PMID:10878804 IMP MGI:1935192 P ATP-binding cassette, sub-family A (ABC1), member 1 ABC1 gene taxon:10090 20050107 MGI relationship(CL:0000595) MGI MGI:109424 Abca4 GO:0045494 MGI:MGI:2136674|PMID:11431429 IMP MGI:1857860 P ATP-binding cassette, sub-family A (ABC1), member 4 Abc10|Rim protein|RmP gene taxon:10090 20050107 MGI relationship(CL:0000604) MGI MGI:1914719 Abhd5 GO:0005811 MGI:MGI:3057082|PMID:15292255 IDA C abhydrolase domain containing 5 CGI-58|IECN5|NCIE2 gene taxon:10090 20060726 MGI relationship(CL:0000136) MGI MGI:1914719 Abhd5 GO:0005811 MGI:MGI:3487148|PMID:15136565 IDA C abhydrolase domain containing 5 CGI-58|IECN5|NCIE2 gene taxon:10090 20060726 MGI relationship(CL:0000057) MGI MGI:1914719 Abhd5 GO:0005829 MGI:MGI:3057082|PMID:15292255 IDA C abhydrolase domain containing 5 CGI-58|IECN5|NCIE2 gene taxon:10090 20060726 MGI relationship(CL:0000057) MGI MGI:1914719 Abhd5 GO:0005829 MGI:MGI:3487148|PMID:15136565 IDA C abhydrolase domain containing 5 CGI-58|IECN5|NCIE2 gene taxon:10090 20060726 MGI relationship(CL:0000057) MGI MGI:1914719 Abhd5 GO:0006629 MGI:MGI:3487148|PMID:15136565 ISS UniProt:Q6QA69 P abhydrolase domain containing 5 CGI-58|IECN5|NCIE2 gene taxon:10090 20060726 MGI relationship(CL:0000057) MGI MGI:106913 Abi2 GO:0005913 MGI:MGI:3525751|PMID:15572692 IDA C abl-interactor 2 gene taxon:10090 20050314 MGI relationship(CL:0000306) MGI MGI:106913 Abi2 GO:0016358 MGI:MGI:3525751|PMID:15572692 IMP MGI:3526871 P abl-interactor 2 gene taxon:10090 20050314 MGI relationship(CL:0000117) MGI MGI:106913 Abi2 GO:0016477 MGI:MGI:3525751|PMID:15572692 IMP MGI:3526871 P abl-interactor 2 gene taxon:10090 20050314 MGI relationship(CL:0000117) MGI MGI:106913 Abi2 GO:0016477 MGI:MGI:3525751|PMID:15572692 IMP MGI:3526871 P abl-interactor 2 gene taxon:10090 20050314 MGI relationship(CL:0000306) MGI MGI:106913 Abi2 GO:0030425 MGI:MGI:3525751|PMID:15572692 IDA C abl-interactor 2 gene taxon:10090 20050314 MGI relationship(CL:0000117) MGI MGI:106913 Abi2 GO:0043010 MGI:MGI:3525751|PMID:15572692 IMP MGI:3526871 P abl-interactor 2 gene taxon:10090 20050314 MGI relationship(CL:0000306) MGI MGI:1100867 Accn1 GO:0043005 MGI:MGI:3530929|PMID:15537887 IDA C amiloride-sensitive cation channel 1, neuronal (degenerin) ASIC2|BNaC1a|BNC1|Mdeg gene taxon:10090 20050511 MGI relationship(CL:0000103) MGI MGI:1100867 Accn1 GO:0043025 MGI:MGI:3530929|PMID:15537887 IDA C amiloride-sensitive cation channel 1, neuronal (degenerin) ASIC2|BNaC1a|BNC1|Mdeg gene taxon:10090 20050511 MGI relationship(CL:0000103) MGI MGI:87877 Ack GO:0009617 MGI:MGI:54337|PMID:892907 IMP P anti-Corynebacterium kutscheri acm gene taxon:10090 20050930 MGI relationship(CL:0000113) MGI MGI:87905 Actc1 GO:0031674 MGI:MGI:3656458|PMID:16481394 IDA C actin, alpha, cardiac Actc-1|alphac-actin gene taxon:10090 20070312 MGI relationship(CL:0000746) MGI MGI:87915 Ad GO:0008285 MGI:MGI:54572|PMID:420754 IMP MGI:87915 P adult obesity and diabetes gene taxon:10090 20050930 MGI relationship(CL:0000136) MGI MGI:87915 Ad GO:0045792 MGI:MGI:54572|PMID:420754 IMP MGI:87915 P adult obesity and diabetes gene taxon:10090 20050930 MGI relationship(CL:0000136) MGI MGI:105377 Adam19 GO:0007507 MGI:MGI:3027294|PMID:14673146 IMP MGI:3028702 P a disintegrin and metallopeptidase domain 19 (meltrin beta) Mltnb gene taxon:10090 20050114 MGI relationship(CL:0000359) MGI MGI:109249 Adamts1 GO:0031012 MGI:MGI:1335998|PMID:9593739 IDA C a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 1 ADAM-TS1|METH-1|METH1 gene taxon:10090 20051201 MGI relationship(CL:0000002) MGI MGI:2685556 Adamts13 GO:0005615 MGI:MGI:3578448|PMID:15136581 IDA C a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin type 1 motif, 13 LOC279028|vWF-CP mRNA for von Willebrand factor-cleaving gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:87920 Adfp GO:0005737 MGI:MGI:3621068|PMID:16581799 IDA C adipose differentiation related protein adipophilin|ADPH|Adrp gene taxon:10090 20060609 MGI relationship(CL:0000351) MGI MGI:106675 Adipoq GO:0005615 MGI:MGI:3055460|PMID:10444069 IDA C adiponectin, C1Q and collagen domain containing Acdc|Acrp30|adipo|adiponectin|apM1|GBP28 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:106675 Adipoq GO:0005783 MGI:MGI:3055460|PMID:10444069 IDA C adiponectin, C1Q and collagen domain containing Acdc|Acrp30|adipo|adiponectin|apM1|GBP28 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:106675 Adipoq GO:0046326 MGI:MGI:2181851|PMID:12068289 IDA P adiponectin, C1Q and collagen domain containing Acdc|Acrp30|adipo|adiponectin|apM1|GBP28 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:104773 Adra1a GO:0004937 MGI:MGI:1206152|PMID:9630362 IDA F adrenergic receptor, alpha 1a [a]1a|Adra1c gene taxon:10090 20051220 MGI relationship(CL:0000002) MGI MGI:104773 Adra1a GO:0005624 MGI:MGI:1206152|PMID:9630362 IDA C adrenergic receptor, alpha 1a [a]1a|Adra1c gene taxon:10090 20051220 MGI relationship(CL:0000002) MGI MGI:104773 Adra1a GO:0007200 MGI:MGI:1203366|PMID:9590558 IDA P adrenergic receptor, alpha 1a [a]1a|Adra1c gene taxon:10090 20051220 MGI relationship(CL:0000002) MGI MGI:104773 Adra1a GO:0016049 MGI:MGI:2664013|PMID:12782680 IGI MGI:104774 P adrenergic receptor, alpha 1a [a]1a|Adra1c gene taxon:10090 20051220 MGI relationship(CL:0000193) MGI MGI:104774 Adra1b GO:0001975 MGI:MGI:2667580|PMID:12871582 IMP MGI:2148638 P adrenergic receptor, alpha 1b [a]1b|alpha1B-adrenergic receptor gene taxon:10090 20051221 MGI relationship(CL:0000700) MGI MGI:104774 Adra1b GO:0016049 MGI:MGI:2664013|PMID:12782680 IGI MGI:104773 P adrenergic receptor, alpha 1b [a]1b|alpha1B-adrenergic receptor gene taxon:10090 20051222 MGI relationship(CL:0000193) MGI MGI:87937 Adrb1 GO:0002024 MGI:MGI:2387786|PMID:12161655 IGI MGI:87938,MGI:87939 P adrenergic receptor, beta 1 Adrb-1|beta 1-AR gene taxon:10090 20051223 MGI relationship(CL:0000449) MGI MGI:87937 Adrb1 GO:0009409 MGI:MGI:2387786|PMID:12161655 IGI MGI:87938,MGI:87939 P adrenergic receptor, beta 1 Adrb-1|beta 1-AR gene taxon:10090 20051223 MGI relationship(CL:0000449) MGI MGI:87937 Adrb1 GO:0031649 MGI:MGI:2387786|PMID:12161655 IGI MGI:87938,MGI:87939 P adrenergic receptor, beta 1 Adrb-1|beta 1-AR gene taxon:10090 20051223 MGI relationship(CL:0000449) MGI MGI:87937 Adrb1 GO:0050873 MGI:MGI:2388907|PMID:12387862 IGI MGI:87938,MGI:87939 P adrenergic receptor, beta 1 Adrb-1|beta 1-AR gene taxon:10090 20051227 MGI relationship(CL:0000449) MGI MGI:87938 Adrb2 GO:0002024 MGI:MGI:2387786|PMID:12161655 IGI MGI:87937,MGI:87939 P adrenergic receptor, beta 2 Adrb-2|Badm|beta 2-adrenoceptor|beta 2-AR gene taxon:10090 20051223 MGI relationship(CL:0000449) MGI MGI:87938 Adrb2 GO:0002028 MGI:MGI:3580729|PMID:15016730 IMP MGI:1859675 P adrenergic receptor, beta 2 Adrb-2|Badm|beta 2-adrenoceptor|beta 2-AR gene taxon:10090 20051228 MGI relationship(CL:0000082) MGI MGI:87938 Adrb2 GO:0004941 MGI:MGI:55803|PMID:6321299 IDA F adrenergic receptor, beta 2 Adrb-2|Badm|beta 2-adrenoceptor|beta 2-AR gene taxon:10090 20051227 MGI relationship(CL:0000182) MGI MGI:87938 Adrb2 GO:0004941 MGI:MGI:77867|PMID:2834198 IDA F adrenergic receptor, beta 2 Adrb-2|Badm|beta 2-adrenoceptor|beta 2-AR gene taxon:10090 20051222 MGI relationship(CL:0000002) MGI MGI:87938 Adrb2 GO:0005624 MGI:MGI:55803|PMID:6321299 IDA C adrenergic receptor, beta 2 Adrb-2|Badm|beta 2-adrenoceptor|beta 2-AR gene taxon:10090 20051227 MGI relationship(CL:0000182) MGI MGI:87938 Adrb2 GO:0005624 MGI:MGI:77867|PMID:2834198 IDA C adrenergic receptor, beta 2 Adrb-2|Badm|beta 2-adrenoceptor|beta 2-AR gene taxon:10090 20051222 MGI relationship(CL:0000002) MGI MGI:87938 Adrb2 GO:0005634 MGI:MGI:3577687|PMID:15791602 IDA C adrenergic receptor, beta 2 Adrb-2|Badm|beta 2-adrenoceptor|beta 2-AR gene taxon:10090 20051222 MGI relationship(CL:0000007) MGI MGI:87938 Adrb2 GO:0007189 MGI:MGI:3575849|PMID:15724149 IMP MGI:1859675 P adrenergic receptor, beta 2 Adrb-2|Badm|beta 2-adrenoceptor|beta 2-AR gene taxon:10090 20051223 MGI relationship(CL:0000001) MGI MGI:87938 Adrb2 GO:0007189 MGI:MGI:77867|PMID:2834198 IDA P adrenergic receptor, beta 2 Adrb-2|Badm|beta 2-adrenoceptor|beta 2-AR gene taxon:10090 20051222 MGI relationship(CL:0000002) MGI MGI:87938 Adrb2 GO:0009409 MGI:MGI:2387786|PMID:12161655 IGI MGI:87937,MGI:87939 P adrenergic receptor, beta 2 Adrb-2|Badm|beta 2-adrenoceptor|beta 2-AR gene taxon:10090 20051223 MGI relationship(CL:0000449) MGI MGI:87938 Adrb2 GO:0016324 MGI:MGI:2683836|PMID:14625387 IDA C adrenergic receptor, beta 2 Adrb-2|Badm|beta 2-adrenoceptor|beta 2-AR gene taxon:10090 20051222 MGI relationship(CL:0000001) MGI MGI:87938 Adrb2 GO:0030501 MGI:MGI:3575849|PMID:15724149 IMP MGI:1859675 P adrenergic receptor, beta 2 Adrb-2|Badm|beta 2-adrenoceptor|beta 2-AR gene taxon:10090 20051223 MGI relationship(CL:0000001) MGI MGI:87938 Adrb2 GO:0031649 MGI:MGI:2387786|PMID:12161655 IGI MGI:87937,MGI:87939 P adrenergic receptor, beta 2 Adrb-2|Badm|beta 2-adrenoceptor|beta 2-AR gene taxon:10090 20051223 MGI relationship(CL:0000449) MGI MGI:87938 Adrb2 GO:0045986 MGI:MGI:2672939|PMID:12925702 IGI MGI:88398,MGI:98496 P adrenergic receptor, beta 2 Adrb-2|Badm|beta 2-adrenoceptor|beta 2-AR gene taxon:10090 20051227 MGI relationship(CL:0000192) MGI MGI:87938 Adrb2 GO:0050873 MGI:MGI:2388907|PMID:12387862 IGI MGI:87937,MGI:87939 P adrenergic receptor, beta 2 Adrb-2|Badm|beta 2-adrenoceptor|beta 2-AR gene taxon:10090 20051227 MGI relationship(CL:0000449) MGI MGI:87939 Adrb3 GO:0002024 MGI:MGI:2387786|PMID:12161655 IGI MGI:87937,MGI:87938 P adrenergic receptor, beta 3 Adrb-3|beta 3-AR|Beta-3 adrenoceptor|Beta-3 AR|beta3-adrenergic receptor gene taxon:10090 20051223 MGI relationship(CL:0000449) MGI MGI:87939 Adrb3 GO:0009409 MGI:MGI:2387786|PMID:12161655 IGI MGI:87937,MGI:87938 P adrenergic receptor, beta 3 Adrb-3|beta 3-AR|Beta-3 adrenoceptor|Beta-3 AR|beta3-adrenergic receptor gene taxon:10090 20051223 MGI relationship(CL:0000449) MGI MGI:87939 Adrb3 GO:0031649 MGI:MGI:2387786|PMID:12161655 IGI MGI:87937,MGI:87938 P adrenergic receptor, beta 3 Adrb-3|beta 3-AR|Beta-3 adrenoceptor|Beta-3 AR|beta3-adrenergic receptor gene taxon:10090 20051223 MGI relationship(CL:0000449) MGI MGI:87939 Adrb3 GO:0050873 MGI:MGI:2388907|PMID:12387862 IGI MGI:87937,MGI:87938 P adrenergic receptor, beta 3 Adrb-3|beta 3-AR|Beta-3 adrenoceptor|Beta-3 AR|beta3-adrenergic receptor gene taxon:10090 20051227 MGI relationship(CL:0000449) MGI MGI:95806 Aes GO:0005634 MGI:MGI:3603095|PMID:16002402 IDA C amino-terminal enhancer of split AES|Grg|Grg5 gene taxon:10090 20051104 MGI relationship(CL:0000002) MGI MGI:95806 Aes GO:0006357 MGI:MGI:3603095|PMID:16002402 IGI MGI:97168 P amino-terminal enhancer of split AES|Grg|Grg5 gene taxon:10090 20051104 MGI relationship(CL:0000002) MGI MGI:95806 Aes GO:0030528 MGI:MGI:3603095|PMID:16002402 IGI MGI:97168 F amino-terminal enhancer of split AES|Grg|Grg5 gene taxon:10090 20051104 MGI relationship(CL:0000002) MGI MGI:2136171 Aff4 GO:0005634 MGI:MGI:3586405|PMID:16024815 IDA C AF4/FMR2 family, member 4 Alf4|Laf4l gene taxon:10090 20060202 MGI relationship(CL:0000216) MGI MGI:2136171 Aff4 GO:0007286 MGI:MGI:3586405|PMID:16024815 IMP MGI:3586991 P AF4/FMR2 family, member 4 Alf4|Laf4l gene taxon:10090 20060202 MGI relationship(CL:0000019) MGI MGI:2142716 Agpat6 GO:0002071 MGI:MGI:3623167|PMID:16449762 IMP MGI:3624276 P 1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta) gene taxon:10090 20060717 MGI relationship(CL:0000150) MGI MGI:2142716 Agpat6 GO:0005783 MGI:MGI:3623167|PMID:16449762 IDA C 1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta) gene taxon:10090 20060717 MGI relationship(CL:0000002) MGI MGI:2142716 Agpat6 GO:0030879 MGI:MGI:3623167|PMID:16449762 IMP MGI:3624276 P 1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta) gene taxon:10090 20060717 MGI relationship(CL:0000150) MGI MGI:87961 Agrn GO:0045944 MGI:MGI:1194472|PMID:9422725 IDA P agrin Agrin gene taxon:10090 20061115 MGI relationship(CL:0000002) MGI MGI:87963 Agt GO:0001658 MGI:MGI:2655949|PMID:12657564 IDA P angiotensinogen (serpin peptidase inhibitor, clade A, member 8) Aogen|Serpina8 gene taxon:10090 20051229 MGI relationship(CL:0000001) MGI MGI:87963 Agt GO:0005615 MGI:MGI:2154640|PMID:11606482 IDA C angiotensinogen (serpin peptidase inhibitor, clade A, member 8) Aogen|Serpina8 gene taxon:10090 20051230 MGI relationship(CL:0000448) MGI MGI:87963 Agt GO:0007160 MGI:MGI:2385816|PMID:9734405 IMP MGI:2136636 P angiotensinogen (serpin peptidase inhibitor, clade A, member 8) Aogen|Serpina8 gene taxon:10090 20051229 MGI relationship(CL:0000127) MGI MGI:87963 Agt GO:0008285 MGI:MGI:1336863|PMID:10318840 IMP MGI:1857121 P angiotensinogen (serpin peptidase inhibitor, clade A, member 8) Aogen|Serpina8 gene taxon:10090 20051230 MGI relationship(CL:0000461) MGI MGI:87963 Agt GO:0008285 MGI:MGI:77583|PMID:8675666 IMP MGI:2183545 P angiotensinogen (serpin peptidase inhibitor, clade A, member 8) Aogen|Serpina8 gene taxon:10090 20051230 MGI relationship(CL:0000359) MGI MGI:87963 Agt GO:0008285 MGI:MGI:77583|PMID:8675666 IMP MGI:2183545 P angiotensinogen (serpin peptidase inhibitor, clade A, member 8) Aogen|Serpina8 gene taxon:10090 20051230 MGI relationship(CL:0000648) MGI MGI:87963 Agt GO:0030198 MGI:MGI:2385816|PMID:9734405 IMP MGI:2136636 P angiotensinogen (serpin peptidase inhibitor, clade A, member 8) Aogen|Serpina8 gene taxon:10090 20051229 MGI relationship(CL:0000127) MGI MGI:87963 Agt GO:0043410 MGI:MGI:892747|PMID:9196031 IMP MGI:2136636 P angiotensinogen (serpin peptidase inhibitor, clade A, member 8) Aogen|Serpina8 gene taxon:10090 20051228 MGI relationship(CL:0000001) MGI MGI:87963 Agt GO:0043524 MGI:MGI:2385817|PMID:9310306 IMP MGI:2136636 P angiotensinogen (serpin peptidase inhibitor, clade A, member 8) Aogen|Serpina8 gene taxon:10090 20051229 MGI relationship(CL:0000001) MGI MGI:87963 Agt GO:0048143 MGI:MGI:2385816|PMID:9734405 IMP MGI:2136636 P angiotensinogen (serpin peptidase inhibitor, clade A, member 8) Aogen|Serpina8 gene taxon:10090 20051229 MGI relationship(CL:0000127) MGI MGI:87963 Agt GO:0048659 MGI:MGI:1313232|PMID:9788961 IDA P angiotensinogen (serpin peptidase inhibitor, clade A, member 8) Aogen|Serpina8 gene taxon:10090 20051230 MGI relationship(CL:0000001) MGI MGI:87963 Agt GO:0048659 MGI:MGI:1313232|PMID:9788961 IMP MGI:2183545 P angiotensinogen (serpin peptidase inhibitor, clade A, member 8) Aogen|Serpina8 gene taxon:10090 20051230 MGI relationship(CL:0000192) MGI MGI:87963 Agt GO:0051145 MGI:MGI:1313232|PMID:9788961 IDA P angiotensinogen (serpin peptidase inhibitor, clade A, member 8) Aogen|Serpina8 gene taxon:10090 20051230 MGI relationship(CL:0000001) MGI MGI:87963 Agt GO:0051145 MGI:MGI:1313232|PMID:9788961 IMP MGI:2183545 P angiotensinogen (serpin peptidase inhibitor, clade A, member 8) Aogen|Serpina8 gene taxon:10090 20051230 MGI relationship(CL:0000192) MGI MGI:2159437 Agtpbp1 GO:0021702 MGI:MGI:1347769|PMID:10630211 IMP MGI:1856535 P ATP/GTP binding protein 1 Nna1 gene taxon:10090 20070116 MGI relationship(CL:0000121) MGI MGI:87964 Agtr1a GO:0005737 MGI:MGI:3610800|PMID:15499027 IDA C angiotensin II receptor, type 1a Agtr-1a|Agtr1a|Angtr-1a|AT1|AT1a gene taxon:10090 20060210 MGI relationship(CL:0000071) MGI MGI:87964 Agtr1a GO:0005886 MGI:MGI:3610800|PMID:15499027 IDA C angiotensin II receptor, type 1a Agtr-1a|Agtr1a|Angtr-1a|AT1|AT1a gene taxon:10090 20060210 MGI relationship(CL:0000071) MGI MGI:87964 Agtr1a NOT GO:0043524 MGI:MGI:2385817|PMID:9310306 IMP P angiotensin II receptor, type 1a Agtr-1a|Agtr1a|Angtr-1a|AT1|AT1a gene taxon:10090 20051229 MGI relationship(CL:0000001) MGI MGI:87965 Agtr1b NOT GO:0043524 MGI:MGI:2385817|PMID:9310306 IMP P angiotensin II receptor, type 1b Agtr-1b|AT1B|AT2R1B gene taxon:10090 20051229 MGI relationship(CL:0000001) MGI MGI:87966 Agtr2 NOT GO:0043524 MGI:MGI:2385817|PMID:9310306 IMP P angiotensin II receptor, type 2 AT2 receptor gene taxon:10090 20051229 MGI relationship(CL:0000001) MGI MGI:1928488 Akap8 GO:0005634 MGI:MGI:3512088|PMID:12082153 IDA C A kinase (PRKA) anchor protein 8 AKAP95 gene taxon:10090 20041230 MGI relationship(CL:0000007) MGI MGI:1929955 Akr1a4 GO:0005829 MGI:MGI:3588122|PMID:15769935 IDA C aldo-keto reductase family 1, member A4 (aldehyde reductase) gene taxon:10090 20051222 MGI relationship(CL:0000182) MGI MGI:1929955 Akr1a4 GO:0016324 MGI:MGI:3588122|PMID:15769935 IDA C aldo-keto reductase family 1, member A4 (aldehyde reductase) gene taxon:10090 20051222 MGI relationship(CL:0000182) MGI MGI:87991 Alb1 GO:0005737 MGI:MGI:3511765|PMID:15576401 IDA C albumin 1 Alb-1 gene taxon:10090 20050105 MGI relationship(CL:0000223) MGI MGI:1313266 Alcam GO:0007411 MGI:MGI:3056232|PMID:15345243 IMP MGI:3056579 P activated leukocyte cell adhesion molecule BEN|CD166|DM-GRASP|MuSC|SC1 gene taxon:10090 20050216 MGI relationship(CL:0000540) MGI MGI:1313266 Alcam GO:0008045 MGI:MGI:3056232|PMID:15345243 IMP MGI:3056579 P activated leukocyte cell adhesion molecule BEN|CD166|DM-GRASP|MuSC|SC1 gene taxon:10090 20050216 MGI relationship(CL:0000100) MGI MGI:1313266 Alcam GO:0009897 MGI:MGI:892661|PMID:9209500 IDA C activated leukocyte cell adhesion molecule BEN|CD166|DM-GRASP|MuSC|SC1 gene taxon:10090 20050216 MGI relationship(CL:0000236) MGI MGI:1313266 Alcam GO:0009897 MGI:MGI:892661|PMID:9209500 IDA C activated leukocyte cell adhesion molecule BEN|CD166|DM-GRASP|MuSC|SC1 gene taxon:10090 20050216 MGI relationship(CL:0000624) MGI MGI:1313266 Alcam GO:0009897 MGI:MGI:892661|PMID:9209500 IDA C activated leukocyte cell adhesion molecule BEN|CD166|DM-GRASP|MuSC|SC1 gene taxon:10090 20050216 MGI relationship(CL:0000625) MGI MGI:1313266 Alcam GO:0030424 MGI:MGI:3607408|PMID:16267219 IDA C activated leukocyte cell adhesion molecule BEN|CD166|DM-GRASP|MuSC|SC1 gene taxon:10090 20060209 MGI relationship(CL:0000741) MGI MGI:1313266 Alcam GO:0043025 MGI:MGI:3607408|PMID:16267219 IDA C activated leukocyte cell adhesion molecule BEN|CD166|DM-GRASP|MuSC|SC1 gene taxon:10090 20060209 MGI relationship(CL:0000741) MGI MGI:1353450 Aldh1a1 GO:0043065 MGI:MGI:3608158|PMID:16207763 IGI MGI:1861722 P aldehyde dehydrogenase family 1, subfamily A1 Ahd-2|Ahd2|ALDH1|E1|Raldh1 gene taxon:10090 20060123 MGI relationship(CL:0000134) MGI MGI:1353450 Aldh1a1 GO:0043065 MGI:MGI:3624188|PMID:16611695 IGI MGI:1861722 P aldehyde dehydrogenase family 1, subfamily A1 Ahd-2|Ahd2|ALDH1|E1|Raldh1 gene taxon:10090 20060627 MGI relationship(CL:0000134) MGI MGI:107928 Aldh1a2 GO:0014032 MGI:MGI:3612223|PMID:16368932 IMP MGI:1857891 P aldehyde dehydrogenase family 1, subfamily A2 Aldh1a7|Raldh2|retinaldehyde dehydrogenase gene taxon:10090 20060321 MGI relationship(CL:0000008) MGI MGI:107928 Aldh1a2 GO:0030182 MGI:MGI:3530707|PMID:15652703 IMP MGI:2180721 P aldehyde dehydrogenase family 1, subfamily A2 Aldh1a7|Raldh2|retinaldehyde dehydrogenase gene taxon:10090 20050510 MGI relationship(CL:0000540) MGI MGI:107928 Aldh1a2 GO:0030182 MGI:MGI:3574740|PMID:15753214 IMP MGI:2451316 P aldehyde dehydrogenase family 1, subfamily A2 Aldh1a7|Raldh2|retinaldehyde dehydrogenase gene taxon:10090 20050509 MGI relationship(CL:0000100) MGI MGI:107928 Aldh1a2 GO:0043010 MGI:MGI:3055706|PMID:15366004 IMP MGI:2180721 P aldehyde dehydrogenase family 1, subfamily A2 Aldh1a7|Raldh2|retinaldehyde dehydrogenase gene taxon:10090 20041201 MGI relationship(CL:0000133) MGI MGI:1861722 Aldh1a3 GO:0043065 MGI:MGI:3608158|PMID:16207763 IGI MGI:1353450 P aldehyde dehydrogenase family 1, subfamily A3 ALDH6|RALDH3|retinaldehyde dehydrogenase 3|V1 gene taxon:10090 20060123 MGI relationship(CL:0000134) MGI MGI:1861722 Aldh1a3 GO:0043065 MGI:MGI:3608158|PMID:16207763 IMP MGI:3043947 P aldehyde dehydrogenase family 1, subfamily A3 ALDH6|RALDH3|retinaldehyde dehydrogenase 3|V1 gene taxon:10090 20060123 MGI relationship(CL:0000134) MGI MGI:1861722 Aldh1a3 GO:0043065 MGI:MGI:3624188|PMID:16611695 IGI MGI:1353450 P aldehyde dehydrogenase family 1, subfamily A3 ALDH6|RALDH3|retinaldehyde dehydrogenase 3|V1 gene taxon:10090 20060627 MGI relationship(CL:0000134) MGI MGI:1934606 Alms1 GO:0045598 MGI:MGI:3588454|PMID:16000322 IMP MGI:3576051 P Alstrom syndrome 1 homolog (human) gene taxon:10090 20051018 MGI relationship(CL:0000448) MGI MGI:1934606 Alms1 GO:0046548 MGI:MGI:3588454|PMID:16000322 IMP MGI:3576051 P Alstrom syndrome 1 homolog (human) gene taxon:10090 20051018 MGI relationship(CL:0000604) MGI MGI:1921268 Als2 GO:0006979 MGI:MGI:3588008|PMID:16107644 IMP MGI:3522476 P amyotrophic lateral sclerosis 2 (juvenile) homolog (human) Als2cr6|Alsin gene taxon:10090 20060727 MGI relationship(CL:0000530) MGI MGI:2447532 Als2cl GO:0007032 MGI:MGI:3054618|PMID:15388334 ISS EMBL:AB107015 P ALS2 C-terminal like mRn.49018 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:88006 Amh GO:0005737 MGI:MGI:3578091|PMID:15789443 IDA C anti-Mullerian hormone MIS|Mullerian inhibiting substance gene taxon:10090 20050607 MGI relationship(CL:0000134) MGI MGI:105062 Amhr2 GO:0005887 MGI:MGI:2178495|PMID:11960012 ISS UniProt:Q62893 C anti-Mullerian hormone type 2 receptor MIS TypeII receptor|MISIIR gene taxon:10090 20060110 MGI relationship(CL:0000002) MGI MGI:1934943 Amn GO:0008104 MGI:MGI:3578036|PMID:15342463 IMP MGI:2135304|MGI:2135454 P amnionless gene taxon:10090 20050607 MGI relationship(CL:0000223) MGI MGI:1934943 Amn GO:0045177 MGI:MGI:3578036|PMID:15342463 IDA C amnionless gene taxon:10090 20050607 MGI relationship(CL:0000223) MGI MGI:1929286 Amotl2 GO:0005923 MGI:MGI:3588603|PMID:16019084 IDA C angiomotin like 2 Lccp|MASCOT gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:1202890 Angpt2 GO:0001525 MGI:MGI:3629544|PMID:16778080 IGI MGI:103178 P angiopoietin 2 Ang-2|Ang2 gene taxon:10090 20060807 MGI relationship(CL:0000001) MGI MGI:1919324 Anks4b GO:0005886 MGI:MGI:2451048|PMID:15461667 IDA C ankyrin repeat and sterile alpha motif domain containing 4B Harp gene taxon:10090 20050503 MGI relationship(CL:0000066) MGI MGI:88031 Anxa7 GO:0005634 MGI:MGI:3578689|PMID:15819996 IDA C annexin A7 Anx7|synexin gene taxon:10090 20050620 MGI relationship(CL:0000117) MGI MGI:88031 Anxa7 GO:0005634 MGI:MGI:3578689|PMID:15819996 IDA C annexin A7 Anx7|synexin gene taxon:10090 20050620 MGI relationship(CL:0000127) MGI MGI:88031 Anxa7 GO:0005829 MGI:MGI:3578689|PMID:15819996 IDA C annexin A7 Anx7|synexin gene taxon:10090 20050620 MGI relationship(CL:0000127) MGI MGI:88031 Anxa7 GO:0005829 MGI:MGI:3578689|PMID:15819996 IDA C annexin A7 Anx7|synexin gene taxon:10090 20050620 MGI relationship(CL:0000710) MGI MGI:101919 Ap1g1 GO:0005802 MGI:MGI:3055460|PMID:10444069 IDA C adaptor protein complex AP-1, gamma 1 subunit Adtg|D8Ertd374e|gamma-adaptin gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:101919 Ap1g1 GO:0048471 MGI:MGI:3055460|PMID:10444069 IDA C adaptor protein complex AP-1, gamma 1 subunit Adtg|D8Ertd374e|gamma-adaptin gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:107765 Apbb1 GO:0001764 MGI:MGI:3614238|PMID:16407979 IGI MGI:108405 P amyloid beta (A4) precursor protein-binding, family B, member 1 Fe65|Rir gene taxon:10090 20060307 MGI relationship(CL:0000117) MGI MGI:107765 Apbb1 GO:0007411 MGI:MGI:3614238|PMID:16407979 IGI MGI:108405 P amyloid beta (A4) precursor protein-binding, family B, member 1 Fe65|Rir gene taxon:10090 20060307 MGI relationship(CL:0000117) MGI MGI:108405 Apbb2 GO:0001764 MGI:MGI:3614238|PMID:16407979 IGI MGI:107765 P amyloid beta (A4) precursor protein-binding, family B, member 2 FE65L1|Rirl1|TR2L|Zfra gene taxon:10090 20060307 MGI relationship(CL:0000117) MGI MGI:108405 Apbb2 GO:0005737 MGI:MGI:3525895|PMID:15629131 IDA C amyloid beta (A4) precursor protein-binding, family B, member 2 FE65L1|Rirl1|TR2L|Zfra gene taxon:10090 20060307 MGI relationship(CL:0000002) MGI MGI:108405 Apbb2 GO:0007411 MGI:MGI:3614238|PMID:16407979 IGI MGI:107765 P amyloid beta (A4) precursor protein-binding, family B, member 2 FE65L1|Rirl1|TR2L|Zfra gene taxon:10090 20060307 MGI relationship(CL:0000117) MGI MGI:108405 Apbb2 GO:0043065 MGI:MGI:3525895|PMID:15629131 IDA P amyloid beta (A4) precursor protein-binding, family B, member 2 FE65L1|Rirl1|TR2L|Zfra gene taxon:10090 20060307 MGI relationship(CL:0000002) MGI MGI:108405 Apbb2 GO:0043066 MGI:MGI:3525895|PMID:15629131 IGI MGI:104798,MGI:99255 P amyloid beta (A4) precursor protein-binding, family B, member 2 FE65L1|Rirl1|TR2L|Zfra gene taxon:10090 20060307 MGI relationship(CL:0000002) MGI MGI:1926788 Apip GO:0043066 MGI:MGI:3056885|PMID:15262985 IMP P APAF1 interacting protein APIP2|CGI-29|Mmrp19 gene taxon:10090 20050103 MGI relationship(CL:0000002) MGI MGI:1926788 Apip GO:0043066 MGI:MGI:3056885|PMID:15262985 IMP P APAF1 interacting protein APIP2|CGI-29|Mmrp19 gene taxon:10090 20050103 MGI relationship(CL:0000188) MGI MGI:88047 Aplp2 GO:0009790 MGI:MGI:3577153|PMID:15689559 IGI MGI:88059 P amyloid beta (A4) precursor-like protein 2 gene taxon:10090 20051206 MGI relationship(CL:0000100) MGI MGI:88047 Aplp2 GO:0030900 MGI:MGI:3577153|PMID:15689559 IGI MGI:88059 P amyloid beta (A4) precursor-like protein 2 gene taxon:10090 20051205 MGI relationship(CL:0000100) MGI MGI:88047 Aplp2 GO:0030901 MGI:MGI:3577153|PMID:15689559 IGI MGI:88059 P amyloid beta (A4) precursor-like protein 2 gene taxon:10090 20051205 MGI relationship(CL:0000100) MGI MGI:88057 Apoe GO:0006874 MGI:MGI:66090|PMID:8185566 IDA P apolipoprotein E gene taxon:10090 20051207 MGI relationship(CL:0000001) MGI MGI:88057 Apoe GO:0042311 MGI:MGI:1314982|PMID:9826706 IMP MGI:2137814 P apolipoprotein E gene taxon:10090 20060222 MGI relationship(CL:0000071) MGI MGI:88059 App GO:0000085 MGI:MGI:3525784|PMID:15561424 IMP MGI:2154535 P amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051202 MGI relationship(CL:0000031) MGI MGI:88059 App GO:0005624 MGI:MGI:1861579|PMID:10845772 IDA C amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051205 MGI relationship(CL:0000188) MGI MGI:88059 App GO:0005737 MGI:MGI:1861579|PMID:10845772 IDA C amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051205 MGI relationship(CL:0000188) MGI MGI:88059 App GO:0006878 MGI:MGI:3056718|PMID:15447675 IGI MGI:88047 P amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051205 MGI relationship(CL:0000001) MGI MGI:88059 App GO:0007409 MGI:MGI:3606204|PMID:9390996 IMP MGI:2136847 P amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051202 MGI relationship(CL:0000001) MGI MGI:88059 App GO:0008088 MGI:MGI:2154812|PMID:11740561 IMP MGI:2136847 P amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051005 MGI relationship(CL:0000540) MGI MGI:88059 App GO:0016020 MGI:MGI:2674181|PMID:12927782 IDA C amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051202 MGI relationship(CL:0000002) MGI MGI:88059 App GO:0016199 MGI:MGI:69837|PMID:8001115 IMP MGI:2154522 P amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051206 MGI relationship(CL:0000117) MGI MGI:88059 App GO:0016322 MGI:MGI:1334893|PMID:10219973 IMP MGI:2136847 P amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051202 MGI relationship(CL:0000117) MGI MGI:88059 App GO:0016358 MGI:MGI:1333449|PMID:10188929 IMP MGI:2136847 P amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051205 MGI relationship(CL:0000598) MGI MGI:88059 App GO:0016358 MGI:MGI:3577153|PMID:15689559 IGI MGI:88047 P amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051205 MGI relationship(CL:0000100) MGI MGI:88059 App GO:0016358 MGI:MGI:3606204|PMID:9390996 IMP MGI:2136847 P amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051202 MGI relationship(CL:0000001) MGI MGI:88059 App GO:0030424 MGI:MGI:2154812|PMID:11740561 IDA C amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051005 MGI relationship(CL:0000540) MGI MGI:88059 App GO:0030424 MGI:MGI:3579206|PMID:15745965 IDA C amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051005 MGI relationship(CL:0000540) MGI MGI:88059 App GO:0030900 MGI:MGI:69837|PMID:8001115 IMP MGI:2154522 P amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051206 MGI relationship(CL:0000117) MGI MGI:88059 App GO:0031410 MGI:MGI:2154812|PMID:11740561 IDA C amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051005 MGI relationship(CL:0000540) MGI MGI:88059 App GO:0031410 MGI:MGI:3579206|PMID:15745965 IDA C amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051005 MGI relationship(CL:0000540) MGI MGI:88059 App GO:0045177 MGI:MGI:3525784|PMID:15561424 IDA C amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051202 MGI relationship(CL:0000710) MGI MGI:88059 App GO:0045931 MGI:MGI:3525784|PMID:15561424 IMP MGI:2154535 P amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051202 MGI relationship(CL:0000031) MGI MGI:88059 App GO:0048471 MGI:MGI:66935|PMID:8207383 IDA C amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051206 MGI relationship(CL:0000540) MGI MGI:88059 App GO:0048669 MGI:MGI:3577153|PMID:15689559 IGI MGI:88047 P amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051205 MGI relationship(CL:0000100) MGI MGI:88059 App GO:0050803 MGI:MGI:1334893|PMID:10219973 IMP MGI:2136847 P amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051202 MGI relationship(CL:0000117) MGI MGI:88059 App GO:0051124 MGI:MGI:3577153|PMID:15689559 IGI MGI:88047 P amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051205 MGI relationship(CL:0000100) MGI MGI:88059 App GO:0051233 MGI:MGI:3525784|PMID:15561424 IDA C amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051202 MGI relationship(CL:0000031) MGI MGI:88059 App GO:0051563 MGI:MGI:2449878|PMID:12431992 IGI MGI:1202717 P amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051206 MGI relationship(CL:0000001) MGI MGI:88059 App NOT GO:0008088 MGI:MGI:3579206|PMID:15745965 IMP MGI:2136847 P amyloid beta (A4) precursor protein Abeta|Adap|appican|betaAPP|Cvap|protease nexin II gene taxon:10090 20051005 MGI relationship(CL:0000540) MGI MGI:2664636 Aqp12 GO:0005737 MGI:MGI:3575463|PMID:15809071 IDA C aquaporin 12 gene taxon:10090 20050503 MGI relationship(CL:0000002) MGI MGI:2445003 Arhgap1 GO:0001726 MGI:MGI:3576987|PMID:15860730 IDA C Rho GTPase activating protein 1 p50rhoGAP gene taxon:10090 20061208 MGI relationship(CL:0000001) MGI MGI:2445003 Arhgap1 GO:0005886 MGI:MGI:3576987|PMID:15860730 IDA C Rho GTPase activating protein 1 p50rhoGAP gene taxon:10090 20061208 MGI relationship(CL:0000001) MGI MGI:2159617 Arr3 GO:0045202 MGI:MGI:3616100|PMID:12486395 IDA C arrestin 3, retinal CAR|mCAR|mCARFL gene taxon:10090 20060727 MGI relationship(CL:0000573) MGI MGI:1097716 Arx GO:0001764 MGI:MGI:2389512|PMID:12379852 IMP MGI:2429693 P aristaless related homeobox gene (Drosophila) gene taxon:10090 20050114 MGI relationship(CL:0000617) MGI MGI:1097716 Arx GO:0042127 MGI:MGI:2389512|PMID:12379852 IMP MGI:2429693 P aristaless related homeobox gene (Drosophila) gene taxon:10090 20050114 MGI relationship(CL:0000710) MGI MGI:96919 Ascl1 GO:0001764 MGI:MGI:3581944|PMID:15976074 IGI MGI:108055 P achaete-scute complex homolog-like 1 (Drosophila) ASH1|Mash1 gene taxon:10090 20050822 MGI relationship(CL:0000100) MGI MGI:96919 Ascl1 GO:0001764 MGI:MGI:3581944|PMID:15976074 IMP MGI:1857470 P achaete-scute complex homolog-like 1 (Drosophila) ASH1|Mash1 gene taxon:10090 20050822 MGI relationship(CL:0000100) MGI MGI:96919 Ascl1 GO:0005634 MGI:MGI:1888698|PMID:10952889 IDA C achaete-scute complex homolog-like 1 (Drosophila) ASH1|Mash1 gene taxon:10090 20061116 MGI relationship(CL:0000165) MGI MGI:96919 Ascl1 GO:0007400 MGI:MGI:2389286|PMID:12397111 IMP MGI:1857470 P achaete-scute complex homolog-like 1 (Drosophila) ASH1|Mash1 gene taxon:10090 20040817 MGI relationship(CL:0000031) MGI MGI:96919 Ascl1 GO:0010001 MGI:MGI:3581944|PMID:15976074 IGI MGI:108055 P achaete-scute complex homolog-like 1 (Drosophila) ASH1|Mash1 gene taxon:10090 20050822 MGI relationship(CL:0000128) MGI MGI:96919 Ascl1 GO:0030154 MGI:MGI:1888698|PMID:10952889 IMP MGI:1857470 P achaete-scute complex homolog-like 1 (Drosophila) ASH1|Mash1 gene taxon:10090 20061116 MGI relationship(CL:0000165) MGI MGI:96919 Ascl1 GO:0030182 MGI:MGI:3045910|PMID:15133515 IMP MGI:1857470 P achaete-scute complex homolog-like 1 (Drosophila) ASH1|Mash1 gene taxon:10090 20040817 MGI relationship(CL:0000403) MGI MGI:96919 Ascl1 GO:0043350 MGI:MGI:3581944|PMID:15976074 IGI MGI:108055 P achaete-scute complex homolog-like 1 (Drosophila) ASH1|Mash1 gene taxon:10090 20050822 MGI relationship(CL:0000031) MGI MGI:96919 Ascl1 GO:0048663 MGI:MGI:2651973|PMID:12629181 IMP MGI:1857470 P achaete-scute complex homolog-like 1 (Drosophila) ASH1|Mash1 gene taxon:10090 20050816 MGI relationship(CL:0000101) MGI MGI:96919 Ascl1 GO:0048663 MGI:MGI:3587461|PMID:16020526 IGI MGI:2151057 P achaete-scute complex homolog-like 1 (Drosophila) ASH1|Mash1 gene taxon:10090 20060202 MGI relationship(CL:0000099) MGI MGI:96920 Ascl2 GO:0030154 MGI:MGI:68639|PMID:8090202 IMP MGI:2153832 P achaete-scute complex homolog-like 2 (Drosophila) Mash2 gene taxon:10090 20040716 MGI relationship(CL:0000351) MGI MGI:1334448 Aspm GO:0000922 MGI:MGI:3654739|PMID:16798874 IDA C asp (abnormal spindle)-like, microcephaly associated (Drosophila) Aspm|Calmbp1|MCPH5|Sha1 gene taxon:10090 20070301 MGI relationship(CL:0000710) MGI MGI:1334448 Aspm GO:0021873 MGI:MGI:3654739|PMID:16798874 IMP P asp (abnormal spindle)-like, microcephaly associated (Drosophila) Aspm|Calmbp1|MCPH5|Sha1 gene taxon:10090 20070301 MGI relationship(CL:0000001) MGI MGI:1334448 Aspm GO:0045769 MGI:MGI:3654739|PMID:16798874 IMP P asp (abnormal spindle)-like, microcephaly associated (Drosophila) Aspm|Calmbp1|MCPH5|Sha1 gene taxon:10090 20070301 MGI relationship(CL:0000001) MGI MGI:1334448 Aspm GO:0051661 MGI:MGI:3654739|PMID:16798874 IMP P asp (abnormal spindle)-like, microcephaly associated (Drosophila) Aspm|Calmbp1|MCPH5|Sha1 gene taxon:10090 20070301 MGI relationship(CL:0000001) MGI MGI:1916188 Aspscr1 GO:0000300 MGI:MGI:3042070|PMID:14562105 IDA C alveolar soft part sarcoma chromosome region, candidate 1 (human) ASPC|ASPCR1|ASPL|RCC17|TUG gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1916188 Aspscr1 GO:0005515 MGI:MGI:3042070|PMID:14562105 IPI UniProt:P14672 F alveolar soft part sarcoma chromosome region, candidate 1 (human) ASPC|ASPCR1|ASPL|RCC17|TUG gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1916188 Aspscr1 GO:0005792 MGI:MGI:3042070|PMID:14562105 IDA C alveolar soft part sarcoma chromosome region, candidate 1 (human) ASPC|ASPCR1|ASPL|RCC17|TUG gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1916188 Aspscr1 GO:0005829 MGI:MGI:3042070|PMID:14562105 IDA C alveolar soft part sarcoma chromosome region, candidate 1 (human) ASPC|ASPCR1|ASPL|RCC17|TUG gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1916188 Aspscr1 GO:0006886 MGI:MGI:3042070|PMID:14562105 IDA P alveolar soft part sarcoma chromosome region, candidate 1 (human) ASPC|ASPCR1|ASPL|RCC17|TUG gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1916188 Aspscr1 GO:0009898 MGI:MGI:3042070|PMID:14562105 IDA C alveolar soft part sarcoma chromosome region, candidate 1 (human) ASPC|ASPCR1|ASPL|RCC17|TUG gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1916188 Aspscr1 GO:0012506 MGI:MGI:3042070|PMID:14562105 IDA C alveolar soft part sarcoma chromosome region, candidate 1 (human) ASPC|ASPCR1|ASPL|RCC17|TUG gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1916188 Aspscr1 GO:0019898 MGI:MGI:3042070|PMID:14562105 IDA C alveolar soft part sarcoma chromosome region, candidate 1 (human) ASPC|ASPCR1|ASPL|RCC17|TUG gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1916188 Aspscr1 GO:0042593 MGI:MGI:3042070|PMID:14562105 IDA P alveolar soft part sarcoma chromosome region, candidate 1 (human) ASPC|ASPCR1|ASPL|RCC17|TUG gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1916188 Aspscr1 GO:0046324 MGI:MGI:3042070|PMID:14562105 IDA P alveolar soft part sarcoma chromosome region, candidate 1 (human) ASPC|ASPCR1|ASPL|RCC17|TUG gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1916188 Aspscr1 GO:0048471 MGI:MGI:3042070|PMID:14562105 IDA C alveolar soft part sarcoma chromosome region, candidate 1 (human) ASPC|ASPCR1|ASPL|RCC17|TUG gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1914045 Atg10 GO:0005515 MGI:MGI:2447271|PMID:12482611 IPI UniProt:Q9D906,UniProt:Q99J83,UniProt:Q9CQY1 F autophagy-related 10 (yeast) APG10|Apg10l|Apg10p gene taxon:10090 20050524 MGI relationship(CL:0000002) MGI MGI:1914045 Atg10 GO:0005515 MGI:MGI:2677578|PMID:12890687 IPI UniProt:O94817,UniProt:O95352 F autophagy-related 10 (yeast) APG10|Apg10l|Apg10p gene taxon:10090 20050524 MGI relationship(CL:0000002) MGI MGI:1914045 Atg10 GO:0006497 MGI:MGI:2677578|PMID:12890687 IDA P autophagy-related 10 (yeast) APG10|Apg10l|Apg10p gene taxon:10090 20050523 MGI relationship(CL:0000002) MGI MGI:1914045 Atg10 GO:0031401 MGI:MGI:2677578|PMID:12890687 IDA P autophagy-related 10 (yeast) APG10|Apg10l|Apg10p gene taxon:10090 20050523 MGI relationship(CL:0000002) MGI MGI:1914776 Atg12 GO:0005515 MGI:MGI:2447271|PMID:12482611 IPI UniProt:Q9D906,UniProt:Q99J83,UniProt:Q8R1P4 F autophagy-related 12 (yeast) Apg12l gene taxon:10090 20050524 MGI relationship(CL:0000002) MGI MGI:1277186 Atg5 GO:0005515 MGI:MGI:2447271|PMID:12482611 IPI UniProt:Q8R1P4,UniProt:Q9CQY1 F autophagy-related 5 (yeast) Apg5l|Paddy gene taxon:10090 20061031 MGI relationship(CL:0000002) MGI MGI:1921494 Atg7 GO:0006497 MGI:MGI:2677578|PMID:12890687 ISS UniProt:O95352 P autophagy-related 7 (yeast) Apg7l gene taxon:10090 20050524 MGI relationship(CL:0000002) MGI MGI:1921494 Atg7 GO:0031401 MGI:MGI:2677578|PMID:12890687 ISS UniProt:O95352 P autophagy-related 7 (yeast) Apg7l gene taxon:10090 20050524 MGI relationship(CL:0000002) MGI MGI:104654 Atoh1 GO:0001764 MGI:MGI:3614298|PMID:16202707 IMP MGI:2155983 P atonal homolog 1 (Drosophila) Hath1|Math1 gene taxon:10090 20060309 MGI relationship(CL:0000031) MGI MGI:104654 Atoh1 GO:0007411 MGI:MGI:3607238|PMID:16145671 IMP MGI:2155984 P atonal homolog 1 (Drosophila) Hath1|Math1 gene taxon:10090 20060221 MGI relationship(CL:0000101) MGI MGI:104654 Atoh1 GO:0007420 MGI:MGI:2387274|PMID:12223565 IMP MGI:2155983 P atonal homolog 1 (Drosophila) Hath1|Math1 gene taxon:10090 20040702 MGI relationship(CL:0000120) MGI MGI:104654 Atoh1 GO:0030154 MGI:MGI:3525036|PMID:15543141 IMP MGI:2155983 P atonal homolog 1 (Drosophila) Hath1|Math1 gene taxon:10090 20050311 MGI relationship(CL:0000630) MGI MGI:104654 Atoh1 GO:0042472 MGI:MGI:3525036|PMID:15543141 IMP MGI:2155983 P atonal homolog 1 (Drosophila) Hath1|Math1 gene taxon:10090 20050309 MGI relationship(CL:0000202) MGI MGI:104654 Atoh1 GO:0042472 MGI:MGI:3525036|PMID:15543141 IMP MGI:2155983 P atonal homolog 1 (Drosophila) Hath1|Math1 gene taxon:10090 20050309 MGI relationship(CL:0000630) MGI MGI:104654 Atoh1 GO:0042491 MGI:MGI:3525036|PMID:15543141 IDA P atonal homolog 1 (Drosophila) Hath1|Math1 gene taxon:10090 20050311 MGI relationship(CL:0000202) MGI MGI:104654 Atoh1 GO:0042491 MGI:MGI:3525036|PMID:15543141 IDA P atonal homolog 1 (Drosophila) Hath1|Math1 gene taxon:10090 20050311 MGI relationship(CL:0000630) MGI MGI:104654 Atoh1 GO:0042491 MGI:MGI:3525036|PMID:15543141 IMP MGI:2155983 P atonal homolog 1 (Drosophila) Hath1|Math1 gene taxon:10090 20050311 MGI relationship(CL:0000202) MGI MGI:104654 Atoh1 GO:0042668 MGI:MGI:3611666|PMID:16407553 IDA P atonal homolog 1 (Drosophila) Hath1|Math1 gene taxon:10090 20060228 MGI relationship(CL:0000001) MGI MGI:88105 Atp1a1 GO:0005886 MGI:MGI:1860042|PMID:10837135 IDA C ATPase, Na+/K+ transporting, alpha 1 polypeptide Atpa-1 gene taxon:10090 20040719 MGI relationship(CL:0000353) MGI MGI:88105 Atp1a1 GO:0045989 MGI:MGI:3688972|PMID:11507009 IMP MGI:2451290 P ATPase, Na+/K+ transporting, alpha 1 polypeptide Atpa-1 gene taxon:10090 20061201 MGI relationship(CL:0000001) MGI MGI:88106 Atp1a2 GO:0002087 MGI:MGI:2450206|PMID:12458206 IMP MGI:2451291 P ATPase, Na+/K+ transporting, alpha 2 polypeptide Atpa-3 gene taxon:10090 20061010 MGI relationship(CL:0000117) MGI MGI:88106 Atp1a2 GO:0002087 MGI:MGI:3521550|PMID:15564586 IMP MGI:3522421 P ATPase, Na+/K+ transporting, alpha 2 polypeptide Atpa-3 gene taxon:10090 20061010 MGI relationship(CL:0000100) MGI MGI:88106 Atp1a2 GO:0006937 MGI:MGI:1337471|PMID:10360172 IMP MGI:2451291 P ATPase, Na+/K+ transporting, alpha 2 polypeptide Atpa-3 gene taxon:10090 20061005 MGI relationship(CL:0000001) MGI MGI:88106 Atp1a2 GO:0006940 MGI:MGI:3525892|PMID:14627611 IMP MGI:2451291 P ATPase, Na+/K+ transporting, alpha 2 polypeptide Atpa-3 gene taxon:10090 20061006 MGI relationship(CL:0000192) MGI MGI:88106 Atp1a2 GO:0045988 MGI:MGI:3688972|PMID:11507009 IMP MGI:2451291 P ATPase, Na+/K+ transporting, alpha 2 polypeptide Atpa-3 gene taxon:10090 20061201 MGI relationship(CL:0000001) MGI MGI:88106 Atp1a2 GO:0051481 MGI:MGI:1337471|PMID:10360172 IMP MGI:2451291 P ATPase, Na+/K+ transporting, alpha 2 polypeptide Atpa-3 gene taxon:10090 20061005 MGI relationship(CL:0000001) MGI MGI:88107 Atp1a3 GO:0005634 MGI:MGI:1860042|PMID:10837135 IDA C ATPase, Na+/K+ transporting, alpha 3 polypeptide Atpa-2 gene taxon:10090 20040719 MGI relationship(CL:0000353) MGI MGI:88107 Atp1a3 GO:0005737 MGI:MGI:1860042|PMID:10837135 IDA C ATPase, Na+/K+ transporting, alpha 3 polypeptide Atpa-2 gene taxon:10090 20040719 MGI relationship(CL:0000353) MGI MGI:88107 Atp1a3 NOT GO:0005886 MGI:MGI:1860042|PMID:10837135 IDA C ATPase, Na+/K+ transporting, alpha 3 polypeptide Atpa-2 gene taxon:10090 20040719 MGI relationship(CL:0000353) MGI MGI:88108 Atp1b1 GO:0005886 MGI:MGI:1860042|PMID:10837135 IDA C ATPase, Na+/K+ transporting, beta 1 polypeptide Atpb|Atpb-1|sodium/potassium ATPase beta subunit gene taxon:10090 20040719 MGI relationship(CL:0000353) MGI MGI:88108 Atp1b1 GO:0016323 MGI:MGI:1860042|PMID:10837135 IDA C ATPase, Na+/K+ transporting, beta 1 polypeptide Atpb|Atpb-1|sodium/potassium ATPase beta subunit gene taxon:10090 20040719 MGI relationship(CL:0000353) MGI MGI:88109 Atp1b2 GO:0005737 MGI:MGI:1860049|PMID:10859164 IDA C ATPase, Na+/K+ transporting, beta 2 polypeptide Amog|Atpb-2 gene taxon:10090 20040719 MGI relationship(CL:0000353) MGI MGI:107788 Atp1b3 GO:0005737 MGI:MGI:1860042|PMID:10837135 IDA C ATPase, Na+/K+ transporting, beta 3 polypeptide gene taxon:10090 20040719 MGI relationship(CL:0000353) MGI MGI:1915071 Atp1b4 GO:0005634 MGI:MGI:3525893|PMID:14656723 IDA C ATPase, (Na+)/K+ transporting, beta 4 polypeptide gene taxon:10090 20050314 MGI relationship(CL:0000187) MGI MGI:88110 Atp2a2 GO:0002026 MGI:MGI:1347184|PMID:10555147 IGI MGI:97622 P ATPase, Ca++ transporting, cardiac muscle, slow twitch 2 D5Wsu150e|sarco/endoplasmic reticulum Ca2+-ATPase 2|SERCA2 gene taxon:10090 20061016 MGI relationship(CL:0000746) MGI MGI:88110 Atp2a2 GO:0006874 MGI:MGI:2670850|PMID:12756243 IGI MGI:96074 P ATPase, Ca++ transporting, cardiac muscle, slow twitch 2 D5Wsu150e|sarco/endoplasmic reticulum Ca2+-ATPase 2|SERCA2 gene taxon:10090 20050603 MGI relationship(CL:0000117) MGI MGI:88110 Atp2a2 GO:0006874 MGI:MGI:2670850|PMID:12756243 IMP P ATPase, Ca++ transporting, cardiac muscle, slow twitch 2 D5Wsu150e|sarco/endoplasmic reticulum Ca2+-ATPase 2|SERCA2 gene taxon:10090 20050603 MGI relationship(CL:0000117) MGI MGI:88110 Atp2a2 GO:0016529 MGI:MGI:85770|PMID:9038922 IDA C ATPase, Ca++ transporting, cardiac muscle, slow twitch 2 D5Wsu150e|sarco/endoplasmic reticulum Ca2+-ATPase 2|SERCA2 gene taxon:10090 20061010 MGI relationship(CL:0000746) MGI MGI:88110 Atp2a2 GO:0045822 MGI:MGI:1347184|PMID:10555147 IGI MGI:97622 P ATPase, Ca++ transporting, cardiac muscle, slow twitch 2 D5Wsu150e|sarco/endoplasmic reticulum Ca2+-ATPase 2|SERCA2 gene taxon:10090 20061016 MGI relationship(CL:0000746) MGI MGI:105368 Atp2b2 GO:0000902 MGI:MGI:1342366|PMID:10441500 IMP MGI:1857092 P ATPase, Ca++ transporting, plasma membrane 2 D6Abb2e|PMCA2|wms gene taxon:10090 20061016 MGI relationship(CL:0000589) MGI MGI:105368 Atp2b2 GO:0005929 MGI:MGI:1342366|PMID:10441500 IDA C ATPase, Ca++ transporting, plasma membrane 2 D6Abb2e|PMCA2|wms gene taxon:10090 20061016 MGI relationship(CL:0000601) MGI MGI:105368 Atp2b2 GO:0006874 MGI:MGI:3608066|PMID:11985881 IMP MGI:1857092 P ATPase, Ca++ transporting, plasma membrane 2 D6Abb2e|PMCA2|wms gene taxon:10090 20061016 MGI relationship(CL:0000117) MGI MGI:105368 Atp2b2 GO:0007605 MGI:MGI:2149509|PMID:10687933 IMP MGI:1857092 P ATPase, Ca++ transporting, plasma membrane 2 D6Abb2e|PMCA2|wms gene taxon:10090 20061016 MGI relationship(CL:0000202) MGI MGI:105368 Atp2b2 GO:0021702 MGI:MGI:1275896|PMID:9668038 IMP MGI:1857876 P ATPase, Ca++ transporting, plasma membrane 2 D6Abb2e|PMCA2|wms gene taxon:10090 20061016 MGI relationship(CL:0000121) MGI MGI:105368 Atp2b2 GO:0021707 MGI:MGI:1275896|PMID:9668038 IMP MGI:1857876 P ATPase, Ca++ transporting, plasma membrane 2 D6Abb2e|PMCA2|wms gene taxon:10090 20061016 MGI relationship(CL:0000120) MGI MGI:105368 Atp2b2 GO:0043025 MGI:MGI:1342366|PMID:10441500 IDA C ATPase, Ca++ transporting, plasma membrane 2 D6Abb2e|PMCA2|wms gene taxon:10090 20061016 MGI relationship(CL:0000589) MGI MGI:105368 Atp2b2 GO:0050808 MGI:MGI:61556|PMID:7683393 IMP MGI:1857092 P ATPase, Ca++ transporting, plasma membrane 2 D6Abb2e|PMCA2|wms gene taxon:10090 20061016 MGI relationship(CL:0000117) MGI MGI:105368 Atp2b2 GO:0050808 MGI:MGI:61556|PMID:7683393 IMP MGI:1857092 P ATPase, Ca++ transporting, plasma membrane 2 D6Abb2e|PMCA2|wms gene taxon:10090 20061016 MGI relationship(CL:0000121) MGI MGI:105368 Atp2b2 GO:0050910 MGI:MGI:3625390|PMID:16529873 IMP MGI:1857876 P ATPase, Ca++ transporting, plasma membrane 2 D6Abb2e|PMCA2|wms gene taxon:10090 20061017 MGI relationship(CL:0000202) MGI MGI:103285 Atp6v1b1 GO:0016324 MGI:MGI:2687341|PMID:14585495 IDA C ATPase, H+ transporting, lysosomal V1 subunit B1 Atp6b1|lysosomal 56/58kDa|Vpp-3|Vpp3 gene taxon:10090 20040719 MGI relationship(CL:0000066) MGI MGI:99400 Atp7a GO:0005794 MGI:MGI:3574155|PMID:15634787 IDA C ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061030 MGI relationship(CL:0000117) MGI MGI:99400 Atp7a GO:0005802 MGI:MGI:3616392|PMID:16371425 IDA C ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061101 MGI relationship(CL:0000001) MGI MGI:99400 Atp7a GO:0005802 MGI:MGI:3689271|PMID:17003121 IDA C ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061212 MGI relationship(CL:0000001) MGI MGI:99400 Atp7a GO:0006878 MGI:MGI:1277426|PMID:9686356 IMP MGI:1856466 P ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061101 MGI relationship(CL:0000066) MGI MGI:99400 Atp7a GO:0006878 MGI:MGI:1277426|PMID:9686356 IMP MGI:1856466 P ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061101 MGI relationship(CL:0000117) MGI MGI:99400 Atp7a GO:0006878 MGI:MGI:1277426|PMID:9686356 IMP MGI:1856466 P ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061101 MGI relationship(CL:0000121) MGI MGI:99400 Atp7a GO:0006878 MGI:MGI:67983|PMID:8025644 IMP MGI:1856098 P ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061108 MGI relationship(CL:0000066) MGI MGI:99400 Atp7a GO:0006878 MGI:MGI:67983|PMID:8025644 IMP MGI:1856098 P ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061108 MGI relationship(CL:0000117) MGI MGI:99400 Atp7a GO:0006878 MGI:MGI:67983|PMID:8025644 IMP MGI:1856098 P ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061108 MGI relationship(CL:0000131) MGI MGI:99400 Atp7a GO:0007005 MGI:MGI:67697|PMID:8009964 IMP MGI:1856466 P ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061108 MGI relationship(CL:0000121) MGI MGI:99400 Atp7a GO:0007005 MGI:MGI:71791|PMID:2288383 IMP MGI:1856466 P ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061107 MGI relationship(CL:0000117) MGI MGI:99400 Atp7a GO:0007005 MGI:MGI:71791|PMID:2288383 IMP MGI:1856466 P ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061107 MGI relationship(CL:0000121) MGI MGI:99400 Atp7a GO:0016020 MGI:MGI:3576400|PMID:15634671 IDA C ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061018 MGI relationship(CL:0000002) MGI MGI:99400 Atp7a GO:0021702 MGI:MGI:71790|PMID:2473662 IMP MGI:1856466 P ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061107 MGI relationship(CL:0000121) MGI MGI:99400 Atp7a GO:0021860 MGI:MGI:71790|PMID:2473662 IMP MGI:1856466 P ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061107 MGI relationship(CL:0000598) MGI MGI:99400 Atp7a GO:0031410 MGI:MGI:3574155|PMID:15634787 IDA C ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061030 MGI relationship(CL:0000001) MGI MGI:99400 Atp7a GO:0031410 MGI:MGI:3689271|PMID:17003121 IDA C ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061212 MGI relationship(CL:0000001) MGI MGI:99400 Atp7a GO:0043005 MGI:MGI:3574155|PMID:15634787 IDA C ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061101 MGI relationship(CL:0000001) MGI MGI:99400 Atp7a GO:0043025 MGI:MGI:3576400|PMID:15634671 IDA C ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061018 MGI relationship(CL:0000644) MGI MGI:99400 Atp7a GO:0043526 MGI:MGI:3689271|PMID:17003121 IMP MGI:1856098 P ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061212 MGI relationship(CL:0000001) MGI MGI:99400 Atp7a GO:0048554 MGI:MGI:2449260|PMID:12488345 IMP MGI:1856098 P ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061101 MGI relationship(CL:0000163) MGI MGI:99400 Atp7a GO:0048813 MGI:MGI:71790|PMID:2473662 IMP MGI:1856466 P ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061107 MGI relationship(CL:0000121) MGI MGI:99400 Atp7a GO:0048813 MGI:MGI:71790|PMID:2473662 IMP MGI:1856466 P ATPase, Cu++ transporting, alpha polypeptide br|Menkes protein|MNK gene taxon:10090 20061107 MGI relationship(CL:0000598) MGI MGI:103297 Atp7b GO:0005802 MGI:MGI:1929057|PMID:11085952 IDA C ATPase, Cu++ transporting, beta polypeptide Atp7a|Wilson protein|WND gene taxon:10090 20061017 MGI relationship(CL:0000150) MGI MGI:103297 Atp7b GO:0006825 MGI:MGI:1929057|PMID:11085952 IMP MGI:1856220 P ATPase, Cu++ transporting, beta polypeptide Atp7a|Wilson protein|WND gene taxon:10090 20061017 MGI relationship(CL:0000150) MGI MGI:103297 Atp7b GO:0016020 MGI:MGI:3576400|PMID:15634671 IDA C ATPase, Cu++ transporting, beta polypeptide Atp7a|Wilson protein|WND gene taxon:10090 20061018 MGI relationship(CL:0000002) MGI MGI:104783 Atxn1 GO:0042405 MGI:MGI:3522382|PMID:15615787 IDA C ataxin 1 Atx1|Sca1 gene taxon:10090 20050512 MGI relationship(CL:0000002) MGI MGI:1913327 Aurkaip1 GO:0005634 MGI:MGI:2445268|PMID:12244051 ISS UniProt:Q9NWT8 C aurora kinase A interacting protein 1 AIP|Aurora-A kinase interacting protein gene taxon:10090 20060110 MGI relationship(CL:0000002) MGI MGI:88121 Avp GO:0030819 MGI:MGI:3612779|PMID:15632412 IDA P arginine vasopressin Vp|Vsp gene taxon:10090 20060223 MGI relationship(CL:0000001) MGI MGI:1270862 Axin2 GO:0001957 MGI:MGI:3578608|PMID:15790973 IMP MGI:3579503 P axin2 Axil|Conductin gene taxon:10090 20050816 MGI relationship(CL:0000062) MGI MGI:1270862 Axin2 GO:0008285 MGI:MGI:3578608|PMID:15790973 IMP MGI:3579503 P axin2 Axil|Conductin gene taxon:10090 20050812 MGI relationship(CL:0000062) MGI MGI:1270862 Axin2 GO:0045668 MGI:MGI:3578608|PMID:15790973 IMP MGI:3579503 P axin2 Axil|Conductin gene taxon:10090 20050812 MGI relationship(CL:0000062) MGI MGI:1891321 Aym1 GO:0001673 MGI:MGI:3522530|PMID:15531368 IDA C activator of yeast meiotic promoters 1 gene taxon:10090 20070213 MGI relationship(CL:0000020) MGI MGI:1891321 Aym1 GO:0001673 MGI:MGI:3522530|PMID:15531368 IDA C activator of yeast meiotic promoters 1 gene taxon:10090 20070213 MGI relationship(CL:0000656) MGI MGI:1891321 Aym1 GO:0001673 MGI:MGI:3522530|PMID:15531368 IDA C activator of yeast meiotic promoters 1 gene taxon:10090 20070213 MGI relationship(CL:0000657) MGI MGI:1891321 Aym1 GO:0001674 MGI:MGI:3522530|PMID:15531368 IDA C activator of yeast meiotic promoters 1 gene taxon:10090 20070213 MGI relationship(CL:0000023) MGI MGI:1889505 B3gnt2 GO:0007411 MGI:MGI:3575344|PMID:15728829 IMP MGI:3576265 P UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2 B3Galt6|B3gnt1 gene taxon:10090 20050513 MGI relationship(CL:0000101) MGI MGI:1342058 B4galnt2 GO:0006047 MGI:MGI:56455|PMID:4031755 IMP MGI:3579308 P beta-1,4-N-acetyl-galactosaminyl transferase 2 CT-Gal NAc transferase|Dlb-1|Dlb1|Galgt2 gene taxon:10090 20070213 MGI relationship(CL:0000071) MGI MGI:1342058 B4galnt2 GO:0006047 MGI:MGI:56455|PMID:4031755 IMP MGI:3579308 P beta-1,4-N-acetyl-galactosaminyl transferase 2 CT-Gal NAc transferase|Dlb-1|Dlb1|Galgt2 gene taxon:10090 20070213 MGI relationship(CL:0000131) MGI MGI:1342058 B4galnt2 GO:0006047 MGI:MGI:65525|PMID:8137279 IMP P beta-1,4-N-acetyl-galactosaminyl transferase 2 CT-Gal NAc transferase|Dlb-1|Dlb1|Galgt2 gene taxon:10090 20070213 MGI relationship(CL:0000131) MGI MGI:95705 B4galt1 GO:0002064 MGI:MGI:87365|PMID:9155011 IMP MGI:2450889 P UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070215 MGI relationship(CL:0000066) MGI MGI:95705 B4galt1 GO:0003831 MGI:MGI:75839|PMID:7641815 IDA F UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070214 MGI relationship(CL:0000002) MGI MGI:95705 B4galt1 GO:0003831 MGI:MGI:84206|PMID:8787759 IMP MGI:2388614 F UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070215 MGI relationship(CL:0000001) MGI MGI:95705 B4galt1 GO:0007155 MGI:MGI:3619189|PMID:12714507 IGI MGI:98280 P UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070216 MGI relationship(CL:0000576) MGI MGI:95705 B4galt1 GO:0007155 MGI:MGI:3619189|PMID:12714507 IGI MGI:98280 P UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070216 MGI relationship(CL:0000738) MGI MGI:95705 B4galt1 GO:0008092 MGI:MGI:65229|PMID:8134355 IDA F UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070213 MGI relationship(CL:0000002) MGI MGI:95705 B4galt1 GO:0008092 MGI:MGI:75839|PMID:7641815 IDA F UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070214 MGI relationship(CL:0000002) MGI MGI:95705 B4galt1 GO:0008285 MGI:MGI:75839|PMID:7641815 IGI MGI:95290|MGI:95294 P UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070214 MGI relationship(CL:0000002) MGI MGI:95705 B4galt1 GO:0008285 MGI:MGI:87365|PMID:9155011 IMP MGI:2450889 P UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070215 MGI relationship(CL:0000066) MGI MGI:95705 B4galt1 GO:0008378 MGI:MGI:65229|PMID:8134355 IDA F UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070213 MGI relationship(CL:0000002) MGI MGI:95705 B4galt1 GO:0008378 MGI:MGI:75839|PMID:7641815 IDA F UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070214 MGI relationship(CL:0000002) MGI MGI:95705 B4galt1 GO:0009101 MGI:MGI:3619189|PMID:12714507 IMP MGI:2450889 P UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070216 MGI relationship(CL:0000738) MGI MGI:95705 B4galt1 GO:0009986 MGI:MGI:65229|PMID:8134355 IDA C UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070213 MGI relationship(CL:0000002) MGI MGI:95705 B4galt1 GO:0009986 MGI:MGI:75839|PMID:7641815 IDA C UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070214 MGI relationship(CL:0000002) MGI MGI:95705 B4galt1 GO:0009986 MGI:MGI:84206|PMID:8787759 IMP MGI:2388614 C UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070215 MGI relationship(CL:0000001) MGI MGI:95705 B4galt1 GO:0030198 MGI:MGI:84206|PMID:8787759 IMP MGI:2388614 P UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070215 MGI relationship(CL:0000001) MGI MGI:95705 B4galt1 GO:0042127 MGI:MGI:75839|PMID:7641815 IMP P UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070214 MGI relationship(CL:0000002) MGI MGI:95705 B4galt1 GO:0050900 MGI:MGI:3038538|PMID:15039218 IMP MGI:2450889 P UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070216 MGI relationship(CL:0000235) MGI MGI:95705 B4galt1 GO:0051270 MGI:MGI:65229|PMID:8134355 IDA P UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070213 MGI relationship(CL:0000002) MGI MGI:95705 B4galt1 GO:0060054 MGI:MGI:3038538|PMID:15039218 IMP MGI:2450889 P UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1 B-1,4-GalT1|b1,4-Galactosyltransferase I|beta 1,4-Galactosyltransferase I|beta-1,4-GalT1|GalT|Ggtb|Ggtb2 gene taxon:10090 20070301 MGI relationship(CL:0000066) MGI MGI:1928704 Baalc GO:0005737 MGI:MGI:3530196|PMID:15749074 IDA C brain and acute leukemia, cytoplasmic gene taxon:10090 20050505 MGI relationship(CL:0000002) MGI MGI:1928704 Baalc GO:0005737 MGI:MGI:3530196|PMID:15749074 IDA C brain and acute leukemia, cytoplasmic gene taxon:10090 20050505 MGI relationship(CL:0000188) MGI MGI:1928704 Baalc GO:0005737 MGI:MGI:3530196|PMID:15749074 IDA C brain and acute leukemia, cytoplasmic gene taxon:10090 20050505 MGI relationship(CL:0000192) MGI MGI:1928704 Baalc GO:0005737 MGI:MGI:3530196|PMID:15749074 IDA C brain and acute leukemia, cytoplasmic gene taxon:10090 20050505 MGI relationship(CL:0000193) MGI MGI:1346542 Bace1 GO:0030424 MGI:MGI:2154812|PMID:11740561 IDA C beta-site APP cleaving enzyme 1 APP beta-secretase gene taxon:10090 20051005 MGI relationship(CL:0000540) MGI MGI:1346542 Bace1 GO:0031410 MGI:MGI:2154812|PMID:11740561 IDA C beta-site APP cleaving enzyme 1 APP beta-secretase gene taxon:10090 20051005 MGI relationship(CL:0000540) MGI MGI:1352493 Bag3 GO:0005515 MGI:MGI:3513163|PMID:11527400 IPI UniProt:Q61698 F Bcl2-associated athanogene 3 Bcl-2-interacting death suppressor|Bis gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1352493 Bag3 GO:0043066 MGI:MGI:3513163|PMID:11527400 IDA P Bcl2-associated athanogene 3 Bcl-2-interacting death suppressor|Bis gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1914634 Bag4 GO:0005515 MGI:MGI:3513163|PMID:11527400 IPI UniProt:Q61698 F BCL2-associated athanogene 4 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1859288 Barhl1 GO:0001764 MGI:MGI:3573845|PMID:15044550 IMP MGI:2181383 P BarH-like 1 (Drosophila) Dres115|MBH2 gene taxon:10090 20050512 MGI relationship(CL:0000117) MGI MGI:1859314 Barhl2 GO:0030182 MGI:MGI:3039051|PMID:14998930 IDA P BarH-like 2 (Drosophila) MBH1 gene taxon:10090 20040520 MGI relationship(CL:0000561) MGI MGI:1859314 Barhl2 GO:0045165 MGI:MGI:3039051|PMID:14998930 IDA P BarH-like 2 (Drosophila) MBH1 gene taxon:10090 20040520 MGI relationship(CL:0000561) MGI MGI:103124 Barx1 GO:0007267 MGI:MGI:3577819|PMID:15809042 IGI MGI:1196625,MGI:1196625 P BarH-like homeobox 1 gene taxon:10090 20050728 MGI relationship(CL:0000001) MGI MGI:103124 Barx1 GO:0007267 MGI:MGI:3577819|PMID:15809042 IMP MGI:3578634 P BarH-like homeobox 1 gene taxon:10090 20050728 MGI relationship(CL:0000001) MGI MGI:103124 Barx1 GO:0030178 MGI:MGI:3577819|PMID:15809042 IGI MGI:1196625,MGI:1196625 P BarH-like homeobox 1 gene taxon:10090 20050728 MGI relationship(CL:0000001) MGI MGI:103124 Barx1 GO:0030855 MGI:MGI:3577819|PMID:15809042 IMP P BarH-like homeobox 1 gene taxon:10090 20050728 MGI relationship(CL:0000001) MGI MGI:99702 Bax GO:0005741 MGI:MGI:3607027|PMID:16227588 IDA C Bcl2-associated X protein gene taxon:10090 20060413 MGI relationship(CL:0000002) MGI MGI:99702 Bax GO:0005829 MGI:MGI:3607027|PMID:16227588 IDA C Bcl2-associated X protein gene taxon:10090 20060413 MGI relationship(CL:0000002) MGI MGI:1277215 Bbs1 GO:0035058 MGI:MGI:3607949|PMID:16170314 IGI MGI:2135272 P Bardet-Biedl syndrome 1 homolog (human) D19Ertd609e gene taxon:10090 20060123 MGI relationship(CL:0000601) MGI MGI:1277215 Bbs1 GO:0035058 MGI:MGI:3607949|PMID:16170314 IMP MGI:3055491 P Bardet-Biedl syndrome 1 homolog (human) D19Ertd609e gene taxon:10090 20060123 MGI relationship(CL:0000601) MGI MGI:2135267 Bbs2 GO:0007288 MGI:MGI:3512844|PMID:15539463 IMP MGI:3521669 P Bardet-Biedl syndrome 2 homolog (human) gene taxon:10090 20050215 MGI relationship(CL:0000018) MGI MGI:2135267 Bbs2 GO:0008104 MGI:MGI:3512844|PMID:15539463 IMP MGI:3521669 P Bardet-Biedl syndrome 2 homolog (human) gene taxon:10090 20050215 MGI relationship(CL:0000210) MGI MGI:2135267 Bbs2 GO:0045494 MGI:MGI:3512844|PMID:15539463 IMP MGI:3521669 P Bardet-Biedl syndrome 2 homolog (human) gene taxon:10090 20050215 MGI relationship(CL:0000210) MGI MGI:2143311 Bbs4 GO:0001895 MGI:MGI:3044824|PMID:15173597 IMP MGI:3045473 P Bardet-Biedl syndrome 4 homolog (human) D9Ertd464e gene taxon:10090 20041223 MGI relationship(CL:0000210) MGI MGI:2143311 Bbs4 GO:0005813 MGI:MGI:3530392|PMID:15649943 IDA C Bardet-Biedl syndrome 4 homolog (human) D9Ertd464e gene taxon:10090 20050424 MGI relationship(CL:0000002) MGI MGI:2143311 Bbs4 GO:0007286 MGI:MGI:3044824|PMID:15173597 IMP MGI:3045473 P Bardet-Biedl syndrome 4 homolog (human) D9Ertd464e gene taxon:10090 20070129 MGI relationship(CL:0000019) MGI MGI:2143311 Bbs4 GO:0035058 MGI:MGI:3607949|PMID:16170314 IMP MGI:3055492 P Bardet-Biedl syndrome 4 homolog (human) D9Ertd464e gene taxon:10090 20060123 MGI relationship(CL:0000601) MGI MGI:2143311 Bbs4 GO:0045724 MGI:MGI:3044824|PMID:15173597 IMP MGI:3045473 P Bardet-Biedl syndrome 4 homolog (human) D9Ertd464e gene taxon:10090 20041223 MGI relationship(CL:0000019) MGI MGI:2143311 Bbs4 GO:0046548 MGI:MGI:3044824|PMID:15173597 IMP MGI:3045473 P Bardet-Biedl syndrome 4 homolog (human) D9Ertd464e gene taxon:10090 20070129 MGI relationship(CL:0000604) MGI MGI:1924210 Bcas1 GO:0005829 MGI:MGI:2679944|PMID:14567997 ISS EMBL:AF041260 C breast carcinoma amplified sequence 1 NABC1 gene taxon:10090 20050510 MGI relationship(CL:0000002) MGI MGI:1924210 Bcas1 GO:0042803 MGI:MGI:2679944|PMID:14567997 ISS EMBL:AF041260 F breast carcinoma amplified sequence 1 NABC1 gene taxon:10090 20050510 MGI relationship(CL:0000002) MGI MGI:1929913 Bcl11b GO:0007409 MGI:MGI:3578473|PMID:15664173 IMP MGI:2663971 P B-cell leukemia/lymphoma 11B COUP-TF interacting protein 2|CTIP2|Rit1 gene taxon:10090 20050722 MGI relationship(CL:0000100) MGI MGI:88140 Bcl3 GO:0002268 MGI:MGI:3655550|PMID:10586052 IMP MGI:2158443 P B-cell leukemia/lymphoma 3 Bcl-3 gene taxon:10090 20061229 MGI relationship(CL:0000442) MGI MGI:107187 Bcl6 GO:0000902 MGI:MGI:3576987|PMID:15860730 IGI MGI:1096342 P B-cell leukemia/lymphoma 6 Bcl5 gene taxon:10090 20061207 MGI relationship(CL:0000001) MGI MGI:107187 Bcl6 GO:0000902 MGI:MGI:3576987|PMID:15860730 IMP MGI:2158438 P B-cell leukemia/lymphoma 6 Bcl5 gene taxon:10090 20061207 MGI relationship(CL:0000001) MGI MGI:107187 Bcl6 GO:0001953 MGI:MGI:3576987|PMID:15860730 IMP MGI:2158438 P B-cell leukemia/lymphoma 6 Bcl5 gene taxon:10090 20061207 MGI relationship(CL:0000001) MGI MGI:107187 Bcl6 GO:0007266 MGI:MGI:3576987|PMID:15860730 IGI MGI:1096342 P B-cell leukemia/lymphoma 6 Bcl5 gene taxon:10090 20061207 MGI relationship(CL:0000001) MGI MGI:107187 Bcl6 GO:0008104 MGI:MGI:3576987|PMID:15860730 IMP MGI:2158438 P B-cell leukemia/lymphoma 6 Bcl5 gene taxon:10090 20061208 MGI relationship(CL:0000001) MGI MGI:107187 Bcl6 GO:0008285 MGI:MGI:3531029|PMID:15507530 IMP MGI:2158439 P B-cell leukemia/lymphoma 6 Bcl5 gene taxon:10090 20061211 MGI relationship(CL:0000001) MGI MGI:107187 Bcl6 GO:0030036 MGI:MGI:3576987|PMID:15860730 IMP MGI:2158438 P B-cell leukemia/lymphoma 6 Bcl5 gene taxon:10090 20061207 MGI relationship(CL:0000001) MGI MGI:107187 Bcl6 GO:0032319 MGI:MGI:3576987|PMID:15860730 IMP MGI:2158438 P B-cell leukemia/lymphoma 6 Bcl5 gene taxon:10090 20061207 MGI relationship(CL:0000001) MGI MGI:107187 Bcl6 GO:0032764 MGI:MGI:3581006|PMID:15950739 IMP MGI:2158436 P B-cell leukemia/lymphoma 6 Bcl5 gene taxon:10090 20061206 MGI relationship(CL:0000001) MGI MGI:107187 Bcl6 GO:0035024 MGI:MGI:3576987|PMID:15860730 IMP MGI:2158438 P B-cell leukemia/lymphoma 6 Bcl5 gene taxon:10090 20061207 MGI relationship(CL:0000001) MGI MGI:107187 Bcl6 GO:0043066 MGI:MGI:1330702|PMID:9927203 IDA P B-cell leukemia/lymphoma 6 Bcl5 gene taxon:10090 20061208 MGI relationship(CL:0000002) MGI MGI:107187 Bcl6 GO:0048821 MGI:MGI:3613333|PMID:15661395 IMP MGI:2158436 P B-cell leukemia/lymphoma 6 Bcl5 gene taxon:10090 20061206 MGI relationship(CL:0000558) MGI MGI:107187 Bcl6 GO:0051272 MGI:MGI:3576987|PMID:15860730 IMP MGI:2158438 P B-cell leukemia/lymphoma 6 Bcl5 gene taxon:10090 20061207 MGI relationship(CL:0000001) MGI MGI:88145 Bdnf GO:0001657 MGI:MGI:3588889|PMID:16018995 IDA P brain derived neurotrophic factor gene taxon:10090 20060306 MGI relationship(CL:0000001) MGI MGI:88145 Bdnf GO:0007411 MGI:MGI:3629534|PMID:15014133 IMP MGI:1929986 P brain derived neurotrophic factor gene taxon:10090 20060807 MGI relationship(CL:0000101) MGI MGI:88145 Bdnf GO:0007412 MGI:MGI:3511733|PMID:15464571 IMP MGI:1930038 P brain derived neurotrophic factor gene taxon:10090 20050110 MGI relationship(CL:0000101) MGI MGI:88145 Bdnf GO:0008038 MGI:MGI:3578094|PMID:15844198 IMP P brain derived neurotrophic factor gene taxon:10090 20050729 MGI relationship(CL:0000101) MGI MGI:88145 Bdnf GO:0016358 MGI:MGI:2669042|PMID:12890780 IMP P brain derived neurotrophic factor gene taxon:10090 20041221 MGI relationship(CL:0000540) MGI MGI:88145 Bdnf GO:0042490 MGI:MGI:3505841|PMID:15376326 IGI MGI:1857232,MGI:1857233 P brain derived neurotrophic factor gene taxon:10090 20050113 MGI relationship(CL:0000199) MGI MGI:88145 Bdnf GO:0043524 MGI:MGI:80051|PMID:8861722 IMP P brain derived neurotrophic factor gene taxon:10090 20070222 MGI relationship(CL:0000001) MGI MGI:2153710 Bhlhb4 GO:0046671 MGI:MGI:3054140|PMID:15363390 IMP MGI:3054837 P basic helix-loop-helix domain containing, class B4 beta-cell E-box transactivating factor 4|BETA4 gene taxon:10090 20041220 MGI relationship(CL:0000103) MGI MGI:2153710 Bhlhb4 GO:0048050 MGI:MGI:3054140|PMID:15363390 IMP MGI:3054837 P basic helix-loop-helix domain containing, class B4 beta-cell E-box transactivating factor 4|BETA4 gene taxon:10090 20041220 MGI relationship(CL:0000103) MGI MGI:891976 Bhlhb8 GO:0005634 MGI:MGI:3611530|PMID:16423820 IDA C basic helix-loop-helix domain containing, class B, 8 Mist1 gene taxon:10090 20060228 MGI relationship(CL:0000152) MGI MGI:891976 Bhlhb8 GO:0007267 MGI:MGI:2671736|PMID:12829745 IMP MGI:2182768 P basic helix-loop-helix domain containing, class B, 8 Mist1 gene taxon:10090 20060228 MGI relationship(CL:0000622) MGI MGI:891976 Bhlhb8 GO:0048469 MGI:MGI:3038031|PMID:15024058 IMP P basic helix-loop-helix domain containing, class B, 8 Mist1 gene taxon:10090 20060228 MGI relationship(CL:0000622) MGI MGI:891976 Bhlhb8 GO:0048469 MGI:MGI:3611530|PMID:16423820 IMP MGI:2182768 P basic helix-loop-helix domain containing, class B, 8 Mist1 gene taxon:10090 20060228 MGI relationship(CL:0000169) MGI MGI:1206591 Bik GO:0005740 MGI:MGI:1202139|PMID:9525867 IDA C Bcl2-interacting killer Biklk|Blk|Nbk gene taxon:10090 20040408 MGI relationship(CL:0000002) MGI MGI:1206591 Bik GO:0006917 MGI:MGI:1202139|PMID:9525867 IDA P Bcl2-interacting killer Biklk|Blk|Nbk gene taxon:10090 20040408 MGI relationship(CL:0000002) MGI MGI:1276108 Birc6 GO:0008284 MGI:MGI:3583045|PMID:15887267 IMP MGI:2678436 P baculoviral IAP repeat-containing 6 apollon|Bruce gene taxon:10090 20060125 MGI relationship(CL:0000523) MGI MGI:88174 Bmi1 GO:0048103 MGI:MGI:3041338|PMID:12714971 IMP MGI:1857632 P Bmi1 polycomb ring finger oncogene Bmi-1|Bmi1|Pcgf4 gene taxon:10090 20040630 MGI relationship(CL:0000037) MGI MGI:88177 Bmp2 GO:0001658 MGI:MGI:3583399|PMID:15925496 IGI MGI:104903 P bone morphogenetic protein 2 Bmp2a gene taxon:10090 20060214 MGI relationship(CL:0000001) MGI MGI:88177 Bmp2 GO:0001837 MGI:MGI:3044331|PMID:15110716 ISS UniProt:P12643 P bone morphogenetic protein 2 Bmp2a gene taxon:10090 20040722 MGI relationship(CL:0000134) MGI MGI:88177 Bmp2 GO:0008285 MGI:MGI:3583399|PMID:15925496 IGI MGI:104903 P bone morphogenetic protein 2 Bmp2a gene taxon:10090 20060214 MGI relationship(CL:0000001) MGI MGI:88177 Bmp2 GO:0035051 MGI:MGI:3044331|PMID:15110716 ISS UniProt:P12643 P bone morphogenetic protein 2 Bmp2a gene taxon:10090 20040722 MGI relationship(CL:0000134) MGI MGI:88177 Bmp2 GO:0045597 MGI:MGI:3513220|PMID:15525533 IDA P bone morphogenetic protein 2 Bmp2a gene taxon:10090 20050121 MGI relationship(CL:0000139) MGI MGI:88177 Bmp2 GO:0045669 MGI:MGI:3587162|PMID:16099986 IDA P bone morphogenetic protein 2 Bmp2a gene taxon:10090 20060201 MGI relationship(CL:0000002) MGI MGI:88177 Bmp2 GO:0048711 MGI:MGI:3577784|PMID:15882580 IDA P bone morphogenetic protein 2 Bmp2a gene taxon:10090 20060214 MGI relationship(CL:0000001) MGI MGI:88177 Bmp2 GO:0048711 MGI:MGI:3577784|PMID:15882580 IGI MGI:99414 P bone morphogenetic protein 2 Bmp2a gene taxon:10090 20060214 MGI relationship(CL:0000001) MGI MGI:88180 Bmp4 GO:0007281 MGI:MGI:3050161|PMID:15289457 IMP MGI:1857137 P bone morphogenetic protein 4 Bmp2b|Bmp2b1 gene taxon:10090 20041007 MGI relationship(CL:0000586) MGI MGI:88180 Bmp4 GO:0030324 MGI:MGI:3618437|PMID:16414041 IMP MGI:2181190|MGI:3574949 P bone morphogenetic protein 4 Bmp2b|Bmp2b1 gene taxon:10090 20060515 MGI relationship(CL:0000082) MGI MGI:88180 Bmp4 GO:0042475 MGI:MGI:3603904|PMID:16179481 IDA P bone morphogenetic protein 4 Bmp2b|Bmp2b1 gene taxon:10090 20051128 MGI relationship(CL:0000001) MGI MGI:88180 Bmp4 GO:0042475 MGI:MGI:3603904|PMID:16179481 IGI MGI:1913292 P bone morphogenetic protein 4 Bmp2b|Bmp2b1 gene taxon:10090 20051128 MGI relationship(CL:0000001) MGI MGI:88180 Bmp4 GO:0045595 MGI:MGI:3513220|PMID:15525533 IGI MGI:95586 P bone morphogenetic protein 4 Bmp2b|Bmp2b1 gene taxon:10090 20050121 MGI relationship(CL:0000139) MGI MGI:88180 Bmp4 GO:0045597 MGI:MGI:3513220|PMID:15525533 IDA P bone morphogenetic protein 4 Bmp2b|Bmp2b1 gene taxon:10090 20050121 MGI relationship(CL:0000139) MGI MGI:88180 Bmp4 GO:0051145 MGI:MGI:3624584|PMID:16546160 IDA P bone morphogenetic protein 4 Bmp2b|Bmp2b1 gene taxon:10090 20060717 MGI relationship(CL:0000001) MGI MGI:103302 Bmp7 GO:0001707 MGI:MGI:3578079|PMID:15843411 IGI MGI:2137520 P bone morphogenetic protein 7 OP1|osteogenic protein 1 gene taxon:10090 20050617 MGI relationship(CL:0000222) MGI MGI:103302 Bmp7 GO:0035239 MGI:MGI:3575981|PMID:15831470 IDA P bone morphogenetic protein 7 OP1|osteogenic protein 1 gene taxon:10090 20050526 MGI relationship(CL:0000002) MGI MGI:103302 Bmp7 GO:0045597 MGI:MGI:3513220|PMID:15525533 IDA P bone morphogenetic protein 7 OP1|osteogenic protein 1 gene taxon:10090 20050121 MGI relationship(CL:0000139) MGI MGI:103302 Bmp7 GO:0048468 MGI:MGI:3575981|PMID:15831470 IDA P bone morphogenetic protein 7 OP1|osteogenic protein 1 gene taxon:10090 20050526 MGI relationship(CL:0000002) MGI MGI:103302 Bmp7 GO:0048754 MGI:MGI:3575981|PMID:15831470 IDA P bone morphogenetic protein 7 OP1|osteogenic protein 1 gene taxon:10090 20051212 MGI relationship(CL:0000002) MGI MGI:1338938 Bmpr1a GO:0009950 MGI:MGI:2670493|PMID:12923052 IMP MGI:2181295 P bone morphogenetic protein receptor, type 1A ALK3|Bmpr|BMPR-IA gene taxon:10090 20050103 MGI relationship(CL:0000221) MGI MGI:1338938 Bmpr1a GO:0030154 MGI:MGI:3487205|PMID:15469980 IGI MGI:107191 P bone morphogenetic protein receptor, type 1A ALK3|Bmpr|BMPR-IA gene taxon:10090 20041214 MGI relationship(CL:0000402) MGI MGI:1338938 Bmpr1a GO:0030324 MGI:MGI:3618437|PMID:16414041 IMP MGI:2158390|MGI:3574949 P bone morphogenetic protein receptor, type 1A ALK3|Bmpr|BMPR-IA gene taxon:10090 20060515 MGI relationship(CL:0000082) MGI MGI:1338938 Bmpr1a GO:0050679 MGI:MGI:3618437|PMID:16414041 IMP MGI:2158390|MGI:3574949 P bone morphogenetic protein receptor, type 1A ALK3|Bmpr|BMPR-IA gene taxon:10090 20060515 MGI relationship(CL:0000082) MGI MGI:107191 Bmpr1b GO:0001654 MGI:MGI:2181740|PMID:12117821 IMP P bone morphogenetic protein receptor, type 1B Acvrlk6|Alk6|BMPR-IB|CFK-43a gene taxon:10090 20050518 MGI relationship(CL:0000306) MGI MGI:107191 Bmpr1b GO:0030154 MGI:MGI:2181740|PMID:12117821 IMP P bone morphogenetic protein receptor, type 1B Acvrlk6|Alk6|BMPR-IB|CFK-43a gene taxon:10090 20050518 MGI relationship(CL:0000306) MGI MGI:107191 Bmpr1b GO:0030154 MGI:MGI:3487205|PMID:15469980 IGI MGI:1338938 P bone morphogenetic protein receptor, type 1B Acvrlk6|Alk6|BMPR-IB|CFK-43a gene taxon:10090 20041214 MGI relationship(CL:0000402) MGI MGI:2151153 Boc GO:0007224 MGI:MGI:3624617|PMID:16647303 IDA P biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding protein gene taxon:10090 20060717 MGI relationship(CL:0000002) MGI MGI:3045315 Bpi GO:0005737 MGI:MGI:3530426|PMID:15590754 IDA C bactericidal permeablility increasing protein gene taxon:10090 20050503 MGI relationship(CL:0000094) MGI MGI:88190 Braf GO:0005737 MGI:MGI:3578616|PMID:15736129 IDA C Braf transforming gene Braf-2|Braf2|D6Ertd631e gene taxon:10090 20050615 MGI relationship(CL:0000007) MGI MGI:88190 Braf GO:0005886 MGI:MGI:3578616|PMID:15736129 IDA C Braf transforming gene Braf-2|Braf2|D6Ertd631e gene taxon:10090 20050615 MGI relationship(CL:0000007) MGI MGI:104537 Brca1 GO:0000793 MGI:MGI:2671746|PMID:12913077 IDA C breast cancer 1 gene taxon:10090 20040902 MGI relationship(CL:0000017) MGI MGI:99495 Brd2 GO:0005634 MGI:MGI:3051972|PMID:15063089 IDA C bromodomain containing 2 D17H6S113E|Frg-1|Fsrg1|Ring3|Rnf3 gene taxon:10090 20060726 MGI relationship(CL:0000031) MGI MGI:99495 Brd2 GO:0005737 MGI:MGI:3051972|PMID:15063089 IDA C bromodomain containing 2 D17H6S113E|Frg-1|Fsrg1|Ring3|Rnf3 gene taxon:10090 20060726 MGI relationship(CL:0000099) MGI MGI:99495 Brd2 GO:0005737 MGI:MGI:3051972|PMID:15063089 IDA C bromodomain containing 2 D17H6S113E|Frg-1|Fsrg1|Ring3|Rnf3 gene taxon:10090 20060726 MGI relationship(CL:0000100) MGI MGI:99495 Brd2 GO:0005737 MGI:MGI:3051972|PMID:15063089 IDA C bromodomain containing 2 D17H6S113E|Frg-1|Fsrg1|Ring3|Rnf3 gene taxon:10090 20060726 MGI relationship(CL:0000101) MGI MGI:2685946 Brsk1 GO:0030010 MGI:MGI:3528781|PMID:15705853 IGI MGI:1923020 P BR serine/threonine kinase 1 LOC381979|SAD-B gene taxon:10090 20050519 MGI relationship(CL:0000117) MGI MGI:2685946 Brsk1 GO:0030182 MGI:MGI:3528781|PMID:15705853 IGI MGI:1923020 P BR serine/threonine kinase 1 LOC381979|SAD-B gene taxon:10090 20050519 MGI relationship(CL:0000117) MGI MGI:1923020 Brsk2 GO:0030010 MGI:MGI:3528781|PMID:15705853 IGI MGI:2685946 P BR serine/threonine kinase 2 SAD-A gene taxon:10090 20050519 MGI relationship(CL:0000117) MGI MGI:1923020 Brsk2 GO:0030182 MGI:MGI:3528781|PMID:15705853 IGI MGI:2685946 P BR serine/threonine kinase 2 SAD-A gene taxon:10090 20050519 MGI relationship(CL:0000117) MGI MGI:1347001 Btd GO:0005730 MGI:MGI:3607479|PMID:16107307 IDA C biotinidase gene taxon:10090 20060221 MGI relationship(CL:0000540) MGI MGI:1347001 Btd GO:0043204 MGI:MGI:3607479|PMID:16107307 IDA C biotinidase gene taxon:10090 20060221 MGI relationship(CL:0000540) MGI MGI:1347001 Btd GO:0045177 MGI:MGI:3607479|PMID:16107307 IDA C biotinidase gene taxon:10090 20060221 MGI relationship(CL:0000067) MGI MGI:88216 Btk GO:0004713 MGI:MGI:1859033|PMID:10872802 IDA F Bruton agammaglobulinemia tyrosine kinase Bruton's tyrosine kinase|X-linked immune deficiency|xid gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:88216 Btk GO:0018108 MGI:MGI:1859033|PMID:10872802 IDA P Bruton agammaglobulinemia tyrosine kinase Bruton's tyrosine kinase|X-linked immune deficiency|xid gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:2658978 Btla GO:0007166 MGI:MGI:3521631|PMID:15568026 IDA P B and T lymphocyte associated gene taxon:10090 20070105 MGI relationship(CL:0000002) MGI MGI:2151071 C1galt1 GO:0001525 MGI:MGI:3531500|PMID:14745002 IMP MGI:3531503 P core 1 UDP-galactose:N-acetylgalactosamine-alpha-R beta 1,3-galactosyltransferase core 1 beta3-Gal-T|T-synthase gene taxon:10090 20050511 MGI relationship(CL:0000071) MGI MGI:109482 Cacna1a GO:0005245 MGI:MGI:1261389|PMID:9614225 IMP MGI:1856210 F calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070115 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0005245 MGI:MGI:1321414|PMID:9857013 IMP MGI:1856210|MGI:1856209 F calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070115 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0005245 MGI:MGI:1350870|PMID:10611370 IMP MGI:2181384 F calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070116 MGI relationship(CL:0000120) MGI MGI:109482 Cacna1a GO:0005245 MGI:MGI:1350870|PMID:10611370 IMP MGI:2181384 F calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070116 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0005245 MGI:MGI:3619817|PMID:12151514 IMP MGI:1856209 F calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070130 MGI relationship(CL:0000117) MGI MGI:109482 Cacna1a GO:0006816 MGI:MGI:1261389|PMID:9614225 IMP MGI:1856210 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070115 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0006816 MGI:MGI:1321414|PMID:9857013 IMP MGI:1856210|MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070115 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0007268 MGI:MGI:3626144|PMID:12040045 IMP MGI:1856211|MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070122 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0007270 MGI:MGI:3619286|PMID:16540584 IMP MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070118 MGI relationship(CL:0000117) MGI MGI:109482 Cacna1a GO:0007416 MGI:MGI:1337561|PMID:10336181 IMP MGI:1856211 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070115 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0007416 MGI:MGI:3042538|PMID:14973254 IMP MGI:2181384 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070117 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0008331 MGI:MGI:1861319|PMID:10908603 IMP MGI:1856211 F calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070116 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0008331 MGI:MGI:2153687|PMID:11718712 IMP MGI:1856210 F calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070116 MGI relationship(CL:0000540) MGI MGI:109482 Cacna1a GO:0008331 MGI:MGI:2179541|PMID:11344116 IMP MGI:2180190 F calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070116 MGI relationship(CL:0000001) MGI MGI:109482 Cacna1a GO:0008331 MGI:MGI:2654957|PMID:12624181 IMP MGI:2181384 F calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070118 MGI relationship(CL:0000100) MGI MGI:109482 Cacna1a GO:0008331 MGI:MGI:3622595|PMID:12401561 IMP MGI:2181384 F calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070122 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0008331 MGI:MGI:3626144|PMID:12040045 IMP MGI:1856211|MGI:1856209 F calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070122 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0008331 MGI:MGI:3655539|PMID:9742139 IMP MGI:1856210 F calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070122 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0014051 MGI:MGI:1353373|PMID:10670432 IMP MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070116 MGI relationship(CL:0000117) MGI MGI:109482 Cacna1a GO:0014056 MGI:MGI:2654957|PMID:12624181 IMP MGI:2181384 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070118 MGI relationship(CL:0000100) MGI MGI:109482 Cacna1a GO:0014056 MGI:MGI:3606714|PMID:10686170 IMP MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070118 MGI relationship(CL:0000100) MGI MGI:109482 Cacna1a GO:0016049 MGI:MGI:62667|PMID:1306163 IMP MGI:1856209|MGI:1856210 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070102 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0019226 MGI:MGI:49712|PMID:1572065 IMP MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20061229 MGI relationship(CL:0000598) MGI MGI:109482 Cacna1a GO:0019226 MGI:MGI:51705|PMID:1469420 IMP MGI:1856211 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20061229 MGI relationship(CL:0000117) MGI MGI:109482 Cacna1a GO:0019226 MGI:MGI:52137|PMID:1355109 IMP MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20061229 MGI relationship(CL:0000598) MGI MGI:109482 Cacna1a GO:0021590 MGI:MGI:2179541|PMID:11344116 IMP MGI:2180190 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070116 MGI relationship(CL:0000120) MGI MGI:109482 Cacna1a GO:0021590 MGI:MGI:2179541|PMID:11344116 IMP MGI:2180190 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070116 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0021680 MGI:MGI:62667|PMID:1306163 IMP MGI:1856209|MGI:1856210 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070102 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0021702 MGI:MGI:1347769|PMID:10630211 IMP MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070116 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0021702 MGI:MGI:62667|PMID:1306163 IMP MGI:1856209|MGI:1856210 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070102 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0021702 MGI:MGI:68980|PMID:7834360 IMP MGI:1856210 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070102 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0021750 MGI:MGI:77774|PMID:8719615 IMP MGI:1856210 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070102 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0021953 MGI:MGI:55090|PMID:6945603 IMP MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070122 MGI relationship(CL:0000459) MGI MGI:109482 Cacna1a GO:0030425 MGI:MGI:3055272|PMID:15451373 IDA C calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20061212 MGI relationship(CL:0000100) MGI MGI:109482 Cacna1a GO:0030644 MGI:MGI:3610944|PMID:10899223 IMP MGI:1856210 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070118 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0035249 MGI:MGI:3042538|PMID:14973254 IMP MGI:2181384 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070117 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0042391 MGI:MGI:1261389|PMID:9614225 IMP MGI:1856210 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070115 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0042391 MGI:MGI:1321414|PMID:9857013 IMP MGI:1856210|MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070115 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0042391 MGI:MGI:1353373|PMID:10670432 IMP MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070116 MGI relationship(CL:0000117) MGI MGI:109482 Cacna1a GO:0042391 MGI:MGI:3619817|PMID:12151514 IMP MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20061227 MGI relationship(CL:0000117) MGI MGI:109482 Cacna1a GO:0042391 MGI:MGI:3622595|PMID:12401561 IMP MGI:2181384 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070122 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0042391 MGI:MGI:49712|PMID:1572065 IMP MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20061229 MGI relationship(CL:0000598) MGI MGI:109482 Cacna1a GO:0042391 MGI:MGI:52137|PMID:1355109 IMP MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20061229 MGI relationship(CL:0000598) MGI MGI:109482 Cacna1a GO:0043025 MGI:MGI:3055272|PMID:15451373 IDA C calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20061212 MGI relationship(CL:0000100) MGI MGI:109482 Cacna1a GO:0043113 MGI:MGI:2654957|PMID:12624181 IMP MGI:2181384 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070116 MGI relationship(CL:0000188) MGI MGI:109482 Cacna1a GO:0043524 MGI:MGI:53718|PMID:4941467 IMP MGI:1856210|MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070122 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0043524 MGI:MGI:84024|PMID:8929530 IMP MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070104 MGI relationship(CL:0000120) MGI MGI:109482 Cacna1a GO:0043524 MGI:MGI:84024|PMID:8929530 IMP MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070104 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0048791 MGI:MGI:1353373|PMID:10670432 IMP MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070116 MGI relationship(CL:0000117) MGI MGI:109482 Cacna1a GO:0048813 MGI:MGI:1337561|PMID:10336181 IMP MGI:1856211 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070115 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0048813 MGI:MGI:2150969|PMID:11160387 IMP MGI:2154404 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070116 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0048813 MGI:MGI:3042538|PMID:14973254 IMP MGI:2181384 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070117 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0050770 MGI:MGI:54631|PMID:572084 IMP MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070122 MGI relationship(CL:0000459) MGI MGI:109482 Cacna1a GO:0051899 MGI:MGI:1861319|PMID:10908603 IMP MGI:1856211 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070116 MGI relationship(CL:0000121) MGI MGI:109482 Cacna1a GO:0051899 MGI:MGI:2153687|PMID:11718712 IMP MGI:1856210 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070116 MGI relationship(CL:0000540) MGI MGI:109482 Cacna1a GO:0051899 MGI:MGI:66121|PMID:8158221 IMP MGI:1856209 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070102 MGI relationship(CL:0000598) MGI MGI:109482 Cacna1a GO:0060024 MGI:MGI:3620292|PMID:16474392 IMP MGI:1856210 P calcium channel, voltage-dependent, P/Q type, alpha 1A subunit alpha1A|Cacnl1a4|Ccha1a|EA2|MHP1|nmf352|SCA6 gene taxon:10090 20070123 MGI relationship(CL:0000121) MGI MGI:88296 Cacna1b GO:0030425 MGI:MGI:3055272|PMID:15451373 IDA C calcium channel, voltage-dependent, N type, alpha 1B subunit alpha(1B)|Cav2.2|Cchn1a gene taxon:10090 20061212 MGI relationship(CL:0000100) MGI MGI:88296 Cacna1b GO:0043025 MGI:MGI:3055272|PMID:15451373 IDA C calcium channel, voltage-dependent, N type, alpha 1B subunit alpha(1B)|Cav2.2|Cchn1a gene taxon:10090 20061212 MGI relationship(CL:0000100) MGI MGI:103013 Cacna1c GO:0002095 MGI:MGI:3628972|PMID:16648270 IDA C calcium channel, voltage-dependent, L type, alpha 1C subunit (alpha)1 subunit|Cav1.2|Cchl1a1|L-type Cav1.2 gene taxon:10090 20070117 MGI relationship(CL:0000187) MGI MGI:103013 Cacna1c GO:0005245 MGI:MGI:2670808|PMID:12881419 IMP MGI:2674119|MGI:2176227 F calcium channel, voltage-dependent, L type, alpha 1C subunit (alpha)1 subunit|Cav1.2|Cchl1a1|L-type Cav1.2 gene taxon:10090 20061212 MGI relationship(CL:0000001) MGI MGI:103013 Cacna1c GO:0005245 MGI:MGI:3663939|PMID:14609949 IMP MGI:2674119|MGI:2389040 F calcium channel, voltage-dependent, L type, alpha 1C subunit (alpha)1 subunit|Cav1.2|Cchl1a1|L-type Cav1.2 gene taxon:10090 20061212 MGI relationship(CL:0000187) MGI MGI:103013 Cacna1c GO:0005886 MGI:MGI:3580191|PMID:15090038 IDA C calcium channel, voltage-dependent, L type, alpha 1C subunit (alpha)1 subunit|Cav1.2|Cchl1a1|L-type Cav1.2 gene taxon:10090 20061212 MGI relationship(CL:0000617) MGI MGI:103013 Cacna1c GO:0005886 MGI:MGI:3580191|PMID:15090038 IDA C calcium channel, voltage-dependent, L type, alpha 1C subunit (alpha)1 subunit|Cav1.2|Cchl1a1|L-type Cav1.2 gene taxon:10090 20061212 MGI relationship(CL:0000679) MGI MGI:103013 Cacna1c GO:0017156 MGI:MGI:2670808|PMID:12881419 IMP MGI:2674119|MGI:2176227 P calcium channel, voltage-dependent, L type, alpha 1C subunit (alpha)1 subunit|Cav1.2|Cchl1a1|L-type Cav1.2 gene taxon:10090 20061212 MGI relationship(CL:0000001) MGI MGI:103013 Cacna1c GO:0030073 MGI:MGI:2670808|PMID:12881419 IMP MGI:2674119|MGI:2176227 P calcium channel, voltage-dependent, L type, alpha 1C subunit (alpha)1 subunit|Cav1.2|Cchl1a1|L-type Cav1.2 gene taxon:10090 20061212 MGI relationship(CL:0000001) MGI MGI:103013 Cacna1c GO:0043025 MGI:MGI:3580191|PMID:15090038 IDA C calcium channel, voltage-dependent, L type, alpha 1C subunit (alpha)1 subunit|Cav1.2|Cchl1a1|L-type Cav1.2 gene taxon:10090 20061212 MGI relationship(CL:0000617) MGI MGI:103013 Cacna1c GO:0043025 MGI:MGI:3580191|PMID:15090038 IDA C calcium channel, voltage-dependent, L type, alpha 1C subunit (alpha)1 subunit|Cav1.2|Cchl1a1|L-type Cav1.2 gene taxon:10090 20061212 MGI relationship(CL:0000679) MGI MGI:103013 Cacna1c GO:0043198 MGI:MGI:3580191|PMID:15090038 IDA C calcium channel, voltage-dependent, L type, alpha 1C subunit (alpha)1 subunit|Cav1.2|Cchl1a1|L-type Cav1.2 gene taxon:10090 20061212 MGI relationship(CL:0000617) MGI MGI:103013 Cacna1c GO:0043198 MGI:MGI:3580191|PMID:15090038 IDA C calcium channel, voltage-dependent, L type, alpha 1C subunit (alpha)1 subunit|Cav1.2|Cchl1a1|L-type Cav1.2 gene taxon:10090 20061212 MGI relationship(CL:0000679) MGI MGI:88293 Cacna1d GO:0005887 MGI:MGI:2678967|PMID:12900400 IC GO:0008331 C calcium channel, voltage-dependent, L type, alpha 1D subunit C79217|Cacnl1a2|Cav1.3alpha1|Cchl1a|Cchl1a2|D-LTCC gene taxon:10090 20061113 MGI relationship(CL:0000002) MGI MGI:88293 Cacna1d GO:0008331 MGI:MGI:2678967|PMID:12900400 IDA F calcium channel, voltage-dependent, L type, alpha 1D subunit C79217|Cacnl1a2|Cav1.3alpha1|Cchl1a|Cchl1a2|D-LTCC gene taxon:10090 20061113 MGI relationship(CL:0000002) MGI MGI:1859639 Cacna1f GO:0007409 MGI:MGI:3608035|PMID:16155113 IMP MGI:3609549 P calcium channel, voltage-dependent, alpha 1F subunit Cav1.4|Sfc17 gene taxon:10090 20061113 MGI relationship(CL:0000745) MGI MGI:1859639 Cacna1f GO:0007409 MGI:MGI:3608035|PMID:16155113 IMP MGI:3609549 P calcium channel, voltage-dependent, alpha 1F subunit Cav1.4|Sfc17 gene taxon:10090 20061113 MGI relationship(CL:0000749) MGI MGI:1859639 Cacna1f GO:0048813 MGI:MGI:3608035|PMID:16155113 IMP MGI:3609549 P calcium channel, voltage-dependent, alpha 1F subunit Cav1.4|Sfc17 gene taxon:10090 20061113 MGI relationship(CL:0000745) MGI MGI:1859639 Cacna1f GO:0048813 MGI:MGI:3608035|PMID:16155113 IMP MGI:3609549 P calcium channel, voltage-dependent, alpha 1F subunit Cav1.4|Sfc17 gene taxon:10090 20061113 MGI relationship(CL:0000749) MGI MGI:88294 Cacna1s GO:0030315 MGI:MGI:1342891|PMID:10444070 IDA C calcium channel, voltage-dependent, L type, alpha 1S subunit Cav1.1|Cchl1a3|DHPR alpha1s|fmd|mdg|muscle dysgenesis|sj gene taxon:10090 20061010 MGI relationship(CL:0000188) MGI MGI:1929813 Cacna2d2 GO:0060024 MGI:MGI:3620292|PMID:16474392 IMP MGI:1856022 P calcium channel, voltage-dependent, alpha 2/delta subunit 2 a2d2 gene taxon:10090 20070123 MGI relationship(CL:0000121) MGI MGI:894644 Cacnb2 GO:0007268 MGI:MGI:2429657|PMID:11980879 IMP MGI:2429694 P calcium channel, voltage-dependent, beta 2 subunit Cchb2 gene taxon:10090 20061227 MGI relationship(CL:0000604) MGI MGI:894644 Cacnb2 GO:0007601 MGI:MGI:2429657|PMID:11980879 IMP MGI:2429694 P calcium channel, voltage-dependent, beta 2 subunit Cchb2 gene taxon:10090 20061227 MGI relationship(CL:0000751) MGI MGI:103301 Cacnb4 GO:0005245 MGI:MGI:3619817|PMID:12151514 IMP MGI:1856936 F calcium channel, voltage-dependent, beta 4 subunit Cchb4 gene taxon:10090 20061227 MGI relationship(CL:0000117) MGI MGI:103301 Cacnb4 GO:0019227 MGI:MGI:55031|PMID:7261997 IMP MGI:1856936 P calcium channel, voltage-dependent, beta 4 subunit Cchb4 gene taxon:10090 20061222 MGI relationship(CL:0000100) MGI MGI:103301 Cacnb4 GO:0042391 MGI:MGI:3619817|PMID:12151514 IMP MGI:1856936 P calcium channel, voltage-dependent, beta 4 subunit Cchb4 gene taxon:10090 20061227 MGI relationship(CL:0000117) MGI MGI:103301 Cacnb4 NOT GO:0030217 MGI:MGI:3691409|PMID:17028169 IMP MGI:1856936 P calcium channel, voltage-dependent, beta 4 subunit Cchb4 gene taxon:10090 20061227 MGI relationship(CL:0000084) MGI MGI:1316660 Cacng2 GO:0005245 MGI:MGI:3619817|PMID:12151514 IMP MGI:1856548 F calcium channel, voltage-dependent, gamma subunit 2 stargazin gene taxon:10090 20061227 MGI relationship(CL:0000117) MGI MGI:1316660 Cacng2 GO:0042391 MGI:MGI:3619817|PMID:12151514 IMP MGI:1856548 P calcium channel, voltage-dependent, gamma subunit 2 stargazin gene taxon:10090 20061227 MGI relationship(CL:0000117) MGI MGI:1889272 Cadm1 GO:0005886 MGI:MGI:3530685|PMID:15707673 IDA C cell adhesion molecule 1 Igsf4|Igsf4a|Necl2|RA175A|RA175B|RA175C|RA175N|SgIGSF|SynCam|Tslc1 gene taxon:10090 20050505 MGI relationship(CL:0000001) MGI MGI:1889272 Cadm1 GO:0030424 MGI:MGI:3530685|PMID:15707673 IDA C cell adhesion molecule 1 Igsf4|Igsf4a|Necl2|RA175A|RA175B|RA175C|RA175N|SgIGSF|SynCam|Tslc1 gene taxon:10090 20050505 MGI relationship(CL:0000001) MGI MGI:1889272 Cadm1 GO:0030425 MGI:MGI:3530685|PMID:15707673 IDA C cell adhesion molecule 1 Igsf4|Igsf4a|Necl2|RA175A|RA175B|RA175C|RA175N|SgIGSF|SynCam|Tslc1 gene taxon:10090 20050505 MGI relationship(CL:0000001) MGI MGI:2137858 Cadm3 GO:0005911 MGI:MGI:3582084|PMID:15893517 IDA C cell adhesion molecule 3 BIgR|Igsf4b|Necl-1|Necl1|SynCAM3|Tsll1 gene taxon:10090 20050812 MGI relationship(CL:0000002) MGI MGI:2137858 Cadm3 GO:0008104 MGI:MGI:3582084|PMID:15893517 IMP P cell adhesion molecule 3 BIgR|Igsf4b|Necl-1|Necl1|SynCAM3|Tsll1 gene taxon:10090 20050812 MGI relationship(CL:0000002) MGI MGI:1350922 Cadps GO:0016050 MGI:MGI:3583730|PMID:15820695 IMP MGI:3583931 P Ca<2+>dependent activator protein for secretion CAPS1 gene taxon:10090 20060202 MGI relationship(CL:0000001) MGI MGI:1350922 Cadps GO:0031410 MGI:MGI:3583730|PMID:15820695 IDA C Ca<2+>dependent activator protein for secretion CAPS1 gene taxon:10090 20060202 MGI relationship(CL:0000336) MGI MGI:1350922 Cadps GO:0050432 MGI:MGI:3583730|PMID:15820695 IMP MGI:3583931 P Ca<2+>dependent activator protein for secretion CAPS1 gene taxon:10090 20060202 MGI relationship(CL:0000001) MGI MGI:1350922 Cadps NOT GO:0006887 MGI:MGI:3583730|PMID:15820695 IMP MGI:3583931 P Ca<2+>dependent activator protein for secretion CAPS1 gene taxon:10090 20060202 MGI relationship(CL:0000001) MGI MGI:2443963 Cadps2 GO:0031410 MGI:MGI:3583508|PMID:15932944 IDA C Ca2+-dependent activator protein for secretion 2 Cadps2|Caps2|cpd2 gene taxon:10090 20060202 MGI relationship(CL:0000336) MGI MGI:2151253 Calca GO:0005622 MGI:MGI:67883|PMID:7955356 IDA C calcitonin/calcitonin-related polypeptide, alpha alpha CGRP|CA|Calc|Calc1|Cgrp|CGRP-1|CGRP1|CT|Ctn gene taxon:10090 20050314 MGI relationship(CL:0000540) MGI MGI:2151253 Calca GO:0005737 MGI:MGI:3028786|PMID:14765981 IDA C calcitonin/calcitonin-related polypeptide, alpha alpha CGRP|CA|Calc|Calc1|Cgrp|CGRP-1|CGRP1|CT|Ctn gene taxon:10090 20061117 MGI relationship(CL:0000070) MGI MGI:2151253 Calca GO:0005737 MGI:MGI:894060|PMID:9271704 IDA C calcitonin/calcitonin-related polypeptide, alpha alpha CGRP|CA|Calc|Calc1|Cgrp|CGRP-1|CGRP1|CT|Ctn gene taxon:10090 20061115 MGI relationship(CL:0000165) MGI MGI:2151253 Calca GO:0005737 MGI:MGI:894060|PMID:9271704 IDA C calcitonin/calcitonin-related polypeptide, alpha alpha CGRP|CA|Calc|Calc1|Cgrp|CGRP-1|CGRP1|CT|Ctn gene taxon:10090 20061115 MGI relationship(CL:0000540) MGI MGI:2151253 Calca GO:0007189 MGI:MGI:77881|PMID:8582325 IGI MGI:1926944 P calcitonin/calcitonin-related polypeptide, alpha alpha CGRP|CA|Calc|Calc1|Cgrp|CGRP-1|CGRP1|CT|Ctn gene taxon:10090 20061114 MGI relationship(CL:0000001) MGI MGI:2151253 Calca GO:0007190 MGI:MGI:77881|PMID:8582325 IDA P calcitonin/calcitonin-related polypeptide, alpha alpha CGRP|CA|Calc|Calc1|Cgrp|CGRP-1|CGRP1|CT|Ctn gene taxon:10090 20061114 MGI relationship(CL:0000001) MGI MGI:2151253 Calca GO:0030424 MGI:MGI:1098517|PMID:1317267 IDA C calcitonin/calcitonin-related polypeptide, alpha alpha CGRP|CA|Calc|Calc1|Cgrp|CGRP-1|CGRP1|CT|Ctn gene taxon:10090 20061116 MGI relationship(CL:0000101) MGI MGI:2151253 Calca GO:0030424 MGI:MGI:62241|PMID:8261138 IDA C calcitonin/calcitonin-related polypeptide, alpha alpha CGRP|CA|Calc|Calc1|Cgrp|CGRP-1|CGRP1|CT|Ctn gene taxon:10090 20061114 MGI relationship(CL:0000207) MGI MGI:2151253 Calca GO:0030424 MGI:MGI:67873|PMID:7521790 IDA C calcitonin/calcitonin-related polypeptide, alpha alpha CGRP|CA|Calc|Calc1|Cgrp|CGRP-1|CGRP1|CT|Ctn gene taxon:10090 20061114 MGI relationship(CL:0000101) MGI MGI:2151253 Calca GO:0030424 MGI:MGI:77881|PMID:8582325 IDA C calcitonin/calcitonin-related polypeptide, alpha alpha CGRP|CA|Calc|Calc1|Cgrp|CGRP-1|CGRP1|CT|Ctn gene taxon:10090 20061114 MGI relationship(CL:0000540) MGI MGI:2151253 Calca GO:0031645 MGI:MGI:2445452|PMID:11717154 IMP MGI:2445489 P calcitonin/calcitonin-related polypeptide, alpha alpha CGRP|CA|Calc|Calc1|Cgrp|CGRP-1|CGRP1|CT|Ctn gene taxon:10090 20061117 MGI relationship(CL:0000700) MGI MGI:2151253 Calca GO:0031716 MGI:MGI:1098356|PMID:9322931 IDA F calcitonin/calcitonin-related polypeptide, alpha alpha CGRP|CA|Calc|Calc1|Cgrp|CGRP-1|CGRP1|CT|Ctn gene taxon:10090 20061115 MGI relationship(CL:0000192) MGI MGI:2151253 Calca GO:0043025 MGI:MGI:1316900|PMID:9838101 IDA C calcitonin/calcitonin-related polypeptide, alpha alpha CGRP|CA|Calc|Calc1|Cgrp|CGRP-1|CGRP1|CT|Ctn gene taxon:10090 20061116 MGI relationship(CL:0000101) MGI MGI:2151253 Calca GO:0043195 MGI:MGI:1306999|PMID:9853118 IDA C calcitonin/calcitonin-related polypeptide, alpha alpha CGRP|CA|Calc|Calc1|Cgrp|CGRP-1|CGRP1|CT|Ctn gene taxon:10090 20061115 MGI relationship(CL:0000100) MGI MGI:2151253 Calca GO:0043195 MGI:MGI:1335275|PMID:10208559 IDA C calcitonin/calcitonin-related polypeptide, alpha alpha CGRP|CA|Calc|Calc1|Cgrp|CGRP-1|CGRP1|CT|Ctn gene taxon:10090 20061116 MGI relationship(CL:0000540) MGI MGI:2151253 Calca GO:0043195 MGI:MGI:1345568|PMID:10532808 IDA C calcitonin/calcitonin-related polypeptide, alpha alpha CGRP|CA|Calc|Calc1|Cgrp|CGRP-1|CGRP1|CT|Ctn gene taxon:10090 20061116 MGI relationship(CL:0000540) MGI MGI:2151253 Calca GO:0043195 MGI:MGI:52986|PMID:8453761 IDA C calcitonin/calcitonin-related polypeptide, alpha alpha CGRP|CA|Calc|Calc1|Cgrp|CGRP-1|CGRP1|CT|Ctn gene taxon:10090 20061114 MGI relationship(CL:0000117) MGI MGI:2151253 Calca GO:0045986 MGI:MGI:1098356|PMID:9322931 IDA P calcitonin/calcitonin-related polypeptide, alpha alpha CGRP|CA|Calc|Calc1|Cgrp|CGRP-1|CGRP1|CT|Ctn gene taxon:10090 20040722 MGI relationship(CL:0000192) MGI MGI:101950 Calcr GO:0004948 MGI:MGI:69977|PMID:7988453 IDA F calcitonin receptor Clr gene taxon:10090 20061114 MGI relationship(CL:0000002) MGI MGI:101950 Calcr GO:0007189 MGI:MGI:69977|PMID:7988453 IDA P calcitonin receptor Clr gene taxon:10090 20061114 MGI relationship(CL:0000002) MGI MGI:101950 Calcr GO:0007204 MGI:MGI:1289525|PMID:9753683 IDA P calcitonin receptor Clr gene taxon:10090 20061114 MGI relationship(CL:0000001) MGI MGI:101950 Calcr GO:0030316 MGI:MGI:76792|PMID:7664679 IDA P calcitonin receptor Clr gene taxon:10090 20061114 MGI relationship(CL:0000092) MGI MGI:1926944 Calcrl GO:0001635 MGI:MGI:77881|PMID:8582325 IGI MGI:2151253 F calcitonin receptor-like CRLR gene taxon:10090 20061114 MGI relationship(CL:0000001) MGI MGI:1926944 Calcrl GO:0007189 MGI:MGI:77881|PMID:8582325 IMP P calcitonin receptor-like CRLR gene taxon:10090 20061114 MGI relationship(CL:0000001) MGI MGI:1926944 Calcrl GO:0048661 MGI:MGI:3619781|PMID:16537897 IMP P calcitonin receptor-like CRLR gene taxon:10090 20060523 MGI relationship(CL:0000359) MGI MGI:107739 Casp3 GO:0006915 MGI:MGI:2150278|PMID:11549719 IMP P caspase 3 Apopain|Caspase-3|CPP32|Yama gene taxon:10090 20051206 MGI relationship(CL:0000540) MGI MGI:107739 Casp3 GO:0008233 MGI:MGI:2150278|PMID:11549719 IMP F caspase 3 Apopain|Caspase-3|CPP32|Yama gene taxon:10090 20051206 MGI relationship(CL:0000540) MGI MGI:107739 Casp3 GO:0030216 MGI:MGI:3042356|PMID:15068794 IMP MGI:2178778 P caspase 3 Apopain|Caspase-3|CPP32|Yama gene taxon:10090 20040702 MGI relationship(CL:0000312) MGI MGI:107739 Casp3 GO:0045165 MGI:MGI:3042356|PMID:15068794 IMP MGI:2178778 P caspase 3 Apopain|Caspase-3|CPP32|Yama gene taxon:10090 20040702 MGI relationship(CL:0000312) MGI MGI:1261423 Casp8 GO:0006915 MGI:MGI:3054336|PMID:15322156 IMP MGI:2176089 P caspase 8 Caspase-8|FLICE|MACH|Mch5 gene taxon:10090 20041101 MGI relationship(CL:0000182) MGI MGI:1261423 Casp8 GO:0007507 MGI:MGI:3609631|PMID:12404118 IMP MGI:3609638 P caspase 8 Caspase-8|FLICE|MACH|Mch5 gene taxon:10090 20060324 MGI relationship(CL:0000746) MGI MGI:1261423 Casp8 GO:0030225 MGI:MGI:3054336|PMID:15322156 IMP MGI:2176089 P caspase 8 Caspase-8|FLICE|MACH|Mch5 gene taxon:10090 20041101 MGI relationship(CL:0000235) MGI MGI:102709 Cav1 GO:0000188 MGI:MGI:2450774|PMID:12388077 IMP MGI:2180364 P caveolin, caveolae protein 1 Cav-1|caveolin-1 gene taxon:10090 20041223 MGI relationship(CL:0000057) MGI MGI:102709 Cav1 GO:0005887 MGI:MGI:78129|PMID:8552590 IDA C caveolin, caveolae protein 1 Cav-1|caveolin-1 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:102709 Cav1 GO:0008285 MGI:MGI:2450774|PMID:12388077 IMP MGI:2180364 P caveolin, caveolae protein 1 Cav-1|caveolin-1 gene taxon:10090 20041223 MGI relationship(CL:0000057) MGI MGI:102709 Cav1 GO:0048471 MGI:MGI:78129|PMID:8552590 IDA C caveolin, caveolae protein 1 Cav-1|caveolin-1 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:102709 Cav1 GO:0051260 MGI:MGI:78129|PMID:8552590 IDA P caveolin, caveolae protein 1 Cav-1|caveolin-1 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:107570 Cav3 GO:0005886 MGI:MGI:1927714|PMID:10988290 ISS UniProt:P51638 C caveolin 3 Cav-3|M-caveolin gene taxon:10090 20060111 MGI relationship(CL:0000002) MGI MGI:107570 Cav3 GO:0005901 MGI:MGI:3628972|PMID:16648270 IDA C caveolin 3 Cav-3|M-caveolin gene taxon:10090 20061212 MGI relationship(CL:0000187) MGI MGI:107570 Cav3 GO:0051925 MGI:MGI:3628972|PMID:16648270 IMP P caveolin 3 Cav-3|M-caveolin gene taxon:10090 20061212 MGI relationship(CL:000018) MGI MGI:1338013 Cbfa2t3h GO:0005622 MGI:MGI:3510739|PMID:15231665 IDA C core-binding factor, runt domain, alpha subunit 2, translocated to, 3 homolog (human) ETO-2|MTGR2 gene taxon:10090 20041213 MGI relationship(CL:0000002) MGI MGI:99851 Cbfb GO:0001649 MGI:MGI:2446761|PMID:12434156 IMP MGI:2447293 P core binding factor beta PEA2|Pebp2|PEBP2b|Pebpb2 gene taxon:10090 20050114 MGI relationship(CL:0000062) MGI MGI:99851 Cbfb GO:0048469 MGI:MGI:2446761|PMID:12434156 IMP MGI:2447293 P core binding factor beta PEA2|Pebp2|PEBP2b|Pebpb2 gene taxon:10090 20050114 MGI relationship(CL:0000138) MGI MGI:1916918 Ccdc115 GO:0005764 MGI:MGI:3616929|PMID:16378758 IDA C coiled-coil domain containing 115 Ccp1 gene taxon:10090 20060501 MGI relationship(CL:0000002) MGI MGI:1914233 Ccdc16 GO:0001832 MGI:MGI:3582017|PMID:15988037 IMP MGI:3583779 P coiled-coil domain containing 16 Omcg1 gene taxon:10090 20050906 MGI relationship(CL:0000007) MGI MGI:1914233 Ccdc16 GO:0005634 MGI:MGI:3582017|PMID:15988037 IDA C coiled-coil domain containing 16 Omcg1 gene taxon:10090 20050906 MGI relationship(CL:0000002) MGI MGI:1914233 Ccdc16 GO:0005634 MGI:MGI:3582017|PMID:15988037 IDA C coiled-coil domain containing 16 Omcg1 gene taxon:10090 20050906 MGI relationship(CL:0000353) MGI MGI:1914233 Ccdc16 GO:0007049 MGI:MGI:3582017|PMID:15988037 IMP MGI:3583779 P coiled-coil domain containing 16 Omcg1 gene taxon:10090 20050906 MGI relationship(CL:0000007) MGI MGI:88297 Cck GO:0001764 MGI:MGI:3573824|PMID:15152034 IDA P cholecystokinin gene taxon:10090 20050505 MGI relationship(CL:0000540) MGI MGI:88297 Cck GO:0007409 MGI:MGI:3573824|PMID:15152034 IDA P cholecystokinin gene taxon:10090 20050505 MGI relationship(CL:0000540) MGI MGI:88297 Cck GO:0030424 MGI:MGI:3573824|PMID:15152034 IDA C cholecystokinin gene taxon:10090 20050505 MGI relationship(CL:0000540) MGI MGI:99478 Cckar GO:0001764 MGI:MGI:3573824|PMID:15152034 IMP P cholecystokinin A receptor gene taxon:10090 20050505 MGI relationship(CL:0000540) MGI MGI:99478 Cckar GO:0007409 MGI:MGI:3573824|PMID:15152034 IMP P cholecystokinin A receptor gene taxon:10090 20050505 MGI relationship(CL:0000540) MGI MGI:99478 Cckar GO:0030900 MGI:MGI:3573824|PMID:15152034 IMP MGI:3051882 P cholecystokinin A receptor gene taxon:10090 20050505 MGI relationship(CL:0000540) MGI MGI:1099448 Ccl25 GO:0050900 MGI:MGI:3530373|PMID:15358618 IDA P chemokine (C-C motif) ligand 25 CKb15|Scya25|TECK gene taxon:10090 20050502 MGI relationship(CL:0000045) MGI MGI:107824 Ccr4 GO:0001764 MGI:MGI:3608233|PMID:16262623 IMP MGI:1934407 P chemokine (C-C motif) receptor 4 CC CKR-4|CCR4|Cmkbr4|fusin|leukocyte-expressed seven-transmembrane-domain receptor|Sdf1r gene taxon:10090 20060327 MGI relationship(CL:0000120) MGI MGI:107824 Ccr4 GO:0001764 MGI:MGI:3608233|PMID:16262623 IMP MGI:1934407 P chemokine (C-C motif) receptor 4 CC CKR-4|CCR4|Cmkbr4|fusin|leukocyte-expressed seven-transmembrane-domain receptor|Sdf1r gene taxon:10090 20060327 MGI relationship(CL:0000498) MGI MGI:107674 Cd1d1 GO:0005515 MGI:MGI:3041278|PMID:11754812 IPI UniProt:P04441-2 F CD1d1 antigen CD1.1|Cd1a|Cd1d gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:107674 Cd1d1 GO:0005764 MGI:MGI:2679144|PMID:14557411 IDA C CD1d1 antigen CD1.1|Cd1a|Cd1d gene taxon:10090 20041008 MGI relationship(CL:0000002) MGI MGI:107674 Cd1d1 GO:0005764 MGI:MGI:3041278|PMID:11754812 IDA C CD1d1 antigen CD1.1|Cd1a|Cd1d gene taxon:10090 20041006 MGI relationship(CL:0000002) MGI MGI:107674 Cd1d1 GO:0009897 MGI:MGI:2679144|PMID:14557411 IDA C CD1d1 antigen CD1.1|Cd1a|Cd1d gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1889024 Cd200r1 GO:0004872 MGI:MGI:3051783|PMID:15274657 IDA F CD200 receptor 1 CD200R|Mox2r|Orexin receptor 2|OX2R gene taxon:10090 20041208 MGI relationship(CL:0000002) MGI MGI:1889024 Cd200r1 GO:0009897 MGI:MGI:3051783|PMID:15274657 IDA C CD200 receptor 1 CD200R|Mox2r|Orexin receptor 2|OX2R gene taxon:10090 20041208 MGI relationship(CL:0000542) MGI MGI:3042847 Cd200r2 GO:0004872 MGI:MGI:3051783|PMID:15274657 IDA F Cd200 receptor 2 CD200 cell surface glycoprotein receptor isoform 2 gene taxon:10090 20041208 MGI relationship(CL:0000002) MGI MGI:3042847 Cd200r2 GO:0009897 MGI:MGI:3051783|PMID:15274657 IDA C Cd200 receptor 2 CD200 cell surface glycoprotein receptor isoform 2 gene taxon:10090 20041208 MGI relationship(CL:0000542) MGI MGI:1921853 Cd200r3 GO:0004872 MGI:MGI:3051783|PMID:15274657 IDA F CD200 receptor 3 mCD200RLb gene taxon:10090 20041208 MGI relationship(CL:0000002) MGI MGI:1921853 Cd200r3 GO:0009897 MGI:MGI:3051783|PMID:15274657 IDA C CD200 receptor 3 mCD200RLb gene taxon:10090 20041208 MGI relationship(CL:0000542) MGI MGI:3036289 Cd200r4 GO:0004872 MGI:MGI:3051783|PMID:15274657 IDA F Cd200 receptor 4 MCD200RLa gene taxon:10090 20041208 MGI relationship(CL:0000002) MGI MGI:3036289 Cd200r4 GO:0009897 MGI:MGI:3051783|PMID:15274657 IDA C Cd200 receptor 4 MCD200RLa gene taxon:10090 20041208 MGI relationship(CL:0000542) MGI MGI:88323 Cd24a GO:0007274 MGI:MGI:3625625|PMID:16606832 IGI MGI:2139434 P CD24a antigen cluster of differentiation 24|heat stable antigen|HSA|Ly-52 gene taxon:10090 20060808 MGI relationship(CL:0000108) MGI MGI:88323 Cd24a GO:0007274 MGI:MGI:3625625|PMID:16606832 IMP MGI:2179996 P CD24a antigen cluster of differentiation 24|heat stable antigen|HSA|Ly-52 gene taxon:10090 20060808 MGI relationship(CL:0000108) MGI MGI:88323 Cd24a GO:0009897 MGI:MGI:1860996|PMID:10943842 IDA C CD24a antigen cluster of differentiation 24|heat stable antigen|HSA|Ly-52 gene taxon:10090 20050617 MGI relationship(CL:0000081) MGI MGI:88323 Cd24a GO:0009897 MGI:MGI:77314|PMID:7477352 IDA C CD24a antigen cluster of differentiation 24|heat stable antigen|HSA|Ly-52 gene taxon:10090 20050117 MGI relationship(CL:0000084) MGI MGI:88323 Cd24a GO:0048488 MGI:MGI:3625625|PMID:16606832 IMP MGI:2179996 P CD24a antigen cluster of differentiation 24|heat stable antigen|HSA|Ly-52 gene taxon:10090 20060808 MGI relationship(CL:0000108) MGI MGI:1926446 Cd274 GO:0009897 MGI:MGI:3521631|PMID:15568026 IDA C CD274 antigen B7-H1|PD-L1|Pdcd1lg1 gene taxon:10090 20070104 MGI relationship(CL:0000002) MGI MGI:88329 Cd34 GO:0009897 MGI:MGI:1860996|PMID:10943842 IDA C CD34 antigen gene taxon:10090 20050617 MGI relationship(CL:0000081) MGI MGI:88329 Cd34 GO:0050900 MGI:MGI:3580935|PMID:15701716 IMP P CD34 antigen gene taxon:10090 20050805 MGI relationship(CL:0000738) MGI MGI:88332 Cd3e GO:0004871 MGI:MGI:75253|PMID:7630421 IDA F CD3 antigen, epsilon polypeptide CD3|CD3epsilon|T3e gene taxon:10090 20050117 MGI relationship(CL:0000084) MGI MGI:88332 Cd3e GO:0007166 MGI:MGI:75253|PMID:7630421 IDA P CD3 antigen, epsilon polypeptide CD3|CD3epsilon|T3e gene taxon:10090 20050117 MGI relationship(CL:0000084) MGI MGI:88332 Cd3e GO:0009897 MGI:MGI:75253|PMID:7630421 IDA C CD3 antigen, epsilon polypeptide CD3|CD3epsilon|T3e gene taxon:10090 20050117 MGI relationship(CL:0000084) MGI MGI:88332 Cd3e GO:0045060 MGI:MGI:75253|PMID:7630421 IDA P CD3 antigen, epsilon polypeptide CD3|CD3epsilon|T3e gene taxon:10090 20050117 MGI relationship(CL:0000084) MGI MGI:88332 Cd3e GO:0045879 MGI:MGI:1888832|PMID:10981962 IDA P CD3 antigen, epsilon polypeptide CD3|CD3epsilon|T3e gene taxon:10090 20061219 MGI relationship(CL:0000001) MGI MGI:88332 Cd3e GO:0050850 MGI:MGI:75253|PMID:7630421 IDA P CD3 antigen, epsilon polypeptide CD3|CD3epsilon|T3e gene taxon:10090 20050117 MGI relationship(CL:0000084) MGI MGI:88335 Cd4 GO:0009897 MGI:MGI:1860996|PMID:10943842 IDA C CD4 antigen L3T4|Ly-4 gene taxon:10090 20050617 MGI relationship(CL:0000081) MGI MGI:88335 Cd4 GO:0009897 MGI:MGI:75253|PMID:7630421 IDA C CD4 antigen L3T4|Ly-4 gene taxon:10090 20050117 MGI relationship(CL:0000084) MGI MGI:88335 Cd4 GO:0009897 MGI:MGI:77314|PMID:7477352 IDA C CD4 antigen L3T4|Ly-4 gene taxon:10090 20050117 MGI relationship(CL:0000084) MGI MGI:88335 Cd4 GO:0009897 MGI:MGI:77315|PMID:7477353 IDA C CD4 antigen L3T4|Ly-4 gene taxon:10090 20050117 MGI relationship(CL:0000084) MGI MGI:88338 Cd44 GO:0009897 MGI:MGI:1860996|PMID:10943842 IDA C CD44 antigen HERMES|Ly-24|Pgp-1 gene taxon:10090 20050617 MGI relationship(CL:0000081) MGI MGI:88338 Cd44 GO:0009897 MGI:MGI:1889048|PMID:7584142 IDA C CD44 antigen HERMES|Ly-24|Pgp-1 gene taxon:10090 20050617 MGI relationship(CL:0000084) MGI MGI:88340 Cd5 GO:0009897 MGI:MGI:77315|PMID:7477353 IDA C CD5 antigen Ly-1|Ly-12|Ly-A|Lyt-1 gene taxon:10090 20050117 MGI relationship(CL:0000236) MGI MGI:88343 Cd69 GO:0009897 MGI:MGI:75253|PMID:7630421 IDA C CD69 antigen AIM|VEA gene taxon:10090 20070323 MGI relationship(CL:0000084) MGI MGI:96534 Cd74 GO:0005515 MGI:MGI:3041278|PMID:11754812 IPI UniProt:P11609 F CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated) CLIP|HLA-DR-GAMMA|Ia-GAMMA|Ii gene taxon:10090 20050110 MGI relationship(CL:0000002) MGI MGI:101774 Cd79a GO:0005515 MGI:MGI:3521842|PMID:1373499 IPI UniProt:P15530 F CD79A antigen (immunoglobulin-associated alpha) Cd79a|Ig alpha|Ig-alpha|Iga|Ly54|mb-1 gene taxon:10090 20050120 MGI relationship(CL:0000002) MGI MGI:101774 Cd79a GO:0005515 MGI:MGI:79455|PMID:8626447 IPI UniProt:P48025,UniProt:P15530 F CD79A antigen (immunoglobulin-associated alpha) Cd79a|Ig alpha|Ig-alpha|Iga|Ly54|mb-1 gene taxon:10090 20050121 MGI relationship(CL:0000002) MGI MGI:101774 Cd79a GO:0009897 MGI:MGI:3521842|PMID:1373499 IDA C CD79A antigen (immunoglobulin-associated alpha) Cd79a|Ig alpha|Ig-alpha|Iga|Ly54|mb-1 gene taxon:10090 20050120 MGI relationship(CL:0000002) MGI MGI:101774 Cd79a GO:0019815 MGI:MGI:3521842|PMID:1373499 IDA C CD79A antigen (immunoglobulin-associated alpha) Cd79a|Ig alpha|Ig-alpha|Iga|Ly54|mb-1 gene taxon:10090 20050120 MGI relationship(CL:0000002) MGI MGI:101774 Cd79a GO:0019815 MGI:MGI:79455|PMID:8626447 IDA C CD79A antigen (immunoglobulin-associated alpha) Cd79a|Ig alpha|Ig-alpha|Iga|Ly54|mb-1 gene taxon:10090 20050121 MGI relationship(CL:0000002) MGI MGI:101774 Cd79a GO:0050853 MGI:MGI:3521842|PMID:1373499 IDA P CD79A antigen (immunoglobulin-associated alpha) Cd79a|Ig alpha|Ig-alpha|Iga|Ly54|mb-1 gene taxon:10090 20050120 MGI relationship(CL:0000002) MGI MGI:101774 Cd79a GO:0050853 MGI:MGI:79455|PMID:8626447 IDA P CD79A antigen (immunoglobulin-associated alpha) Cd79a|Ig alpha|Ig-alpha|Iga|Ly54|mb-1 gene taxon:10090 20050121 MGI relationship(CL:0000002) MGI MGI:96431 Cd79b GO:0005515 MGI:MGI:3521842|PMID:1373499 IPI UniProt:P11911 F CD79B antigen B29|Ig-beta|Igb|Igbeta gene taxon:10090 20050120 MGI relationship(CL:0000002) MGI MGI:96431 Cd79b GO:0005515 MGI:MGI:79455|PMID:8626447 IPI UniProt:P11911 F CD79B antigen B29|Ig-beta|Igb|Igbeta gene taxon:10090 20050121 MGI relationship(CL:0000002) MGI MGI:96431 Cd79b GO:0009897 MGI:MGI:3521842|PMID:1373499 IDA C CD79B antigen B29|Ig-beta|Igb|Igbeta gene taxon:10090 20050120 MGI relationship(CL:0000002) MGI MGI:96431 Cd79b GO:0019815 MGI:MGI:3521842|PMID:1373499 IDA C CD79B antigen B29|Ig-beta|Igb|Igbeta gene taxon:10090 20050120 MGI relationship(CL:0000002) MGI MGI:96431 Cd79b GO:0019815 MGI:MGI:79455|PMID:8626447 IDA C CD79B antigen B29|Ig-beta|Igb|Igbeta gene taxon:10090 20050121 MGI relationship(CL:0000002) MGI MGI:96431 Cd79b GO:0050853 MGI:MGI:3521842|PMID:1373499 IDA P CD79B antigen B29|Ig-beta|Igb|Igbeta gene taxon:10090 20050120 MGI relationship(CL:0000002) MGI MGI:96431 Cd79b GO:0050853 MGI:MGI:79455|PMID:8626447 IDA P CD79B antigen B29|Ig-beta|Igb|Igbeta gene taxon:10090 20050121 MGI relationship(CL:0000002) MGI MGI:101775 Cd80 GO:0009897 MGI:MGI:3521631|PMID:15568026 IDA C CD80 antigen B7-1|B7.1|Cd28l|Ly-53|Ly53 gene taxon:10090 20070104 MGI relationship(CL:0000002) MGI MGI:88346 Cd8a GO:0009897 MGI:MGI:1860996|PMID:10943842 IDA C CD8 antigen, alpha chain Ly-2|Ly-35|Ly-B|Lyt-2 gene taxon:10090 20050617 MGI relationship(CL:0000081) MGI MGI:99701 Cdc25b GO:0001556 MGI:MGI:2682954|PMID:11912493 IMP MGI:2682953 P cell division cycle 25 homolog B (S. pombe) gene taxon:10090 20060821 MGI relationship(CL:0000023) MGI MGI:99701 Cdc25b GO:0007144 MGI:MGI:2682954|PMID:11912493 IMP MGI:2682953 P cell division cycle 25 homolog B (S. pombe) gene taxon:10090 20060821 MGI relationship(CL:0000023) MGI MGI:99701 Cdc25b GO:0045860 MGI:MGI:2682954|PMID:11912493 IMP MGI:2682953 P cell division cycle 25 homolog B (S. pombe) gene taxon:10090 20060821 MGI relationship(CL:0000023) MGI MGI:88354 Cdh1 GO:0005886 MGI:MGI:3614372|PMID:16418220 IDA C cadherin 1 E-cadherin|Ecad|L-CAM|UM|uvomorulin gene taxon:10090 20060309 MGI relationship(CL:1000274) MGI MGI:88354 Cdh1 GO:0005913 MGI:MGI:3578587|PMID:15788452 IDA C cadherin 1 E-cadherin|Ecad|L-CAM|UM|uvomorulin gene taxon:10090 20050727 MGI relationship(CL:1000274) MGI MGI:88354 Cdh1 GO:0016323 MGI:MGI:3578587|PMID:15788452 IDA C cadherin 1 E-cadherin|Ecad|L-CAM|UM|uvomorulin gene taxon:10090 20050727 MGI relationship(CL:1000274) MGI MGI:88354 Cdh1 GO:0045177 MGI:MGI:3033551|PMID:14758363 IDA C cadherin 1 E-cadherin|Ecad|L-CAM|UM|uvomorulin gene taxon:10090 20040421 MGI relationship(CL:0000066) MGI MGI:88355 Cdh2 GO:0048514 MGI:MGI:3578460|PMID:15809310 IMP MGI:3522469 P cadherin 2 N-cadherin|Ncad gene taxon:10090 20050705 MGI relationship(CL:0000071) MGI MGI:1890219 Cdh23 GO:0005929 MGI:MGI:3577782|PMID:15882574 IDA C cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070322 MGI relationship(CL:0000202) MGI MGI:1890219 Cdh23 GO:0005932 MGI:MGI:3577782|PMID:15882574 IDA C cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20050620 MGI relationship(CL:0000202) MGI MGI:1890219 Cdh23 GO:0032420 MGI:MGI:3577782|PMID:15882574 IDA C cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070322 MGI relationship(CL:0000589) MGI MGI:1890219 Cdh23 GO:0032420 MGI:MGI:3577782|PMID:15882574 IDA C cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070322 MGI relationship(CL:0000601) MGI MGI:1890219 Cdh23 GO:0032420 MGI:MGI:3686545|PMID:17050716 IDA C cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070322 MGI relationship(CL:0000609) MGI MGI:1890219 Cdh23 GO:0032426 MGI:MGI:3686545|PMID:17050716 IDA C cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070322 MGI relationship(CL:0000609) MGI MGI:1890219 Cdh23 GO:0042472 MGI:MGI:3579755|PMID:15925194 IMP MGI:2665714 P cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070322 MGI relationship(CL:0000635) MGI MGI:1890219 Cdh23 GO:0042472 MGI:MGI:3579755|PMID:15925194 IMP MGI:2665714 P cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070322 MGI relationship(CL:1000191) MGI MGI:1890219 Cdh23 GO:0042472 MGI:MGI:75953|PMID:7610888 IMP MGI:1856681 P cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070321 MGI relationship(CL:0000601) MGI MGI:1890219 Cdh23 GO:0060088 MGI:MGI:1929001|PMID:11138008 IMP MGI:2154548 P cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070322 MGI relationship(CL:0000589) MGI MGI:1890219 Cdh23 GO:0060088 MGI:MGI:1929001|PMID:11138008 IMP MGI:2154548 P cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070322 MGI relationship(CL:0000601) MGI MGI:1890219 Cdh23 GO:0060088 MGI:MGI:1933915|PMID:11322776 IMP MGI:2154549 P cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070322 MGI relationship(CL:0000601) MGI MGI:1890219 Cdh23 GO:0060088 MGI:MGI:3526751|PMID:15537665 IGI MGI:1891428 P cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070322 MGI relationship(CL:0000589) MGI MGI:1890219 Cdh23 GO:0060088 MGI:MGI:3526751|PMID:15537665 IGI MGI:1891428 P cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070322 MGI relationship(CL:0000601) MGI MGI:1890219 Cdh23 GO:0060088 MGI:MGI:3686545|PMID:17050716 IMP MGI:2154548 P cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070322 MGI relationship(CL:0000589) MGI MGI:1890219 Cdh23 GO:0060088 MGI:MGI:3686545|PMID:17050716 IMP MGI:2154548 P cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070322 MGI relationship(CL:0000601) MGI MGI:1890219 Cdh23 GO:0060088 MGI:MGI:75953|PMID:7610888 IMP MGI:1856681 P cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070322 MGI relationship(CL:0000589) MGI MGI:1890219 Cdh23 GO:0060088 MGI:MGI:75953|PMID:7610888 IMP MGI:1856681 P cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070322 MGI relationship(CL:0000601) MGI MGI:1890219 Cdh23 GO:0060088 MGI:MGI:81497|PMID:8790740 IMP MGI:1856681 P cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070322 MGI relationship(CL:0000589) MGI MGI:1890219 Cdh23 GO:0060088 MGI:MGI:81497|PMID:8790740 IMP MGI:1856681 P cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070322 MGI relationship(CL:0000601) MGI MGI:1890219 Cdh23 GO:0060088 MGI:MGI:86134|PMID:9039475 IMP MGI:1856681 P cadherin 23 (otocadherin) ahl|ahl1|bob|mdfw|nmf112|nmf181|nmf252|USH1D gene taxon:10090 20070322 MGI relationship(CL:0000609) MGI MGI:105057 Cdh5 GO:0005911 MGI:MGI:3577866|PMID:15861137 IDA C cadherin 5 7B4/cadherin-5|CD144|VE-Cad|VE-cadherin|VEC gene taxon:10090 20050531 MGI relationship(CL:0000002) MGI MGI:105057 Cdh5 GO:0005923 MGI:MGI:3513971|PMID:10508865 IDA C cadherin 5 7B4/cadherin-5|CD144|VE-Cad|VE-cadherin|VEC gene taxon:10090 20050201 MGI relationship(CL:0000071) MGI MGI:105057 Cdh5 GO:0008285 MGI:MGI:3577866|PMID:15861137 IGI MGI:88537 P cadherin 5 7B4/cadherin-5|CD144|VE-Cad|VE-cadherin|VEC gene taxon:10090 20050531 MGI relationship(CL:0000002) MGI MGI:105057 Cdh5 GO:0016337 MGI:MGI:3513971|PMID:10508865 IC GO:0005923 P cadherin 5 7B4/cadherin-5|CD144|VE-Cad|VE-cadherin|VEC gene taxon:10090 20050201 MGI relationship(CL:0000071) MGI MGI:88357 Cdk4 GO:0005634 MGI:MGI:3528104|PMID:15645444 IDA C cyclin-dependent kinase 4 Crk3|p34/cdk4 gene taxon:10090 20050308 MGI relationship(CL:0000131) MGI MGI:88357 Cdk4 GO:0005634 MGI:MGI:3528104|PMID:15645444 IDA C cyclin-dependent kinase 4 Crk3|p34/cdk4 gene taxon:10090 20050308 MGI relationship(CL:0000499) MGI MGI:104565 Cdkn1b GO:0051271 MGI:MGI:3529385|PMID:15652749 IDA P cyclin-dependent kinase inhibitor 1B p27|p27Kip1 gene taxon:10090 20050503 MGI relationship(CL:0000002) MGI MGI:104564 Cdkn1c GO:0005634 MGI:MGI:3611010|PMID:11737597 IDA C cyclin-dependent kinase inhibitor 1C (P57) CDKI|Kip2|p57Kip2 gene taxon:10090 20060510 MGI relationship(CL:0000653) MGI MGI:104564 Cdkn1c GO:0042551 MGI:MGI:3029599|PMID:14671317 IMP MGI:1933757 P cyclin-dependent kinase inhibitor 1C (P57) CDKI|Kip2|p57Kip2 gene taxon:10090 20051005 MGI relationship(CL:0000700) MGI MGI:1921846 Cds1 GO:0005783 MGI:MGI:3587961|PMID:16023307 IDA C CDP-diacylglycerol synthase 1 phosphatidate cytidylyltransferase gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:1332236 Cds2 GO:0005783 MGI:MGI:3587961|PMID:16023307 IDA C CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2 D2Wsu127e gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:88361 Cdx2 GO:0001824 MGI:MGI:3578587|PMID:15788452 IMP MGI:1857928 P caudal type homeo box 2 Cdx-2 gene taxon:10090 20050727 MGI relationship(CL:1000274) MGI MGI:88361 Cdx2 GO:0030154 MGI:MGI:3578587|PMID:15788452 IMP MGI:1857928 P caudal type homeo box 2 Cdx-2 gene taxon:10090 20050727 MGI relationship(CL:1000274) MGI MGI:99480 Cebpa GO:0005634 MGI:MGI:3522690|PMID:15519652 IDA C CCAAT/enhancer binding protein (C/EBP), alpha C/EBP alpha|Cebp gene taxon:10090 20050308 MGI relationship(CL:0000182) MGI MGI:99480 Cebpa GO:0005634 MGI:MGI:3522690|PMID:15519652 IDA C CCAAT/enhancer binding protein (C/EBP), alpha C/EBP alpha|Cebp gene taxon:10090 20050308 MGI relationship(CL:0000223) MGI MGI:99480 Cebpa GO:0008285 MGI:MGI:3055255|PMID:15073037 IMP MGI:2177135 P CCAAT/enhancer binding protein (C/EBP), alpha C/EBP alpha|Cebp gene taxon:10090 20050105 MGI relationship(CL:0000037) MGI MGI:99480 Cebpa GO:0030324 MGI:MGI:3618952|PMID:16467360 IMP MGI:2177133|MGI:2445716 P CCAAT/enhancer binding protein (C/EBP), alpha C/EBP alpha|Cebp gene taxon:10090 20060606 MGI relationship(CL:0000082) MGI MGI:99480 Cebpa GO:0048469 MGI:MGI:3618952|PMID:16467360 IMP MGI:2177133|MGI:2445716 P CCAAT/enhancer binding protein (C/EBP), alpha C/EBP alpha|Cebp gene taxon:10090 20060606 MGI relationship(CL:0000082) MGI MGI:1100883 Celsr1 GO:0045176 MGI:MGI:3624469|PMID:16687519 IMP MGI:2668337 P cadherin EGF LAG seven-pass G-type receptor 1 Scy gene taxon:10090 20060629 MGI relationship(CL:0000601) MGI MGI:1313302 Cenpf GO:0005634 MGI:MGI:1339480|PMID:10373470 IDA C centromere protein F Lek1 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1313302 Cenpf GO:0016202 MGI:MGI:1339480|PMID:10373470 IDA P centromere protein F Lek1 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1201414 Cer1 GO:0008285 MGI:MGI:3042338|PMID:15004567 IGI MGI:107405 P cerberus 1 homolog (Xenopus laevis) cer-1|Cerberus-like|Cerr1 gene taxon:10090 20060125 MGI relationship(CL:0000223) MGI MGI:101757 Cfl1 GO:0001755 MGI:MGI:3530675|PMID:15649475 IMP MGI:3574399 P cofilin 1, non-muscle Cof|cofilin gene taxon:10090 20050511 MGI relationship(CL:0000333) MGI MGI:101757 Cfl1 GO:0001842 MGI:MGI:3530675|PMID:15649475 IMP MGI:3574399 P cofilin 1, non-muscle Cof|cofilin gene taxon:10090 20050511 MGI relationship(CL:0000133) MGI MGI:1336166 Cflar GO:0005737 MGI:MGI:3612311|PMID:16263940 IDA C CASP8 and FADD-like apoptosis regulator c-Flip|Casper|Flip|I-FLICE gene taxon:10090 20060301 MGI relationship(CL:0000670) MGI MGI:1336166 Cflar GO:0043066 MGI:MGI:3612311|PMID:16263940 IMP P CASP8 and FADD-like apoptosis regulator c-Flip|Casper|Flip|I-FLICE gene taxon:10090 20060301 MGI relationship(CL:0000670) MGI MGI:1336166 Cflar GO:0043154 MGI:MGI:3612311|PMID:16263940 IMP P CASP8 and FADD-like apoptosis regulator c-Flip|Casper|Flip|I-FLICE gene taxon:10090 20060301 MGI relationship(CL:0000670) MGI MGI:1927237 Cgn GO:0043296 MGI:MGI:3512870|PMID:15292197 IDA C cingulin gene taxon:10090 20050217 MGI relationship(CL:0000066) MGI MGI:1915428 Cgnl1 GO:0015629 MGI:MGI:3512870|PMID:15292197 IDA C cingulin-like 1 Jacop gene taxon:10090 20050217 MGI relationship(CL:0000002) MGI MGI:1915428 Cgnl1 GO:0015629 MGI:MGI:3512870|PMID:15292197 IDA C cingulin-like 1 Jacop gene taxon:10090 20050217 MGI relationship(CL:0000066) MGI MGI:1915428 Cgnl1 GO:0043296 MGI:MGI:3512870|PMID:15292197 IDA C cingulin-like 1 Jacop gene taxon:10090 20050217 MGI relationship(CL:0000066) MGI MGI:88392 Chat GO:0043025 MGI:MGI:1306999|PMID:9853118 IDA C choline acetyltransferase gene taxon:10090 20061115 MGI relationship(CL:0000540) MGI MGI:88392 Chat GO:0043179 MGI:MGI:3577822|PMID:15820692 IMP MGI:2450310 P choline acetyltransferase gene taxon:10090 20050609 MGI relationship(CL:0000099) MGI MGI:1355321 Chek2 GO:0010332 MGI:MGI:3032464|PMID:14744935 IDA P CHK2 checkpoint homolog (S. pombe) Cds1|CHK2|Rad53 gene taxon:10090 20070314 MGI relationship(CL:0000002) MGI MGI:1355321 Chek2 GO:0042770 MGI:MGI:3032464|PMID:14744935 IDA P CHK2 checkpoint homolog (S. pombe) Cds1|CHK2|Rad53 gene taxon:10090 20070314 MGI relationship(CL:0000002) MGI MGI:1098266 Chl1 GO:0001764 MGI:MGI:3530933|PMID:15504324 IMP MGI:2429688 P cell adhesion molecule with homology to L1CAM CALL|close homolog of L1|LICAM2 gene taxon:10090 20050412 MGI relationship(CL:0000117) MGI MGI:1098266 Chl1 GO:0030425 MGI:MGI:3530933|PMID:15504324 IDA C cell adhesion molecule with homology to L1CAM CALL|close homolog of L1|LICAM2 gene taxon:10090 20050412 MGI relationship(CL:0000598) MGI MGI:1098266 Chl1 GO:0045177 MGI:MGI:3530933|PMID:15504324 IDA C cell adhesion molecule with homology to L1CAM CALL|close homolog of L1|LICAM2 gene taxon:10090 20050412 MGI relationship(CL:0000598) MGI MGI:1098266 Chl1 NOT GO:0007156 MGI:MGI:1339859|PMID:10103075 IDA P cell adhesion molecule with homology to L1CAM CALL|close homolog of L1|LICAM2 gene taxon:10090 20050414 MGI relationship(CL:0000002) MGI MGI:1924209 Chmp5 GO:0007040 MGI:MGI:3622513|PMID:16567502 IMP MGI:3626293 P chromatin modifying protein 5 gene taxon:10090 20060814 MGI relationship(CL:0000001) MGI MGI:1924209 Chmp5 GO:0008333 MGI:MGI:3622513|PMID:16567502 IMP MGI:3626293 P chromatin modifying protein 5 gene taxon:10090 20060814 MGI relationship(CL:0000001) MGI MGI:1313268 Chrd GO:0001707 MGI:MGI:2662951|PMID:12810603 IMP MGI:2157350 P chordin Chd gene taxon:10090 20050114 MGI relationship(CL:0000222) MGI MGI:1313268 Chrd GO:0005615 MGI:MGI:3577114|PMID:15780974 IDA C chordin Chd gene taxon:10090 20050928 MGI relationship(CL:0000002) MGI MGI:1313268 Chrd GO:0030514 MGI:MGI:3577114|PMID:15780974 IDA P chordin Chd gene taxon:10090 20050928 MGI relationship(CL:0000002) MGI MGI:1313268 Chrd GO:0045668 MGI:MGI:3577114|PMID:15780974 IDA P chordin Chd gene taxon:10090 20050928 MGI relationship(CL:0000002) MGI MGI:88398 Chrm3 GO:0045987 MGI:MGI:2672939|PMID:12925702 IDA P cholinergic receptor, muscarinic 3, cardiac AChR M3|Chrm-3|M3|M3R|muscarinic acetylcholine receptor 3 gene taxon:10090 20051227 MGI relationship(CL:0000192) MGI MGI:87894 Chrne GO:0045211 MGI:MGI:3577805|PMID:15883046 IDA C cholinergic receptor, nicotinic, epsilon polypeptide AChrepsilon|Acre gene taxon:10090 20050531 MGI relationship(CL:0000188) MGI MGI:87895 Chrng GO:0045211 MGI:MGI:3577805|PMID:15883046 IDA C cholinergic receptor, nicotinic, gamma polypeptide Achr-3|Acrg gene taxon:10090 20050531 MGI relationship(CL:0000188) MGI MGI:99484 Chuk GO:0002011 MGI:MGI:3042351|PMID:14960276 IMP MGI:3045616 P conserved helix-loop-helix ubiquitous kinase Chuk1|IkappaB kinase alpha|IKK 1|IKK alpha|IKK-1|IKK-alpha|IKK[a]|IKK1|IKKalpha gene taxon:10090 20040729 MGI relationship(CL:0000066) MGI MGI:99484 Chuk GO:0030316 MGI:MGI:3525391|PMID:15485831 IGI MGI:1100089,MGI:104798 P conserved helix-loop-helix ubiquitous kinase Chuk1|IkappaB kinase alpha|IKK 1|IKK alpha|IKK-1|IKK-alpha|IKK[a]|IKK1|IKKalpha gene taxon:10090 20050317 MGI relationship(CL:0000092) MGI MGI:99484 Chuk GO:0030316 MGI:MGI:3525391|PMID:15485831 IMP MGI:1857735 P conserved helix-loop-helix ubiquitous kinase Chuk1|IkappaB kinase alpha|IKK 1|IKK alpha|IKK-1|IKK-alpha|IKK[a]|IKK1|IKKalpha gene taxon:10090 20050317 MGI relationship(CL:0000092) MGI MGI:88401 Chx10 GO:0008285 MGI:MGI:3611606|PMID:16384989 IMP MGI:1856112 P C. elegans ceh-10 homeo domain containing homolog Hox-10|Hox10 gene taxon:10090 20060228 MGI relationship(CL:0000031) MGI MGI:88401 Chx10 GO:0045165 MGI:MGI:3512656|PMID:15576400 IMP MGI:1856112 P C. elegans ceh-10 homeo domain containing homolog Hox-10|Hox10 gene taxon:10090 20050214 MGI relationship(CL:0000540) MGI MGI:105313 Cit GO:0000910 MGI:MGI:2181325|PMID:11086988 IMP MGI:2447844 P citron Cit-k|citron kinase|citron-N|CRIK-SK gene taxon:10090 20060328 MGI relationship(CL:0000117) MGI MGI:105313 Cit GO:0000910 MGI:MGI:2447488|PMID:12432070 IMP MGI:2447844 P citron Cit-k|citron kinase|citron-N|CRIK-SK gene taxon:10090 20060328 MGI relationship(CL:0000015) MGI MGI:105313 Cit GO:0001726 MGI:MGI:3608100|PMID:12781320 IDA C citron Cit-k|citron kinase|citron-N|CRIK-SK gene taxon:10090 20060328 MGI relationship(CL:0000001) MGI MGI:105313 Cit GO:0005737 MGI:MGI:3608100|PMID:12781320 IDA C citron Cit-k|citron kinase|citron-N|CRIK-SK gene taxon:10090 20060328 MGI relationship(CL:0000001) MGI MGI:105313 Cit GO:0007283 MGI:MGI:2447488|PMID:12432070 IMP MGI:2447844 P citron Cit-k|citron kinase|citron-N|CRIK-SK gene taxon:10090 20060328 MGI relationship(CL:0000015) MGI MGI:105313 Cit GO:0016358 MGI:MGI:3608100|PMID:12781320 IMP MGI:2447844 P citron Cit-k|citron kinase|citron-N|CRIK-SK gene taxon:10090 20060328 MGI relationship(CL:0000598) MGI MGI:105313 Cit GO:0050774 MGI:MGI:3608100|PMID:12781320 IDA P citron Cit-k|citron kinase|citron-N|CRIK-SK gene taxon:10090 20060328 MGI relationship(CL:0000001) MGI MGI:2139758 Clca5 GO:0005886 MGI:MGI:3057090|PMID:15284223 IDA C chloride channel calcium activated 5 gene taxon:10090 20041202 MGI relationship(CL:0000002) MGI MGI:2139744 Clca6 GO:0005886 MGI:MGI:3057090|PMID:15284223 IDA C chloride channel calcium activated 6 gene taxon:10090 20041202 MGI relationship(CL:0000002) MGI MGI:1276112 Cldn5 GO:0016337 MGI:MGI:3513971|PMID:10508865 IC GO:0005923 P claudin 5 Tmvcf gene taxon:10090 20050201 MGI relationship(CL:0000071) MGI MGI:2136650 Clec2i GO:0009986 MGI:MGI:3589064|PMID:15963483 IDA C C-type lectin domain family 2, member i Clr-g|Clrg|Dcl1|OCILrP2 gene taxon:10090 20060719 MGI relationship(CL:0000002) MGI MGI:1861431 Clec7a GO:0009897 MGI:MGI:3027358|PMID:14707091 IDA C C-type lectin domain family 7, member a beta-glucan receptor|beta-GR|BGR|Clecsf12|dectin-1 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1861431 Clec7a GO:0009897 MGI:MGI:3027358|PMID:14707091 IDA C C-type lectin domain family 7, member a beta-glucan receptor|beta-GR|BGR|Clecsf12|dectin-1 gene taxon:10090 20060726 MGI relationship(CL:0000235) MGI MGI:107537 Cln3 GO:0005764 MGI:MGI:3527911|PMID:15588329 IDA C ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) battenin gene taxon:10090 20060913 MGI relationship(CL:0000002) MGI MGI:107537 Cln3 GO:0005769 MGI:MGI:3527911|PMID:15588329 IDA C ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) battenin gene taxon:10090 20060913 MGI relationship(CL:0000002) MGI MGI:107537 Cln3 GO:0005770 MGI:MGI:3527911|PMID:15588329 IDA C ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) battenin gene taxon:10090 20060913 MGI relationship(CL:0000002) MGI MGI:107537 Cln3 GO:0007040 MGI:MGI:1346962|PMID:10527801 IMP MGI:1933976 P ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) battenin gene taxon:10090 20060912 MGI relationship(CL:0000117) MGI MGI:107537 Cln3 GO:0007040 MGI:MGI:3527911|PMID:15588329 IMP MGI:2388887 P ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) battenin gene taxon:10090 20060913 MGI relationship(CL:0000002) MGI MGI:107537 Cln3 GO:0016044 MGI:MGI:3527911|PMID:15588329 IMP MGI:2388887 P ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) battenin gene taxon:10090 20060913 MGI relationship(CL:0000002) MGI MGI:107537 Cln3 GO:0016236 MGI:MGI:3690270|PMID:16714284 IMP MGI:2388888 P ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) battenin gene taxon:10090 20061214 MGI relationship(CL:0000121) MGI MGI:107537 Cln3 GO:0016236 MGI:MGI:3690270|PMID:16714284 IMP MGI:2388888 P ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) battenin gene taxon:10090 20061214 MGI relationship(CL:0000598) MGI MGI:107537 Cln3 GO:0016242 MGI:MGI:3690270|PMID:16714284 IMP MGI:2388888 P ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) battenin gene taxon:10090 20061214 MGI relationship(CL:0000121) MGI MGI:107537 Cln3 GO:0016242 MGI:MGI:3690270|PMID:16714284 IMP MGI:2388888 P ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) battenin gene taxon:10090 20061214 MGI relationship(CL:0000598) MGI MGI:107537 Cln3 GO:0016485 MGI:MGI:3527911|PMID:15588329 IMP MGI:2388887 P ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) battenin gene taxon:10090 20060913 MGI relationship(CL:0000002) MGI MGI:107537 Cln3 GO:0035235 MGI:MGI:3653554|PMID:16483786 IMP MGI:1933976 P ceroid lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) battenin gene taxon:10090 20060913 MGI relationship(CL:0000001) MGI MGI:2442253 Cln5 GO:0005764 MGI:MGI:3046133|PMID:15207259 IDA C ceroid-lipofuscinosis, neuronal 5 gene taxon:10090 20040811 MGI relationship(CL:0000540) MGI MGI:1349447 Cln8 GO:0006644 MGI:MGI:1095703|PMID:9245501 IMP MGI:1856959 P ceroid-lipofuscinosis, neuronal 8 gene taxon:10090 20060919 MGI relationship(CL:0000182) MGI MGI:1349447 Cln8 GO:0007040 MGI:MGI:1333651|PMID:10087069 IMP MGI:1856959 P ceroid-lipofuscinosis, neuronal 8 gene taxon:10090 20060919 MGI relationship(CL:0000099) MGI MGI:1349447 Cln8 GO:0007040 MGI:MGI:66707|PMID:8160780 IMP MGI:1856959 P ceroid-lipofuscinosis, neuronal 8 gene taxon:10090 20060919 MGI relationship(CL:0000117) MGI MGI:1349447 Cln8 GO:0044257 MGI:MGI:53233|PMID:8389815 IMP MGI:1856959 P ceroid-lipofuscinosis, neuronal 8 gene taxon:10090 20060915 MGI relationship(CL:0000100) MGI MGI:1349447 Cln8 GO:0044267 MGI:MGI:49160|PMID:1658691 IMP MGI:1856959 P ceroid-lipofuscinosis, neuronal 8 gene taxon:10090 20060915 MGI relationship(CL:0000100) MGI MGI:1349447 Cln8 GO:0045494 MGI:MGI:1096072|PMID:9151333 IMP MGI:1856959 P ceroid-lipofuscinosis, neuronal 8 gene taxon:10090 20060919 MGI relationship(CL:0000604) MGI MGI:1333878 Cmya1 GO:0005916 MGI:MGI:1329802|PMID:10021346 IDA C cardiomyopathy associated 1 mXin alpha|Xin gene taxon:10090 20070105 MGI relationship(CL:0000513) MGI MGI:1333878 Cmya1 GO:0005916 MGI:MGI:3655786|PMID:16708114 IDA C cardiomyopathy associated 1 mXin alpha|Xin gene taxon:10090 20070105 MGI relationship(CL:0000513) MGI MGI:88439 Cntf GO:0046533 MGI:MGI:3045481|PMID:15207851 IDA P ciliary neurotrophic factor gene taxon:10090 20040818 MGI relationship(CL:0000604) MGI MGI:1095415 Col19a1 GO:0007519 MGI:MGI:3053247|PMID:15302855 IMP MGI:3053870 P procollagen, type XIX, alpha 1 gene taxon:10090 20041101 MGI relationship(CL:0000188) MGI MGI:88461 Col6a3 GO:0005615 MGI:MGI:3055460|PMID:10444069 IDA C procollagen, type VI, alpha 3 Col6a-3 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:88463 Col8a1 GO:0050673 MGI:MGI:3587134|PMID:16051690 IGI MGI:88464 P procollagen, type VIII, alpha 1 Col8a-1 gene taxon:10090 20050923 MGI relationship(CL:0000001) MGI MGI:88464 Col8a2 GO:0050673 MGI:MGI:3587134|PMID:16051690 IGI MGI:88463 P procollagen, type VIII, alpha 2 gene taxon:10090 20050923 MGI relationship(CL:0000001) MGI MGI:1917599 Copb1 GO:0005794 MGI:MGI:3055460|PMID:10444069 IDA C coatomer protein complex, subunit beta 1 Copb1 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1349415 Cops5 GO:0000074 MGI:MGI:3510484|PMID:15299027 IMP MGI:3511260 P COP9 (constitutive photomorphogenic) homolog, subunit 5 (Arabidopsis thaliana) COP9 complex S5|CSN5|Jab1|JUN activation binding protein|Sgn5 gene taxon:10090 20041220 MGI relationship(CL:0000007) MGI MGI:1926135 Coro7 GO:0000299 MGI:MGI:3051202|PMID:15327992 IDA C coronin 7 gene taxon:10090 20041026 MGI relationship(CL:0000002) MGI MGI:1926135 Coro7 GO:0005625 MGI:MGI:3051202|PMID:15327992 IDA C coronin 7 gene taxon:10090 20041026 MGI relationship(CL:0000002) MGI MGI:1926135 Coro7 GO:0005794 MGI:MGI:3051202|PMID:15327992 IDA C coronin 7 gene taxon:10090 20041026 MGI relationship(CL:0000002) MGI MGI:108442 Cpeb1 GO:0007130 MGI:MGI:3606735|PMID:11702780 IMP MGI:3606747 P cytoplasmic polyadenylation element binding protein 1 mCPEB gene taxon:10090 20060314 MGI relationship(CL:0000017) MGI MGI:108442 Cpeb1 GO:0007130 MGI:MGI:3606735|PMID:11702780 IMP MGI:3606747 P cytoplasmic polyadenylation element binding protein 1 mCPEB gene taxon:10090 20060314 MGI relationship(CL:0000023) MGI MGI:108442 Cpeb1 GO:0048168 MGI:MGI:3606369|PMID:15169862 IMP MGI:3606747 P cytoplasmic polyadenylation element binding protein 1 mCPEB gene taxon:10090 20060314 MGI relationship(CL:0000117) MGI MGI:2384571 Cplx3 GO:0045202 MGI:MGI:3582382|PMID:15911881 IDA C complexin 3 CpxIII gene taxon:10090 20050816 MGI relationship(CL:0000573) MGI MGI:1334445 Cpne6 GO:0030424 MGI:MGI:1321417|PMID:9886090 IDA C copine VI neuronal copine gene taxon:10090 20040721 MGI relationship(CL:0000117) MGI MGI:1334445 Cpne6 GO:0030425 MGI:MGI:1321417|PMID:9886090 IDA C copine VI neuronal copine gene taxon:10090 20040721 MGI relationship(CL:0000120) MGI MGI:2136343 Crb1 GO:0016044 MGI:MGI:2675211|PMID:12915475 IMP MGI:2676366 P crumbs homolog 1 (Drosophila) gene taxon:10090 20040721 MGI relationship(CL:0000210) MGI MGI:2136343 Crb1 GO:0042462 MGI:MGI:2675211|PMID:12915475 IMP MGI:2676366 P crumbs homolog 1 (Drosophila) gene taxon:10090 20040721 MGI relationship(CL:0000210) MGI MGI:1916603 Creb3l4 GO:0005783 MGI:MGI:3611598|PMID:15938716 IDA C cAMP responsive element binding protein 3-like 4 ATCE1|CREB3|CREB4|JAL|mJAL|Tisp40|Tisp40alpha|Tisp40beta gene taxon:10090 20060309 MGI relationship(CL:0000002) MGI MGI:1339758 Csf1r GO:0005886 MGI:MGI:3576987|PMID:15860730 IDA C colony stimulating factor 1 receptor CD115|CSF-1R|Csfmr|Fim-2|Fms|M-CSFR gene taxon:10090 20061208 MGI relationship(CL:0000001) MGI MGI:88537 Csk GO:0005911 MGI:MGI:3577866|PMID:15861137 IDA C c-src tyrosine kinase gene taxon:10090 20050531 MGI relationship(CL:0000002) MGI MGI:88537 Csk GO:0008285 MGI:MGI:3577866|PMID:15861137 IGI MGI:105057 P c-src tyrosine kinase gene taxon:10090 20050531 MGI relationship(CL:0000002) MGI MGI:88537 Csk GO:0008285 MGI:MGI:3577866|PMID:15861137 IMP P c-src tyrosine kinase gene taxon:10090 20050531 MGI relationship(CL:0000002) MGI MGI:1352747 Cspg5 GO:0050804 MGI:MGI:3583729|PMID:15848802 IMP MGI:3583953 P chondroitin sulfate proteoglycan 5 CALEB|neuroglycan C|NGC gene taxon:10090 20050825 MGI relationship(CL:0000617) MGI MGI:1330824 Csrp3 GO:0002026 MGI:MGI:1347184|PMID:10555147 IGI MGI:97622 P cysteine and glycine-rich protein 3 CRP3|MLP|muscle LIM protein gene taxon:10090 20061016 MGI relationship(CL:0000746) MGI MGI:1330824 Csrp3 GO:0006874 MGI:MGI:1347184|PMID:10555147 IGI MGI:97622 P cysteine and glycine-rich protein 3 CRP3|MLP|muscle LIM protein gene taxon:10090 20061016 MGI relationship(CL:0000746) MGI MGI:1330824 Csrp3 GO:0048738 MGI:MGI:1347184|PMID:10555147 IGI MGI:97622 P cysteine and glycine-rich protein 3 CRP3|MLP|muscle LIM protein gene taxon:10090 20061013 MGI relationship(CL:0000746) MGI MGI:2684607 Ctf2 GO:0008284 MGI:MGI:3039221|PMID:15051883 IGI MGI:95516,MGI:95290 P cardiotrophin 2 LOC244218|neuropoietin|NP gene taxon:10090 20060125 MGI relationship(CL:0000001) MGI MGI:88274 Ctnna1 GO:0007163 MGI:MGI:3619284|PMID:16543460 IMP MGI:2677796|MGI:2176173 P catenin (cadherin associated protein), alpha 1 alpha E catenin|alpha(E)-catenin|Catna1 gene taxon:10090 20061220 MGI relationship(CL:0000337) MGI MGI:88274 Ctnna1 GO:0007406 MGI:MGI:3619284|PMID:16543460 IGI MGI:108075 P catenin (cadherin associated protein), alpha 1 alpha E catenin|alpha(E)-catenin|Catna1 gene taxon:10090 20061220 MGI relationship(CL:0000337) MGI MGI:88274 Ctnna1 GO:0007406 MGI:MGI:3619284|PMID:16543460 IMP MGI:2677796|MGI:2176173 P catenin (cadherin associated protein), alpha 1 alpha E catenin|alpha(E)-catenin|Catna1 gene taxon:10090 20061220 MGI relationship(CL:0000337) MGI MGI:88274 Ctnna1 GO:0043066 MGI:MGI:3619284|PMID:16543460 IMP MGI:2677796|MGI:2176173 P catenin (cadherin associated protein), alpha 1 alpha E catenin|alpha(E)-catenin|Catna1 gene taxon:10090 20061220 MGI relationship(CL:0000337) MGI MGI:88274 Ctnna1 GO:0043297 MGI:MGI:3619284|PMID:16543460 IMP MGI:2677796|MGI:2176173 P catenin (cadherin associated protein), alpha 1 alpha E catenin|alpha(E)-catenin|Catna1 gene taxon:10090 20061220 MGI relationship(CL:0000337) MGI MGI:88274 Ctnna1 GO:0045880 MGI:MGI:3619284|PMID:16543460 IGI MGI:108075 P catenin (cadherin associated protein), alpha 1 alpha E catenin|alpha(E)-catenin|Catna1 gene taxon:10090 20061220 MGI relationship(CL:0000337) MGI MGI:88276 Ctnnb1 GO:0000904 MGI:MGI:3603687|PMID:16102745 IMP MGI:2148567|MGI:3045749 P catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20051129 MGI relationship(CL:0000066) MGI MGI:88276 Ctnnb1 GO:0001709 MGI:MGI:3529734|PMID:15708565 IMP MGI:2148567|MGI:2176173 P catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20050519 MGI relationship(CL:0000117) MGI MGI:88276 Ctnnb1 GO:0001711 MGI:MGI:3625553|PMID:12194849 IMP MGI:2148567|MGI:1858007 P catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20060724 MGI relationship(CL:0000223) MGI MGI:88276 Ctnnb1 GO:0003682 MGI:MGI:3579620|PMID:15778706 IDA F catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20050824 MGI relationship(CL:0000510) MGI MGI:88276 Ctnnb1 GO:0003682 MGI:MGI:3582095|PMID:15907834 IDA F catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20060727 MGI relationship(CL:0000001) MGI MGI:88276 Ctnnb1 GO:0005634 MGI:MGI:2670493|PMID:12923052 IDA C catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20050103 MGI relationship(CL:0000221) MGI MGI:88276 Ctnnb1 GO:0005634 MGI:MGI:3055626|PMID:15371327 IDA C catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20041206 MGI relationship(CL:0000134) MGI MGI:88276 Ctnnb1 GO:0005634 MGI:MGI:3579620|PMID:15778706 IDA C catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20050824 MGI relationship(CL:0000510) MGI MGI:88276 Ctnnb1 GO:0005634 MGI:MGI:3617131|PMID:16439479 IDA C catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20060605 MGI relationship(CL:0000131) MGI MGI:88276 Ctnnb1 GO:0005634 MGI:MGI:3640895|PMID:16678815 IDA C catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20060921 MGI relationship(CL:0000070) MGI MGI:88276 Ctnnb1 GO:0005634 MGI:MGI:3640895|PMID:16678815 IDA C catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20060921 MGI relationship(CL:0000134) MGI MGI:88276 Ctnnb1 GO:0005737 MGI:MGI:2670493|PMID:12923052 IDA C catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20050103 MGI relationship(CL:0000221) MGI MGI:88276 Ctnnb1 GO:0005886 MGI:MGI:3614372|PMID:16418220 IDA C catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20060309 MGI relationship(CL:1000274) MGI MGI:88276 Ctnnb1 GO:0005913 MGI:MGI:2154851|PMID:11731229 IDA C catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20060912 MGI relationship(CL:0000353) MGI MGI:88276 Ctnnb1 GO:0005913 MGI:MGI:3528104|PMID:15645444 IDA C catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20050308 MGI relationship(CL:0000131) MGI MGI:88276 Ctnnb1 GO:0005916 MGI:MGI:3656458|PMID:16481394 IDA C catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20070312 MGI relationship(CL:0000746) MGI MGI:88276 Ctnnb1 GO:0007398 MGI:MGI:77405|PMID:8582267 IMP MGI:1857678 P catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20040716 MGI relationship(CL:0000221) MGI MGI:88276 Ctnnb1 GO:0009950 MGI:MGI:2670493|PMID:12923052 IMP MGI:2148594|MGI:2158470 P catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20050103 MGI relationship(CL:0000221) MGI MGI:88276 Ctnnb1 GO:0010003 MGI:MGI:77405|PMID:8582267 IMP MGI:1857678 P catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20040716 MGI relationship(CL:0000221) MGI MGI:88276 Ctnnb1 GO:0016020 MGI:MGI:81460|PMID:8821035 IDA C catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20070222 MGI relationship(CL:0000746) MGI MGI:88276 Ctnnb1 GO:0016331 MGI:MGI:3603687|PMID:16102745 IMP MGI:2148567|MGI:3045749 P catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20051129 MGI relationship(CL:0000066) MGI MGI:88276 Ctnnb1 GO:0016337 MGI:MGI:3603687|PMID:16102745 IMP MGI:2148567|MGI:3045749 P catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20051129 MGI relationship(CL:0000066) MGI MGI:88276 Ctnnb1 GO:0030018 MGI:MGI:81460|PMID:8821035 IDA C catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20070222 MGI relationship(CL:0000188) MGI MGI:88276 Ctnnb1 GO:0030018 MGI:MGI:81460|PMID:8821035 IDA C catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20070222 MGI relationship(CL:0000746) MGI MGI:88276 Ctnnb1 GO:0030154 MGI:MGI:3607950|PMID:16192304 IMP MGI:2148569 P catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20060412 MGI relationship(CL:0000622) MGI MGI:88276 Ctnnb1 GO:0030316 MGI:MGI:3578468|PMID:15866165 IMP MGI:1858008 P catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20050620 MGI relationship(CL:0000092) MGI MGI:88276 Ctnnb1 GO:0030858 MGI:MGI:3613282|PMID:16040629 IMP MGI:1858008|MGI:2679524|MGI:2445707 P catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20060307 MGI relationship(CL:0000082) MGI MGI:88276 Ctnnb1 GO:0031528 MGI:MGI:3617131|PMID:16439479 IDA C catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20060605 MGI relationship(CL:0000131) MGI MGI:88276 Ctnnb1 GO:0045177 MGI:MGI:3033551|PMID:14758363 IDA C catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20040421 MGI relationship(CL:0000066) MGI MGI:88276 Ctnnb1 GO:0045177 MGI:MGI:3037622|PMID:15037549 IDA C catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20040630 MGI relationship(CL:0000117) MGI MGI:88276 Ctnnb1 GO:0045453 MGI:MGI:3578468|PMID:15866165 IMP MGI:1858008|MGI:2148567|MGI:3041864 P catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20050620 MGI relationship(CL:0000092) MGI MGI:88276 Ctnnb1 GO:0045596 MGI:MGI:3603687|PMID:16102745 IMP MGI:2148567|MGI:3045749 P catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20051129 MGI relationship(CL:0000306) MGI MGI:88276 Ctnnb1 GO:0045667 MGI:MGI:3511731|PMID:15576404 IMP MGI:2148567|MGI:3044412 P catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20050110 MGI relationship(CL:0000062) MGI MGI:88276 Ctnnb1 GO:0045892 MGI:MGI:3578464|PMID:15866163 IMP MGI:2148594 P catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20050728 MGI relationship(CL:0000134) MGI MGI:88276 Ctnnb1 GO:0045941 MGI:MGI:3578464|PMID:15866163 IMP MGI:1858008 P catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20050728 MGI relationship(CL:0000134) MGI MGI:88276 Ctnnb1 GO:0045944 MGI:MGI:3582095|PMID:15907834 IDA P catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20050912 MGI relationship(CL:0000001) MGI MGI:88276 Ctnnb1 GO:0048593 MGI:MGI:3603687|PMID:16102745 IMP MGI:2148567|MGI:3045749 P catenin (cadherin associated protein), beta 1 beta catenin|beta-catenin|Catnb gene taxon:10090 20051129 MGI relationship(CL:0000066) MGI MGI:88562 Ctsd GO:0004192 MGI:MGI:3527911|PMID:15588329 IDA F cathepsin D CatD|CD gene taxon:10090 20060913 MGI relationship(CL:0000002) MGI MGI:88562 Ctsd GO:0005764 MGI:MGI:1352198|PMID:10591619 IDA C cathepsin D CatD|CD gene taxon:10090 20050712 MGI relationship(CL:0000067) MGI MGI:88562 Ctsd GO:0005764 MGI:MGI:2673081|PMID:12775715 IDA C cathepsin D CatD|CD gene taxon:10090 20050609 MGI relationship(CL:0000075) MGI MGI:88562 Ctsd GO:0005764 MGI:MGI:3608104|PMID:16242638 IDA C cathepsin D CatD|CD gene taxon:10090 20060913 MGI relationship(CL:0000001) MGI MGI:88562 Ctsd GO:0006508 MGI:MGI:3527911|PMID:15588329 IC GO:0004192 P cathepsin D CatD|CD gene taxon:10090 20060913 MGI relationship(CL:0000002) MGI MGI:1931256 Cubn GO:0005737 MGI:MGI:2179173|PMID:11856751 IDA C cubilin (intrinsic factor-cobalamin receptor) D2Wsu88e gene taxon:10090 20050607 MGI relationship(CL:0000623) MGI MGI:1931256 Cubn GO:0005783 MGI:MGI:3577702|PMID:15616221 IDA C cubilin (intrinsic factor-cobalamin receptor) D2Wsu88e gene taxon:10090 20050609 MGI relationship(CL:0000007) MGI MGI:1931256 Cubn GO:0005794 MGI:MGI:3577702|PMID:15616221 IDA C cubilin (intrinsic factor-cobalamin receptor) D2Wsu88e gene taxon:10090 20050609 MGI relationship(CL:0000223) MGI MGI:1931256 Cubn GO:0005905 MGI:MGI:3577702|PMID:15616221 IDA C cubilin (intrinsic factor-cobalamin receptor) D2Wsu88e gene taxon:10090 20050609 MGI relationship(CL:0000223) MGI MGI:1931256 Cubn GO:0006898 MGI:MGI:3577702|PMID:15616221 IMP P cubilin (intrinsic factor-cobalamin receptor) D2Wsu88e gene taxon:10090 20050609 MGI relationship(CL:1000274) MGI MGI:1931256 Cubn GO:0016324 MGI:MGI:3577702|PMID:15616221 IDA C cubilin (intrinsic factor-cobalamin receptor) D2Wsu88e gene taxon:10090 20050609 MGI relationship(CL:0000223) MGI MGI:1931256 Cubn GO:0016324 MGI:MGI:3577702|PMID:15616221 IDA C cubilin (intrinsic factor-cobalamin receptor) D2Wsu88e gene taxon:10090 20050609 MGI relationship(CL:1000274) MGI MGI:1931256 Cubn GO:0030139 MGI:MGI:3577702|PMID:15616221 IDA C cubilin (intrinsic factor-cobalamin receptor) D2Wsu88e gene taxon:10090 20050609 MGI relationship(CL:0000223) MGI MGI:1931256 Cubn GO:0042953 MGI:MGI:3577702|PMID:15616221 IDA P cubilin (intrinsic factor-cobalamin receptor) D2Wsu88e gene taxon:10090 20050609 MGI relationship(CL:1000274) MGI MGI:1931256 Cubn GO:0045177 MGI:MGI:2179173|PMID:11856751 IDA C cubilin (intrinsic factor-cobalamin receptor) D2Wsu88e gene taxon:10090 20050607 MGI relationship(CL:0000623) MGI MGI:1931256 Cubn GO:0045177 MGI:MGI:3577702|PMID:15616221 IDA C cubilin (intrinsic factor-cobalamin receptor) D2Wsu88e gene taxon:10090 20050609 MGI relationship(CL:0000710) MGI MGI:1931256 Cubn GO:0045177 MGI:MGI:3578036|PMID:15342463 IDA C cubilin (intrinsic factor-cobalamin receptor) D2Wsu88e gene taxon:10090 20050609 MGI relationship(CL:0000223) MGI MGI:1201679 Cxadr GO:0007005 MGI:MGI:3587448|PMID:16079292 IMP MGI:3587803 P coxsackievirus and adenovirus receptor CAR|MCAR|MCVADR gene taxon:10090 20051129 MGI relationship(CL:0000193) MGI MGI:1201679 Cxadr GO:0048739 MGI:MGI:3587448|PMID:16079292 IMP MGI:3587803 P coxsackievirus and adenovirus receptor CAR|MCAR|MCVADR gene taxon:10090 20051129 MGI relationship(CL:0000002) MGI MGI:1201679 Cxadr GO:0048739 MGI:MGI:3587448|PMID:16079292 IMP MGI:3587803 P coxsackievirus and adenovirus receptor CAR|MCAR|MCVADR gene taxon:10090 20051129 MGI relationship(CL:0000193) MGI MGI:103556 Cxcl12 GO:0001667 MGI:MGI:3578491|PMID:15626744 IMP MGI:1934384 P chemokine (C-X-C motif) ligand 12 PBSF|PBSF/SDF-1|Scyb12|SDF-1|Sdf1|Sdf1a|Sdf1b|TLSF-a|TLSF-b|TPAR1 gene taxon:10090 20050805 MGI relationship(CL:0000071) MGI MGI:103556 Cxcl12 GO:0008045 MGI:MGI:3590395|PMID:16129397 IMP MGI:1934384 P chemokine (C-X-C motif) ligand 12 PBSF|PBSF/SDF-1|Scyb12|SDF-1|Sdf1|Sdf1a|Sdf1b|TLSF-a|TLSF-b|TPAR1 gene taxon:10090 20060123 MGI relationship(CL:0000100) MGI MGI:109563 Cxcr4 GO:0001667 MGI:MGI:3578491|PMID:15626744 IMP MGI:1934442 P chemokine (C-X-C motif) receptor 4 CD184|Cmkar4|CXCR4|fusin|PB-CKR gene taxon:10090 20050805 MGI relationship(CL:0000071) MGI MGI:109563 Cxcr4 GO:0008045 MGI:MGI:3590395|PMID:16129397 IMP MGI:1934442 P chemokine (C-X-C motif) receptor 4 CD184|Cmkar4|CXCR4|fusin|PB-CKR gene taxon:10090 20060123 MGI relationship(CL:0000100) MGI MGI:109563 Cxcr4 GO:0030334 MGI:MGI:2389283|PMID:12183377 IMP MGI:1934407 P chemokine (C-X-C motif) receptor 4 CD184|Cmkar4|CXCR4|fusin|PB-CKR gene taxon:10090 20050114 MGI relationship(CL:0000120) MGI MGI:109563 Cxcr4 GO:0030334 MGI:MGI:3589965|PMID:16166380 IGI MGI:108088 P chemokine (C-X-C motif) receptor 4 CD184|Cmkar4|CXCR4|fusin|PB-CKR gene taxon:10090 20060116 MGI relationship(CL:0000056) MGI MGI:109563 Cxcr4 GO:0030426 MGI:MGI:3590395|PMID:16129397 IDA C chemokine (C-X-C motif) receptor 4 CD184|Cmkar4|CXCR4|fusin|PB-CKR gene taxon:10090 20060123 MGI relationship(CL:0000001) MGI MGI:88574 Cybb GO:0005737 MGI:MGI:3610800|PMID:15499027 IDA C cytochrome b-245, beta polypeptide gp91|gp91phox|Nox2 gene taxon:10090 20060210 MGI relationship(CL:0000071) MGI MGI:88574 Cybb GO:0005886 MGI:MGI:3610800|PMID:15499027 IDA C cytochrome b-245, beta polypeptide gp91|gp91phox|Nox2 gene taxon:10090 20060210 MGI relationship(CL:0000071) MGI MGI:1859320 Cyhr1 GO:0005635 MGI:MGI:1355019|PMID:10745073 IDA C cysteine and histidine rich 1 Chrp gene taxon:10090 20041228 MGI relationship(CL:0000002) MGI MGI:1859320 Cyhr1 GO:0005737 MGI:MGI:1355019|PMID:10745073 IDA C cysteine and histidine rich 1 Chrp gene taxon:10090 20041228 MGI relationship(CL:0000002) MGI MGI:108554 Dab1 GO:0001764 MGI:MGI:3042322|PMID:15091337 IMP MGI:1856801 P disabled homolog 1 (Drosophila) gene taxon:10090 20050114 MGI relationship(CL:0000117) MGI MGI:108554 Dab1 GO:0001764 MGI:MGI:3574745|PMID:15703280 IMP MGI:1856801 P disabled homolog 1 (Drosophila) gene taxon:10090 20050509 MGI relationship(CL:0000100) MGI MGI:108554 Dab1 GO:0007162 MGI:MGI:3042322|PMID:15091337 IMP MGI:1856801 P disabled homolog 1 (Drosophila) gene taxon:10090 20070301 MGI relationship(CL:0000117) MGI MGI:108554 Dab1 GO:0021799 MGI:MGI:1098179|PMID:9338785 IMP MGI:1861918 P disabled homolog 1 (Drosophila) gene taxon:10090 20070301 MGI relationship(CL:0000117) MGI MGI:108554 Dab1 GO:0021799 MGI:MGI:1098179|PMID:9338785 IMP MGI:1861918 P disabled homolog 1 (Drosophila) gene taxon:10090 20070301 MGI relationship(CL:0000598) MGI MGI:108554 Dab1 GO:0021813 MGI:MGI:3042322|PMID:15091337 IMP MGI:1856801 P disabled homolog 1 (Drosophila) gene taxon:10090 20070301 MGI relationship(CL:0000117) MGI MGI:108554 Dab1 GO:0021942 MGI:MGI:1098179|PMID:9338785 IMP MGI:1861918 P disabled homolog 1 (Drosophila) gene taxon:10090 20070301 MGI relationship(CL:0000121) MGI MGI:108554 Dab1 GO:0045860 MGI:MGI:3629864|PMID:12526740 IGI MGI:103022 P disabled homolog 1 (Drosophila) gene taxon:10090 20060807 MGI relationship(CL:0000001) MGI MGI:109175 Dab2 GO:0000904 MGI:MGI:2389502|PMID:12413896 IMP MGI:2429678 P disabled homolog 2 (Drosophila) D15Wsu122e|Doc-2|Doc2|p96 gene taxon:10090 20060130 MGI relationship(CL:0000223) MGI MGI:109175 Dab2 GO:0006907 MGI:MGI:3610714|PMID:16263760 IMP MGI:2387168 P disabled homolog 2 (Drosophila) D15Wsu122e|Doc-2|Doc2|p96 gene taxon:10090 20060130 MGI relationship(CL:0000001) MGI MGI:101864 Dag1 GO:0005626 MGI:MGI:3028713|PMID:14627610 IDA C dystroglycan 1 alpha-dystroglycan|beta-dystroglycan|D9Wsu13e|DG|dystrophin associated glycoprotein 1 gene taxon:10090 20060726 MGI relationship(CL:0000188) MGI MGI:101864 Dag1 GO:0005886 MGI:MGI:1927714|PMID:10988290 IDA C dystroglycan 1 alpha-dystroglycan|beta-dystroglycan|D9Wsu13e|DG|dystrophin associated glycoprotein 1 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:101864 Dag1 GO:0005886 MGI:MGI:3028713|PMID:14627610 IDA C dystroglycan 1 alpha-dystroglycan|beta-dystroglycan|D9Wsu13e|DG|dystrophin associated glycoprotein 1 gene taxon:10090 20060726 MGI relationship(CL:0000188) MGI MGI:1342328 Dazl GO:0007281 MGI:MGI:3612913|PMID:16310179 IMP MGI:2181904 P deleted in azoospermia-like Dazla|Tpx-2|Tpx2 gene taxon:10090 20060411 MGI relationship(CL:0000015) MGI MGI:94864 Dbh GO:0001816 MGI:MGI:1332340|PMID:10051631 IMP MGI:1857556 P dopamine beta hydroxylase gene taxon:10090 20051209 MGI relationship(CL:0000084) MGI MGI:94864 Dbh GO:0042127 MGI:MGI:3587974|PMID:15849236 IMP MGI:1857556 P dopamine beta hydroxylase gene taxon:10090 20051214 MGI relationship(CL:0000071) MGI MGI:94864 Dbh GO:0042127 MGI:MGI:3587974|PMID:15849236 IMP MGI:1857556 P dopamine beta hydroxylase gene taxon:10090 20051214 MGI relationship(CL:0000359) MGI MGI:102563 Dct GO:0048066 MGI:MGI:3041903|PMID:15060160 IMP MGI:1856379 P dopachrome tautomerase TRP-2|TRP2|tyrosinase-related protein-2|Tyrp-2|Tyrp2 gene taxon:10090 20050513 MGI relationship(CL:0000148) MGI MGI:102563 Dct GO:0048468 MGI:MGI:3041903|PMID:15060160 IMP MGI:1856379 P dopachrome tautomerase TRP-2|TRP2|tyrosinase-related protein-2|Tyrp-2|Tyrp2 gene taxon:10090 20050513 MGI relationship(CL:0000148) MGI MGI:102670 Ddx4 GO:0005737 MGI:MGI:3530170|PMID:15749075 IDA C DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 Mvh|mvh / m'vasa|VASA gene taxon:10090 20050424 MGI relationship(CL:0000039) MGI MGI:102670 Ddx4 GO:0005737 MGI:MGI:3578091|PMID:15789443 IDA C DEAD (Asp-Glu-Ala-Asp) box polypeptide 4 Mvh|mvh / m'vasa|VASA gene taxon:10090 20050607 MGI relationship(CL:0000586) MGI MGI:1889850 Dfna5h GO:0035315 MGI:MGI:3583372|PMID:16023581 IMP MGI:3583715 P deafness, autosomal dominant 5 homolog (human) Fin15 gene taxon:10090 20060918 MGI relationship(CL:0000202) MGI MGI:3045345 Dgat2l4 GO:0005789 MGI:MGI:3054255|PMID:15220349 IDA C diacylglycerol O-acyltransferase 2-like 4 gene taxon:10090 20050112 MGI relationship(CL:0000002) MGI MGI:1298378 Dhcr7 GO:0030154 MGI:MGI:3056828|PMID:15005800 IMP MGI:2387406 P 7-dehydrocholesterol reductase gene taxon:10090 20050216 MGI relationship(CL:0000082) MGI MGI:1913843 Diablo GO:0005737 MGI:MGI:3577836|PMID:15882989 IDA C diablo homolog (Drosophila) Smac gene taxon:10090 20051208 MGI relationship(CL:0000001) MGI MGI:1913843 Diablo GO:0005737 MGI:MGI:3587135|PMID:16085184 IDA C diablo homolog (Drosophila) Smac gene taxon:10090 20051208 MGI relationship(CL:0000002) MGI MGI:1913843 Diablo GO:0005739 MGI:MGI:3577836|PMID:15882989 IDA C diablo homolog (Drosophila) Smac gene taxon:10090 20051208 MGI relationship(CL:0000001) MGI MGI:1913843 Diablo GO:0005739 MGI:MGI:3587135|PMID:16085184 IDA C diablo homolog (Drosophila) Smac gene taxon:10090 20051208 MGI relationship(CL:0000002) MGI MGI:1913843 Diablo GO:0006919 MGI:MGI:3587135|PMID:16085184 IDA P diablo homolog (Drosophila) Smac gene taxon:10090 20051208 MGI relationship(CL:0000002) MGI MGI:1913843 Diablo GO:0006919 MGI:MGI:3587135|PMID:16085184 IMP P diablo homolog (Drosophila) Smac gene taxon:10090 20051208 MGI relationship(CL:0000002) MGI MGI:1913843 Diablo GO:0008631 MGI:MGI:3587135|PMID:16085184 IDA P diablo homolog (Drosophila) Smac gene taxon:10090 20051208 MGI relationship(CL:0000002) MGI MGI:2177178 Dicer1 GO:0019827 MGI:MGI:2679763|PMID:14528307 IMP MGI:2681012 P Dicer1, Dcr-1 homolog (Drosophila) D12Ertd7e gene taxon:10090 20050114 MGI relationship(CL:0000034) MGI MGI:2177178 Dicer1 GO:0035116 MGI:MGI:3609457|PMID:16319892 IMP MGI:3589208|MGI:2450929 P Dicer1, Dcr-1 homolog (Drosophila) D12Ertd7e gene taxon:10090 20060130 MGI relationship(CL:0000134) MGI MGI:1916147 Disp1 GO:0007389 MGI:MGI:3051703|PMID:15269168 IMP MGI:2448055|MGI:3052133 P dispatched homolog 1 (Drosophila) DispA gene taxon:10090 20050114 MGI relationship(CL:0000134) MGI MGI:1329040 Dkk1 GO:0030178 MGI:MGI:3603992|PMID:16126904 IDA P dickkopf homolog 1 (Xenopus laevis) mdkk-1 gene taxon:10090 20060119 MGI relationship(CL:0000002) MGI MGI:1277959 Dlg4 GO:0005515 MGI:MGI:2138004|PMID:11483650 IPI UniProt:Q9Z123 F discs, large homolog 4 (Drosophila) Dlgh4|PSD-95|PSD95|SAP90|SAP90A gene taxon:10090 20050429 MGI relationship(CL:0000002) MGI MGI:1277959 Dlg4 GO:0005737 MGI:MGI:2138004|PMID:11483650 IDA C discs, large homolog 4 (Drosophila) Dlgh4|PSD-95|PSD95|SAP90|SAP90A gene taxon:10090 20050429 MGI relationship(CL:0000002) MGI MGI:1277959 Dlg4 GO:0016188 MGI:MGI:3521633|PMID:15603741 IDA P discs, large homolog 4 (Drosophila) Dlgh4|PSD-95|PSD95|SAP90|SAP90A gene taxon:10090 20050315 MGI relationship(CL:0000117) MGI MGI:1277959 Dlg4 GO:0016188 MGI:MGI:3521633|PMID:15603741 IGI MGI:1915336 P discs, large homolog 4 (Drosophila) Dlgh4|PSD-95|PSD95|SAP90|SAP90A gene taxon:10090 20050315 MGI relationship(CL:0000117) MGI MGI:1277959 Dlg4 GO:0031234 MGI:MGI:2138004|PMID:11483650 IDA C discs, large homolog 4 (Drosophila) Dlgh4|PSD-95|PSD95|SAP90|SAP90A gene taxon:10090 20050429 MGI relationship(CL:0000002) MGI MGI:1277959 Dlg4 GO:0045202 MGI:MGI:3653273|PMID:16818724 IDA C discs, large homolog 4 (Drosophila) Dlgh4|PSD-95|PSD95|SAP90|SAP90A gene taxon:10090 20070228 MGI relationship(CL:0000117) MGI MGI:1277959 Dlg4 GO:0048169 MGI:MGI:3580530|PMID:12427827 IGI MGI:3039785 P discs, large homolog 4 (Drosophila) Dlgh4|PSD-95|PSD95|SAP90|SAP90A gene taxon:10090 20060308 MGI relationship(CL:0000117) MGI MGI:104659 Dll1 GO:0005886 MGI:MGI:3603078|PMID:16000382 IDA C delta-like 1 (Drosophila) Delta1 gene taxon:10090 20051117 MGI relationship(CL:0000002) MGI MGI:104659 Dll1 GO:0031410 MGI:MGI:3603078|PMID:16000382 IDA C delta-like 1 (Drosophila) Delta1 gene taxon:10090 20051117 MGI relationship(CL:0000002) MGI MGI:104659 Dll1 GO:0045596 MGI:MGI:3621102|PMID:16495313 IMP MGI:3044907|MGI:1932522 P delta-like 1 (Drosophila) Delta1 gene taxon:10090 20060810 MGI relationship(CL:0000635) MGI MGI:104659 Dll1 GO:0045596 MGI:MGI:3621102|PMID:16495313 IMP MGI:3044907|MGI:1932522 P delta-like 1 (Drosophila) Delta1 gene taxon:10090 20060810 MGI relationship(CL:1000191) MGI MGI:104659 Dll1 GO:0045608 MGI:MGI:3621102|PMID:16495313 IMP MGI:3044907|MGI:1932522 P delta-like 1 (Drosophila) Delta1 gene taxon:10090 20060810 MGI relationship(CL:0000589) MGI MGI:104659 Dll1 GO:0045608 MGI:MGI:3621102|PMID:16495313 IMP MGI:3044907|MGI:1932522 P delta-like 1 (Drosophila) Delta1 gene taxon:10090 20060810 MGI relationship(CL:0000601) MGI MGI:104659 Dll1 GO:0048839 MGI:MGI:3621102|PMID:16495313 IMP MGI:3044907|MGI:1932522 P delta-like 1 (Drosophila) Delta1 gene taxon:10090 20060810 MGI relationship(CL:0000589) MGI MGI:104659 Dll1 GO:0048839 MGI:MGI:3621102|PMID:16495313 IMP MGI:3044907|MGI:1932522 P delta-like 1 (Drosophila) Delta1 gene taxon:10090 20060810 MGI relationship(CL:0000601) MGI MGI:104659 Dll1 GO:0048839 MGI:MGI:3621102|PMID:16495313 IMP MGI:3044907|MGI:1932522 P delta-like 1 (Drosophila) Delta1 gene taxon:10090 20060810 MGI relationship(CL:0000635) MGI MGI:104659 Dll1 GO:0048839 MGI:MGI:3621102|PMID:16495313 IMP MGI:3044907|MGI:1932522 P delta-like 1 (Drosophila) Delta1 gene taxon:10090 20060810 MGI relationship(CL:1000191) MGI MGI:1859388 Dll4 GO:0001525 MGI:MGI:3056004|PMID:15466160 IMP MGI:3056460 P delta-like 4 (Drosophila) Delta4 gene taxon:10090 20041117 MGI relationship(CL:0000071) MGI MGI:94901 Dlx1 GO:0030154 MGI:MGI:2389286|PMID:12397111 IMP MGI:1857826 P distal-less homeobox 1 DII B|Dlx|Dlx-1 gene taxon:10090 20060125 MGI relationship(CL:0000031) MGI MGI:94901 Dlx1 GO:0043524 MGI:MGI:3604035|PMID:16007083 IMP MGI:1857826 P distal-less homeobox 1 DII B|Dlx|Dlx-1 gene taxon:10090 20060125 MGI relationship(CL:0000617) MGI MGI:94902 Dlx2 GO:0030154 MGI:MGI:2389286|PMID:12397111 IMP MGI:1857828 P distal-less homeobox 2 DII A|Dlx-2|Tes-1 gene taxon:10090 20060125 MGI relationship(CL:0000031) MGI MGI:106210 Dmbt1 GO:0005578 MGI:MGI:3057099|PMID:15452149 IDA C deleted in malignant brain tumors 1 CRP-[a]|CRP-[b]|Crpd|ebnerin|gp300|hensin|MUCLIN|vomeroglandin gene taxon:10090 20050124 MGI relationship(CL:0000007) MGI MGI:106210 Dmbt1 GO:0005622 MGI:MGI:3057099|PMID:15452149 IDA C deleted in malignant brain tumors 1 CRP-[a]|CRP-[b]|Crpd|ebnerin|gp300|hensin|MUCLIN|vomeroglandin gene taxon:10090 20050124 MGI relationship(CL:0000007) MGI MGI:1329019 Dnase2a GO:0006308 MGI:MGI:3521632|PMID:15568025 IMP MGI:2449811 P deoxyribonuclease II alpha gene taxon:10090 20050208 MGI relationship(CL:0000235) MGI MGI:2447763 Dnd1 GO:0007281 MGI:MGI:3578711|PMID:15902260 IMP MGI:2158668 P dead end homolog 1 (zebrafish) RBMS4|Ter gene taxon:10090 20050818 MGI relationship(CL:0000586) MGI MGI:94912 Dnmt1 GO:0005634 MGI:MGI:3051927|PMID:15063176 IDA C DNA methyltransferase (cytosine-5) 1 Cxxc9|Dnmt1o|MTase gene taxon:10090 20040930 MGI relationship(CL:0000586) MGI MGI:1261827 Dnmt3a GO:0000792 MGI:MGI:3611125|PMID:16322236 IDA C DNA methyltransferase 3A gene taxon:10090 20060724 MGI relationship(CL:0000002) MGI MGI:1261827 Dnmt3a GO:0005634 MGI:MGI:3574237|PMID:15739230 IDA C DNA methyltransferase 3A gene taxon:10090 20050513 MGI relationship(CL:0000020) MGI MGI:1261827 Dnmt3a GO:0005634 MGI:MGI:3574237|PMID:15739230 IDA C DNA methyltransferase 3A gene taxon:10090 20050513 MGI relationship(CL:0000023) MGI MGI:1261827 Dnmt3a GO:0005737 MGI:MGI:3574237|PMID:15739230 IDA C DNA methyltransferase 3A gene taxon:10090 20050513 MGI relationship(CL:0000020) MGI MGI:1261827 Dnmt3a GO:0005737 MGI:MGI:3574237|PMID:15739230 IDA C DNA methyltransferase 3A gene taxon:10090 20050513 MGI relationship(CL:0000023) MGI MGI:1261819 Dnmt3b GO:0005634 MGI:MGI:3623538|PMID:16543361 IDA C DNA methyltransferase 3B gene taxon:10090 20060728 MGI relationship(CL:0000002) MGI MGI:1261819 Dnmt3b GO:0031503 MGI:MGI:3623538|PMID:16543361 IDA P DNA methyltransferase 3B gene taxon:10090 20060728 MGI relationship(CL:0000002) MGI MGI:1859287 Dnmt3l GO:0005737 MGI:MGI:3623538|PMID:16543361 IDA C DNA (cytosine-5-)-methyltransferase 3-like D6Ertd14e|ecat7 gene taxon:10090 20060728 MGI relationship(CL:0000002) MGI MGI:3584043 Dok7 GO:0007528 MGI:MGI:3630229|PMID:16794080 IGI MGI:103581 P docking protein 7 Dok-7 gene taxon:10090 20060814 MGI relationship(CL:0000188) MGI MGI:3584043 Dok7 GO:0031594 MGI:MGI:3630229|PMID:16794080 IDA C docking protein 7 Dok-7 gene taxon:10090 20060814 MGI relationship(CL:0000188) MGI MGI:3584043 Dok7 GO:0043113 MGI:MGI:3630229|PMID:16794080 IDA P docking protein 7 Dok-7 gene taxon:10090 20060814 MGI relationship(CL:0000188) MGI MGI:3584043 Dok7 GO:0043113 MGI:MGI:3630229|PMID:16794080 IGI MGI:103581 P docking protein 7 Dok-7 gene taxon:10090 20060814 MGI relationship(CL:0000188) MGI MGI:1919104 Dpep3 GO:0005624 MGI:MGI:2669357|PMID:12738806 IDA C dipeptidase 3 MBD-3 gene taxon:10090 20040510 MGI relationship(CL:0000002) MGI MGI:1920958 Dppa3 GO:0005634 MGI:MGI:2178884|PMID:11900980 IDA C developmental pluripotency-associated 3 PGC7|stella gene taxon:10090 20050117 MGI relationship(CL:0000007) MGI MGI:1920958 Dppa3 GO:0005737 MGI:MGI:2178884|PMID:11900980 IDA C developmental pluripotency-associated 3 PGC7|stella gene taxon:10090 20050117 MGI relationship(CL:0000007) MGI MGI:1920958 Dppa3 GO:0040016 MGI:MGI:3056827|PMID:15018652 IMP MGI:3057184 P developmental pluripotency-associated 3 PGC7|stella gene taxon:10090 20050117 MGI relationship(CL:0000007) MGI MGI:1194993 Dsc3 GO:0005737 MGI:MGI:3614372|PMID:16418220 IDA C desmocollin 3 gene taxon:10090 20060309 MGI relationship(CL:0000023) MGI MGI:1194993 Dsc3 GO:0005886 MGI:MGI:3614372|PMID:16418220 IDA C desmocollin 3 gene taxon:10090 20060309 MGI relationship(CL:1000274) MGI MGI:109611 Dsp GO:0030057 MGI:MGI:3614372|PMID:16418220 IDA C desmoplakin DP gene taxon:10090 20060309 MGI relationship(CL:1000274) MGI MGI:104627 Dst GO:0008017 MGI:MGI:1341473|PMID:10428034 IDA F dystonin ah|athetoid|Bpag|BPAG1|BPAG1-n|bullous pemphigoid antigen 1|Macf2|nmf203|nmf339 gene taxon:10090 20070302 MGI relationship(CL:0000101) MGI MGI:104627 Dst GO:0015629 MGI:MGI:1341473|PMID:10428034 IDA C dystonin ah|athetoid|Bpag|BPAG1|BPAG1-n|bullous pemphigoid antigen 1|Macf2|nmf203|nmf339 gene taxon:10090 20070302 MGI relationship(CL:0000002) MGI MGI:104627 Dst GO:0015630 MGI:MGI:1341473|PMID:10428034 IDA C dystonin ah|athetoid|Bpag|BPAG1|BPAG1-n|bullous pemphigoid antigen 1|Macf2|nmf203|nmf339 gene taxon:10090 20070302 MGI relationship(CL:0000001) MGI MGI:104627 Dst GO:0031110 MGI:MGI:1341473|PMID:10428034 IMP MGI:2429314 P dystonin ah|athetoid|Bpag|BPAG1|BPAG1-n|bullous pemphigoid antigen 1|Macf2|nmf203|nmf339 gene taxon:10090 20070302 MGI relationship(CL:0000001) MGI MGI:104627 Dst GO:0031122 MGI:MGI:1341473|PMID:10428034 IMP MGI:2429314 P dystonin ah|athetoid|Bpag|BPAG1|BPAG1-n|bullous pemphigoid antigen 1|Macf2|nmf203|nmf339 gene taxon:10090 20070302 MGI relationship(CL:0000101) MGI MGI:104627 Dst GO:0060053 MGI:MGI:1341473|PMID:10428034 IDA C dystonin ah|athetoid|Bpag|BPAG1|BPAG1-n|bullous pemphigoid antigen 1|Macf2|nmf203|nmf339 gene taxon:10090 20070302 MGI relationship(CL:0000001) MGI MGI:94941 Dvl1 GO:0001505 MGI:MGI:3653273|PMID:16818724 IMP MGI:2137230 P dishevelled, dsh homolog 1 (Drosophila) gene taxon:10090 20070228 MGI relationship(CL:0000117) MGI MGI:94941 Dvl1 GO:0005515 MGI:MGI:2384358|PMID:12165471 IPI UniProt:Q61006|UniProt:O88643 F dishevelled, dsh homolog 1 (Drosophila) gene taxon:10090 20070228 MGI relationship(CL:0000002) MGI MGI:94941 Dvl1 GO:0007269 MGI:MGI:3653273|PMID:16818724 IGI MGI:98961 P dishevelled, dsh homolog 1 (Drosophila) gene taxon:10090 20070228 MGI relationship(CL:0000117) MGI MGI:94941 Dvl1 GO:0045202 MGI:MGI:3653273|PMID:16818724 IDA C dishevelled, dsh homolog 1 (Drosophila) gene taxon:10090 20070228 MGI relationship(CL:0000117) MGI MGI:94941 Dvl1 GO:0050808 MGI:MGI:3653273|PMID:16818724 IGI MGI:98961 P dishevelled, dsh homolog 1 (Drosophila) gene taxon:10090 20070228 MGI relationship(CL:0000117) MGI MGI:94941 Dvl1 GO:0050808 MGI:MGI:3653273|PMID:16818724 IMP MGI:2137230 P dishevelled, dsh homolog 1 (Drosophila) gene taxon:10090 20070228 MGI relationship(CL:0000117) MGI MGI:107736 Dync2h1 GO:0008105 MGI:MGI:3610248|PMID:16229832 IMP P dynein cytoplasmic 2 heavy chain 1 DHC1b|DHC2|Dnchc2 gene taxon:10090 20060203 MGI relationship(CL:0000064) MGI MGI:107736 Dync2h1 GO:0042384 MGI:MGI:3588600|PMID:16061793 IMP MGI:3578144 P dynein cytoplasmic 2 heavy chain 1 DHC1b|DHC2|Dnchc2 gene taxon:10090 20060203 MGI relationship(CL:0000064) MGI MGI:107736 Dync2h1 GO:0042384 MGI:MGI:3610248|PMID:16229832 IMP P dynein cytoplasmic 2 heavy chain 1 DHC1b|DHC2|Dnchc2 gene taxon:10090 20060203 MGI relationship(CL:0000133) MGI MGI:107736 Dync2h1 GO:0042384 MGI:MGI:3610248|PMID:16229832 IMP P dynein cytoplasmic 2 heavy chain 1 DHC1b|DHC2|Dnchc2 gene taxon:10090 20060203 MGI relationship(CL:0000134) MGI MGI:105091 E2f5 GO:0005634 MGI:MGI:3616424|PMID:16172982 IDA C E2F transcription factor 5 E2F-5 gene taxon:10090 20060517 MGI relationship(CL:0000710) MGI MGI:105091 E2f5 GO:0005737 MGI:MGI:3616424|PMID:16172982 IDA C E2F transcription factor 5 E2F-5 gene taxon:10090 20060517 MGI relationship(CL:0000710) MGI MGI:1349469 Ecsit GO:0001707 MGI:MGI:2682456|PMID:14633973 IMP MGI:2683025 P ECSIT homolog (Drosophila) Sitpec gene taxon:10090 20050725 MGI relationship(CL:0000222) MGI MGI:1096355 Edg1 GO:0030155 MGI:MGI:3055628|PMID:15371328 IDA P endothelial differentiation sphingolipid G-protein-coupled receptor 1 S1P1 gene taxon:10090 20060726 MGI relationship(CL:0000071) MGI MGI:1096355 Edg1 GO:0030155 MGI:MGI:3055628|PMID:15371328 IDA P endothelial differentiation sphingolipid G-protein-coupled receptor 1 S1P1 gene taxon:10090 20060726 MGI relationship(CL:0000359) MGI MGI:95283 Edn1 GO:0001701 MGI:MGI:3510064|PMID:15327783 IMP MGI:1857637 P endothelin 1 ET-1 gene taxon:10090 20060222 MGI relationship(CL:0000008) MGI MGI:95283 Edn1 GO:0005102 MGI:MGI:70451|PMID:2542249 IDA F endothelin 1 ET-1 gene taxon:10090 20060223 MGI relationship(CL:0000002) MGI MGI:95283 Edn1 GO:0007205 MGI:MGI:70451|PMID:2542249 IDA P endothelin 1 ET-1 gene taxon:10090 20060223 MGI relationship(CL:0000002) MGI MGI:95283 Edn1 GO:0008284 MGI:MGI:70451|PMID:2542249 IDA P endothelin 1 ET-1 gene taxon:10090 20060223 MGI relationship(CL:0000002) MGI MGI:95283 Edn1 GO:0014032 MGI:MGI:1277800|PMID:9671575 IMP MGI:1857637 P endothelin 1 ET-1 gene taxon:10090 20060223 MGI relationship(CL:0000008) MGI MGI:95283 Edn1 GO:0014032 MGI:MGI:3510064|PMID:15327783 IMP MGI:1857637 P endothelin 1 ET-1 gene taxon:10090 20060222 MGI relationship(CL:0000008) MGI MGI:95283 Edn1 GO:0030818 MGI:MGI:3612779|PMID:15632412 IGI MGI:88121 P endothelin 1 ET-1 gene taxon:10090 20060223 MGI relationship(CL:0000001) MGI MGI:95283 Edn1 GO:0030818 MGI:MGI:70451|PMID:2542249 IDA P endothelin 1 ET-1 gene taxon:10090 20060223 MGI relationship(CL:0000002) MGI MGI:95283 Edn1 GO:0031583 MGI:MGI:84748|PMID:8978712 IDA P endothelin 1 ET-1 gene taxon:10090 20060222 MGI relationship(CL:0000127) MGI MGI:95283 Edn1 GO:0051482 MGI:MGI:70451|PMID:2542249 IDA P endothelin 1 ET-1 gene taxon:10090 20060223 MGI relationship(CL:0000002) MGI MGI:95284 Edn2 GO:0045987 MGI:MGI:65983|PMID:2768235 IDA P endothelin 2 vasoactive intestinal contractor peptide|VIC gene taxon:10090 20060223 MGI relationship(CL:0000192) MGI MGI:95285 Edn3 GO:0001755 MGI:MGI:1267304|PMID:9624616 IMP MGI:1856392 P endothelin 3 gene taxon:10090 20070226 MGI relationship(CL:0000333) MGI MGI:95285 Edn3 GO:0008284 MGI:MGI:1934508|PMID:11401406 IDA P endothelin 3 gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:95285 Edn3 GO:0030182 MGI:MGI:1267304|PMID:9624616 IMP MGI:1856392 P endothelin 3 gene taxon:10090 20070226 MGI relationship(CL:0000029) MGI MGI:105923 Ednra GO:0001701 MGI:MGI:3510064|PMID:15327783 IMP P endothelin receptor type A ET-AR|ETa|Gpcr10 gene taxon:10090 20060222 MGI relationship(CL:0000008) MGI MGI:105923 Ednra GO:0014032 MGI:MGI:3510064|PMID:15327783 IMP P endothelin receptor type A ET-AR|ETa|Gpcr10 gene taxon:10090 20060222 MGI relationship(CL:0000008) MGI MGI:102720 Ednrb GO:0001755 MGI:MGI:1349495|PMID:10591209 IMP P endothelin receptor type B ETb|Sox10m1 gene taxon:10090 20041022 MGI relationship(CL:0000031) MGI MGI:102720 Ednrb GO:0007422 MGI:MGI:77408|PMID:8582288 IMP MGI:1856149 P endothelin receptor type B ETb|Sox10m1 gene taxon:10090 20041022 MGI relationship(CL:0000029) MGI MGI:102720 Ednrb GO:0007497 MGI:MGI:77408|PMID:8582288 IMP MGI:1856149 P endothelin receptor type B ETb|Sox10m1 gene taxon:10090 20041022 MGI relationship(CL:0000029) MGI MGI:2442192 Eea1 GO:0005769 MGI:MGI:3527911|PMID:15588329 IDA C early endosome antigen 1 ZFYVE2 gene taxon:10090 20060913 MGI relationship(CL:0000002) MGI MGI:103236 Efna1 GO:0000187 MGI:MGI:3050703|PMID:15145949 IDA P ephrin A1 B61|EFL-1|Epl1|Eplg1|LERK-1|Lerk1 gene taxon:10090 20040930 MGI relationship(CL:0000117) MGI MGI:103236 Efna1 GO:0030182 MGI:MGI:3050703|PMID:15145949 IDA P ephrin A1 B61|EFL-1|Epl1|Eplg1|LERK-1|Lerk1 gene taxon:10090 20040930 MGI relationship(CL:0000117) MGI MGI:103236 Efna1 GO:0048013 MGI:MGI:3050703|PMID:15145949 IDA P ephrin A1 B61|EFL-1|Epl1|Eplg1|LERK-1|Lerk1 gene taxon:10090 20040930 MGI relationship(CL:0000117) MGI MGI:107444 Efna5 GO:0007411 MGI:MGI:1931133|PMID:11222144 IMP MGI:2429768 P ephrin A5 AL-1|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS gene taxon:10090 20070305 MGI relationship(CL:0000540) MGI MGI:107444 Efna5 GO:0031290 MGI:MGI:3583377|PMID:15996548 IDA P ephrin A5 AL-1|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS gene taxon:10090 20060202 MGI relationship(CL:0000001) MGI MGI:107444 Efna5 GO:0045499 MGI:MGI:3583377|PMID:15996548 IDA F ephrin A5 AL-1|EFL-5|Ephrin-A5|Epl7|LERK-7|RAGS gene taxon:10090 20060202 MGI relationship(CL:0000001) MGI MGI:95290 Egf GO:0007173 MGI:MGI:75839|PMID:7641815 IGI MGI:95294 P epidermal growth factor gene taxon:10090 20070214 MGI relationship(CL:0000002) MGI MGI:95290 Egf GO:0008284 MGI:MGI:3521553|PMID:15509736 IGI MGI:96522 P epidermal growth factor gene taxon:10090 20050309 MGI relationship(CL:0000710) MGI MGI:95290 Egf GO:0008284 MGI:MGI:75839|PMID:7641815 IGI MGI:95705|MGI:95294 P epidermal growth factor gene taxon:10090 20070214 MGI relationship(CL:0000002) MGI MGI:95290 Egf GO:0021940 MGI:MGI:1329746|PMID:10027293 IDA P epidermal growth factor gene taxon:10090 20061218 MGI relationship(CL:0000001) MGI MGI:95290 Egf GO:0048754 MGI:MGI:3575981|PMID:15831470 IDA P epidermal growth factor gene taxon:10090 20051212 MGI relationship(CL:0000002) MGI MGI:95294 Egfr GO:0005886 MGI:MGI:75839|PMID:7641815 IDA C epidermal growth factor receptor avian erythroblastic leukemia viral (v-erb-b) oncogene homolog|Erbb|Wa5 gene taxon:10090 20070214 MGI relationship(CL:0000002) MGI MGI:95294 Egfr GO:0007173 MGI:MGI:75839|PMID:7641815 IGI MGI:95290 P epidermal growth factor receptor avian erythroblastic leukemia viral (v-erb-b) oncogene homolog|Erbb|Wa5 gene taxon:10090 20070214 MGI relationship(CL:0000002) MGI MGI:95294 Egfr GO:0008284 MGI:MGI:75839|PMID:7641815 IGI MGI:95290|MGI:95705 P epidermal growth factor receptor avian erythroblastic leukemia viral (v-erb-b) oncogene homolog|Erbb|Wa5 gene taxon:10090 20070214 MGI relationship(CL:0000002) MGI MGI:1306780 Egr3 GO:0007422 MGI:MGI:3527364|PMID:15582775 IMP MGI:2180063 P early growth response 3 Pilot gene taxon:10090 20050308 MGI relationship(CL:0000100) MGI MGI:1921453 Eif4enif1 GO:0005634 MGI:MGI:3616756|PMID:16343815 IDA C eukaryotic translation initiation factor 4E nuclear import factor 1 Clast4|D11Ertd166e gene taxon:10090 20060523 MGI relationship(CL:0000501) MGI MGI:1921453 Eif4enif1 GO:0005829 MGI:MGI:3616756|PMID:16343815 IDA C eukaryotic translation initiation factor 4E nuclear import factor 1 Clast4|D11Ertd166e gene taxon:10090 20060523 MGI relationship(CL:0000023) MGI MGI:1335079 Elf5 GO:0007398 MGI:MGI:3578082|PMID:15829518 IMP MGI:3578666 P E74-like factor 5 ESE-5 gene taxon:10090 20050729 MGI relationship(CL:0000349) MGI MGI:106912 Emr1 GO:0009897 MGI:MGI:1860996|PMID:10943842 IDA C EGF-like module containing, mucin-like, hormone receptor-like sequence 1 DD7A5-7|EGF-TM7|F4/80|TM7LN3 gene taxon:10090 20050617 MGI relationship(CL:0000081) MGI MGI:95389 En1 GO:0030182 MGI:MGI:3522127|PMID:15340832 IGI MGI:95390 P engrailed 1 En-1|engrailed-1|Mo-en.1 gene taxon:10090 20050218 MGI relationship(CL:0000117) MGI MGI:95389 En1 GO:0030182 MGI:MGI:3525936|PMID:15607945 IGI MGI:95390 P engrailed 1 En-1|engrailed-1|Mo-en.1 gene taxon:10090 20050502 MGI relationship(CL:0000403) MGI MGI:95389 En1 GO:0030182 MGI:MGI:3578062|PMID:15175251 IGI MGI:95390 P engrailed 1 En-1|engrailed-1|Mo-en.1 gene taxon:10090 20050803 MGI relationship(CL:0000700) MGI MGI:95389 En1 GO:0030901 MGI:MGI:3578062|PMID:15175251 IGI MGI:95390 P engrailed 1 En-1|engrailed-1|Mo-en.1 gene taxon:10090 20050803 MGI relationship(CL:0000700) MGI MGI:95389 En1 GO:0048666 MGI:MGI:1933708|PMID:11312297 IGI MGI:95390 P engrailed 1 En-1|engrailed-1|Mo-en.1 gene taxon:10090 20050908 MGI relationship(CL:0000700) MGI MGI:95390 En2 GO:0030182 MGI:MGI:3522127|PMID:15340832 IGI MGI:95389 P engrailed 2 En-2 gene taxon:10090 20050218 MGI relationship(CL:0000117) MGI MGI:95390 En2 GO:0030182 MGI:MGI:3525936|PMID:15607945 IGI MGI:95389 P engrailed 2 En-2 gene taxon:10090 20050502 MGI relationship(CL:0000403) MGI MGI:95390 En2 GO:0030182 MGI:MGI:3578062|PMID:15175251 IGI MGI:95389 P engrailed 2 En-2 gene taxon:10090 20050803 MGI relationship(CL:0000700) MGI MGI:95390 En2 GO:0030901 MGI:MGI:3578062|PMID:15175251 IGI MGI:95389 P engrailed 2 En-2 gene taxon:10090 20050803 MGI relationship(CL:0000700) MGI MGI:95390 En2 GO:0048666 MGI:MGI:1933708|PMID:11312297 IGI MGI:95389 P engrailed 2 En-2 gene taxon:10090 20050908 MGI relationship(CL:0000700) MGI MGI:108360 Enah GO:0007411 MGI:MGI:3054149|PMID:15371503 IGI MGI:109268 P enabled homolog (Drosophila) Mena|Ndpp1|WBP8 gene taxon:10090 20041026 MGI relationship(CL:0000117) MGI MGI:108360 Enah GO:0007411 MGI:MGI:3054149|PMID:15371503 IMP MGI:3056050 P enabled homolog (Drosophila) Mena|Ndpp1|WBP8 gene taxon:10090 20041104 MGI relationship(CL:0000117) MGI MGI:108360 Enah GO:0030036 MGI:MGI:3054149|PMID:15371503 IGI MGI:109268 P enabled homolog (Drosophila) Mena|Ndpp1|WBP8 gene taxon:10090 20041026 MGI relationship(CL:0000075) MGI MGI:108360 Enah GO:0030175 MGI:MGI:1331576|PMID:10069337 IDA C enabled homolog (Drosophila) Mena|Ndpp1|WBP8 gene taxon:10090 20041104 MGI relationship(CL:0000117) MGI MGI:106645 Enpep GO:0005903 MGI:MGI:3624074|PMID:16286663 IDA C glutamyl aminopeptidase aminopeptidase-A|APA|Bp-1/6C3|Ly-51|Ly51 gene taxon:10090 20060728 MGI relationship(CL:0000075) MGI MGI:106645 Enpep GO:0016324 MGI:MGI:3624074|PMID:16286663 IDA C glutamyl aminopeptidase aminopeptidase-A|APA|Bp-1/6C3|Ly-51|Ly51 gene taxon:10090 20060728 MGI relationship(CL:0000075) MGI MGI:106645 Enpep GO:0016324 MGI:MGI:3624074|PMID:16286663 IDA C glutamyl aminopeptidase aminopeptidase-A|APA|Bp-1/6C3|Ly-51|Ly51 gene taxon:10090 20060728 MGI relationship(CL:0000653) MGI MGI:106645 Enpep GO:0031410 MGI:MGI:3624074|PMID:16286663 IDA C glutamyl aminopeptidase aminopeptidase-A|APA|Bp-1/6C3|Ly-51|Ly51 gene taxon:10090 20060728 MGI relationship(CL:0000075) MGI MGI:106645 Enpep GO:0045177 MGI:MGI:3624074|PMID:16286663 IDA C glutamyl aminopeptidase aminopeptidase-A|APA|Bp-1/6C3|Ly-51|Ly51 gene taxon:10090 20060728 MGI relationship(CL:0000075) MGI MGI:106645 Enpep GO:0045177 MGI:MGI:3624074|PMID:16286663 IDA C glutamyl aminopeptidase aminopeptidase-A|APA|Bp-1/6C3|Ly-51|Ly51 gene taxon:10090 20060728 MGI relationship(CL:0000653) MGI MGI:1201683 Eomes GO:0005634 MGI:MGI:3582144|PMID:15880683 IDA C eomesodermin homolog (Xenopus laevis) Tbr2 gene taxon:10090 20050819 MGI relationship(CL:1000274) MGI MGI:1201683 Eomes GO:0030154 MGI:MGI:3578587|PMID:15788452 IMP MGI:3579497 P eomesodermin homolog (Xenopus laevis) Tbr2 gene taxon:10090 20050727 MGI relationship(CL:0000001) MGI MGI:95278 Epha2 GO:0030182 MGI:MGI:3050703|PMID:15145949 IDA P Eph receptor A2 Eck|Myk2|Sek-2|Sek2 gene taxon:10090 20040930 MGI relationship(CL:0000117) MGI MGI:95278 Epha2 GO:0030182 MGI:MGI:3050703|PMID:15145949 IMP P Eph receptor A2 Eck|Myk2|Sek-2|Sek2 gene taxon:10090 20040930 MGI relationship(CL:0000117) MGI MGI:99612 Epha3 GO:0005003 MGI:MGI:3050703|PMID:15145949 IDA F Eph receptor A3 Cek4|End3|Hek|Hek4|Mek4|Tyro4 gene taxon:10090 20040930 MGI relationship(CL:0000117) MGI MGI:95276 Epha7 GO:0031290 MGI:MGI:3583377|PMID:15996548 IMP MGI:3583808 P Eph receptor A7 Cek11|Ebk|Ehk3|Hek11|MDK1 gene taxon:10090 20060202 MGI relationship(CL:0000740) MGI MGI:95276 Epha7 GO:0045499 MGI:MGI:3583377|PMID:15996548 IDA F Eph receptor A7 Cek11|Ebk|Ehk3|Hek11|MDK1 gene taxon:10090 20060202 MGI relationship(CL:0000001) MGI MGI:95276 Epha7 GO:0048755 MGI:MGI:3583377|PMID:15996548 IMP MGI:3583808 P Eph receptor A7 Cek11|Ebk|Ehk3|Hek11|MDK1 gene taxon:10090 20060202 MGI relationship(CL:0000740) MGI MGI:95410 Erbb2 GO:0005737 MGI:MGI:3512707|PMID:15306553 IDA C v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) c-erbB2|c-neu|ErbB-2|HER-2|HER2|Neu|Neu oncogene gene taxon:10090 20050215 MGI relationship(CL:0000007) MGI MGI:95410 Erbb2 GO:0007399 MGI:MGI:3512703|PMID:15496447 IMP MGI:3521860|MGI:3521857|MGI:1929071 P v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) c-erbB2|c-neu|ErbB-2|HER-2|HER2|Neu|Neu oncogene gene taxon:10090 20050127 MGI relationship(CL:0000101) MGI MGI:95410 Erbb2 GO:0007399 MGI:MGI:3512703|PMID:15496447 IMP MGI:3521860|MGI:3521857|MGI:1929071 P v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) c-erbB2|c-neu|ErbB-2|HER-2|HER2|Neu|Neu oncogene gene taxon:10090 20050127 MGI relationship(CL:0000540) MGI MGI:95410 Erbb2 GO:0016324 MGI:MGI:3512707|PMID:15306553 IDA C v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) c-erbB2|c-neu|ErbB-2|HER-2|HER2|Neu|Neu oncogene gene taxon:10090 20050215 MGI relationship(CL:0000007) MGI MGI:95411 Erbb3 GO:0016324 MGI:MGI:3512707|PMID:15306553 IDA C v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) Erbb-3|Erbb3r gene taxon:10090 20050215 MGI relationship(CL:0000007) MGI MGI:95411 Erbb3 GO:0016328 MGI:MGI:3512707|PMID:15306553 IDA C v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) Erbb-3|Erbb3r gene taxon:10090 20050215 MGI relationship(CL:0000007) MGI MGI:1916774 Esam1 GO:0016337 MGI:MGI:1934405|PMID:11279107 IDA P endothelial cell-specific adhesion molecule W117m gene taxon:10090 20060106 MGI relationship(CL:0000002) MGI MGI:1352467 Esr1 GO:0005634 MGI:MGI:2178020|PMID:11897499 IDA C estrogen receptor 1 (alpha) ER-alpha|ER[a]|ERa|ERalpha|ESR|Estr|Estra|Nr3a1 gene taxon:10090 20041007 MGI relationship(CL:0000075) MGI MGI:109392 Esr2 GO:0001764 MGI:MGI:2449269|PMID:12515851 IMP MGI:2152217 P estrogen receptor 2 (beta) ER beta|ERbeta|Estrb|oestrogen receptor beta gene taxon:10090 20050209 MGI relationship(CL:0000117) MGI MGI:109392 Esr2 GO:0007420 MGI:MGI:2449269|PMID:12515851 IMP MGI:2152217 P estrogen receptor 2 (beta) ER beta|ERbeta|Estrb|oestrogen receptor beta gene taxon:10090 20050209 MGI relationship(CL:0000117) MGI MGI:108050 Ext2 GO:0015012 MGI:MGI:3608483|PMID:16236767 IMP MGI:3608690 P exostoses (multiple) 2 gene taxon:10090 20060315 MGI relationship(CL:0000351) MGI MGI:109344 Eya1 GO:0042472 MGI:MGI:3577160|PMID:15817220 IMP MGI:1857803 P eyes absent 1 homolog (Drosophila) bor gene taxon:10090 20050602 MGI relationship(CL:0000031) MGI MGI:109344 Eya1 GO:0043066 MGI:MGI:3577160|PMID:15817220 IMP MGI:1857803 P eyes absent 1 homolog (Drosophila) bor gene taxon:10090 20050602 MGI relationship(CL:0000066) MGI MGI:109344 Eya1 GO:0045165 MGI:MGI:3577160|PMID:15817220 IMP MGI:1857803 P eyes absent 1 homolog (Drosophila) bor gene taxon:10090 20050602 MGI relationship(CL:0000031) MGI MGI:109344 Eya1 GO:0045165 MGI:MGI:3588889|PMID:16018995 IMP MGI:2150426 P eyes absent 1 homolog (Drosophila) bor gene taxon:10090 20060306 MGI relationship(CL:0000134) MGI MGI:109344 Eya1 GO:0045664 MGI:MGI:3512702|PMID:15496442 IMP MGI:2150426 P eyes absent 1 homolog (Drosophila) bor gene taxon:10090 20050315 MGI relationship(CL:0000101) MGI MGI:107940 Ezh2 GO:0005634 MGI:MGI:3057067|PMID:15520282 IDA C enhancer of zeste homolog 2 (Drosophila) Enx-1|Enx1h gene taxon:10090 20041207 MGI relationship(CL:0000002) MGI MGI:107940 Ezh2 GO:0051154 MGI:MGI:3057067|PMID:15520282 IDA P enhancer of zeste homolog 2 (Drosophila) Enx-1|Enx1h gene taxon:10090 20041207 MGI relationship(CL:0000002) MGI MGI:1321398 F11r GO:0005923 MGI:MGI:3057232|PMID:15494378 IMP C F11 receptor BV11 antigen|ESTM33|JAM-1|JAM-A|Jcam1|Ly106 gene taxon:10090 20060726 MGI relationship(CL:0000007) MGI MGI:1321398 F11r GO:0005923 MGI:MGI:3057232|PMID:15494378 IMP C F11 receptor BV11 antigen|ESTM33|JAM-1|JAM-A|Jcam1|Ly106 gene taxon:10090 20060726 MGI relationship(CL:0000066) MGI MGI:1321398 F11r GO:0007155 MGI:MGI:3057232|PMID:15494378 IDA P F11 receptor BV11 antigen|ESTM33|JAM-1|JAM-A|Jcam1|Ly106 gene taxon:10090 20060726 MGI relationship(CL:0000007) MGI MGI:1321398 F11r GO:0007155 MGI:MGI:3057232|PMID:15494378 IDA P F11 receptor BV11 antigen|ESTM33|JAM-1|JAM-A|Jcam1|Ly106 gene taxon:10090 20060726 MGI relationship(CL:0000066) MGI MGI:1321398 F11r GO:0030855 MGI:MGI:3057232|PMID:15494378 IDA P F11 receptor BV11 antigen|ESTM33|JAM-1|JAM-A|Jcam1|Ly106 gene taxon:10090 20060726 MGI relationship(CL:0000007) MGI MGI:1321398 F11r GO:0030855 MGI:MGI:3057232|PMID:15494378 IDA P F11 receptor BV11 antigen|ESTM33|JAM-1|JAM-A|Jcam1|Ly106 gene taxon:10090 20060726 MGI relationship(CL:0000066) MGI MGI:109419 Faf1 GO:0030155 MGI:MGI:2154851|PMID:11731229 IMP P Fas-associated factor 1 Dffrx|Fam gene taxon:10090 20060912 MGI relationship(CL:0000353) MGI MGI:1341823 Fanca GO:0007140 MGI:MGI:2671746|PMID:12913077 IMP MGI:2674095 P Fanconi anemia, complementation group A gene taxon:10090 20050720 MGI relationship(CL:0000017) MGI MGI:1341823 Fanca GO:0008584 MGI:MGI:2671746|PMID:12913077 IMP MGI:2674095 P Fanconi anemia, complementation group A gene taxon:10090 20050209 MGI relationship(CL:0000178) MGI MGI:1341823 Fanca GO:0008584 MGI:MGI:2671746|PMID:12913077 IMP MGI:2674095 P Fanconi anemia, complementation group A gene taxon:10090 20050209 MGI relationship(CL:0000216) MGI MGI:1341823 Fanca GO:0008585 MGI:MGI:2671746|PMID:12913077 IMP MGI:2674095 P Fanconi anemia, complementation group A gene taxon:10090 20050209 MGI relationship(CL:0000023) MGI MGI:1341823 Fanca GO:0042127 MGI:MGI:2671746|PMID:12913077 IMP MGI:2674095 P Fanconi anemia, complementation group A gene taxon:10090 20050209 MGI relationship(CL:0000586) MGI MGI:95484 Fas GO:0043065 MGI:MGI:3038547|PMID:15039234 IGI MGI:96974 P Fas (TNF receptor superfamily member) APO-1|CD95|TNFR6|Tnfrsf6 gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:99255 Fasl GO:0008624 MGI:MGI:3038547|PMID:15039234 IDA P Fas ligand (TNF superfamily, member 6) APT1LG1|CD178|CD95L|Fas-L|Tnfsf6 gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:99255 Fasl GO:0008624 MGI:MGI:3525895|PMID:15629131 IDA P Fas ligand (TNF superfamily, member 6) APT1LG1|CD178|CD95L|Fas-L|Tnfsf6 gene taxon:10090 20060307 MGI relationship(CL:0000002) MGI MGI:99255 Fasl GO:0043065 MGI:MGI:3038547|PMID:15039234 IGI MGI:97306,MGI:97583 P Fas ligand (TNF superfamily, member 6) APT1LG1|CD178|CD95L|Fas-L|Tnfsf6 gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:95485 Fasn GO:0042587 MGI:MGI:3603489|PMID:15169678 IDA C fatty acid synthase FAS gene taxon:10090 20060119 MGI relationship(CL:0000326) MGI MGI:2670976 Fez1 GO:0005737 MGI:MGI:3530392|PMID:15649943 IDA C fasciculation and elongation protein zeta 1 (zygin I) UNC-76|UNC76 gene taxon:10090 20050424 MGI relationship(CL:0000002) MGI MGI:2670976 Fez1 GO:0005813 MGI:MGI:3530392|PMID:15649943 IDA C fasciculation and elongation protein zeta 1 (zygin I) UNC-76|UNC76 gene taxon:10090 20050424 MGI relationship(CL:0000002) MGI MGI:2670976 Fez1 GO:0043015 MGI:MGI:3530392|PMID:15649943 IDA F fasciculation and elongation protein zeta 1 (zygin I) UNC-76|UNC76 gene taxon:10090 20050424 MGI relationship(CL:0000002) MGI MGI:1920441 Fezf1 GO:0001764 MGI:MGI:3621093|PMID:16540508 IMP P Fez family zinc finger 1 fez|fez-like|Zfp312-like gene taxon:10090 20060522 MGI relationship(CL:0000099) MGI MGI:1920441 Fezf1 GO:0007411 MGI:MGI:3621093|PMID:16540508 IMP P Fez family zinc finger 1 fez|fez-like|Zfp312-like gene taxon:10090 20060519 MGI relationship(CL:0000101) MGI MGI:1859823 Fezf2 GO:0007411 MGI:MGI:3611736|PMID:16314561 IMP P Fez family zinc finger 2 Fez|Fezl|forebrain embryonic zinc finger|Zfp312 gene taxon:10090 20060227 MGI relationship(CL:0000598) MGI MGI:1859823 Fezf2 GO:0016358 MGI:MGI:3611736|PMID:16314561 IMP P Fez family zinc finger 2 Fez|Fezl|forebrain embryonic zinc finger|Zfp312 gene taxon:10090 20060227 MGI relationship(CL:0000598) MGI MGI:1859823 Fezf2 GO:0030900 MGI:MGI:3046163|PMID:15188439 IMP MGI:3046867 P Fez family zinc finger 2 Fez|Fezl|forebrain embryonic zinc finger|Zfp312 gene taxon:10090 20040820 MGI relationship(CL:0000117) MGI MGI:95515 Fgf1 GO:0001759 MGI:MGI:3511765|PMID:15576401 IDA P fibroblast growth factor 1 Dffrx|Fam|Fgf-1|Fgfa|fibroblast growth factor 1 (acidic) gene taxon:10090 20050105 MGI relationship(CL:0000134) MGI MGI:95515 Fgf1 GO:0001759 MGI:MGI:3511765|PMID:15576401 IDA P fibroblast growth factor 1 Dffrx|Fam|Fgf-1|Fgfa|fibroblast growth factor 1 (acidic) gene taxon:10090 20050105 MGI relationship(CL:0000223) MGI MGI:1099809 Fgf10 GO:0006935 MGI:MGI:3609523|PMID:16169547 IDA P fibroblast growth factor 10 FGF-10 gene taxon:10090 20060125 MGI relationship(CL:0000002) MGI MGI:1099809 Fgf10 GO:0007267 MGI:MGI:1101385|PMID:9428423 IDA P fibroblast growth factor 10 FGF-10 gene taxon:10090 20051214 MGI relationship(CL:0000082) MGI MGI:1099809 Fgf10 GO:0007267 MGI:MGI:1101385|PMID:9428423 IDA P fibroblast growth factor 10 FGF-10 gene taxon:10090 20051214 MGI relationship(CL:0000134) MGI MGI:1099809 Fgf10 GO:0007267 MGI:MGI:3045497|PMID:15199404 IMP MGI:1927833 P fibroblast growth factor 10 FGF-10 gene taxon:10090 20060726 MGI relationship(CL:0000066) MGI MGI:1099809 Fgf10 GO:0007267 MGI:MGI:3045497|PMID:15199404 IMP MGI:1927833 P fibroblast growth factor 10 FGF-10 gene taxon:10090 20060726 MGI relationship(CL:0000134) MGI MGI:1099809 Fgf10 GO:0008284 MGI:MGI:1101385|PMID:9428423 IDA P fibroblast growth factor 10 FGF-10 gene taxon:10090 20051214 MGI relationship(CL:0000082) MGI MGI:1099809 Fgf10 GO:0008284 MGI:MGI:3045497|PMID:15199404 IDA P fibroblast growth factor 10 FGF-10 gene taxon:10090 20060726 MGI relationship(CL:0000066) MGI MGI:1099809 Fgf10 GO:0008284 MGI:MGI:3045497|PMID:15199404 IDA P fibroblast growth factor 10 FGF-10 gene taxon:10090 20060726 MGI relationship(CL:0000134) MGI MGI:1099809 Fgf10 GO:0008285 MGI:MGI:3604918|PMID:16141225 IDA P fibroblast growth factor 10 FGF-10 gene taxon:10090 20060113 MGI relationship(CL:0000134) MGI MGI:1099809 Fgf10 GO:0042056 MGI:MGI:3609523|PMID:16169547 IDA F fibroblast growth factor 10 FGF-10 gene taxon:10090 20060125 MGI relationship(CL:0000002) MGI MGI:1099809 Fgf10 GO:0048754 MGI:MGI:3609523|PMID:16169547 IDA P fibroblast growth factor 10 FGF-10 gene taxon:10090 20060125 MGI relationship(CL:0000002) MGI MGI:1099809 Fgf10 GO:0050679 MGI:MGI:3621094|PMID:16540513 IDA P fibroblast growth factor 10 FGF-10 gene taxon:10090 20060522 MGI relationship(CL:0000001) MGI MGI:1096383 Fgf15 GO:0001755 MGI:MGI:3575218|PMID:15789410 IMP MGI:3044957 P fibroblast growth factor 15 gene taxon:10090 20050510 MGI relationship(CL:0000333) MGI MGI:1202401 Fgf17 GO:0008284 MGI:MGI:1340078|PMID:10381577 IDA P fibroblast growth factor 17 gene taxon:10090 20070302 MGI relationship(CL:0000002) MGI MGI:1202401 Fgf17 GO:0008543 MGI:MGI:1340078|PMID:10381577 IDA P fibroblast growth factor 17 gene taxon:10090 20070302 MGI relationship(CL:0000002) MGI MGI:95516 Fgf2 GO:0001759 MGI:MGI:3511765|PMID:15576401 IDA P fibroblast growth factor 2 bFGF|Fgf-2|Fgfb gene taxon:10090 20050105 MGI relationship(CL:0000134) MGI MGI:95516 Fgf2 GO:0001759 MGI:MGI:3511765|PMID:15576401 IDA P fibroblast growth factor 2 bFGF|Fgf-2|Fgfb gene taxon:10090 20050105 MGI relationship(CL:0000223) MGI MGI:95516 Fgf2 GO:0008284 MGI:MGI:3039221|PMID:15051883 IGI MGI:95290 P fibroblast growth factor 2 bFGF|Fgf-2|Fgfb gene taxon:10090 20060125 MGI relationship(CL:0000001) MGI MGI:95516 Fgf2 GO:0008284 MGI:MGI:3521553|PMID:15509736 IGI MGI:97363,MGI:96522 P fibroblast growth factor 2 bFGF|Fgf-2|Fgfb gene taxon:10090 20050309 MGI relationship(CL:0000710) MGI MGI:95516 Fgf2 GO:0008284 MGI:MGI:3604918|PMID:16141225 IDA P fibroblast growth factor 2 bFGF|Fgf-2|Fgfb gene taxon:10090 20060116 MGI relationship(CL:0000134) MGI MGI:95516 Fgf2 GO:0008285 MGI:MGI:1329746|PMID:10027293 IGI MGI:98297 P fibroblast growth factor 2 bFGF|Fgf-2|Fgfb gene taxon:10090 20061218 MGI relationship(CL:0000001) MGI MGI:95516 Fgf2 GO:0021940 MGI:MGI:1329746|PMID:10027293 IDA P fibroblast growth factor 2 bFGF|Fgf-2|Fgfb gene taxon:10090 20061218 MGI relationship(CL:0000001) MGI MGI:95516 Fgf2 GO:0045597 MGI:MGI:2429373|PMID:12417662 IDA P fibroblast growth factor 2 bFGF|Fgf-2|Fgfb gene taxon:10090 20060116 MGI relationship(CL:0000001) MGI MGI:95516 Fgf2 GO:0045766 MGI:MGI:3629251|PMID:16648142 IGI MGI:97306 P fibroblast growth factor 2 bFGF|Fgf-2|Fgfb gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:95518 Fgf4 GO:0008284 MGI:MGI:3608165|PMID:16245339 IGI MGI:99604 P fibroblast growth factor 4 Fgf-4|Fgfk|hst|hst-1|Hstf-1|kFGF|KS3 gene taxon:10090 20060118 MGI relationship(CL:0000134) MGI MGI:95518 Fgf4 GO:0019827 MGI:MGI:3052627|PMID:15328412 IGI MGI:97359 P fibroblast growth factor 4 Fgf-4|Fgfk|hst|hst-1|Hstf-1|kFGF|KS3 gene taxon:10090 20041209 MGI relationship(CL:0000351) MGI MGI:95518 Fgf4 GO:0043066 MGI:MGI:3608165|PMID:16245339 IGI MGI:99604 P fibroblast growth factor 4 Fgf-4|Fgfk|hst|hst-1|Hstf-1|kFGF|KS3 gene taxon:10090 20060118 MGI relationship(CL:0000134) MGI MGI:99604 Fgf8 GO:0000165 MGI:MGI:3628999|PMID:16720880 IMP MGI:2686864|MGI:2654594 P fibroblast growth factor 8 Aigf|Fgf-8 gene taxon:10090 20060807 MGI relationship(CL:0000222) MGI MGI:99604 Fgf8 GO:0008284 MGI:MGI:1340078|PMID:10381577 IDA P fibroblast growth factor 8 Aigf|Fgf-8 gene taxon:10090 20070302 MGI relationship(CL:0000002) MGI MGI:99604 Fgf8 GO:0008284 MGI:MGI:3608165|PMID:16245339 IGI MGI:95518 P fibroblast growth factor 8 Aigf|Fgf-8 gene taxon:10090 20060118 MGI relationship(CL:0000134) MGI MGI:99604 Fgf8 GO:0008284 MGI:MGI:3628999|PMID:16720880 IMP MGI:2686864|MGI:2654594 P fibroblast growth factor 8 Aigf|Fgf-8 gene taxon:10090 20060807 MGI relationship(CL:0000222) MGI MGI:99604 Fgf8 GO:0008284 MGI:MGI:3628999|PMID:16720880 IMP MGI:2686864|MGI:2654594 P fibroblast growth factor 8 Aigf|Fgf-8 gene taxon:10090 20060807 MGI relationship(CL:0000223) MGI MGI:99604 Fgf8 GO:0008543 MGI:MGI:1340078|PMID:10381577 IDA P fibroblast growth factor 8 Aigf|Fgf-8 gene taxon:10090 20070302 MGI relationship(CL:0000002) MGI MGI:99604 Fgf8 GO:0008543 MGI:MGI:3608165|PMID:16245339 IMP MGI:95518 P fibroblast growth factor 8 Aigf|Fgf-8 gene taxon:10090 20060130 MGI relationship(CL:0000540) MGI MGI:99604 Fgf8 GO:0043066 MGI:MGI:3608165|PMID:16245339 IGI MGI:95518 P fibroblast growth factor 8 Aigf|Fgf-8 gene taxon:10090 20060118 MGI relationship(CL:0000134) MGI MGI:99604 Fgf8 GO:0043066 MGI:MGI:3628999|PMID:16720880 IMP MGI:2686864|MGI:2654594 P fibroblast growth factor 8 Aigf|Fgf-8 gene taxon:10090 20060807 MGI relationship(CL:0000008) MGI MGI:99604 Fgf8 GO:0043524 MGI:MGI:3608165|PMID:16245339 IMP MGI:95518 P fibroblast growth factor 8 Aigf|Fgf-8 gene taxon:10090 20060130 MGI relationship(CL:0000540) MGI MGI:99604 Fgf8 GO:0045165 MGI:MGI:3577817|PMID:15809037 IGI MGI:1345138 P fibroblast growth factor 8 Aigf|Fgf-8 gene taxon:10090 20050608 MGI relationship(CL:1000191) MGI MGI:99604 Fgf8 GO:0048699 MGI:MGI:3608481|PMID:16267092 IMP MGI:2150347 P fibroblast growth factor 8 Aigf|Fgf-8 gene taxon:10090 20060130 MGI relationship(CL:0000540) MGI MGI:104723 Fgf9 GO:0001525 MGI:MGI:3629544|PMID:16778080 IDA P fibroblast growth factor 9 glia activating factor gene taxon:10090 20060807 MGI relationship(CL:0000001) MGI MGI:104723 Fgf9 GO:0002053 MGI:MGI:3621094|PMID:16540513 IDA P fibroblast growth factor 9 glia activating factor gene taxon:10090 20060522 MGI relationship(CL:0000001) MGI MGI:104723 Fgf9 GO:0006606 MGI:MGI:3051710|PMID:15229180 IMP MGI:2135961 P fibroblast growth factor 9 glia activating factor gene taxon:10090 20041001 MGI relationship(CL:0000216) MGI MGI:104723 Fgf9 GO:0007267 MGI:MGI:3056034|PMID:15328018 IMP MGI:2135961 P fibroblast growth factor 9 glia activating factor gene taxon:10090 20060726 MGI relationship(CL:0000066) MGI MGI:104723 Fgf9 GO:0007267 MGI:MGI:3056034|PMID:15328018 IMP MGI:2135961 P fibroblast growth factor 9 glia activating factor gene taxon:10090 20060726 MGI relationship(CL:0000134) MGI MGI:104723 Fgf9 GO:0008284 MGI:MGI:3051710|PMID:15229180 IMP MGI:2135961 P fibroblast growth factor 9 glia activating factor gene taxon:10090 20041001 MGI relationship(CL:0000216) MGI MGI:104723 Fgf9 GO:0008284 MGI:MGI:3629544|PMID:16778080 IMP MGI:2135961 P fibroblast growth factor 9 glia activating factor gene taxon:10090 20060807 MGI relationship(CL:0000746) MGI MGI:104723 Fgf9 GO:0008543 MGI:MGI:3051710|PMID:15229180 IMP MGI:2135961 P fibroblast growth factor 9 glia activating factor gene taxon:10090 20041001 MGI relationship(CL:0000216) MGI MGI:104723 Fgf9 GO:0008584 MGI:MGI:3621114|PMID:16540514 IMP MGI:2135961 P fibroblast growth factor 9 glia activating factor gene taxon:10090 20060522 MGI relationship(CL:0000015) MGI MGI:104723 Fgf9 GO:0030324 MGI:MGI:3621094|PMID:16540513 IDA P fibroblast growth factor 9 glia activating factor gene taxon:10090 20060522 MGI relationship(CL:0000001) MGI MGI:104723 Fgf9 GO:0042472 MGI:MGI:3056034|PMID:15328018 IMP MGI:2135961 P fibroblast growth factor 9 glia activating factor gene taxon:10090 20041117 MGI relationship(CL:0000134) MGI MGI:104723 Fgf9 GO:0045880 MGI:MGI:3621094|PMID:16540513 IDA P fibroblast growth factor 9 glia activating factor gene taxon:10090 20060522 MGI relationship(CL:0000001) MGI MGI:104723 Fgf9 GO:0045880 MGI:MGI:3629544|PMID:16778080 IMP MGI:2135961 P fibroblast growth factor 9 glia activating factor gene taxon:10090 20060807 MGI relationship(CL:0000222) MGI MGI:104723 Fgf9 GO:0045880 MGI:MGI:3629544|PMID:16778080 IMP MGI:2135961 P fibroblast growth factor 9 glia activating factor gene taxon:10090 20060807 MGI relationship(CL:0000746) MGI MGI:104723 Fgf9 GO:0050679 MGI:MGI:3621094|PMID:16540513 IDA P fibroblast growth factor 9 glia activating factor gene taxon:10090 20060522 MGI relationship(CL:0000001) MGI MGI:95522 Fgfr1 GO:0001759 MGI:MGI:3511765|PMID:15576401 IMP P fibroblast growth factor receptor 1 Fgfr-1|Flt-2 gene taxon:10090 20050105 MGI relationship(CL:0000134) MGI MGI:95522 Fgfr1 GO:0001759 MGI:MGI:3511765|PMID:15576401 IMP P fibroblast growth factor receptor 1 Fgfr-1|Flt-2 gene taxon:10090 20050105 MGI relationship(CL:0000223) MGI MGI:95522 Fgfr1 GO:0002053 MGI:MGI:3621094|PMID:16540513 IGI MGI:95523 P fibroblast growth factor receptor 1 Fgfr-1|Flt-2 gene taxon:10090 20060522 MGI relationship(CL:0000001) MGI MGI:95522 Fgfr1 GO:0008284 MGI:MGI:3629544|PMID:16778080 IGI MGI:95523 P fibroblast growth factor receptor 1 Fgfr-1|Flt-2 gene taxon:10090 20060807 MGI relationship(CL:0000746) MGI MGI:95522 Fgfr1 GO:0008543 MGI:MGI:3629544|PMID:16778080 IGI MGI:95523 P fibroblast growth factor receptor 1 Fgfr-1|Flt-2 gene taxon:10090 20060807 MGI relationship(CL:0000746) MGI MGI:95522 Fgfr1 GO:0030324 MGI:MGI:3621094|PMID:16540513 IGI MGI:95523 P fibroblast growth factor receptor 1 Fgfr-1|Flt-2 gene taxon:10090 20060522 MGI relationship(CL:0000001) MGI MGI:95522 Fgfr1 GO:0030326 MGI:MGI:3608262|PMID:16207751 IMP MGI:2181474|MGI:2176216 P fibroblast growth factor receptor 1 Fgfr-1|Flt-2 gene taxon:10090 20060123 MGI relationship(CL:0000134) MGI MGI:95522 Fgfr1 GO:0042127 MGI:MGI:2386422|PMID:12194867 IMP MGI:2153351 P fibroblast growth factor receptor 1 Fgfr-1|Flt-2 gene taxon:10090 20050209 MGI relationship(CL:0000066) MGI MGI:95522 Fgfr1 GO:0043066 MGI:MGI:3608262|PMID:16207751 IMP MGI:2181474|MGI:2176216 P fibroblast growth factor receptor 1 Fgfr-1|Flt-2 gene taxon:10090 20060123 MGI relationship(CL:0000134) MGI MGI:95522 Fgfr1 GO:0043066 MGI:MGI:3608262|PMID:16207751 IMP MGI:2181474|MGI:2176216 P fibroblast growth factor receptor 1 Fgfr-1|Flt-2 gene taxon:10090 20060123 MGI relationship(CL:0000221) MGI MGI:95522 Fgfr1 GO:0048469 MGI:MGI:3608763|PMID:10373225 IMP MGI:1857123 P fibroblast growth factor receptor 1 Fgfr-1|Flt-2 gene taxon:10090 20060123 MGI relationship(CL:0000359) MGI MGI:95523 Fgfr2 GO:0002053 MGI:MGI:3621094|PMID:16540513 IGI MGI:95522 P fibroblast growth factor receptor 2 Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFRTr gene taxon:10090 20060522 MGI relationship(CL:0000001) MGI MGI:95523 Fgfr2 GO:0005634 MGI:MGI:3051710|PMID:15229180 IDA C fibroblast growth factor receptor 2 Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFRTr gene taxon:10090 20041001 MGI relationship(CL:0000216) MGI MGI:95523 Fgfr2 GO:0005634 MGI:MGI:3583842|PMID:15944199 IDA C fibroblast growth factor receptor 2 Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFRTr gene taxon:10090 20060913 MGI relationship(CL:0000216) MGI MGI:95523 Fgfr2 GO:0007267 MGI:MGI:3045497|PMID:15199404 IMP MGI:2153811 P fibroblast growth factor receptor 2 Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFRTr gene taxon:10090 20060726 MGI relationship(CL:0000066) MGI MGI:95523 Fgfr2 GO:0007267 MGI:MGI:3045497|PMID:15199404 IMP MGI:2153811 P fibroblast growth factor receptor 2 Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFRTr gene taxon:10090 20060726 MGI relationship(CL:0000134) MGI MGI:95523 Fgfr2 GO:0008284 MGI:MGI:3045497|PMID:15199404 IMP MGI:2153811 P fibroblast growth factor receptor 2 Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFRTr gene taxon:10090 20060726 MGI relationship(CL:0000066) MGI MGI:95523 Fgfr2 GO:0008284 MGI:MGI:3045497|PMID:15199404 IMP MGI:2153811 P fibroblast growth factor receptor 2 Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFRTr gene taxon:10090 20060726 MGI relationship(CL:0000134) MGI MGI:95523 Fgfr2 GO:0008284 MGI:MGI:3629544|PMID:16778080 IGI MGI:95522 P fibroblast growth factor receptor 2 Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFRTr gene taxon:10090 20060807 MGI relationship(CL:0000746) MGI MGI:95523 Fgfr2 GO:0008543 MGI:MGI:3629544|PMID:16778080 IGI MGI:95522 P fibroblast growth factor receptor 2 Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFRTr gene taxon:10090 20060807 MGI relationship(CL:0000746) MGI MGI:95523 Fgfr2 GO:0030324 MGI:MGI:3621094|PMID:16540513 IGI MGI:95522 P fibroblast growth factor receptor 2 Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFRTr gene taxon:10090 20060522 MGI relationship(CL:0000001) MGI MGI:95523 Fgfr2 GO:0042127 MGI:MGI:3043470|PMID:12756187 IMP MGI:3044427 P fibroblast growth factor receptor 2 Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFRTr gene taxon:10090 20040730 MGI relationship(CL:0000062) MGI MGI:95523 Fgfr2 GO:0045165 MGI:MGI:3521553|PMID:15509736 IDA P fibroblast growth factor receptor 2 Bek|Fgfr-2|Fgfr-7|Fgfr7|KGFRTr gene taxon:10090 20050309 MGI relationship(CL:0000681) MGI MGI:95524 Fgfr3 GO:0008285 MGI:MGI:3529735|PMID:15708559 IMP MGI:2135676 P fibroblast growth factor receptor 3 Fgfr-3|HBGFR gene taxon:10090 20050503 MGI relationship(CL:0000117) MGI MGI:95524 Fgfr3 GO:0008285 MGI:MGI:3529735|PMID:15708559 IMP MGI:2135676 P fibroblast growth factor receptor 3 Fgfr-3|HBGFR gene taxon:10090 20050503 MGI relationship(CL:0000337) MGI MGI:95524 Fgfr3 GO:0009898 MGI:MGI:3032479|PMID:14699054 IDA C fibroblast growth factor receptor 3 Fgfr-3|HBGFR gene taxon:10090 20050428 MGI relationship(CL:0000002) MGI MGI:95524 Fgfr3 GO:0043065 MGI:MGI:3529735|PMID:15708559 IMP MGI:2135676 P fibroblast growth factor receptor 3 Fgfr-3|HBGFR gene taxon:10090 20050503 MGI relationship(CL:0000117) MGI MGI:95524 Fgfr3 GO:0043065 MGI:MGI:3529735|PMID:15708559 IMP MGI:2135676 P fibroblast growth factor receptor 3 Fgfr-3|HBGFR gene taxon:10090 20050503 MGI relationship(CL:0000337) MGI MGI:95524 Fgfr3 GO:0048471 MGI:MGI:3032479|PMID:14699054 IDA C fibroblast growth factor receptor 3 Fgfr-3|HBGFR gene taxon:10090 20050428 MGI relationship(CL:0000002) MGI MGI:95525 Fgfr4 GO:0001759 MGI:MGI:3511765|PMID:15576401 IMP P fibroblast growth factor receptor 4 Fgfr-4 gene taxon:10090 20050105 MGI relationship(CL:0000134) MGI MGI:95525 Fgfr4 GO:0001759 MGI:MGI:3511765|PMID:15576401 IMP P fibroblast growth factor receptor 4 Fgfr-4 gene taxon:10090 20050105 MGI relationship(CL:0000223) MGI MGI:1341907 Fjx1 GO:0005615 MGI:MGI:3607225|PMID:16145673 IDA C four jointed box 1 (Drosophila) gene taxon:10090 20060113 MGI relationship(CL:0000002) MGI MGI:2444782 Fkbp15 GO:0030424 MGI:MGI:3640241|PMID:16756961 IDA C FK506 binding protein 15 FKBP133 gene taxon:10090 20061114 MGI relationship(CL:0000001) MGI MGI:2444782 Fkbp15 GO:0030426 MGI:MGI:3640241|PMID:16756961 IDA C FK506 binding protein 15 FKBP133 gene taxon:10090 20061114 MGI relationship(CL:0000001) MGI MGI:2444782 Fkbp15 colocalizes_with GO:0005884 MGI:MGI:3640241|PMID:16756961 IDA C FK506 binding protein 15 FKBP133 gene taxon:10090 20061114 MGI relationship(CL:0000001) MGI MGI:1353460 Fkbp3 GO:0005634 MGI:MGI:3579700|PMID:15908283 IDA C FK506 binding protein 3 25kDa|FKBP25 gene taxon:10090 20050823 MGI relationship(CL:0000001) MGI MGI:1341070 Fkbp8 GO:0001708 MGI:MGI:3039989|PMID:15105374 IMP MGI:3042750 P FK506 binding protein 8 38kDa|Fkbp38 gene taxon:10090 20040707 MGI relationship(CL:0000117) MGI MGI:1341070 Fkbp8 GO:0043010 MGI:MGI:3039989|PMID:15105374 IMP MGI:3042750 P FK506 binding protein 8 38kDa|Fkbp38 gene taxon:10090 20040707 MGI relationship(CL:0000066) MGI MGI:95558 Flt1 GO:0016477 MGI:MGI:3525930|PMID:15601856 IGI MGI:103178 P FMS-like tyrosine kinase 1 Flt-1|sFlt1|vascular endothelial growth factor receptor|vascular permeability factor receptor|VEGFR-1|VEGFR1 gene taxon:10090 20050303 MGI relationship(CL:0000007) MGI MGI:1919257 Fndc3b GO:0045600 MGI:MGI:3511725|PMID:15527760 IPI P fibronectin type III domain containing 3B fad104 gene taxon:10090 20050609 MGI relationship(CL:0000002) MGI MGI:1861305 Fntb GO:0008284 MGI:MGI:3580759|PMID:15837621 IMP MGI:3581448 P farnesyltransferase, CAAX box, beta gene taxon:10090 20050721 MGI relationship(CL:0000007) MGI MGI:1347472 Foxa1 GO:0005634 MGI:MGI:3510582|PMID:15567715 IDA C forkhead box A1 Hnf-3a|Hnf3a|Tcf-3a|Tcf3a gene taxon:10090 20041229 MGI relationship(CL:0000121) MGI MGI:1347472 Foxa1 GO:0030855 MGI:MGI:3579763|PMID:15668254 IGI MGI:1347476 P forkhead box A1 Hnf-3a|Hnf3a|Tcf-3a|Tcf3a gene taxon:10090 20050823 MGI relationship(CL:0000082) MGI MGI:1347476 Foxa2 GO:0030855 MGI:MGI:3579763|PMID:15668254 IGI MGI:1347472 P forkhead box A2 Hnf-3b|HNF3-beta|Hnf3b|HNF3beta|Tcf-3b|Tcf3b gene taxon:10090 20050823 MGI relationship(CL:0000082) MGI MGI:1347481 Foxc2 GO:0048468 MGI:MGI:3619287|PMID:16498405 IMP MGI:1857740 P forkhead box C2 Fkh14|Hfhbf3|MFH-1|Mfh1 gene taxon:10090 20060607 MGI relationship(CL:0000115) MGI MGI:1347481 Foxc2 GO:0048468 MGI:MGI:3619287|PMID:16498405 IMP MGI:1857740 P forkhead box C2 Fkh14|Hfhbf3|MFH-1|Mfh1 gene taxon:10090 20060607 MGI relationship(CL:0000650) MGI MGI:1347481 Foxc2 GO:0048468 MGI:MGI:3619287|PMID:16498405 IMP MGI:1857740 P forkhead box C2 Fkh14|Hfhbf3|MFH-1|Mfh1 gene taxon:10090 20060607 MGI relationship(CL:0000653) MGI MGI:1347463 Foxd1 GO:0007411 MGI:MGI:3512698|PMID:15509772 IMP MGI:2180362 P forkhead box D1 BF-2|FREAC4|Hfh10|Hfhbf2 gene taxon:10090 20050202 MGI relationship(CL:0000410) MGI MGI:1353569 Foxe3 GO:0048468 MGI:MGI:3603877|PMID:16199865 IMP MGI:3604211 P forkhead box E3 FREAC8 gene taxon:10090 20051128 MGI relationship(CL:0000306) MGI MGI:1353569 Foxe3 GO:0050679 MGI:MGI:3603877|PMID:16199865 IMP MGI:3604211 P forkhead box E3 FREAC8 gene taxon:10090 20051128 MGI relationship(CL:0000066) MGI MGI:1347470 Foxf1a GO:0030198 MGI:MGI:3617131|PMID:16439479 IGI MGI:1347479 P forkhead box F1a Foxf1|Freac-1|FREAC1|HFH-8|Hfh8 gene taxon:10090 20060605 MGI relationship(CL:0000057) MGI MGI:1347470 Foxf1a GO:0045198 MGI:MGI:3617131|PMID:16439479 IGI MGI:1347479 P forkhead box F1a Foxf1|Freac-1|FREAC1|HFH-8|Hfh8 gene taxon:10090 20060605 MGI relationship(CL:0000131) MGI MGI:1347479 Foxf2 GO:0030198 MGI:MGI:3617131|PMID:16439479 IGI MGI:1347470 P forkhead box F2 Fkh20|FREAC2|LUN gene taxon:10090 20060605 MGI relationship(CL:0000057) MGI MGI:1347479 Foxf2 GO:0030198 MGI:MGI:3617131|PMID:16439479 IMP MGI:2667134 P forkhead box F2 Fkh20|FREAC2|LUN gene taxon:10090 20060605 MGI relationship(CL:0000057) MGI MGI:1347479 Foxf2 GO:0042249 MGI:MGI:3617131|PMID:16439479 IGI MGI:1347470 P forkhead box F2 Fkh20|FREAC2|LUN gene taxon:10090 20060605 MGI relationship(CL:0000131) MGI MGI:1347479 Foxf2 GO:0042249 MGI:MGI:3617131|PMID:16439479 IMP MGI:2667134 P forkhead box F2 Fkh20|FREAC2|LUN gene taxon:10090 20060605 MGI relationship(CL:0000131) MGI MGI:1347464 Foxg1 GO:0002052 MGI:MGI:3581994|PMID:15893304 IMP MGI:1932522 P forkhead box G1 BF-1|Bf1|Hfh9|Hfhbf1 gene taxon:10090 20070302 MGI relationship(CL:0000133) MGI MGI:1347464 Foxg1 GO:0007346 MGI:MGI:2183356|PMID:12151532 IMP MGI:1857771 P forkhead box G1 BF-1|Bf1|Hfh9|Hfhbf1 gene taxon:10090 20050817 MGI relationship(CL:0000133) MGI MGI:1347464 Foxg1 GO:0009953 MGI:MGI:2679162|PMID:14566948 IMP MGI:1857771 P forkhead box G1 BF-1|Bf1|Hfh9|Hfhbf1 gene taxon:10090 20050817 MGI relationship(CL:0000001) MGI MGI:1347464 Foxg1 GO:0016199 MGI:MGI:3051707|PMID:15240555 IMP MGI:1857771 P forkhead box G1 BF-1|Bf1|Hfh9|Hfhbf1 gene taxon:10090 20050825 MGI relationship(CL:0000740) MGI MGI:1347464 Foxg1 GO:0030900 MGI:MGI:2679162|PMID:14566948 IMP MGI:1857771 P forkhead box G1 BF-1|Bf1|Hfh9|Hfhbf1 gene taxon:10090 20050817 MGI relationship(CL:0000001) MGI MGI:1347464 Foxg1 GO:0045665 MGI:MGI:2686852|PMID:14704420 IMP MGI:1932522 P forkhead box G1 BF-1|Bf1|Hfh9|Hfhbf1 gene taxon:10090 20040930 MGI relationship(CL:0000117) MGI MGI:1347464 Foxg1 GO:0045665 MGI:MGI:74152|PMID:7605629 IMP MGI:1857771 P forkhead box G1 BF-1|Bf1|Hfh9|Hfhbf1 gene taxon:10090 20050817 MGI relationship(CL:0000117) MGI MGI:1347464 Foxg1 GO:0045787 MGI:MGI:3581994|PMID:15893304 IMP MGI:1932522 P forkhead box G1 BF-1|Bf1|Hfh9|Hfhbf1 gene taxon:10090 20050817 MGI relationship(CL:0000133) MGI MGI:1347464 Foxg1 GO:0048667 MGI:MGI:3654570|PMID:16691564 IMP MGI:2388671 P forkhead box G1 BF-1|Bf1|Hfh9|Hfhbf1 gene taxon:10090 20070302 MGI relationship(CL:0000540) MGI MGI:1347487 Foxm1 GO:0001889 MGI:MGI:3522012|PMID:15531365 IMP MGI:3522201 P forkhead box M1 Fkh16|Foxm1b|HFH-11B|Mpm2|Trident|WIN gene taxon:10090 20050314 MGI relationship(CL:0000055) MGI MGI:1347487 Foxm1 GO:0008284 MGI:MGI:3587543|PMID:15817462 IMP MGI:3522201 P forkhead box M1 Fkh16|Foxm1b|HFH-11B|Mpm2|Trident|WIN gene taxon:10090 20060202 MGI relationship(CL:0000134) MGI MGI:1347487 Foxm1 GO:0042127 MGI:MGI:3522012|PMID:15531365 IMP MGI:3522201 P forkhead box M1 Fkh16|Foxm1b|HFH-11B|Mpm2|Trident|WIN gene taxon:10090 20050314 MGI relationship(CL:0000055) MGI MGI:2151057 Foxn4 GO:0030154 MGI:MGI:3054139|PMID:15363391 IMP MGI:3054789 P forkhead box N4 gene taxon:10090 20060726 MGI relationship(CL:0000561) MGI MGI:2151057 Foxn4 GO:0048663 MGI:MGI:3587461|PMID:16020526 IGI MGI:96919 P forkhead box N4 gene taxon:10090 20060202 MGI relationship(CL:0000099) MGI MGI:1890081 Foxo3a GO:0005634 MGI:MGI:2675571|PMID:12857750 IDA C forkhead box O3a Fkhr2|FKHRL1 gene taxon:10090 20050720 MGI relationship(CL:0000002) MGI MGI:1890081 Foxo3a GO:0005737 MGI:MGI:2675571|PMID:12857750 IDA C forkhead box O3a Fkhr2|FKHRL1 gene taxon:10090 20050720 MGI relationship(CL:0000002) MGI MGI:1891436 Foxp3 GO:0050672 MGI:MGI:3662823|PMID:16227984 IMP MGI:2654936 P forkhead box P3 JM2|scurfin gene taxon:10090 20070111 MGI relationship(CL:0000542) MGI MGI:1921373 Foxp4 GO:0000122 MGI:MGI:3606794|PMID:14701752 IDA P forkhead box P4 gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:1921373 Foxp4 GO:0016564 MGI:MGI:3606794|PMID:14701752 IDA F forkhead box P4 gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:109166 Freq GO:0030424 MGI:MGI:85512|PMID:9030700 IDA C frequenin homolog (Drosophila) NCS-1 gene taxon:10090 20040330 MGI relationship(CL:0000540) MGI MGI:109166 Freq GO:0030425 MGI:MGI:85512|PMID:9030700 IDA C frequenin homolog (Drosophila) NCS-1 gene taxon:10090 20040330 MGI relationship(CL:0000540) MGI MGI:1100860 Frs2 GO:0000187 MGI:MGI:3580203|PMID:15870281 IMP MGI:3580390 P fibroblast growth factor receptor substrate 2 Frs2alpha|SNT1 gene taxon:10090 20050722 MGI relationship(CL:0000221) MGI MGI:1100860 Frs2 GO:0005737 MGI:MGI:3578616|PMID:15736129 IDA C fibroblast growth factor receptor substrate 2 Frs2alpha|SNT1 gene taxon:10090 20050615 MGI relationship(CL:0000007) MGI MGI:1100860 Frs2 GO:0005886 MGI:MGI:3578616|PMID:15736129 IDA C fibroblast growth factor receptor substrate 2 Frs2alpha|SNT1 gene taxon:10090 20050615 MGI relationship(CL:0000007) MGI MGI:1100860 Frs2 GO:0043350 MGI:MGI:3608243|PMID:16239343 IGI MGI:95516 P fibroblast growth factor receptor substrate 2 Frs2alpha|SNT1 gene taxon:10090 20060123 MGI relationship(CL:0000001) MGI MGI:1100860 Frs2 GO:0043350 MGI:MGI:3608243|PMID:16239343 IMP MGI:3521833 P fibroblast growth factor receptor substrate 2 Frs2alpha|SNT1 gene taxon:10090 20060123 MGI relationship(CL:0000337) MGI MGI:95586 Fst GO:0007276 MGI:MGI:3042808|PMID:15162500 IGI MGI:98957 P follistatin gene taxon:10090 20040715 MGI relationship(CL:0000021) MGI MGI:95586 Fst GO:0030509 MGI:MGI:3513220|PMID:15525533 IGI MGI:88180 P follistatin gene taxon:10090 20050121 MGI relationship(CL:0000139) MGI MGI:95586 Fst GO:0042475 MGI:MGI:3050251|PMID:15305290 IMP MGI:1857467 P follistatin gene taxon:10090 20040903 MGI relationship(CL:0000066) MGI MGI:95586 Fst GO:0045596 MGI:MGI:3513220|PMID:15525533 IGI MGI:88180 P follistatin gene taxon:10090 20050121 MGI relationship(CL:0000139) MGI MGI:95586 Fst GO:0045596 MGI:MGI:3513220|PMID:15525533 IMP MGI:1857467 P follistatin gene taxon:10090 20050121 MGI relationship(CL:0000139) MGI MGI:95594 Fut4 GO:0009986 MGI:MGI:3051927|PMID:15063176 IDA C fucosyltransferase 4 3-fucosyl-N-acetyl-lactosamine epitope|FAL|FucT-IV|LeX|SSEA-1 gene taxon:10090 20040930 MGI relationship(CL:0000586) MGI MGI:95602 Fyn GO:0001764 MGI:MGI:3590439|PMID:16162939 IGI MGI:98397 P Fyn proto-oncogene Src Kinase p59 gene taxon:10090 20060123 MGI relationship(CL:0000117) MGI MGI:95602 Fyn GO:0001764 MGI:MGI:3590439|PMID:16162939 IGI MGI:98397 P Fyn proto-oncogene Src Kinase p59 gene taxon:10090 20060123 MGI relationship(CL:0000121) MGI MGI:95602 Fyn GO:0001764 MGI:MGI:3610430|PMID:15073522 IMP MGI:1930480 P Fyn proto-oncogene Src Kinase p59 gene taxon:10090 20060301 MGI relationship(CL:0000117) MGI MGI:95602 Fyn GO:0004713 MGI:MGI:1859033|PMID:10872802 IDA F Fyn proto-oncogene Src Kinase p59 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:95602 Fyn GO:0018108 MGI:MGI:1859033|PMID:10872802 IDA P Fyn proto-oncogene Src Kinase p59 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1196625 Fzd1 GO:0007267 MGI:MGI:3577819|PMID:15809042 IDA P frizzled homolog 1 (Drosophila) FZ-1 gene taxon:10090 20050728 MGI relationship(CL:0000001) MGI MGI:1196625 Fzd1 GO:0016055 MGI:MGI:3581375|PMID:15923619 IGI MGI:98961,MGI:1278315,MGI:2136761 P frizzled homolog 1 (Drosophila) FZ-1 gene taxon:10090 20050816 MGI relationship(CL:0000002) MGI MGI:1196625 Fzd1 GO:0030855 MGI:MGI:3577819|PMID:15809042 IDA P frizzled homolog 1 (Drosophila) FZ-1 gene taxon:10090 20050728 MGI relationship(CL:0000001) MGI MGI:1196625 Fzd1 GO:0030855 MGI:MGI:3577819|PMID:15809042 IGI MGI:103124 P frizzled homolog 1 (Drosophila) FZ-1 gene taxon:10090 20050728 MGI relationship(CL:0000001) MGI MGI:2136761 Fzd10 GO:0016055 MGI:MGI:3581375|PMID:15923619 IGI MGI:1278315,MGI:98961,MGI:1196625 P frizzled homolog 10 (Drosophila) Fz-10 gene taxon:10090 20050816 MGI relationship(CL:0000002) MGI MGI:1888513 Fzd2 GO:0007267 MGI:MGI:3577819|PMID:15809042 IDA P frizzled homolog 2 (Drosophila) Fz10|Mfz10|Mfz10a gene taxon:10090 20050728 MGI relationship(CL:0000001) MGI MGI:1888513 Fzd2 GO:0030855 MGI:MGI:3577819|PMID:15809042 IDA P frizzled homolog 2 (Drosophila) Fz10|Mfz10|Mfz10a gene taxon:10090 20050728 MGI relationship(CL:0000001) MGI MGI:1888513 Fzd2 GO:0030855 MGI:MGI:3577819|PMID:15809042 IGI MGI:103124 P frizzled homolog 2 (Drosophila) Fz10|Mfz10|Mfz10a gene taxon:10090 20050728 MGI relationship(CL:0000001) MGI MGI:108476 Fzd3 GO:0042472 MGI:MGI:3616416|PMID:16495441 IGI MGI:108474 P frizzled homolog 3 (Drosophila) Fz3 gene taxon:10090 20060329 MGI relationship(CL:0000202) MGI MGI:108476 Fzd3 GO:0045177 MGI:MGI:3616416|PMID:16495441 IDA C frizzled homolog 3 (Drosophila) Fz3 gene taxon:10090 20060329 MGI relationship(CL:0000202) MGI MGI:108476 Fzd3 GO:0045177 MGI:MGI:3624469|PMID:16687519 IDA C frizzled homolog 3 (Drosophila) Fz3 gene taxon:10090 20060629 MGI relationship(CL:0000601) MGI MGI:108571 Fzd5 GO:0048469 MGI:MGI:3579620|PMID:15778706 IMP P frizzled homolog 5 (Drosophila) Fz5 gene taxon:10090 20050824 MGI relationship(CL:0000510) MGI MGI:108474 Fzd6 GO:0001736 MGI:MGI:3616416|PMID:16495441 IGI MGI:108476 P frizzled homolog 6 (Drosophila) Fz6 gene taxon:10090 20060329 MGI relationship(CL:0000202) MGI MGI:108474 Fzd6 GO:0042472 MGI:MGI:3616416|PMID:16495441 IGI MGI:108476 P frizzled homolog 6 (Drosophila) Fz6 gene taxon:10090 20060329 MGI relationship(CL:0000202) MGI MGI:108474 Fzd6 GO:0045177 MGI:MGI:3616416|PMID:16495441 IDA C frizzled homolog 6 (Drosophila) Fz6 gene taxon:10090 20060329 MGI relationship(CL:0000202) MGI MGI:1313278 Fzd9 GO:0043350 MGI:MGI:3584195|PMID:15930120 IMP MGI:3586504 P frizzled homolog 9 (Drosophila) frizzled 9|mfz9 gene taxon:10090 20050907 MGI relationship(CL:0000031) MGI MGI:108088 Gab1 GO:0005737 MGI:MGI:3578616|PMID:15736129 IDA C growth factor receptor bound protein 2-associated protein 1 gene taxon:10090 20050615 MGI relationship(CL:0000007) MGI MGI:108088 Gab1 GO:0030334 MGI:MGI:3589965|PMID:16166380 IGI MGI:109563 P growth factor receptor bound protein 2-associated protein 1 gene taxon:10090 20060116 MGI relationship(CL:0000056) MGI MGI:95610 Gabpa GO:0005634 MGI:MGI:1861311|PMID:11004506 IDA C GA repeat binding protein, alpha gene taxon:10090 20060817 MGI relationship(CL:0000002) MGI MGI:1337018 Galr2 GO:0031175 MGI:MGI:2449895|PMID:12533601 IDA P galanin receptor 2 GalR2|mGalR gene taxon:10090 20050209 MGI relationship(CL:0000101) MGI MGI:95639 Gap43 GO:0007411 MGI:MGI:1353240|PMID:10662636 IMP MGI:2448337 P growth associated protein 43 B-50|GAP-43|neuromodulin gene taxon:10090 20070227 MGI relationship(CL:0000001) MGI MGI:95639 Gap43 GO:0010001 MGI:MGI:3531391|PMID:15234344 IMP MGI:2180341 P growth associated protein 43 B-50|GAP-43|neuromodulin gene taxon:10090 20050720 MGI relationship(CL:0000002) MGI MGI:95639 Gap43 GO:0010001 MGI:MGI:3531391|PMID:15234344 IMP MGI:2180341 P growth associated protein 43 B-50|GAP-43|neuromodulin gene taxon:10090 20050720 MGI relationship(CL:0000127) MGI MGI:95639 Gap43 GO:0010001 MGI:MGI:3531391|PMID:15234344 IMP MGI:2180341 P growth associated protein 43 B-50|GAP-43|neuromodulin gene taxon:10090 20050720 MGI relationship(CL:0000681) MGI MGI:95639 Gap43 GO:0016198 MGI:MGI:70834|PMID:7859286 IMP MGI:2448337 P growth associated protein 43 B-50|GAP-43|neuromodulin gene taxon:10090 20070227 MGI relationship(CL:0000740) MGI MGI:95639 Gap43 GO:0045165 MGI:MGI:3531391|PMID:15234344 IMP P growth associated protein 43 B-50|GAP-43|neuromodulin gene taxon:10090 20050720 MGI relationship(CL:0000002) MGI MGI:1202388 Gas7 GO:0001726 MGI:MGI:2159085|PMID:11795944 IDA C growth arrest specific 7 Gas7-cb gene taxon:10090 20050331 MGI relationship(CL:0000002) MGI MGI:1202388 Gas7 GO:0005884 MGI:MGI:2159085|PMID:11795944 IDA C growth arrest specific 7 Gas7-cb gene taxon:10090 20050331 MGI relationship(CL:0000002) MGI MGI:1202388 Gas7 GO:0030182 MGI:MGI:3698406|PMID:15725398 IDA P growth arrest specific 7 Gas7-cb gene taxon:10090 20070302 MGI relationship(CL:0000002) MGI MGI:1202388 Gas7 GO:0048812 MGI:MGI:1289379|PMID:9736752 IMP P growth arrest specific 7 Gas7-cb gene taxon:10090 20070227 MGI relationship(CL:0000001) MGI MGI:95662 Gata2 GO:0021983 MGI:MGI:3625416|PMID:16543408 IMP MGI:3628639|MGI:2179995 P GATA binding protein 2 Gata-2 gene taxon:10090 20060823 MGI relationship(CL:0000437) MGI MGI:95662 Gata2 GO:0021983 MGI:MGI:3625416|PMID:16543408 IMP MGI:3628639|MGI:2179995 P GATA binding protein 2 Gata-2 gene taxon:10090 20060823 MGI relationship(CL:0000476) MGI MGI:95662 Gata2 GO:0030154 MGI:MGI:3625416|PMID:16543408 IMP MGI:3628639|MGI:2179995 P GATA binding protein 2 Gata-2 gene taxon:10090 20060823 MGI relationship(CL:0000437) MGI MGI:95662 Gata2 GO:0030154 MGI:MGI:3625416|PMID:16543408 IMP MGI:3628639|MGI:2179995 P GATA binding protein 2 Gata-2 gene taxon:10090 20060823 MGI relationship(CL:0000476) MGI MGI:95662 Gata2 GO:0048469 MGI:MGI:3625416|PMID:16543408 IMP MGI:3628639|MGI:2179995 P GATA binding protein 2 Gata-2 gene taxon:10090 20060823 MGI relationship(CL:0000437) MGI MGI:95663 Gata3 GO:0005634 MGI:MGI:1338150|PMID:10447238 IDA C GATA binding protein 3 Gata-3 gene taxon:10090 20050426 MGI relationship(CL:0000066) MGI MGI:95663 Gata3 GO:0005634 MGI:MGI:1338150|PMID:10447238 IDA C GATA binding protein 3 Gata-3 gene taxon:10090 20050426 MGI relationship(CL:0000631) MGI MGI:95663 Gata3 GO:0005634 MGI:MGI:1338150|PMID:10447238 IDA C GATA binding protein 3 Gata-3 gene taxon:10090 20050426 MGI relationship(CL:0000635) MGI MGI:95663 Gata3 GO:0005634 MGI:MGI:3037230|PMID:15003631 IDA C GATA binding protein 3 Gata-3 gene taxon:10090 20050428 MGI relationship(CL:0000002) MGI MGI:95664 Gata4 GO:0005634 MGI:MGI:3575862|PMID:15767668 IDA C GATA binding protein 4 Gata-4 gene taxon:10090 20050519 MGI relationship(CL:0000223) MGI MGI:95664 Gata4 GO:0007267 MGI:MGI:3590399|PMID:16127717 IMP MGI:2386764 P GATA binding protein 4 Gata-4 gene taxon:10090 20060116 MGI relationship(CL:0000131) MGI MGI:107516 Gata6 GO:0003682 MGI:MGI:3603876|PMID:16199866 IDA F GATA binding protein 6 gene taxon:10090 20051201 MGI relationship(CL:0000002) MGI MGI:107516 Gata6 GO:0005634 MGI:MGI:3603876|PMID:16199866 IDA C GATA binding protein 6 gene taxon:10090 20051201 MGI relationship(CL:0000002) MGI MGI:107516 Gata6 GO:0045944 MGI:MGI:3603876|PMID:16199866 IDA P GATA binding protein 6 gene taxon:10090 20051201 MGI relationship(CL:0000002) MGI MGI:95668 Gbx2 GO:0001755 MGI:MGI:3588904|PMID:15996652 IMP MGI:1857634 P gastrulation brain homeobox 2 Gbx-2|MMoxA|Stra7 gene taxon:10090 20051024 MGI relationship(CL:0000333) MGI MGI:95668 Gbx2 GO:0035239 MGI:MGI:3588904|PMID:15996652 IMP MGI:1857634 P gastrulation brain homeobox 2 Gbx-2|MMoxA|Stra7 gene taxon:10090 20051024 MGI relationship(CL:0000071) MGI MGI:1270854 Gck GO:0004340 MGI:MGI:3691164|PMID:9873043 IDA F glucokinase Gk|hexokinase 4|HK4|MODY2 gene taxon:10090 20061222 MGI relationship(CL:0000001) MGI MGI:1270854 Gck GO:0006739 MGI:MGI:3691164|PMID:9873043 IMP P glucokinase Gk|hexokinase 4|HK4|MODY2 gene taxon:10090 20061222 MGI relationship(CL:0000001) MGI MGI:104990 Gclc GO:0006750 MGI:MGI:1858542|PMID:10805773 IMP MGI:2387010 P glutamate-cysteine ligase, catalytic subunit D9Wsu168e|gamma GCS-HS|GLCL-H|Glclc gene taxon:10090 20061114 MGI relationship(CL:0000001) MGI MGI:108045 Gcm1 GO:0060018 MGI:MGI:3630207|PMID:14573516 IDA P glial cells missing homolog 1 (Drosophila) Gcm 1|Gcm a|Gcm1-rs1|GCMa|glial cell deficient|glide gene taxon:10090 20061208 MGI relationship(CL:0000001) MGI MGI:105113 Gcna1 GO:0005634 MGI:MGI:3628699|PMID:16564520 IDA C germ cell nuclear antigen 1 gene taxon:10090 20060807 MGI relationship(CL:0000017) MGI MGI:105113 Gcna1 GO:0005634 MGI:MGI:3628699|PMID:16564520 IDA C germ cell nuclear antigen 1 gene taxon:10090 20060807 MGI relationship(CL:0000020) MGI MGI:105113 Gcna1 GO:0043073 MGI:MGI:3056006|PMID:15467367 IDA C germ cell nuclear antigen 1 gene taxon:10090 20050615 MGI relationship(CL:0000020) MGI MGI:1338027 Gdf11 GO:0045596 MGI:MGI:3581514|PMID:15976303 IDA P growth differentiation factor 11 Bmp11 gene taxon:10090 20060727 MGI relationship(CL:0000001) MGI MGI:1338027 Gdf11 GO:0045596 MGI:MGI:3581514|PMID:15976303 IDA P growth differentiation factor 11 Bmp11 gene taxon:10090 20060727 MGI relationship(CL:0000561) MGI MGI:1338027 Gdf11 GO:0045596 MGI:MGI:3581514|PMID:15976303 IDA P growth differentiation factor 11 Bmp11 gene taxon:10090 20060727 MGI relationship(CL:0000740) MGI MGI:1338027 Gdf11 GO:0048469 MGI:MGI:3512831|PMID:15548585 IMP MGI:2449672 P growth differentiation factor 11 Bmp11 gene taxon:10090 20050315 MGI relationship(CL:0000169) MGI MGI:95688 Gdf5 GO:0030326 MGI:MGI:3513212|PMID:15542031 IMP MGI:1855974 P growth differentiation factor 5 bp|cartilage-derived morphogenetic protein-1|CDMP-1 gene taxon:10090 20050120 MGI relationship(CL:0000134) MGI MGI:95688 Gdf5 GO:0042981 MGI:MGI:3513212|PMID:15542031 IMP MGI:1855974 P growth differentiation factor 5 bp|cartilage-derived morphogenetic protein-1|CDMP-1 gene taxon:10090 20050120 MGI relationship(CL:0000134) MGI MGI:95690 Gdf7 GO:0045165 MGI:MGI:3581508|PMID:15883363 IDA P growth differentiation factor 7 BMP12 gene taxon:10090 20050805 MGI relationship(CL:0000101) MGI MGI:107430 Gdnf GO:0001657 MGI:MGI:3582141|PMID:15905075 IDA P glial cell line derived neurotrophic factor glial cell line-derived neurotrophic factor gene taxon:10090 20051014 MGI relationship(CL:0000001) MGI MGI:107430 Gdnf GO:0007422 MGI:MGI:2157194|PMID:11774071 IMP MGI:2136846 P glial cell line derived neurotrophic factor glial cell line-derived neurotrophic factor gene taxon:10090 20050308 MGI relationship(CL:0000107) MGI MGI:103170 Gfi1 GO:0009996 MGI:MGI:3606816|PMID:16230531 IMP MGI:2449921 P growth factor independent 1 Pal-1|Pal1 gene taxon:10090 20060130 MGI relationship(CL:0000160) MGI MGI:103170 Gfi1 GO:0042472 MGI:MGI:2429425|PMID:12441305 IMP MGI:2449921 P growth factor independent 1 Pal-1|Pal1 gene taxon:10090 20050209 MGI relationship(CL:0000589) MGI MGI:103170 Gfi1 GO:0042472 MGI:MGI:2429425|PMID:12441305 IMP MGI:2449921 P growth factor independent 1 Pal-1|Pal1 gene taxon:10090 20050209 MGI relationship(CL:0000601) MGI MGI:103170 Gfi1 GO:0042491 MGI:MGI:2429425|PMID:12441305 IMP MGI:2449921 P growth factor independent 1 Pal-1|Pal1 gene taxon:10090 20050209 MGI relationship(CL:0000589) MGI MGI:103170 Gfi1 GO:0042491 MGI:MGI:2429425|PMID:12441305 IMP MGI:2449921 P growth factor independent 1 Pal-1|Pal1 gene taxon:10090 20050209 MGI relationship(CL:0000601) MGI MGI:103170 Gfi1 GO:0042660 MGI:MGI:3606816|PMID:16230531 IMP MGI:2449921 P growth factor independent 1 Pal-1|Pal1 gene taxon:10090 20060221 MGI relationship(CL:0000164) MGI MGI:103170 Gfi1 GO:0045165 MGI:MGI:3606816|PMID:16230531 IMP MGI:2449921 P growth factor independent 1 Pal-1|Pal1 gene taxon:10090 20060130 MGI relationship(CL:0000510) MGI MGI:1201403 Gfra3 GO:0001764 MGI:MGI:1344239|PMID:10482239 IMP MGI:2136781 P glial cell line derived neurotrophic factor family receptor alpha 3 gene taxon:10090 20061116 MGI relationship(CL:0000540) MGI MGI:1201403 Gfra3 GO:0005515 MGI:MGI:1195875|PMID:9452475 IPI UniProt:P35546 F glial cell line derived neurotrophic factor family receptor alpha 3 gene taxon:10090 20050609 MGI relationship(CL:0000002) MGI MGI:1201403 Gfra3 GO:0007411 MGI:MGI:1344239|PMID:10482239 IMP MGI:2136781 P glial cell line derived neurotrophic factor family receptor alpha 3 gene taxon:10090 20061116 MGI relationship(CL:0000540) MGI MGI:1201403 Gfra3 GO:0009897 MGI:MGI:1195875|PMID:9452475 IDA C glial cell line derived neurotrophic factor family receptor alpha 3 gene taxon:10090 20050609 MGI relationship(CL:0000002) MGI MGI:1201403 Gfra3 GO:0048485 MGI:MGI:1344239|PMID:10482239 IMP MGI:2136781 P glial cell line derived neurotrophic factor family receptor alpha 3 gene taxon:10090 20061116 MGI relationship(CL:0000540) MGI MGI:1201403 Gfra3 GO:0048666 MGI:MGI:1344239|PMID:10482239 IMP MGI:2136781 P glial cell line derived neurotrophic factor family receptor alpha 3 gene taxon:10090 20061116 MGI relationship(CL:0000540) MGI MGI:2181461 Ggn GO:0048471 MGI:MGI:3529646|PMID:15642376 IDA C gametogenetin gene taxon:10090 20050325 MGI relationship(CL:0000002) MGI MGI:3055306 Ggnbp1 GO:0005794 MGI:MGI:3529646|PMID:15642376 IDA C gametogenetin binding protein 1 gene taxon:10090 20050325 MGI relationship(CL:0000002) MGI MGI:3055306 Ggnbp1 GO:0005886 MGI:MGI:3529646|PMID:15642376 IDA C gametogenetin binding protein 1 gene taxon:10090 20050325 MGI relationship(CL:0000002) MGI MGI:2387356 Ggnbp2 GO:0005737 MGI:MGI:3529646|PMID:15642376 IDA C gametogenetin binding protein 2 DIF-3|Zfp403 gene taxon:10090 20050325 MGI relationship(CL:0000002) MGI MGI:95713 Gja1 GO:0001764 MGI:MGI:3612915|PMID:12638734 IMP MGI:1857177 P gap junction membrane channel protein alpha 1 alpha 1 connexin|connexin 43|connexin43|Cx43|Cx43alpha1|Gja-1 gene taxon:10090 20060309 MGI relationship(CL:0000031) MGI MGI:95713 Gja1 GO:0002070 MGI:MGI:3624198|PMID:16624854 IMP MGI:3051881|MGI:2176205 P gap junction membrane channel protein alpha 1 alpha 1 connexin|connexin 43|connexin43|Cx43|Cx43alpha1|Gja-1 gene taxon:10090 20060727 MGI relationship(CL:0000710) MGI MGI:95713 Gja1 GO:0005921 MGI:MGI:3607852|PMID:11922902 IDA C gap junction membrane channel protein alpha 1 alpha 1 connexin|connexin 43|connexin43|Cx43|Cx43alpha1|Gja-1 gene taxon:10090 20060116 MGI relationship(CL:0000746) MGI MGI:1339969 Gja10 GO:0005243 MGI:MGI:1336986|PMID:10329667 IDA F gap junction membrane channel protein alpha 10 connexin-57|Cx-57|Cx59 gene taxon:10090 20070216 MGI relationship(CL:0000002) MGI MGI:1339969 Gja10 GO:0005921 MGI:MGI:1336986|PMID:10329667 IDA C gap junction membrane channel protein alpha 10 connexin-57|Cx-57|Cx59 gene taxon:10090 20070216 MGI relationship(CL:0000002) MGI MGI:1339969 Gja10 GO:0007276 MGI:MGI:1336986|PMID:10329667 IDA P gap junction membrane channel protein alpha 10 connexin-57|Cx-57|Cx59 gene taxon:10090 20070216 MGI relationship(CL:0000002) MGI MGI:1339969 Gja10 GO:0007416 MGI:MGI:3654563|PMID:16820008 IMP MGI:3043946 P gap junction membrane channel protein alpha 10 connexin-57|Cx-57|Cx59 gene taxon:10090 20070216 MGI relationship(CL:0000745) MGI MGI:95718 Gja7 GO:0005921 MGI:MGI:3607852|PMID:11922902 IDA C gap junction membrane channel protein alpha 7 connexin 45|Cx45|Gja-7 gene taxon:10090 20060116 MGI relationship(CL:0000746) MGI MGI:95718 Gja7 GO:0007507 MGI:MGI:3608436|PMID:14681043 IMP MGI:3608701|MGI:2177600 P gap junction membrane channel protein alpha 7 connexin 45|Cx45|Gja-7 gene taxon:10090 20060130 MGI relationship(CL:0000746) MGI MGI:95718 Gja7 GO:0048468 MGI:MGI:3608436|PMID:14681043 IMP MGI:3608701|MGI:2177600 P gap junction membrane channel protein alpha 7 connexin 45|Cx45|Gja-7 gene taxon:10090 20060130 MGI relationship(CL:0000746) MGI MGI:95718 Gja7 GO:0048738 MGI:MGI:3608436|PMID:14681043 IMP MGI:3608701|MGI:2177600 P gap junction membrane channel protein alpha 7 connexin 45|Cx45|Gja-7 gene taxon:10090 20060130 MGI relationship(CL:0000746) MGI MGI:95719 Gjb1 GO:0005886 MGI:MGI:2671736|PMID:12829745 IDA C gap junction membrane channel protein beta 1 connexin 32|connexin-32|Cx32|Gjb-1 gene taxon:10090 20060228 MGI relationship(CL:0000622) MGI MGI:95727 Gli1 GO:0021938 MGI:MGI:3624180|PMID:16571625 IGI MGI:95728 P GLI-Kruppel family member GLI1 Gli1|Zfp-5|Zfp5 gene taxon:10090 20061221 MGI relationship(CL:0000120) MGI MGI:95728 Gli2 GO:0002076 MGI:MGI:3653954|PMID:16880529 IDA P GLI-Kruppel family member GLI2 gene taxon:10090 20061221 MGI relationship(CL:0000002) MGI MGI:95728 Gli2 GO:0002076 MGI:MGI:3653954|PMID:16880529 IMP P GLI-Kruppel family member GLI2 gene taxon:10090 20061221 MGI relationship(CL:0000002) MGI MGI:95728 Gli2 GO:0007411 MGI:MGI:1340208|PMID:10409510 IMP MGI:1857509 P GLI-Kruppel family member GLI2 gene taxon:10090 20061218 MGI relationship(CL:0000117) MGI MGI:95728 Gli2 GO:0008284 MGI:MGI:1277743|PMID:9731531 IMP MGI:1857509 P GLI-Kruppel family member GLI2 gene taxon:10090 20061218 MGI relationship(CL:0000066) MGI MGI:95728 Gli2 GO:0008284 MGI:MGI:1277743|PMID:9731531 IMP MGI:1857509 P GLI-Kruppel family member GLI2 gene taxon:10090 20061218 MGI relationship(CL:0000134) MGI MGI:95728 Gli2 GO:0008284 MGI:MGI:3512837|PMID:15496441 IGI MGI:98297 P GLI-Kruppel family member GLI2 gene taxon:10090 20050204 MGI relationship(CL:0000120) MGI MGI:95728 Gli2 GO:0008284 MGI:MGI:3512837|PMID:15496441 IMP MGI:1857509 P GLI-Kruppel family member GLI2 gene taxon:10090 20050204 MGI relationship(CL:0000120) MGI MGI:95728 Gli2 GO:0008284 MGI:MGI:3589306|PMID:16054035 IGI MGI:98297 P GLI-Kruppel family member GLI2 gene taxon:10090 20061220 MGI relationship(CL:0000362) MGI MGI:95728 Gli2 GO:0021775 MGI:MGI:3051712|PMID:15215207 IGI MGI:95729 P GLI-Kruppel family member GLI2 gene taxon:10090 20061220 MGI relationship(CL:0000099) MGI MGI:95728 Gli2 GO:0021776 MGI:MGI:3051712|PMID:15215207 IGI MGI:95729 P GLI-Kruppel family member GLI2 gene taxon:10090 20061220 MGI relationship(CL:0000100) MGI MGI:95728 Gli2 GO:0021938 MGI:MGI:3624180|PMID:16571625 IGI MGI:95727 P GLI-Kruppel family member GLI2 gene taxon:10090 20061221 MGI relationship(CL:0000120) MGI MGI:95728 Gli2 GO:0021938 MGI:MGI:3624180|PMID:16571625 IMP MGI:3664541|MGI:2446434 P GLI-Kruppel family member GLI2 gene taxon:10090 20061221 MGI relationship(CL:0000120) MGI MGI:95728 Gli2 GO:0021965 MGI:MGI:1340208|PMID:10409510 IMP MGI:1857509 P GLI-Kruppel family member GLI2 gene taxon:10090 20061218 MGI relationship(CL:0000117) MGI MGI:95728 Gli2 GO:0030902 MGI:MGI:3512837|PMID:15496441 IGI MGI:98297 P GLI-Kruppel family member GLI2 gene taxon:10090 20050204 MGI relationship(CL:0000120) MGI MGI:95728 Gli2 GO:0030902 MGI:MGI:3512837|PMID:15496441 IMP MGI:1857509 P GLI-Kruppel family member GLI2 gene taxon:10090 20050204 MGI relationship(CL:0000120) MGI MGI:95728 Gli2 GO:0045666 MGI:MGI:3663573|PMID:16950124 IGI MGI:97490 P GLI-Kruppel family member GLI2 gene taxon:10090 20061221 MGI relationship(CL:0000540) MGI MGI:95728 Gli2 GO:0045944 MGI:MGI:3653954|PMID:16880529 IGI MGI:98297 P GLI-Kruppel family member GLI2 gene taxon:10090 20061221 MGI relationship(CL:0000002) MGI MGI:95728 Gli2 GO:0048666 MGI:MGI:3607408|PMID:16267219 IMP MGI:1857509 P GLI-Kruppel family member GLI2 gene taxon:10090 20060209 MGI relationship(CL:0000741) MGI MGI:95729 Gli3 GO:0021775 MGI:MGI:3051712|PMID:15215207 IGI MGI:95728 P GLI-Kruppel family member GLI3 Bph|brachyphalangy gene taxon:10090 20061220 MGI relationship(CL:0000099) MGI MGI:95729 Gli3 GO:0021776 MGI:MGI:3051712|PMID:15215207 IGI MGI:95728 P GLI-Kruppel family member GLI3 Bph|brachyphalangy gene taxon:10090 20061220 MGI relationship(CL:0000100) MGI MGI:95729 Gli3 GO:0045595 MGI:MGI:3608261|PMID:16284117 IGI MGI:96533 P GLI-Kruppel family member GLI3 Bph|brachyphalangy gene taxon:10090 20060131 MGI relationship(CL:0000743) MGI MGI:95729 Gli3 GO:0045596 MGI:MGI:3608261|PMID:16284117 IGI MGI:96533 P GLI-Kruppel family member GLI3 Bph|brachyphalangy gene taxon:10090 20060131 MGI relationship(CL:0000744) MGI MGI:95729 Gli3 GO:0048663 MGI:MGI:3610448|PMID:16168404 IMP MGI:1856276 P GLI-Kruppel family member GLI3 Bph|brachyphalangy gene taxon:10090 20060228 MGI relationship(CL:0000695) MGI MGI:2444289 Glis3 GO:0000122 MGI:MGI:3033266|PMID:14500813 IDA P GLIS family zinc finger 3 gene taxon:10090 20060814 MGI relationship(CL:0000002) MGI MGI:2444289 Glis3 GO:0003700 MGI:MGI:3033266|PMID:14500813 IDA F GLIS family zinc finger 3 gene taxon:10090 20060814 MGI relationship(CL:0000002) MGI MGI:2444289 Glis3 GO:0044428 MGI:MGI:3033266|PMID:14500813 IDA C GLIS family zinc finger 3 gene taxon:10090 20060814 MGI relationship(CL:0000002) MGI MGI:2444289 Glis3 GO:0045944 MGI:MGI:3033266|PMID:14500813 IDA P GLIS family zinc finger 3 gene taxon:10090 20060814 MGI relationship(CL:0000002) MGI MGI:3696042 Glp1 GO:0005634 MGI:MGI:3695332|PMID:16982049 IDA C GATA-like 1 gene taxon:10090 20070209 MGI relationship(CL:0000002) MGI MGI:95747 Glra1 GO:0001508 MGI:MGI:3622577|PMID:11742725 IMP MGI:1856177 P glycine receptor, alpha 1 subunit nmf11|oscillator|ot gene taxon:10090 20061129 MGI relationship(CL:0000540) MGI MGI:95747 Glra1 GO:0001508 MGI:MGI:3654385|PMID:16800867 IMP MGI:1856362 P glycine receptor, alpha 1 subunit nmf11|oscillator|ot gene taxon:10090 20061128 MGI relationship(CL:0000117) MGI MGI:95747 Glra1 GO:0002087 MGI:MGI:3654385|PMID:16800867 IMP MGI:1856362 P glycine receptor, alpha 1 subunit nmf11|oscillator|ot gene taxon:10090 20061128 MGI relationship(CL:0000117) MGI MGI:95747 Glra1 GO:0007268 MGI:MGI:3615703|PMID:12837931 IMP MGI:1856177|MGI:1856363 P glycine receptor, alpha 1 subunit nmf11|oscillator|ot gene taxon:10090 20061129 MGI relationship(CL:0000540) MGI MGI:95747 Glra1 GO:0016594 MGI:MGI:68467|PMID:8062927 IMP MGI:1856362 F glycine receptor, alpha 1 subunit nmf11|oscillator|ot gene taxon:10090 20061129 MGI relationship(CL:0000540) MGI MGI:95747 Glra1 GO:0016934 MGI:MGI:3623689|PMID:16672662 IMP MGI:1856177|MGI:1856362 F glycine receptor, alpha 1 subunit nmf11|oscillator|ot gene taxon:10090 20061201 MGI relationship(CL:0000540) MGI MGI:95747 Glra1 GO:0042391 MGI:MGI:3623689|PMID:16672662 IMP MGI:1856177|MGI:1856362 P glycine receptor, alpha 1 subunit nmf11|oscillator|ot gene taxon:10090 20061201 MGI relationship(CL:0000540) MGI MGI:95747 Glra1 GO:0043576 MGI:MGI:3622577|PMID:11742725 IMP MGI:1856177 P glycine receptor, alpha 1 subunit nmf11|oscillator|ot gene taxon:10090 20061129 MGI relationship(CL:0000540) MGI MGI:95747 Glra1 GO:0045211 MGI:MGI:3663854|PMID:16964444 IDA C glycine receptor, alpha 1 subunit nmf11|oscillator|ot gene taxon:10090 20061128 MGI relationship(CL:0000100) MGI MGI:95747 Glra1 GO:0060012 MGI:MGI:3623689|PMID:16672662 IMP MGI:1856177|MGI:1856362 P glycine receptor, alpha 1 subunit nmf11|oscillator|ot gene taxon:10090 20061201 MGI relationship(CL:0000540) MGI MGI:95751 Glrb GO:0007601 MGI:MGI:49331|PMID:1338094 IMP MGI:1856363 P glycine receptor, beta subunit gene taxon:10090 20061201 MGI relationship(CL:0000740) MGI MGI:95751 Glrb GO:0016934 MGI:MGI:3621380|PMID:12809985 IMP MGI:1856363 F glycine receptor, beta subunit gene taxon:10090 20061204 MGI relationship(CL:0000540) MGI MGI:95751 Glrb GO:0016934 MGI:MGI:3623689|PMID:16672662 IMP MGI:1856363 F glycine receptor, beta subunit gene taxon:10090 20061201 MGI relationship(CL:0000540) MGI MGI:95751 Glrb GO:0042391 MGI:MGI:3623689|PMID:16672662 IMP MGI:1856363 P glycine receptor, beta subunit gene taxon:10090 20061201 MGI relationship(CL:0000540) MGI MGI:95751 Glrb GO:0060012 MGI:MGI:3621380|PMID:12809985 IMP MGI:1856363 P glycine receptor, beta subunit gene taxon:10090 20061204 MGI relationship(CL:0000540) MGI MGI:95751 Glrb GO:0060012 MGI:MGI:3623689|PMID:16672662 IMP MGI:1856363 P glycine receptor, beta subunit gene taxon:10090 20061201 MGI relationship(CL:0000540) MGI MGI:95751 Glrb GO:0060012 MGI:MGI:49331|PMID:1338094 IMP P glycine receptor, beta subunit gene taxon:10090 20061201 MGI relationship(CL:0000740) MGI MGI:95762 Gm2a GO:0019915 MGI:MGI:894862|PMID:9223328 IMP MGI:1861930 P GM2 ganglioside activator protein gene taxon:10090 20050602 MGI relationship(CL:0000117) MGI MGI:95762 Gm2a GO:0019915 MGI:MGI:894862|PMID:9223328 IMP MGI:1861930 P GM2 ganglioside activator protein gene taxon:10090 20050602 MGI relationship(CL:0000121) MGI MGI:95762 Gm2a GO:0019915 MGI:MGI:894862|PMID:9223328 IMP MGI:1861930 P GM2 ganglioside activator protein gene taxon:10090 20050602 MGI relationship(CL:0000243) MGI MGI:95762 Gm2a GO:0019915 MGI:MGI:894862|PMID:9223328 IMP MGI:1861930 P GM2 ganglioside activator protein gene taxon:10090 20050602 MGI relationship(CL:0000598) MGI MGI:95768 Gna13 GO:0001569 MGI:MGI:3583513|PMID:15919816 IMP MGI:3583876|MGI:2450311 P guanine nucleotide binding protein, alpha 13 Galpha13 gene taxon:10090 20060303 MGI relationship(CL:0000071) MGI MGI:101849 Gnb2l1 GO:0043025 MGI:MGI:3616942|PMID:16414032 IDA C guanine nucleotide binding protein (G protein), beta polypeptide 2 like 1 GB-like|Gnb2-rs1|p205|Rack1 gene taxon:10090 20060518 MGI relationship(CL:0000117) MGI MGI:101849 Gnb2l1 GO:0043025 MGI:MGI:3616942|PMID:16414032 IDA C guanine nucleotide binding protein (G protein), beta polypeptide 2 like 1 GB-like|Gnb2-rs1|p205|Rack1 gene taxon:10090 20060518 MGI relationship(CL:0000121) MGI MGI:101849 Gnb2l1 GO:0043025 MGI:MGI:3616942|PMID:16414032 IDA C guanine nucleotide binding protein (G protein), beta polypeptide 2 like 1 GB-like|Gnb2-rs1|p205|Rack1 gene taxon:10090 20060518 MGI relationship(CL:0000598) MGI MGI:2139395 Golga2 GO:0005801 MGI:MGI:3624072|PMID:16399995 IDA C golgi autoantigen, golgin subfamily a, 2 GM130 gene taxon:10090 20060706 MGI relationship(CL:0000002) MGI MGI:104903 Gpc3 GO:0001658 MGI:MGI:3583399|PMID:15925496 IGI MGI:88177,MGI:894293 P glypican 3 OCI-5 gene taxon:10090 20060202 MGI relationship(CL:0000001) MGI MGI:104903 Gpc3 GO:0008285 MGI:MGI:3583399|PMID:15925496 IGI MGI:88177,MGI:894293 P glypican 3 OCI-5 gene taxon:10090 20060202 MGI relationship(CL:0000001) MGI MGI:104903 Gpc3 GO:0030513 MGI:MGI:3583399|PMID:15925496 IMP MGI:2159356 P glypican 3 OCI-5 gene taxon:10090 20060202 MGI relationship(CL:0000001) MGI MGI:2685341 Gpr139 GO:0007200 MGI:MGI:3619839|PMID:16378626 IDA P G protein-coupled receptor 139 GPRg1|LOC209776 gene taxon:10090 20060607 MGI relationship(CL:0000002) MGI MGI:2685341 Gpr139 GO:0008188 MGI:MGI:3619839|PMID:16378626 IDA F G protein-coupled receptor 139 GPRg1|LOC209776 gene taxon:10090 20060607 MGI relationship(CL:0000002) MGI MGI:2685341 Gpr139 GO:0046983 MGI:MGI:3619839|PMID:16378626 IDA F G protein-coupled receptor 139 GPRg1|LOC209776 gene taxon:10090 20060607 MGI relationship(CL:0000002) MGI MGI:1274784 Gpr98 GO:0005886 MGI:MGI:3629345|PMID:16775142 IDA C G protein-coupled receptor 98 Mass1|Mgr1|VLGR1 gene taxon:10090 20070312 MGI relationship(CL:0000589) MGI MGI:1274784 Gpr98 GO:0005886 MGI:MGI:3629345|PMID:16775142 IDA C G protein-coupled receptor 98 Mass1|Mgr1|VLGR1 gene taxon:10090 20070312 MGI relationship(CL:0000601) MGI MGI:1274784 Gpr98 GO:0048839 MGI:MGI:3629345|PMID:16775142 IMP MGI:3046273 P G protein-coupled receptor 98 Mass1|Mgr1|VLGR1 gene taxon:10090 20070312 MGI relationship(CL:0000589) MGI MGI:1274784 Gpr98 GO:0048839 MGI:MGI:3629345|PMID:16775142 IMP MGI:3046273 P G protein-coupled receptor 98 Mass1|Mgr1|VLGR1 gene taxon:10090 20070312 MGI relationship(CL:0000601) MGI MGI:1274784 Gpr98 GO:0050910 MGI:MGI:3629345|PMID:16775142 IMP MGI:3046273 P G protein-coupled receptor 98 Mass1|Mgr1|VLGR1 gene taxon:10090 20070312 MGI relationship(CL:0000589) MGI MGI:1274784 Gpr98 GO:0050910 MGI:MGI:3629345|PMID:16775142 IMP MGI:3046273 P G protein-coupled receptor 98 Mass1|Mgr1|VLGR1 gene taxon:10090 20070312 MGI relationship(CL:0000601) MGI MGI:95805 Grb2 GO:0005515 MGI:MGI:3613261|PMID:16405865 IPI UniProt:P46662 F growth factor receptor bound protein 2 gene taxon:10090 20070119 MGI relationship(CL:0000002) MGI MGI:95805 Grb2 GO:0005737 MGI:MGI:3578616|PMID:15736129 IDA C growth factor receptor bound protein 2 gene taxon:10090 20050615 MGI relationship(CL:0000007) MGI MGI:1344337 Grem1 GO:0007267 MGI:MGI:3045644|PMID:15201225 IMP MGI:3046937 P gremlin 1 Cktsf1b1|Drm|gremlin gene taxon:10090 20060726 MGI relationship(CL:0000066) MGI MGI:1344337 Grem1 GO:0007267 MGI:MGI:3045644|PMID:15201225 IMP MGI:3046937 P gremlin 1 Cktsf1b1|Drm|gremlin gene taxon:10090 20060726 MGI relationship(CL:0000134) MGI MGI:2655333 Grhl3 GO:0008544 MGI:MGI:3575446|PMID:15831758 IMP MGI:2684328 P grainyhead-like 3 (Drosophila) Get1|Som gene taxon:10090 20050510 MGI relationship(CL:0000312) MGI MGI:1929494 Grlf1 GO:0005737 MGI:MGI:1926242|PMID:11044403 IDA C glucocorticoid receptor DNA binding factor 1 P190 RhoGAP gene taxon:10090 20050209 MGI relationship(CL:0000002) MGI MGI:1929494 Grlf1 GO:0043010 MGI:MGI:1926242|PMID:11044403 IMP MGI:2448591 P glucocorticoid receptor DNA binding factor 1 P190 RhoGAP gene taxon:10090 20050209 MGI relationship(CL:0000066) MGI MGI:95832 Grn GO:0005615 MGI:MGI:3589098|PMID:15901638 IDA C granulin acrogranulin|epithelin|PC cell-derived growth factor|progranulin gene taxon:10090 20051128 MGI relationship(CL:0000001) MGI MGI:95832 Grn GO:0005615 MGI:MGI:3589098|PMID:15901638 IDA C granulin acrogranulin|epithelin|PC cell-derived growth factor|progranulin gene taxon:10090 20051128 MGI relationship(CL:0000002) MGI MGI:95832 Grn GO:0005615 MGI:MGI:3589098|PMID:15901638 IDA C granulin acrogranulin|epithelin|PC cell-derived growth factor|progranulin gene taxon:10090 20051128 MGI relationship(CL:1000274) MGI MGI:95832 Grn GO:0050679 MGI:MGI:3589098|PMID:15901638 IDA P granulin acrogranulin|epithelin|PC cell-derived growth factor|progranulin gene taxon:10090 20051128 MGI relationship(CL:0000002) MGI MGI:95843 Gsh2 GO:0007389 MGI:MGI:3579956|PMID:15930101 IMP MGI:2150162 P genomic screened homeo box 2 Gsh-2 gene taxon:10090 20050815 MGI relationship(CL:0000099) MGI MGI:95843 Gsh2 GO:0048665 MGI:MGI:3579956|PMID:15930101 IMP MGI:2150162 P genomic screened homeo box 2 Gsh-2 gene taxon:10090 20050816 MGI relationship(CL:0000402) MGI MGI:1861437 Gsk3b GO:0006983 MGI:MGI:3032464|PMID:14744935 IDA P glycogen synthase kinase 3 beta GSK-3|GSK-3beta|GSK3 gene taxon:10090 20070316 MGI relationship(CL:0000002) MGI MGI:1861437 Gsk3b GO:0016055 MGI:MGI:3640889|PMID:16815997 IGI MGI:108559 P glycogen synthase kinase 3 beta GSK-3|GSK-3beta|GSK3 gene taxon:10090 20060921 MGI relationship(CL:0000001) MGI MGI:95865 Gstp1 GO:0004364 MGI:MGI:69635|PMID:7982937 IDA F glutathione S-transferase, pi 1 Gst p-1|GstpiB gene taxon:10090 20050325 MGI relationship(CL:0000002) MGI MGI:95865 Gstp1 GO:0006749 MGI:MGI:69635|PMID:7982937 IDA P glutathione S-transferase, pi 1 Gst p-1|GstpiB gene taxon:10090 20050325 MGI relationship(CL:0000002) MGI MGI:95864 Gstp2 GO:0004364 MGI:MGI:69635|PMID:7982937 IDA F glutathione S-transferase, pi 2 Gst p-2|Gst-3|Gst3|GSTpiA gene taxon:10090 20050325 MGI relationship(CL:0000002) MGI MGI:95864 Gstp2 GO:0006749 MGI:MGI:69635|PMID:7982937 IDA P glutathione S-transferase, pi 2 Gst p-2|Gst-3|Gst3|GSTpiA gene taxon:10090 20050325 MGI relationship(CL:0000002) MGI MGI:96010 Hal GO:0005625 MGI:MGI:52899|PMID:8486363 IDA C histidine ammonia lyase histidase|Hsd gene taxon:10090 20070308 MGI relationship(CL:0000002) MGI MGI:103577 Hand1 GO:0007507 MGI:MGI:3513216|PMID:15576406 IGI MGI:103580 P heart and neural crest derivatives expressed transcript 1 eHAND|Ehand1|Hxt|Th1|Thing1 gene taxon:10090 20050120 MGI relationship(CL:0000193) MGI MGI:103580 Hand2 GO:0007507 MGI:MGI:3513216|PMID:15576406 IGI MGI:103577 P heart and neural crest derivatives expressed transcript 2 dHAND|Ehand2|Hed|Thing2 gene taxon:10090 20050120 MGI relationship(CL:0000193) MGI MGI:103580 Hand2 GO:0045944 MGI:MGI:3607868|PMID:12392994 IDA P heart and neural crest derivatives expressed transcript 2 dHAND|Ehand2|Hed|Thing2 gene taxon:10090 20060119 MGI relationship(CL:0000002) MGI MGI:103580 Hand2 GO:0045944 MGI:MGI:3607868|PMID:12392994 IGI MGI:97350 P heart and neural crest derivatives expressed transcript 2 dHAND|Ehand2|Hed|Thing2 gene taxon:10090 20060119 MGI relationship(CL:0000002) MGI MGI:1202306 Hcrt GO:0048471 MGI:MGI:2156321|PMID:11748295 IDA C hypocretin orexin gene taxon:10090 20061116 MGI relationship(CL:0000163) MGI MGI:108086 Hdac1 GO:0000792 MGI:MGI:2682503|PMID:14643676 IDA C histone deacetylase 1 HD1|RPD3 gene taxon:10090 20060724 MGI relationship(CL:0000007) MGI MGI:108086 Hdac1 GO:0000792 MGI:MGI:2682503|PMID:14643676 IDA C histone deacetylase 1 HD1|RPD3 gene taxon:10090 20060724 MGI relationship(CL:1000274) MGI MGI:108086 Hdac1 GO:0007492 MGI:MGI:3041938|PMID:15060137 IDA P histone deacetylase 1 HD1|RPD3 gene taxon:10090 20040630 MGI relationship(CL:0000131) MGI MGI:108086 Hdac1 GO:0007492 MGI:MGI:3041938|PMID:15060137 IMP P histone deacetylase 1 HD1|RPD3 gene taxon:10090 20040630 MGI relationship(CL:0000131) MGI MGI:1097691 Hdac2 GO:0000792 MGI:MGI:2682503|PMID:14643676 IDA C histone deacetylase 2 D10Wsu179e|mRPD3|YAF1|Yy1bp gene taxon:10090 20060724 MGI relationship(CL:0000007) MGI MGI:1097691 Hdac2 GO:0000792 MGI:MGI:2682503|PMID:14643676 IDA C histone deacetylase 2 D10Wsu179e|mRPD3|YAF1|Yy1bp gene taxon:10090 20060724 MGI relationship(CL:1000274) MGI MGI:3036234 Hdac4 GO:0001501 MGI:MGI:3513625|PMID:15537544 IMP MGI:3525071 P histone deacetylase 4 gene taxon:10090 20050315 MGI relationship(CL:0000138) MGI MGI:1194494 Hdgf GO:0005615 MGI:MGI:3046368|PMID:15140875 IDA C hepatoma-derived growth factor D3Ertd299e gene taxon:10090 20040818 MGI relationship(CL:0000117) MGI MGI:1194494 Hdgf GO:0005634 MGI:MGI:3028819|PMID:14572309 IDA C hepatoma-derived growth factor D3Ertd299e gene taxon:10090 20060726 MGI relationship(CL:0000117) MGI MGI:1194494 Hdgf GO:0009987 MGI:MGI:3046368|PMID:15140875 IDA P hepatoma-derived growth factor D3Ertd299e gene taxon:10090 20060726 MGI relationship(CL:0000117) MGI MGI:96067 Hdh GO:0016234 MGI:MGI:3522382|PMID:15615787 IDA C Huntington disease gene homolog HD|htt|huntingtin|IT15 gene taxon:10090 20050512 MGI relationship(CL:0000002) MGI MGI:96067 Hdh GO:0048341 MGI:MGI:3609520|PMID:16109169 IMP MGI:1857180 P Huntington disease gene homolog HD|htt|huntingtin|IT15 gene taxon:10090 20060221 MGI relationship(CL:0000222) MGI MGI:104853 Hes1 GO:0005634 MGI:MGI:3528104|PMID:15645444 IDA C hairy and enhancer of split 1 (Drosophila) Hry gene taxon:10090 20050308 MGI relationship(CL:0000499) MGI MGI:104853 Hes1 GO:0007155 MGI:MGI:3512697|PMID:15496443 IGI MGI:104876 P hairy and enhancer of split 1 (Drosophila) Hry gene taxon:10090 20050121 MGI relationship(CL:0000681) MGI MGI:104853 Hes1 GO:0008284 MGI:MGI:3588911|PMID:16038893 IMP MGI:2149672 P hairy and enhancer of split 1 (Drosophila) Hry gene taxon:10090 20051031 MGI relationship(CL:0000306) MGI MGI:104853 Hes1 GO:0030324 MGI:MGI:1888698|PMID:10952889 IMP MGI:2149672 P hairy and enhancer of split 1 (Drosophila) Hry gene taxon:10090 20061116 MGI relationship(CL:0000158) MGI MGI:104853 Hes1 GO:0030324 MGI:MGI:1888698|PMID:10952889 IMP MGI:2149672 P hairy and enhancer of split 1 (Drosophila) Hry gene taxon:10090 20061116 MGI relationship(CL:0000165) MGI MGI:104853 Hes1 GO:0045165 MGI:MGI:1888698|PMID:10952889 IMP MGI:2149672 P hairy and enhancer of split 1 (Drosophila) Hry gene taxon:10090 20061116 MGI relationship(CL:0000158) MGI MGI:104853 Hes1 GO:0045596 MGI:MGI:1888698|PMID:10952889 IMP MGI:2149672 P hairy and enhancer of split 1 (Drosophila) Hry gene taxon:10090 20061116 MGI relationship(CL:0000165) MGI MGI:104853 Hes1 GO:0045665 MGI:MGI:3512697|PMID:15496443 IGI MGI:104876 P hairy and enhancer of split 1 (Drosophila) Hry gene taxon:10090 20050121 MGI relationship(CL:0000117) MGI MGI:104853 Hes1 GO:0045665 MGI:MGI:3588911|PMID:16038893 IMP MGI:2149672 P hairy and enhancer of split 1 (Drosophila) Hry gene taxon:10090 20060209 MGI relationship(CL:0000561) MGI MGI:104853 Hes1 GO:0045665 MGI:MGI:3588911|PMID:16038893 IMP MGI:2149672 P hairy and enhancer of split 1 (Drosophila) Hry gene taxon:10090 20060209 MGI relationship(CL:0000745) MGI MGI:104853 Hes1 GO:0048469 MGI:MGI:3512697|PMID:15496443 IGI MGI:104876 P hairy and enhancer of split 1 (Drosophila) Hry gene taxon:10090 20050121 MGI relationship(CL:0000681) MGI MGI:104876 Hes5 GO:0007155 MGI:MGI:3512697|PMID:15496443 IGI MGI:104853 P hairy and enhancer of split 5 (Drosophila) gene taxon:10090 20050121 MGI relationship(CL:0000681) MGI MGI:104876 Hes5 GO:0045665 MGI:MGI:3512697|PMID:15496443 IGI MGI:104853 P hairy and enhancer of split 5 (Drosophila) gene taxon:10090 20050121 MGI relationship(CL:0000117) MGI MGI:104876 Hes5 GO:0048469 MGI:MGI:3512697|PMID:15496443 IGI MGI:104853 P hairy and enhancer of split 5 (Drosophila) gene taxon:10090 20050121 MGI relationship(CL:0000681) MGI MGI:96073 Hexa GO:0005764 MGI:MGI:3033879|PMID:11854359 IDA C hexosaminidase A Hex-1 gene taxon:10090 20050712 MGI relationship(CL:0000236) MGI MGI:96073 Hexa GO:0007040 MGI:MGI:1097747|PMID:9302266 IMP MGI:2429698 P hexosaminidase A Hex-1 gene taxon:10090 20050712 MGI relationship(CL:0000117) MGI MGI:96073 Hexa GO:0007040 MGI:MGI:1352198|PMID:10591619 IMP MGI:2429698 P hexosaminidase A Hex-1 gene taxon:10090 20050712 MGI relationship(CL:0000067) MGI MGI:96073 Hexa GO:0007040 MGI:MGI:3033296|PMID:14972652 IMP MGI:2429698 P hexosaminidase A Hex-1 gene taxon:10090 20050714 MGI relationship(CL:0000117) MGI MGI:96073 Hexa GO:0007040 MGI:MGI:69059|PMID:7937929 IMP MGI:1857181 P hexosaminidase A Hex-1 gene taxon:10090 20050719 MGI relationship(CL:0000117) MGI MGI:96073 Hexa GO:0007040 MGI:MGI:83770|PMID:8896570 IGI MGI:96074 P hexosaminidase A Hex-1 gene taxon:10090 20050719 MGI relationship(CL:0000540) MGI MGI:96073 Hexa GO:0007040 MGI:MGI:894634|PMID:9184660 IGI MGI:96074 P hexosaminidase A Hex-1 gene taxon:10090 20050719 MGI relationship(CL:0000066) MGI MGI:96073 Hexa GO:0007040 MGI:MGI:894634|PMID:9184660 IGI MGI:96074 P hexosaminidase A Hex-1 gene taxon:10090 20050719 MGI relationship(CL:0000111) MGI MGI:96073 Hexa GO:0007040 MGI:MGI:894634|PMID:9184660 IGI MGI:96074 P hexosaminidase A Hex-1 gene taxon:10090 20050719 MGI relationship(CL:0000117) MGI MGI:96073 Hexa GO:0007040 MGI:MGI:894634|PMID:9184660 IGI MGI:96074 P hexosaminidase A Hex-1 gene taxon:10090 20050719 MGI relationship(CL:0000129) MGI MGI:96073 Hexa GO:0007040 MGI:MGI:894634|PMID:9184660 IGI MGI:96074 P hexosaminidase A Hex-1 gene taxon:10090 20050719 MGI relationship(CL:0000137) MGI MGI:96073 Hexa GO:0007040 MGI:MGI:894634|PMID:9184660 IGI MGI:96074 P hexosaminidase A Hex-1 gene taxon:10090 20050719 MGI relationship(CL:0000138) MGI MGI:96073 Hexa GO:0007040 MGI:MGI:894634|PMID:9184660 IGI MGI:96074 P hexosaminidase A Hex-1 gene taxon:10090 20050719 MGI relationship(CL:0000235) MGI MGI:96073 Hexa GO:0007040 MGI:MGI:894634|PMID:9184660 IGI MGI:96074 P hexosaminidase A Hex-1 gene taxon:10090 20050719 MGI relationship(CL:0000540) MGI MGI:96073 Hexa GO:0016020 MGI:MGI:3033879|PMID:11854359 IDA C hexosaminidase A Hex-1 gene taxon:10090 20050712 MGI relationship(CL:0000236) MGI MGI:96073 Hexa GO:0019915 MGI:MGI:3033296|PMID:14972652 IMP MGI:2429698 P hexosaminidase A Hex-1 gene taxon:10090 20050714 MGI relationship(CL:0000117) MGI MGI:96073 Hexa GO:0019915 MGI:MGI:894862|PMID:9223328 IMP MGI:1857181 P hexosaminidase A Hex-1 gene taxon:10090 20050602 MGI relationship(CL:0000598) MGI MGI:96074 Hexb GO:0005764 MGI:MGI:3033879|PMID:11854359 IDA C hexosaminidase B gene taxon:10090 20050607 MGI relationship(CL:0000002) MGI MGI:96074 Hexb GO:0006689 MGI:MGI:3041658|PMID:12657883 IMP MGI:1857438 P hexosaminidase B gene taxon:10090 20050609 MGI relationship(CL:0000117) MGI MGI:96074 Hexb GO:0006689 MGI:MGI:3573807|PMID:15748167 IMP MGI:1857438 P hexosaminidase B gene taxon:10090 20050610 MGI relationship(CL:0000117) MGI MGI:96074 Hexb GO:0006689 MGI:MGI:3573807|PMID:15748167 IMP MGI:1857438 P hexosaminidase B gene taxon:10090 20050610 MGI relationship(CL:0000120) MGI MGI:96074 Hexb GO:0006689 MGI:MGI:3573807|PMID:15748167 IMP MGI:1857438 P hexosaminidase B gene taxon:10090 20050610 MGI relationship(CL:0000243) MGI MGI:96074 Hexb GO:0006689 MGI:MGI:3573807|PMID:15748167 IMP MGI:1857438 P hexosaminidase B gene taxon:10090 20050610 MGI relationship(CL:0000598) MGI MGI:96074 Hexb GO:0006874 MGI:MGI:2670850|PMID:12756243 IGI MGI:88110 P hexosaminidase B gene taxon:10090 20050603 MGI relationship(CL:0000117) MGI MGI:96074 Hexb GO:0006874 MGI:MGI:2670850|PMID:12756243 IMP MGI:1857438 P hexosaminidase B gene taxon:10090 20050603 MGI relationship(CL:0000117) MGI MGI:96074 Hexb GO:0007040 MGI:MGI:78473|PMID:8789434 IMP MGI:2429701 P hexosaminidase B gene taxon:10090 20050714 MGI relationship(CL:0000066) MGI MGI:96074 Hexb GO:0007040 MGI:MGI:78473|PMID:8789434 IMP MGI:2429701 P hexosaminidase B gene taxon:10090 20050714 MGI relationship(CL:0000091) MGI MGI:96074 Hexb GO:0007040 MGI:MGI:78473|PMID:8789434 IMP MGI:2429701 P hexosaminidase B gene taxon:10090 20050714 MGI relationship(CL:0000115) MGI MGI:96074 Hexb GO:0007040 MGI:MGI:83770|PMID:8896570 IGI MGI:96073 P hexosaminidase B gene taxon:10090 20050719 MGI relationship(CL:0000540) MGI MGI:96074 Hexb GO:0007040 MGI:MGI:894634|PMID:9184660 IGI MGI:96073 P hexosaminidase B gene taxon:10090 20050719 MGI relationship(CL:0000066) MGI MGI:96074 Hexb GO:0007040 MGI:MGI:894634|PMID:9184660 IGI MGI:96073 P hexosaminidase B gene taxon:10090 20050719 MGI relationship(CL:0000111) MGI MGI:96074 Hexb GO:0007040 MGI:MGI:894634|PMID:9184660 IGI MGI:96073 P hexosaminidase B gene taxon:10090 20050719 MGI relationship(CL:0000117) MGI MGI:96074 Hexb GO:0007040 MGI:MGI:894634|PMID:9184660 IGI MGI:96073 P hexosaminidase B gene taxon:10090 20050719 MGI relationship(CL:0000129) MGI MGI:96074 Hexb GO:0007040 MGI:MGI:894634|PMID:9184660 IGI MGI:96073 P hexosaminidase B gene taxon:10090 20050719 MGI relationship(CL:0000137) MGI MGI:96074 Hexb GO:0007040 MGI:MGI:894634|PMID:9184660 IGI MGI:96073 P hexosaminidase B gene taxon:10090 20050719 MGI relationship(CL:0000138) MGI MGI:96074 Hexb GO:0007040 MGI:MGI:894634|PMID:9184660 IGI MGI:96073 P hexosaminidase B gene taxon:10090 20050719 MGI relationship(CL:0000235) MGI MGI:96074 Hexb GO:0007040 MGI:MGI:894634|PMID:9184660 IGI MGI:96073 P hexosaminidase B gene taxon:10090 20050719 MGI relationship(CL:0000540) MGI MGI:96074 Hexb GO:0008654 MGI:MGI:3047051|PMID:15198669 IMP MGI:1857438 P hexosaminidase B gene taxon:10090 20050603 MGI relationship(CL:0000117) MGI MGI:96074 Hexb GO:0009313 MGI:MGI:1331265|PMID:10021458 IMP MGI:1857438 P hexosaminidase B gene taxon:10090 20050603 MGI relationship(CL:0000117) MGI MGI:96074 Hexb GO:0009313 MGI:MGI:1331265|PMID:10021458 IMP MGI:1857438 P hexosaminidase B gene taxon:10090 20050603 MGI relationship(CL:0000121) MGI MGI:96074 Hexb GO:0009313 MGI:MGI:3573807|PMID:15748167 IMP MGI:1857438 P hexosaminidase B gene taxon:10090 20050711 MGI relationship(CL:0000243) MGI MGI:96074 Hexb GO:0016020 MGI:MGI:3033879|PMID:11854359 IDA C hexosaminidase B gene taxon:10090 20050607 MGI relationship(CL:0000002) MGI MGI:96074 Hexb GO:0019915 MGI:MGI:76799|PMID:7550345 IMP MGI:1857438 P hexosaminidase B gene taxon:10090 20050712 MGI relationship(CL:0000117) MGI MGI:96074 Hexb GO:0019915 MGI:MGI:76799|PMID:7550345 IMP MGI:1857438 P hexosaminidase B gene taxon:10090 20050712 MGI relationship(CL:0000540) MGI MGI:96074 Hexb GO:0019915 MGI:MGI:78473|PMID:8789434 IMP MGI:2429701 P hexosaminidase B gene taxon:10090 20050714 MGI relationship(CL:0000540) MGI MGI:96074 Hexb GO:0019915 MGI:MGI:894862|PMID:9223328 IMP MGI:1857438 P hexosaminidase B gene taxon:10090 20050712 MGI relationship(CL:0000117) MGI MGI:96074 Hexb GO:0019915 MGI:MGI:894862|PMID:9223328 IMP MGI:1857438 P hexosaminidase B gene taxon:10090 20050712 MGI relationship(CL:0000121) MGI MGI:96074 Hexb GO:0031323 MGI:MGI:3047051|PMID:15198669 IMP MGI:1857438 P hexosaminidase B gene taxon:10090 20050603 MGI relationship(CL:0000117) MGI MGI:96074 Hexb GO:0044267 MGI:MGI:3041658|PMID:12657883 IMP MGI:1857438 P hexosaminidase B gene taxon:10090 20050609 MGI relationship(CL:0000117) MGI MGI:1341800 Hey1 GO:0001570 MGI:MGI:3040159|PMID:15107403 IGI MGI:1341884 P hairy/enhancer-of-split related with YRPW motif 1 Hairy/E(spl)-related with YRPW motif 1|Herp2|hesr-1|HRT1 gene taxon:10090 20040601 MGI relationship(CL:0000071) MGI MGI:1341884 Hey2 GO:0001570 MGI:MGI:3040159|PMID:15107403 IGI MGI:1341800 P hairy/enhancer-of-split related with YRPW motif 2 CHF1|Hairy-E(spl)-related with YRPW motif 2|Herp1|Hesr2|Hrt2 gene taxon:10090 20040601 MGI relationship(CL:0000071) MGI MGI:96079 Hgf GO:0051450 MGI:MGI:3618663|PMID:11061428 IDA P hepatocyte growth factor HGF/SF|NK1|NK2|scatter factor|SF/HGF gene taxon:10090 20060606 MGI relationship(CL:0000001) MGI MGI:96079 Hgf GO:0051450 MGI:MGI:3618663|PMID:11061428 IDA P hepatocyte growth factor HGF/SF|NK1|NK2|scatter factor|SF/HGF gene taxon:10090 20060606 MGI relationship(CL:0000002) MGI MGI:96086 Hhex GO:0042127 MGI:MGI:3027468|PMID:14736744 IMP MGI:2177762 P hematopoietically expressed homeobox Hex|Prhx gene taxon:10090 20041006 MGI relationship(CL:0000223) MGI MGI:1341847 Hhip GO:0007405 MGI:MGI:3511726|PMID:15576403 IGI MGI:105373 P Hedgehog-interacting protein Hhip1|Hip|Hip1 gene taxon:10090 20050110 MGI relationship(CL:0000031) MGI MGI:1341847 Hhip GO:0009953 MGI:MGI:3511726|PMID:15576403 IGI MGI:105373 P Hedgehog-interacting protein Hhip1|Hip|Hip1 gene taxon:10090 20050110 MGI relationship(CL:0000117) MGI MGI:1341847 Hhip GO:0009986 MGI:MGI:3511726|PMID:15576403 IDA C Hedgehog-interacting protein Hhip1|Hip|Hip1 gene taxon:10090 20050110 MGI relationship(CL:0000002) MGI MGI:106918 Hif1a GO:0005634 MGI:MGI:2153426|PMID:11691837 IDA C hypoxia inducible factor 1, alpha subunit HIF-1alpha|MOP1 gene taxon:10090 20070131 MGI relationship(CL:0000138) MGI MGI:1314873 Hipk1 GO:0007224 MGI:MGI:3619785|PMID:16537918 IGI MGI:1314872 P homeodomain interacting protein kinase 1 Myak gene taxon:10090 20060512 MGI relationship(CL:0000001) MGI MGI:1314873 Hipk1 GO:0008284 MGI:MGI:3619785|PMID:16537918 IGI MGI:1314872 P homeodomain interacting protein kinase 1 Myak gene taxon:10090 20060512 MGI relationship(CL:0000133) MGI MGI:1314873 Hipk1 GO:0008284 MGI:MGI:3619785|PMID:16537918 IGI MGI:1314872 P homeodomain interacting protein kinase 1 Myak gene taxon:10090 20060512 MGI relationship(CL:0000222) MGI MGI:1314872 Hipk2 GO:0007224 MGI:MGI:3619785|PMID:16537918 IGI MGI:1314872 P homeodomain interacting protein kinase 2 Stank gene taxon:10090 20060512 MGI relationship(CL:0000001) MGI MGI:1314872 Hipk2 GO:0008284 MGI:MGI:3619785|PMID:16537918 IGI MGI:1314872 P homeodomain interacting protein kinase 2 Stank gene taxon:10090 20060512 MGI relationship(CL:0000133) MGI MGI:1314872 Hipk2 GO:0008284 MGI:MGI:3619785|PMID:16537918 IGI MGI:1314872 P homeodomain interacting protein kinase 2 Stank gene taxon:10090 20060512 MGI relationship(CL:0000222) MGI MGI:96113 Hmgb1 GO:0005615 MGI:MGI:3046368|PMID:15140875 IDA C high mobility group box 1 Hmg1 gene taxon:10090 20040818 MGI relationship(CL:0000117) MGI MGI:1098219 Hmgb3 GO:0005634 MGI:MGI:2670545|PMID:12714519 IDA C high mobility group box 3 Hmg2a|Hmg4 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:109128 Hnf4a GO:0005634 MGI:MGI:3575862|PMID:15767668 IDA C hepatic nuclear factor 4, alpha HNF-4|Hnf4|HNF4 alpha|MODY1|Nr2a1|Nuclear receptor 2A1|Tcf14|Tcf4 gene taxon:10090 20050519 MGI relationship(CL:0000223) MGI MGI:109128 Hnf4a GO:0005634 MGI:MGI:3619787|PMID:16537911 IDA C hepatic nuclear factor 4, alpha HNF-4|Hnf4|HNF4 alpha|MODY1|Nr2a1|Nuclear receptor 2A1|Tcf14|Tcf4 gene taxon:10090 20060512 MGI relationship(CL:0000182) MGI MGI:104820 Hnrpa1 GO:0005634 MGI:MGI:3522382|PMID:15615787 IDA C heterogeneous nuclear ribonucleoprotein A1 D15Ertd119e|Hdp|hnrnp-A gene taxon:10090 20050512 MGI relationship(CL:0000002) MGI MGI:1916782 Hod GO:0005634 MGI:MGI:2387286|PMID:12297045 IDA C homeobox only domain Cameo|Hop|Ob1|Toto gene taxon:10090 20050720 MGI relationship(CL:0000002) MGI MGI:1916782 Hod GO:0007507 MGI:MGI:2387285|PMID:12297046 IMP MGI:2389233 P homeobox only domain Cameo|Hop|Ob1|Toto gene taxon:10090 20050720 MGI relationship(CL:0000193) MGI MGI:1925213 Hook1 GO:0007286 MGI:MGI:2180892|PMID:12075009 IMP MGI:1856652 P hook homolog 1 (Drosophila) abnormal spermatozoon head shape|azh gene taxon:10090 20050720 MGI relationship(CL:0000019) MGI MGI:96170 Hoxa1 GO:0007399 MGI:MGI:3055618|PMID:15367676 IMP MGI:3056069 P homeo box A1 early retinoic acid|ERA1|Hox-1.6 gene taxon:10090 20041108 MGI relationship(CL:0000117) MGI MGI:96173 Hoxa13 GO:0005634 MGI:MGI:3527920|PMID:15617687 IDA C homeo box A13 Hox-1.10 gene taxon:10090 20050412 MGI relationship(CL:0000134) MGI MGI:96175 Hoxa3 GO:0008284 MGI:MGI:3613407|PMID:15714286 IMP MGI:1857992 P homeo box A3 Hox-1.5|Mo-10 gene taxon:10090 20060307 MGI relationship(CL:0000134) MGI MGI:96175 Hoxa3 GO:0030878 MGI:MGI:1197395|PMID:9524238 IGI MGI:96207,MGI:96184 P homeo box A3 Hox-1.5|Mo-10 gene taxon:10090 20061116 MGI relationship(CL:0000570) MGI MGI:96175 Hoxa3 GO:0030878 MGI:MGI:1201272|PMID:9520319 IMP MGI:1857992 P homeo box A3 Hox-1.5|Mo-10 gene taxon:10090 20061116 MGI relationship(CL:0000570) MGI MGI:96180 Hoxa9 GO:0005634 MGI:MGI:3032461|PMID:15161102 IDA C homeo box A9 D6a9|Hox-1.7 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96180 Hoxa9 GO:0005737 MGI:MGI:3032461|PMID:15161102 IDA C homeo box A9 D6a9|Hox-1.7 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96184 Hoxb3 GO:0030878 MGI:MGI:1201272|PMID:9520319 IGI MGI:96175 P homeo box B3 Hox-2.7 gene taxon:10090 20061116 MGI relationship(CL:0000570) MGI MGI:96198 Hoxc8 GO:0030182 MGI:MGI:3574740|PMID:15753214 IMP MGI:3574938 P homeo box C8 Hox-3.1 gene taxon:10090 20050509 MGI relationship(CL:0000100) MGI MGI:96205 Hoxd13 GO:0005634 MGI:MGI:3527920|PMID:15617687 IDA C homeo box D13 Hox-4.8|spdh gene taxon:10090 20050412 MGI relationship(CL:0000134) MGI MGI:96207 Hoxd3 GO:0030878 MGI:MGI:1201272|PMID:9520319 IGI MGI:96175 P homeo box D3 Hox-4.1|Hox-5.5 gene taxon:10090 20061116 MGI relationship(CL:0000570) MGI MGI:96212 hpc GO:0000904 MGI:MGI:55518|PMID:6841964 IMP MGI:1856902 P hyperspiny Purkinje cell gene taxon:10090 20051003 MGI relationship(CL:0000121) MGI MGI:96217 Hprt1 GO:0004422 MGI:MGI:1331314|PMID:10037486 IMP MGI:1857299 F hypoxanthine guanine phosphoribosyl transferase 1 HPGRT gene taxon:10090 20060823 MGI relationship(CL:0000001) MGI MGI:96217 Hprt1 GO:0005737 MGI:MGI:65752|PMID:8193672 IDA C hypoxanthine guanine phosphoribosyl transferase 1 HPGRT gene taxon:10090 20060824 MGI relationship(CL:0000121) MGI MGI:96217 Hprt1 GO:0005737 MGI:MGI:65752|PMID:8193672 IDA C hypoxanthine guanine phosphoribosyl transferase 1 HPGRT gene taxon:10090 20060824 MGI relationship(CL:0000598) MGI MGI:96217 Hprt1 GO:0006166 MGI:MGI:1331314|PMID:10037486 IMP MGI:1857299 P hypoxanthine guanine phosphoribosyl transferase 1 HPGRT gene taxon:10090 20060823 MGI relationship(CL:0000001) MGI MGI:96217 Hprt1 GO:0006168 MGI:MGI:1331314|PMID:10037486 IMP MGI:1857299 P hypoxanthine guanine phosphoribosyl transferase 1 HPGRT gene taxon:10090 20060823 MGI relationship(CL:0000001) MGI MGI:96217 Hprt1 GO:0006178 MGI:MGI:1331314|PMID:10037486 IMP MGI:1857299 P hypoxanthine guanine phosphoribosyl transferase 1 HPGRT gene taxon:10090 20060823 MGI relationship(CL:0000001) MGI MGI:96217 Hprt1 GO:0021756 MGI:MGI:1321418|PMID:9886073 IMP MGI:1857299 P hypoxanthine guanine phosphoribosyl transferase 1 HPGRT gene taxon:10090 20060823 MGI relationship(CL:0000700) MGI MGI:96217 Hprt1 GO:0021895 MGI:MGI:3622601|PMID:11297820 IMP MGI:1857299 P hypoxanthine guanine phosphoribosyl transferase 1 HPGRT gene taxon:10090 20060823 MGI relationship(CL:0000001) MGI MGI:96217 Hprt1 GO:0021954 MGI:MGI:1321418|PMID:9886073 IMP MGI:1857299 P hypoxanthine guanine phosphoribosyl transferase 1 HPGRT gene taxon:10090 20060823 MGI relationship(CL:0000700) MGI MGI:96217 Hprt1 GO:0042417 MGI:MGI:1321418|PMID:9886073 IMP MGI:1857299 P hypoxanthine guanine phosphoribosyl transferase 1 HPGRT gene taxon:10090 20060823 MGI relationship(CL:0000700) MGI MGI:96217 Hprt1 GO:0046100 MGI:MGI:1331314|PMID:10037486 IMP MGI:1857299 P hypoxanthine guanine phosphoribosyl transferase 1 HPGRT gene taxon:10090 20060823 MGI relationship(CL:0000001) MGI MGI:96217 Hprt1 GO:0048813 MGI:MGI:3622601|PMID:11297820 IMP MGI:1857299 P hypoxanthine guanine phosphoribosyl transferase 1 HPGRT gene taxon:10090 20060823 MGI relationship(CL:0000001) MGI MGI:96224 Hras1 GO:0043524 MGI:MGI:1861510|PMID:10845775 IDA P Harvey rat sarcoma virus oncogene 1 c-H-ras|c-rasHa|H-ras|Ha-ras|Harvey-ras|Hras-1|ras gene taxon:10090 20070130 MGI relationship(CL:0000001) MGI MGI:96224 Hras1 GO:0043524 MGI:MGI:1861510|PMID:10845775 IGI MGI:97306|MGI:96680 P Harvey rat sarcoma virus oncogene 1 c-H-ras|c-rasHa|H-ras|Ha-ras|Harvey-ras|Hras-1|ras gene taxon:10090 20070130 MGI relationship(CL:0000001) MGI MGI:96224 Hras1 GO:0048169 MGI:MGI:3580530|PMID:12427827 IMP MGI:3580632 P Harvey rat sarcoma virus oncogene 1 c-H-ras|c-rasHa|H-ras|Ha-ras|Harvey-ras|Hras-1|ras gene taxon:10090 20060308 MGI relationship(CL:0000117) MGI MGI:96238 Hsf1 GO:0008285 MGI:MGI:3056833|PMID:15483628 IGI MGI:1347058 P heat shock factor 1 heat shock transcription factor 1 gene taxon:10090 20050216 MGI relationship(CL:0000066) MGI MGI:1347058 Hsf4 GO:0008284 MGI:MGI:3056833|PMID:15483628 IGI MGI:96238 P heat shock transcription factor 4 gene taxon:10090 20050216 MGI relationship(CL:0000066) MGI MGI:1347058 Hsf4 GO:0008284 MGI:MGI:3056833|PMID:15483628 IMP MGI:3057199 P heat shock transcription factor 4 gene taxon:10090 20050216 MGI relationship(CL:0000066) MGI MGI:1347058 Hsf4 GO:0045597 MGI:MGI:3056833|PMID:15483628 IMP MGI:3057199 P heat shock transcription factor 4 gene taxon:10090 20050216 MGI relationship(CL:0000306) MGI MGI:1347058 Hsf4 GO:0048468 MGI:MGI:3526483|PMID:15593327 IMP MGI:3527211 P heat shock transcription factor 4 gene taxon:10090 20060130 MGI relationship(CL:0000306) MGI MGI:98817 Hsp90b1 GO:0005783 MGI:MGI:3055460|PMID:10444069 IDA C heat shock protein 90kDa beta (Grp94), member 1 endoplasmin|ERp99|gp96|GRP94|Targ2|Tra-1|Tra1|tumor rejection antigen (gp96) 1 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:99517 Hspa1b GO:0005515 MGI:MGI:3513163|PMID:11527400 IPI UniProt:Q8CI61,UniProt:Q9JLV1 F heat shock protein 1B hsp68|Hsp70|Hsp70-1|Hsp70.1|HSP70A1 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1928676 Htra2 GO:0007005 MGI:MGI:3511734|PMID:15574596 IMP MGI:3512633 P HtrA serine peptidase 2 HtrA2|mnd2|OMI|Prss25 gene taxon:10090 20051208 MGI relationship(CL:0000001) MGI MGI:1928676 Htra2 GO:0008629 MGI:MGI:3511636|PMID:15509788 IMP MGI:3512633 P HtrA serine peptidase 2 HtrA2|mnd2|OMI|Prss25 gene taxon:10090 20051208 MGI relationship(CL:0000001) MGI MGI:1928676 Htra2 GO:0030900 MGI:MGI:3511636|PMID:15509788 IMP MGI:3512633 P HtrA serine peptidase 2 HtrA2|mnd2|OMI|Prss25 gene taxon:10090 20051208 MGI relationship(CL:0000117) MGI MGI:1928676 Htra2 GO:0048666 MGI:MGI:60999|PMID:8325640 IMP MGI:1856960 P HtrA serine peptidase 2 HtrA2|mnd2|OMI|Prss25 gene taxon:10090 20051208 MGI relationship(CL:0000100) MGI MGI:96382 Iapp GO:0043025 MGI:MGI:1316900|PMID:9838101 IDA C islet amyloid polypeptide amylin gene taxon:10090 20061116 MGI relationship(CL:0000101) MGI MGI:96382 Iapp GO:0045596 MGI:MGI:3037515|PMID:14970190 IGI MGI:1346858 P islet amyloid polypeptide amylin gene taxon:10090 20061114 MGI relationship(CL:0000001) MGI MGI:96382 Iapp GO:0045596 MGI:MGI:3037515|PMID:14970190 IMP MGI:2656235 P islet amyloid polypeptide amylin gene taxon:10090 20061114 MGI relationship(CL:0000001) MGI MGI:1354701 Icosl GO:0005515 MGI:MGI:1353163|PMID:10657606 IPI UniProt:Q9WVS0 F icos ligand B7-H2|B7h|B7RP-1|GL50|GL50-B|ICOS-L|LICOS gene taxon:10090 20070111 MGI relationship(CL:0000002) MGI MGI:1354701 Icosl GO:0005887 MGI:MGI:1353163|PMID:10657606 IDA C icos ligand B7-H2|B7h|B7RP-1|GL50|GL50-B|ICOS-L|LICOS gene taxon:10090 20070111 MGI relationship(CL:0000002) MGI MGI:1354701 Icosl GO:0009897 MGI:MGI:1353163|PMID:10657606 IDA C icos ligand B7-H2|B7h|B7RP-1|GL50|GL50-B|ICOS-L|LICOS gene taxon:10090 20070111 MGI relationship(CL:0000002) MGI MGI:96397 Id2 GO:0005634 MGI:MGI:3525032|PMID:15616565 IDA C inhibitor of DNA binding 2 C78922|Id2|Idb2|inhibitor of differentiation 2 gene taxon:10090 20070131 MGI relationship(CL:0000235) MGI MGI:96398 Id3 GO:0030855 MGI:MGI:3611666|PMID:16407553 IDA P inhibitor of DNA binding 3 HLH462|Id3|Idb3 gene taxon:10090 20060228 MGI relationship(CL:0000001) MGI MGI:99414 Id4 GO:0008284 MGI:MGI:3577784|PMID:15882580 IMP MGI:3579084 P inhibitor of DNA binding 4 Id4|Idb4 gene taxon:10090 20060214 MGI relationship(CL:0000001) MGI MGI:99414 Id4 GO:0043350 MGI:MGI:3577784|PMID:15882580 IMP MGI:3579084 P inhibitor of DNA binding 4 Id4|Idb4 gene taxon:10090 20060214 MGI relationship(CL:0000031) MGI MGI:99414 Id4 GO:0045665 MGI:MGI:3577784|PMID:15882580 IMP MGI:3579084 P inhibitor of DNA binding 4 Id4|Idb4 gene taxon:10090 20060214 MGI relationship(CL:0000117) MGI MGI:99414 Id4 GO:0048712 MGI:MGI:3577784|PMID:15882580 IGI MGI:88177 P inhibitor of DNA binding 4 Id4|Idb4 gene taxon:10090 20060214 MGI relationship(CL:0000001) MGI MGI:96429 Ifi204 GO:0045669 MGI:MGI:3530710|PMID:15557274 IGI MGI:88177 P interferon activated gene 204 p204 gene taxon:10090 20050505 MGI relationship(CL:0000002) MGI MGI:96432 Igf1 GO:0021940 MGI:MGI:1329746|PMID:10027293 IDA P insulin-like growth factor 1 Igf-1|Igf-I gene taxon:10090 20061218 MGI relationship(CL:0000001) MGI MGI:96432 Igf1 GO:0048468 MGI:MGI:3624910|PMID:10465256 IMP MGI:1857466 P insulin-like growth factor 1 Igf-1|Igf-I gene taxon:10090 20060717 MGI relationship(CL:0000439) MGI MGI:96432 Igf1 GO:0048468 MGI:MGI:3624910|PMID:10465256 IMP MGI:1857466 P insulin-like growth factor 1 Igf-1|Igf-I gene taxon:10090 20060717 MGI relationship(CL:0000471) MGI MGI:96447 Igh-5 GO:0009897 MGI:MGI:77314|PMID:7477352 IDA C immunoglobulin heavy chain 5 (delta-like heavy chain) IgD gene taxon:10090 20060726 MGI relationship(CL:0000236) MGI MGI:96447 Igh-5 GO:0019815 MGI:MGI:77314|PMID:7477352 IDA C immunoglobulin heavy chain 5 (delta-like heavy chain) IgD gene taxon:10090 20060726 MGI relationship(CL:0000236) MGI MGI:96448 Igh-6 GO:0000187 MGI:MGI:79455|PMID:8626447 IDA P immunoglobulin heavy chain 6 (heavy chain of IgM) Ig mu|Igh-M|Igh6|IgM|muH gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96448 Igh-6 GO:0004888 MGI:MGI:3521842|PMID:1373499 IDA F immunoglobulin heavy chain 6 (heavy chain of IgM) Ig mu|Igh-M|Igh6|IgM|muH gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96448 Igh-6 GO:0005515 MGI:MGI:3521842|PMID:1373499 IPI UniProt:P01843 F immunoglobulin heavy chain 6 (heavy chain of IgM) Ig mu|Igh-M|Igh6|IgM|muH gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96448 Igh-6 GO:0009897 MGI:MGI:3521842|PMID:1373499 IDA C immunoglobulin heavy chain 6 (heavy chain of IgM) Ig mu|Igh-M|Igh6|IgM|muH gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96448 Igh-6 GO:0009897 MGI:MGI:77314|PMID:7477352 IDA C immunoglobulin heavy chain 6 (heavy chain of IgM) Ig mu|Igh-M|Igh6|IgM|muH gene taxon:10090 20060726 MGI relationship(CL:0000236) MGI MGI:96448 Igh-6 GO:0009897 MGI:MGI:77315|PMID:7477353 IDA C immunoglobulin heavy chain 6 (heavy chain of IgM) Ig mu|Igh-M|Igh6|IgM|muH gene taxon:10090 20060726 MGI relationship(CL:0000236) MGI MGI:96448 Igh-6 GO:0009897 MGI:MGI:79455|PMID:8626447 IDA C immunoglobulin heavy chain 6 (heavy chain of IgM) Ig mu|Igh-M|Igh6|IgM|muH gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96448 Igh-6 GO:0019815 MGI:MGI:3521842|PMID:1373499 IDA C immunoglobulin heavy chain 6 (heavy chain of IgM) Ig mu|Igh-M|Igh6|IgM|muH gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96448 Igh-6 GO:0019815 MGI:MGI:77314|PMID:7477352 IDA C immunoglobulin heavy chain 6 (heavy chain of IgM) Ig mu|Igh-M|Igh6|IgM|muH gene taxon:10090 20060726 MGI relationship(CL:0000236) MGI MGI:96448 Igh-6 GO:0019815 MGI:MGI:79455|PMID:8626447 IDA C immunoglobulin heavy chain 6 (heavy chain of IgM) Ig mu|Igh-M|Igh6|IgM|muH gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96448 Igh-6 GO:0048471 MGI:MGI:3521842|PMID:1373499 IDA C immunoglobulin heavy chain 6 (heavy chain of IgM) Ig mu|Igh-M|Igh6|IgM|muH gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96448 Igh-6 GO:0050731 MGI:MGI:3521842|PMID:1373499 IDA P immunoglobulin heavy chain 6 (heavy chain of IgM) Ig mu|Igh-M|Igh6|IgM|muH gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96448 Igh-6 GO:0050731 MGI:MGI:79455|PMID:8626447 IDA P immunoglobulin heavy chain 6 (heavy chain of IgM) Ig mu|Igh-M|Igh6|IgM|muH gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96448 Igh-6 GO:0050853 MGI:MGI:3521842|PMID:1373499 IDA P immunoglobulin heavy chain 6 (heavy chain of IgM) Ig mu|Igh-M|Igh6|IgM|muH gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96448 Igh-6 GO:0050853 MGI:MGI:79455|PMID:8626447 IDA P immunoglobulin heavy chain 6 (heavy chain of IgM) Ig mu|Igh-M|Igh6|IgM|muH gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:99954 Ighmbp2 GO:0005634 MGI:MGI:3054621|PMID:15269181 IDA C immunoglobulin mu binding protein 2 AEP|Catf1|p110 subunit|RIPE3b1|sma|Smbp-2|Smbp2|Smubp2 gene taxon:10090 20041101 MGI relationship(CL:0000100) MGI MGI:99954 Ighmbp2 GO:0030424 MGI:MGI:3054621|PMID:15269181 IDA C immunoglobulin mu binding protein 2 AEP|Catf1|p110 subunit|RIPE3b1|sma|Smbp-2|Smbp2|Smubp2 gene taxon:10090 20041101 MGI relationship(CL:0000100) MGI MGI:99954 Ighmbp2 GO:0043025 MGI:MGI:3054621|PMID:15269181 IDA C immunoglobulin mu binding protein 2 AEP|Catf1|p110 subunit|RIPE3b1|sma|Smbp-2|Smbp2|Smubp2 gene taxon:10090 20041101 MGI relationship(CL:0000100) MGI MGI:99546 Igl-C1 GO:0005515 MGI:MGI:3521842|PMID:1373499 IPI UniProt:Q8VCX7 F immunoglobulin lambda chain, constant region 1 Clambda1 gene taxon:10090 20050120 MGI relationship(CL:0000002) MGI MGI:99546 Igl-C1 GO:0009897 MGI:MGI:3521842|PMID:1373499 IDA C immunoglobulin lambda chain, constant region 1 Clambda1 gene taxon:10090 20050120 MGI relationship(CL:0000002) MGI MGI:99546 Igl-C1 GO:0019815 MGI:MGI:3521842|PMID:1373499 IDA C immunoglobulin lambda chain, constant region 1 Clambda1 gene taxon:10090 20050120 MGI relationship(CL:0000002) MGI MGI:96533 Ihh GO:0001569 MGI:MGI:3574706|PMID:15689378 IMP MGI:1934258 P Indian hedgehog gene taxon:10090 20050513 MGI relationship(CL:0000001) MGI MGI:96533 Ihh GO:0008284 MGI:MGI:3608261|PMID:16284117 IMP MGI:1934258 P Indian hedgehog gene taxon:10090 20060131 MGI relationship(CL:0000744) MGI MGI:96533 Ihh GO:0030154 MGI:MGI:3583389|PMID:15951842 IDA P Indian hedgehog gene taxon:10090 20051202 MGI relationship(CL:0000744) MGI MGI:96533 Ihh GO:0045596 MGI:MGI:3608261|PMID:16284117 IMP MGI:1934258 P Indian hedgehog gene taxon:10090 20060131 MGI relationship(CL:0000743) MGI MGI:1342540 Ikzf1 GO:0005634 MGI:MGI:3617295|PMID:16467156 IDA C IKAROS family zinc finger 1 hlk-1|Ikaros|LyF-1|Zfpn1a1 gene taxon:10090 20060728 MGI relationship(CL:0000167) MGI MGI:1342540 Ikzf1 GO:0030900 MGI:MGI:3575374|PMID:15841184 IMP MGI:2158690 P IKAROS family zinc finger 1 hlk-1|Ikaros|LyF-1|Zfpn1a1 gene taxon:10090 20050512 MGI relationship(CL:0000640) MGI MGI:1342540 Ikzf1 GO:0030900 MGI:MGI:3617295|PMID:16467156 IMP MGI:2158690 P IKAROS family zinc finger 1 hlk-1|Ikaros|LyF-1|Zfpn1a1 gene taxon:10090 20060728 MGI relationship(CL:0000295) MGI MGI:1342540 Ikzf1 GO:0045944 MGI:MGI:3617295|PMID:16467156 IDA P IKAROS family zinc finger 1 hlk-1|Ikaros|LyF-1|Zfpn1a1 gene taxon:10090 20060728 MGI relationship(CL:0000002) MGI MGI:1342540 Ikzf1 GO:0048732 MGI:MGI:3617295|PMID:16467156 IMP MGI:2158690 P IKAROS family zinc finger 1 hlk-1|Ikaros|LyF-1|Zfpn1a1 gene taxon:10090 20060728 MGI relationship(CL:0000295) MGI MGI:107426 Il11ra1 GO:0001779 MGI:MGI:3505799|PMID:15499555 IMP MGI:2177774 P interleukin 11 receptor, alpha chain 1 Il11ra|NR1 gene taxon:10090 20041214 MGI relationship(CL:0000623) MGI MGI:96548 Il2 GO:0050672 MGI:MGI:3662823|PMID:16227984 IMP MGI:1857191 P interleukin 2 IL-2 gene taxon:10090 20070111 MGI relationship(CL:0000542) MGI MGI:96549 Il2ra GO:0009897 MGI:MGI:64265|PMID:8262055 IDA C interleukin 2 receptor, alpha chain CD25|IL-2R alpha chain|Il2r|Ly-43 gene taxon:10090 20050616 MGI relationship(CL:0000002) MGI MGI:96549 Il2ra GO:0009897 MGI:MGI:77314|PMID:7477352 IDA C interleukin 2 receptor, alpha chain CD25|IL-2R alpha chain|Il2r|Ly-43 gene taxon:10090 20050117 MGI relationship(CL:0000236) MGI MGI:96549 Il2ra GO:0050672 MGI:MGI:3662823|PMID:16227984 IMP MGI:1857192 P interleukin 2 receptor, alpha chain CD25|IL-2R alpha chain|Il2r|Ly-43 gene taxon:10090 20070111 MGI relationship(CL:0000542) MGI MGI:96550 Il2rb GO:0009897 MGI:MGI:64265|PMID:8262055 IDA C interleukin 2 receptor, beta chain CD122|IL-15 receptor beta chain|IL-15Rbeta|IL-2 receptor beta chain|IL-2/15Rbeta|Il-2Rbeta|IL15Rbeta|p70 gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:96551 Il2rg GO:0009897 MGI:MGI:64265|PMID:8262055 IDA C interleukin 2 receptor, gamma chain [g]c|CD132|common cytokine receptor gamma chain|common gamma chain|gamma C receptor|gamma(c) gene taxon:10090 20050616 MGI relationship(CL:0000002) MGI MGI:1339973 Ilf3 GO:0005634 MGI:MGI:1860344|PMID:10749851 ISS UniProt:Q12906 C interleukin enhancer binding factor 3 NF90 gene taxon:10090 20060111 MGI relationship(CL:0000002) MGI MGI:1195267 Ilk GO:0001658 MGI:MGI:3575981|PMID:15831470 IDA P integrin linked kinase ESTM24 gene taxon:10090 20050526 MGI relationship(CL:0000069) MGI MGI:96568 Ina GO:0005883 MGI:MGI:1336062|PMID:10221457 IDA C internexin neuronal intermediate filament protein, alpha NF-66 gene taxon:10090 20070226 MGI relationship(CL:0000029) MGI MGI:96568 Ina GO:0060052 MGI:MGI:1339419|PMID:10350642 IGI MGI:97313 P internexin neuronal intermediate filament protein, alpha NF-66 gene taxon:10090 20070302 MGI relationship(CL:0000540) MGI MGI:1277960 Inadl GO:0045177 MGI:MGI:3033551|PMID:14758363 IDA C InaD-like (Drosophila) Cipp gene taxon:10090 20040421 MGI relationship(CL:0000066) MGI MGI:1859980 Insm1 GO:0030154 MGI:MGI:3619850|PMID:16511571 IMP P insulinoma-associated 1 IA-1 gene taxon:10090 20060517 MGI relationship(CL:0000001) MGI MGI:1859980 Insm1 GO:0031018 MGI:MGI:3619850|PMID:16511571 IMP P insulinoma-associated 1 IA-1 gene taxon:10090 20060517 MGI relationship(CL:0000001) MGI MGI:96575 Insr GO:0005886 MGI:MGI:3042070|PMID:14562105 IDA C insulin receptor CD220|IR gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1916968 Ipmk GO:0046853 MGI:MGI:3583505|PMID:15939867 IMP MGI:3583918 P inositol polyphosphate multikinase gene taxon:10090 20060303 MGI relationship(CL:0000001) MGI MGI:1916968 Ipmk GO:0050516 MGI:MGI:3583505|PMID:15939867 IMP MGI:3583918 F inositol polyphosphate multikinase gene taxon:10090 20060303 MGI relationship(CL:0000001) MGI MGI:101791 Isl1 GO:0005634 MGI:MGI:2686820|PMID:14702043 IDA C ISL1 transcription factor, LIM/homeodomain Islet 1 gene taxon:10090 20041006 MGI relationship(CL:0000169) MGI MGI:96601 Itga2b GO:0005925 MGI:MGI:3051967|PMID:15031111 IDA C integrin alpha 2b alphaIIb|CD41|GP IIb|GpIIb|platelet glycoprotein IIb gene taxon:10090 20040928 MGI relationship(CL:0000351) MGI MGI:96601 Itga2b GO:0007160 MGI:MGI:3051967|PMID:15031111 IMP P integrin alpha 2b alphaIIb|CD41|GP IIb|GpIIb|platelet glycoprotein IIb gene taxon:10090 20040928 MGI relationship(CL:0000351) MGI MGI:96602 Itga3 GO:0001764 MGI:MGI:3042322|PMID:15091337 IMP P integrin alpha 3 alpha3-integrin|VLA-3 alpha 3 gene taxon:10090 20050720 MGI relationship(CL:0000117) MGI MGI:96602 Itga3 GO:0016323 MGI:MGI:2159597|PMID:11891657 IDA C integrin alpha 3 alpha3-integrin|VLA-3 alpha 3 gene taxon:10090 20060726 MGI relationship(CL:0000066) MGI MGI:96603 Itga4 GO:0016477 MGI:MGI:3624077|PMID:16529735 IMP MGI:1857206 P integrin alpha 4 VLA-4 receptor, alpha 4 subunit gene taxon:10090 20060627 MGI relationship(CL:0000001) MGI MGI:96603 Itga4 GO:0016477 MGI:MGI:3624077|PMID:16529735 IMP MGI:1857206 P integrin alpha 4 VLA-4 receptor, alpha 4 subunit gene taxon:10090 20060627 MGI relationship(CL:0000184) MGI MGI:96603 Itga4 GO:0016477 MGI:MGI:3624077|PMID:16529735 IMP MGI:1857206 P integrin alpha 4 VLA-4 receptor, alpha 4 subunit gene taxon:10090 20060627 MGI relationship(CL:0000359) MGI MGI:96605 Itga6 GO:0005886 MGI:MGI:2159597|PMID:11891657 IDA C integrin alpha 6 Cd49f gene taxon:10090 20060726 MGI relationship(CL:0000066) MGI MGI:96605 Itga6 GO:0007160 MGI:MGI:3623696|PMID:16365040 IMP P integrin alpha 6 Cd49f gene taxon:10090 20060706 MGI relationship(CL:0000001) MGI MGI:96605 Itga6 GO:0016323 MGI:MGI:2159597|PMID:11891657 IDA C integrin alpha 6 Cd49f gene taxon:10090 20060726 MGI relationship(CL:0000066) MGI MGI:96605 Itga6 GO:0042475 MGI:MGI:3623696|PMID:16365040 IMP P integrin alpha 6 Cd49f gene taxon:10090 20060706 MGI relationship(CL:0000001) MGI MGI:96605 Itga6 GO:0046847 MGI:MGI:3623696|PMID:16365040 IMP P integrin alpha 6 Cd49f gene taxon:10090 20060706 MGI relationship(CL:0000001) MGI MGI:96605 Itga6 GO:0050900 MGI:MGI:74269|PMID:7621877 IMP P integrin alpha 6 Cd49f gene taxon:10090 20060824 MGI relationship(CL:0000827) MGI MGI:102700 Itga7 GO:0048514 MGI:MGI:3587516|PMID:16003770 IMP MGI:3512077 P integrin alpha 7 [a]7|alpha7 gene taxon:10090 20051129 MGI relationship(CL:0000359) MGI MGI:96610 Itgb1 GO:0008284 MGI:MGI:3573843|PMID:15056720 IMP MGI:2156945 P integrin beta 1 (fibronectin receptor beta) beta1 integrin|CD29 gene taxon:10090 20050504 MGI relationship(CL:0000031) MGI MGI:96610 Itgb1 GO:0045214 MGI:MGI:84974|PMID:9004034 IMP MGI:2154539 P integrin beta 1 (fibronectin receptor beta) beta1 integrin|CD29 gene taxon:10090 20060926 MGI relationship(CL:0000513) MGI MGI:96610 Itgb1 GO:0045596 MGI:MGI:3573843|PMID:15056720 IMP MGI:2156945 P integrin beta 1 (fibronectin receptor beta) beta1 integrin|CD29 gene taxon:10090 20050504 MGI relationship(CL:0000120) MGI MGI:96612 Itgb3 GO:0030334 MGI:MGI:3051967|PMID:15031111 IMP P integrin beta 3 CD61|platelet glycoprotein IIIa (GP3A) gene taxon:10090 20040928 MGI relationship(CL:0000351) MGI MGI:96613 Itgb4 GO:0009925 MGI:MGI:2159597|PMID:11891657 IDA C integrin beta 4 CD104 gene taxon:10090 20060726 MGI relationship(CL:0000066) MGI MGI:96613 Itgb4 GO:0046847 MGI:MGI:3623696|PMID:16365040 IMP P integrin beta 4 CD104 gene taxon:10090 20060706 MGI relationship(CL:0000001) MGI MGI:1095416 Jag1 GO:0005886 MGI:MGI:3603078|PMID:16000382 IDA C jagged 1 Headturner|Htu|Ozz|Serrate-1 gene taxon:10090 20051117 MGI relationship(CL:0000002) MGI MGI:1095416 Jag1 GO:0005886 MGI:MGI:3621102|PMID:16495313 IDA C jagged 1 Headturner|Htu|Ozz|Serrate-1 gene taxon:10090 20060810 MGI relationship(CL:0000635) MGI MGI:1095416 Jag1 GO:0005886 MGI:MGI:3621102|PMID:16495313 IDA C jagged 1 Headturner|Htu|Ozz|Serrate-1 gene taxon:10090 20060810 MGI relationship(CL:1000191) MGI MGI:1095416 Jag1 GO:0042491 MGI:MGI:3621102|PMID:16495313 IMP MGI:3623344|MGI:1932522 P jagged 1 Headturner|Htu|Ozz|Serrate-1 gene taxon:10090 20060810 MGI relationship(CL:0000202) MGI MGI:1095416 Jag1 GO:0042491 MGI:MGI:3621102|PMID:16495313 IMP MGI:3623344|MGI:1932522 P jagged 1 Headturner|Htu|Ozz|Serrate-1 gene taxon:10090 20060810 MGI relationship(CL:0000601) MGI MGI:1095416 Jag1 GO:0045596 MGI:MGI:3529381|PMID:15064243 IMP P jagged 1 Headturner|Htu|Ozz|Serrate-1 gene taxon:10090 20050322 MGI relationship(CL:0000165) MGI MGI:1095416 Jag1 GO:0048839 MGI:MGI:3621102|PMID:16495313 IMP MGI:3623344|MGI:1932522 P jagged 1 Headturner|Htu|Ozz|Serrate-1 gene taxon:10090 20060810 MGI relationship(CL:0000066) MGI MGI:1095416 Jag1 GO:0048839 MGI:MGI:3621102|PMID:16495313 IMP MGI:3623344|MGI:1932522 P jagged 1 Headturner|Htu|Ozz|Serrate-1 gene taxon:10090 20060810 MGI relationship(CL:0000601) MGI MGI:1098270 Jag2 GO:0030155 MGI:MGI:3624929|PMID:16607638 IMP MGI:2657215 P jagged 2 D12Ggc2e|Serh gene taxon:10090 20060705 MGI relationship(CL:0000066) MGI MGI:1098270 Jag2 GO:0042981 MGI:MGI:3624929|PMID:16607638 IMP MGI:2657215 P jagged 2 D12Ggc2e|Serh gene taxon:10090 20060705 MGI relationship(CL:0000066) MGI MGI:96628 Jak1 GO:0004713 MGI:MGI:1859033|PMID:10872802 IDA F Janus kinase 1 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96628 Jak1 GO:0018108 MGI:MGI:1859033|PMID:10872802 IDA P Janus kinase 1 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96629 Jak2 GO:0004713 MGI:MGI:1859033|PMID:10872802 IDA F Janus kinase 2 C81284|Fd17 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96629 Jak2 GO:0005515 MGI:MGI:1859033|PMID:10872802 IPI UniProt:Q9JID9 F Janus kinase 2 C81284|Fd17 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96629 Jak2 GO:0018108 MGI:MGI:1859033|PMID:10872802 IDA P Janus kinase 2 C81284|Fd17 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:99928 Jak3 GO:0004713 MGI:MGI:1859033|PMID:10872802 IDA F Janus kinase 3 gene taxon:10090 20041115 MGI relationship(CL:0000002) MGI MGI:99928 Jak3 GO:0005515 MGI:MGI:1859033|PMID:10872802 IPI UniProt:Q9JID9 F Janus kinase 3 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:99928 Jak3 GO:0018108 MGI:MGI:1859033|PMID:10872802 IDA P Janus kinase 3 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:104813 Jarid2 GO:0000122 MGI:MGI:3589998|PMID:15870077 IGI MGI:97874 P jumonji, AT rich interactive domain 2 Jmj|jumonji gene taxon:10090 20060306 MGI relationship(CL:0000001) MGI MGI:104813 Jarid2 GO:0008285 MGI:MGI:3589998|PMID:15870077 IMP MGI:1856923 P jumonji, AT rich interactive domain 2 Jmj|jumonji gene taxon:10090 20060306 MGI relationship(CL:0000001) MGI MGI:96650 Jup GO:0030018 MGI:MGI:81460|PMID:8821035 IDA C junction plakoglobin gamma-catenin|PG|plakoglobin gene taxon:10090 20070222 MGI relationship(CL:0000188) MGI MGI:96650 Jup GO:0030018 MGI:MGI:81460|PMID:8821035 IDA C junction plakoglobin gamma-catenin|PG|plakoglobin gene taxon:10090 20070222 MGI relationship(CL:0000746) MGI MGI:1344353 Katna1 GO:0030424 MGI:MGI:3579921|PMID:15944385 IDA C katanin p60 (ATPase-containing) subunit A1 gene taxon:10090 20060118 MGI relationship(CL:0000540) MGI MGI:1344353 Katna1 GO:0031122 MGI:MGI:3579921|PMID:15944385 IDA P katanin p60 (ATPase-containing) subunit A1 gene taxon:10090 20060118 MGI relationship(CL:0000002) MGI MGI:1921437 Katnb1 GO:0030424 MGI:MGI:3579921|PMID:15944385 IDA C katanin p80 (WD40-containing) subunit B 1 KAT gene taxon:10090 20060118 MGI relationship(CL:0000540) MGI MGI:1921437 Katnb1 GO:0030424 MGI:MGI:3608033|PMID:16203747 IDA C katanin p80 (WD40-containing) subunit B 1 KAT gene taxon:10090 20060118 MGI relationship(CL:0000117) MGI MGI:109322 Kcnk1 GO:0005267 MGI:MGI:3525805|PMID:15540117 IDA F potassium channel, subfamily K, member 1 TWIK-1 gene taxon:10090 20050321 MGI relationship(CL:0000002) MGI MGI:109322 Kcnk1 GO:0005768 MGI:MGI:3525805|PMID:15540117 IDA C potassium channel, subfamily K, member 1 TWIK-1 gene taxon:10090 20050321 MGI relationship(CL:0000002) MGI MGI:99923 Kcnma1 GO:0001666 MGI:MGI:3611743|PMID:16306267 IDA P potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070313 MGI relationship(CL:0000002) MGI MGI:99923 Kcnma1 GO:0005249 MGI:MGI:3053479|PMID:15184377 IMP MGI:3053849 F potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070313 MGI relationship(CL:0000192) MGI MGI:99923 Kcnma1 GO:0005267 MGI:MGI:3695228|PMID:16873365 IGI MGI:1277957 F potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070314 MGI relationship(CL:0000622) MGI MGI:99923 Kcnma1 GO:0005267 MGI:MGI:3697763|PMID:17135251 IMP MGI:3053849 F potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070314 MGI relationship(CL:0000589) MGI MGI:99923 Kcnma1 GO:0005886 MGI:MGI:1346192|PMID:10517674 IDA C potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070312 MGI relationship(CL:0000002) MGI MGI:99923 Kcnma1 GO:0005886 MGI:MGI:2680842|PMID:12952984 IDA C potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070313 MGI relationship(CL:0000192) MGI MGI:99923 Kcnma1 GO:0006813 MGI:MGI:1346192|PMID:10517674 IDA P potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070312 MGI relationship(CL:0000002) MGI MGI:99923 Kcnma1 GO:0007268 MGI:MGI:3047034|PMID:15194823 IMP MGI:3050114 P potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070313 MGI relationship(CL:0000121) MGI MGI:99923 Kcnma1 GO:0008076 MGI:MGI:2450799|PMID:12388098 IGI MGI:1913272,MGI:1334203 C potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070312 MGI relationship(CL:0000002) MGI MGI:99923 Kcnma1 GO:0015269 MGI:MGI:1346192|PMID:10517674 IDA F potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070312 MGI relationship(CL:0000002) MGI MGI:99923 Kcnma1 GO:0015269 MGI:MGI:2450799|PMID:12388098 IGI MGI:1334203,MGI:1913272 F potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070312 MGI relationship(CL:0000002) MGI MGI:99923 Kcnma1 GO:0015269 MGI:MGI:3053479|PMID:15184377 IMP MGI:3053849 F potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070313 MGI relationship(CL:0000192) MGI MGI:99923 Kcnma1 GO:0015269 MGI:MGI:3611743|PMID:16306267 IDA F potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070313 MGI relationship(CL:0000002) MGI MGI:99923 Kcnma1 GO:0016021 MGI:MGI:2450799|PMID:12388098 IDA C potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070312 MGI relationship(CL:0000622) MGI MGI:99923 Kcnma1 GO:0016324 MGI:MGI:3697763|PMID:17135251 IDA C potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070314 MGI relationship(CL:0000589) MGI MGI:99923 Kcnma1 GO:0042391 MGI:MGI:3047034|PMID:15194823 IMP MGI:3050114 P potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070313 MGI relationship(CL:0000121) MGI MGI:99923 Kcnma1 GO:0042391 MGI:MGI:3626129|PMID:16763026 IMP MGI:3050114 P potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070314 MGI relationship(CL:0000002) MGI MGI:99923 Kcnma1 GO:0042491 MGI:MGI:3052624|PMID:15328414 IMP MGI:3050114 P potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070313 MGI relationship(CL:0000601) MGI MGI:99923 Kcnma1 GO:0042491 MGI:MGI:3697555|PMID:17074442 IMP MGI:3050114 P potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070314 MGI relationship(CL:0000601) MGI MGI:99923 Kcnma1 GO:0043195 MGI:MGI:3052624|PMID:15328414 IDA C potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070313 MGI relationship(CL:0000601) MGI MGI:99923 Kcnma1 GO:0044444 MGI:MGI:2680842|PMID:12952984 IDA C potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070313 MGI relationship(CL:0000192) MGI MGI:99923 Kcnma1 GO:0045211 MGI:MGI:3052624|PMID:15328414 IDA C potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070313 MGI relationship(CL:0000601) MGI MGI:99923 Kcnma1 GO:0045794 MGI:MGI:3695228|PMID:16873365 IMP MGI:3053849 P potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070314 MGI relationship(CL:0000622) MGI MGI:99923 Kcnma1 GO:0046541 MGI:MGI:3695228|PMID:16873365 IGI MGI:1277957 P potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070314 MGI relationship(CL:0000622) MGI MGI:99923 Kcnma1 GO:0048469 MGI:MGI:3052624|PMID:15328414 IMP MGI:3050114 P potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070313 MGI relationship(CL:0000601) MGI MGI:99923 Kcnma1 GO:0048469 MGI:MGI:3052624|PMID:15328414 IMP MGI:3050114 P potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070313 MGI relationship(CL:0000635) MGI MGI:99923 Kcnma1 GO:0060072 MGI:MGI:2450799|PMID:12388098 IDA F potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070314 MGI relationship(CL:0000622) MGI MGI:99923 Kcnma1 GO:0060072 MGI:MGI:3695228|PMID:16873365 IMP MGI:3053849 F potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070314 MGI relationship(CL:0000622) MGI MGI:99923 Kcnma1 GO:0060087 MGI:MGI:3695011|PMID:15867178 IMP MGI:3050114 P potassium large conductance calcium-activated channel, subfamily M, alpha member 1 BK channel alpha subunit|MaxiK|mSlo1|Slo|Slo1 gene taxon:10090 20070319 MGI relationship(CL:0000359) MGI MGI:1334203 Kcnmb1 GO:0008076 MGI:MGI:2450799|PMID:12388098 IGI MGI:99923 C potassium large conductance calcium-activated channel, subfamily M, beta member 1 BK channel beta subunit|BKbeta1 gene taxon:10090 20070312 MGI relationship(CL:0000002) MGI MGI:1334203 Kcnmb1 GO:0015269 MGI:MGI:2450799|PMID:12388098 IGI MGI:99923 F potassium large conductance calcium-activated channel, subfamily M, beta member 1 BK channel beta subunit|BKbeta1 gene taxon:10090 20070312 MGI relationship(CL:0000002) MGI MGI:1334203 Kcnmb1 GO:0016021 MGI:MGI:2450799|PMID:12388098 IDA C potassium large conductance calcium-activated channel, subfamily M, beta member 1 BK channel beta subunit|BKbeta1 gene taxon:10090 20070312 MGI relationship(CL:0000622) MGI MGI:1913272 Kcnmb4 GO:0008076 MGI:MGI:2450799|PMID:12388098 IGI MGI:99923 C potassium large conductance calcium-activated channel, subfamily M, beta member 4 Slowpoke beta 4 gene taxon:10090 20070312 MGI relationship(CL:0000002) MGI MGI:1913272 Kcnmb4 GO:0015269 MGI:MGI:2450799|PMID:12388098 IGI MGI:99923 F potassium large conductance calcium-activated channel, subfamily M, beta member 4 Slowpoke beta 4 gene taxon:10090 20070312 MGI relationship(CL:0000002) MGI MGI:1277957 Kcnn4 GO:0005267 MGI:MGI:3695228|PMID:16873365 IGI MGI:99923 F potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4 IK1|IKCA1|KCA4|mIKCa1|SK4 gene taxon:10090 20070314 MGI relationship(CL:0000622) MGI MGI:1277957 Kcnn4 GO:0015269 MGI:MGI:2450799|PMID:12388098 IDA F potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4 IK1|IKCA1|KCA4|mIKCa1|SK4 gene taxon:10090 20070312 MGI relationship(CL:0000622) MGI MGI:1277957 Kcnn4 GO:0046541 MGI:MGI:3695228|PMID:16873365 IGI MGI:99923 P potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4 IK1|IKCA1|KCA4|mIKCa1|SK4 gene taxon:10090 20070314 MGI relationship(CL:0000622) MGI MGI:96683 Kdr GO:0001570 MGI:MGI:3529425|PMID:15644447 IMP MGI:3530468 P kinase insert domain protein receptor Flk-1|Flk1|vascular endothelial growth factor receptor- 2|VEGF receptor-2|VEGFR-2|VEGFR2 gene taxon:10090 20050505 MGI relationship(CL:0000071) MGI MGI:96683 Kdr GO:0016477 MGI:MGI:3525930|PMID:15601856 IGI MGI:103178 P kinase insert domain protein receptor Flk-1|Flk1|vascular endothelial growth factor receptor- 2|VEGF receptor-2|VEGFR-2|VEGFR2 gene taxon:10090 20050303 MGI relationship(CL:0000007) MGI MGI:107566 Kifap3 GO:0008104 MGI:MGI:3578508|PMID:15834408 IMP MGI:3579410|MGI:3579409|MGI:3043822 P kinesin-associated protein 3 KAP3|Smg GDS gene taxon:10090 20051107 MGI relationship(CL:0000031) MGI MGI:107566 Kifap3 GO:0008285 MGI:MGI:3578508|PMID:15834408 IMP MGI:3579410|MGI:3579409|MGI:3043822 P kinesin-associated protein 3 KAP3|Smg GDS gene taxon:10090 20051107 MGI relationship(CL:0000031) MGI MGI:96677 Kit GO:0005020 MGI:MGI:1859033|PMID:10872802 IDA F kit oncogene belly-spot|c-KIT|CD117|Dominant white spotting|Steel Factor Receptor|Tr-kit gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96677 Kit GO:0005515 MGI:MGI:1859033|PMID:10872802 IPI UniProt:Q9JID9 F kit oncogene belly-spot|c-KIT|CD117|Dominant white spotting|Steel Factor Receptor|Tr-kit gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96677 Kit GO:0007243 MGI:MGI:1859033|PMID:10872802 IDA P kit oncogene belly-spot|c-KIT|CD117|Dominant white spotting|Steel Factor Receptor|Tr-kit gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96677 Kit GO:0008284 MGI:MGI:1351242|PMID:10620616 IGI MGI:96974|MGI:97306 P kit oncogene belly-spot|c-KIT|CD117|Dominant white spotting|Steel Factor Receptor|Tr-kit gene taxon:10090 20070129 MGI relationship(CL:0000001) MGI MGI:96677 Kit GO:0018108 MGI:MGI:1859033|PMID:10872802 IDA P kit oncogene belly-spot|c-KIT|CD117|Dominant white spotting|Steel Factor Receptor|Tr-kit gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96677 Kit GO:0019221 MGI:MGI:1859033|PMID:10872802 IDA P kit oncogene belly-spot|c-KIT|CD117|Dominant white spotting|Steel Factor Receptor|Tr-kit gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96677 Kit GO:0043406 MGI:MGI:1351242|PMID:10620616 IGI MGI:96974|MGI:97306 P kit oncogene belly-spot|c-KIT|CD117|Dominant white spotting|Steel Factor Receptor|Tr-kit gene taxon:10090 20070129 MGI relationship(CL:0000001) MGI MGI:96974 Kitl GO:0001755 MGI:MGI:1934508|PMID:11401406 IDA P kit ligand Gb|grizzle-belly|Mgf|SF|Sl|SLF|Steel|Steel factor|stem cell factor gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:96974 Kitl GO:0005173 MGI:MGI:1859033|PMID:10872802 IDA F kit ligand Gb|grizzle-belly|Mgf|SF|Sl|SLF|Steel|Steel factor|stem cell factor gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96974 Kitl GO:0008284 MGI:MGI:1351242|PMID:10620616 IGI MGI:97306|MGI:96677 P kit ligand Gb|grizzle-belly|Mgf|SF|Sl|SLF|Steel|Steel factor|stem cell factor gene taxon:10090 20070129 MGI relationship(CL:0000001) MGI MGI:96974 Kitl GO:0008284 MGI:MGI:1934508|PMID:11401406 IDA P kit ligand Gb|grizzle-belly|Mgf|SF|Sl|SLF|Steel|Steel factor|stem cell factor gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:96974 Kitl GO:0008284 MGI:MGI:1934508|PMID:11401406 IGI MGI:97306 P kit ligand Gb|grizzle-belly|Mgf|SF|Sl|SLF|Steel|Steel factor|stem cell factor gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:96974 Kitl GO:0008284 MGI:MGI:2149663|PMID:11435472 IDA P kit ligand Gb|grizzle-belly|Mgf|SF|Sl|SLF|Steel|Steel factor|stem cell factor gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:96974 Kitl GO:0008284 MGI:MGI:2149663|PMID:11435472 IGI MGI:97306 P kit ligand Gb|grizzle-belly|Mgf|SF|Sl|SLF|Steel|Steel factor|stem cell factor gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:96974 Kitl GO:0043066 MGI:MGI:3038547|PMID:15039234 IGI MGI:97306,MGI:95484 P kit ligand Gb|grizzle-belly|Mgf|SF|Sl|SLF|Steel|Steel factor|stem cell factor gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:96974 Kitl GO:0043406 MGI:MGI:1351242|PMID:10620616 IGI MGI:97306|MGI:96677 P kit ligand Gb|grizzle-belly|Mgf|SF|Sl|SLF|Steel|Steel factor|stem cell factor gene taxon:10090 20070129 MGI relationship(CL:0000001) MGI MGI:96974 Kitl GO:0046579 MGI:MGI:2149663|PMID:11435472 IDA P kit ligand Gb|grizzle-belly|Mgf|SF|Sl|SLF|Steel|Steel factor|stem cell factor gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:96974 Kitl GO:0050731 MGI:MGI:1859033|PMID:10872802 IDA P kit ligand Gb|grizzle-belly|Mgf|SF|Sl|SLF|Steel|Steel factor|stem cell factor gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:107978 Klc1 GO:0008088 MGI:MGI:2154812|PMID:11740561 IMP MGI:2136259 P kinesin light chain 1 Kns2 gene taxon:10090 20051005 MGI relationship(CL:0000540) MGI MGI:107978 Klc1 GO:0030424 MGI:MGI:2154812|PMID:11740561 IDA C kinesin light chain 1 Kns2 gene taxon:10090 20051005 MGI relationship(CL:0000540) MGI MGI:107978 Klc1 GO:0031410 MGI:MGI:2154812|PMID:11740561 IDA C kinesin light chain 1 Kns2 gene taxon:10090 20051005 MGI relationship(CL:0000540) MGI MGI:1342771 Klf1 GO:0043249 MGI:MGI:73365|PMID:7753195 IMP P Kruppel-like factor 1 (erythroid) Eklf gene taxon:10090 20060824 MGI relationship(CL:0000232) MGI MGI:1346318 Klf6 GO:0005634 MGI:MGI:3522536|PMID:15557439 IDA C Kruppel-like factor 6 BCD1|Copeb|CPBP|FM2|FM6|Ierepo1|Ierepo3|Zf9 gene taxon:10090 20050208 MGI relationship(CL:0000066) MGI MGI:1346318 Klf6 GO:0005737 MGI:MGI:3522536|PMID:15557439 IDA C Kruppel-like factor 6 BCD1|Copeb|CPBP|FM2|FM6|Ierepo1|Ierepo3|Zf9 gene taxon:10090 20050208 MGI relationship(CL:0000066) MGI MGI:1346318 Klf6 GO:0005737 MGI:MGI:3522536|PMID:15557439 IDA C Kruppel-like factor 6 BCD1|Copeb|CPBP|FM2|FM6|Ierepo1|Ierepo3|Zf9 gene taxon:10090 20050208 MGI relationship(CL:0000134) MGI MGI:1336161 Klrc1 GO:0009897 MGI:MGI:2687118|PMID:14707119 IDA C killer cell lectin-like receptor subfamily C, member 1 CD159a|NKG2A|NKG2B gene taxon:10090 20070117 MGI relationship(CL:0000002) MGI MGI:1336162 Klrc2 GO:0009897 MGI:MGI:2687118|PMID:14707119 IDA C killer cell lectin-like receptor subfamily C, member 2 NKG2C gene taxon:10090 20070117 MGI relationship(CL:0000002) MGI MGI:1929720 Klrc3 GO:0009897 MGI:MGI:2687118|PMID:14707119 IDA C killer cell lectin-like receptor subfamily C, member 3 NKG2E gene taxon:10090 20070117 MGI relationship(CL:0000002) MGI MGI:1196250 Klrk1 GO:0009897 MGI:MGI:2450811|PMID:12645935 IDA C killer cell lectin-like receptor subfamily K, member 1 D6H12S2489E|NKG2-D|NKG2D gene taxon:10090 20070115 MGI relationship(CL:0000002) MGI MGI:1196250 Klrk1 GO:0009897 MGI:MGI:2687118|PMID:14707119 IDA C killer cell lectin-like receptor subfamily K, member 1 D6H12S2489E|NKG2-D|NKG2D gene taxon:10090 20070117 MGI relationship(CL:0000002) MGI MGI:96680 Kras GO:0003924 MGI:MGI:3526457|PMID:15665300 IGI MGI:97306 F v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog K-ras|Ki-ras|Kras-2|Kras2 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:96680 Kras GO:0007265 MGI:MGI:3526457|PMID:15665300 IGI MGI:97306 P v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog K-ras|Ki-ras|Kras-2|Kras2 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:96680 Kras GO:0008284 MGI:MGI:3526457|PMID:15665300 IGI MGI:97306 P v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog K-ras|Ki-ras|Kras-2|Kras2 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:96680 Kras GO:0030036 MGI:MGI:3526457|PMID:15665300 IGI MGI:97306 P v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog K-ras|Ki-ras|Kras-2|Kras2 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:96680 Kras GO:0032228 MGI:MGI:2157992|PMID:11793011 IGI MGI:97306 P v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog K-ras|Ki-ras|Kras-2|Kras2 gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:96680 Kras GO:0035022 MGI:MGI:3526457|PMID:15665300 IGI MGI:97306 P v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog K-ras|Ki-ras|Kras-2|Kras2 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:96680 Kras GO:0043524 MGI:MGI:1861510|PMID:10845775 IGI MGI:97306|MGI:96224 P v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog K-ras|Ki-ras|Kras-2|Kras2 gene taxon:10090 20070130 MGI relationship(CL:0000001) MGI MGI:96680 Kras GO:0048169 MGI:MGI:2157992|PMID:11793011 IGI MGI:97306 P v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog K-ras|Ki-ras|Kras-2|Kras2 gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:96680 Kras GO:0051146 MGI:MGI:3511080|PMID:15542848 IGI MGI:97874 P v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog K-ras|Ki-ras|Kras-2|Kras2 gene taxon:10090 20050121 MGI relationship(CL:0000188) MGI MGI:96738 l7Rn6 GO:0005737 MGI:MGI:3614242|PMID:16157679 IDA C lethal, Chr 7, Rinchik 6 l(7)6Rn gene taxon:10090 20060912 MGI relationship(CL:0000158) MGI MGI:99892 Lama1 GO:0045198 MGI:MGI:3529401|PMID:15668394 IMP MGI:3530455 P laminin, alpha 1 Lama gene taxon:10090 20050505 MGI relationship(CL:0000066) MGI MGI:105382 Lama5 GO:0001658 MGI:MGI:2678847|PMID:14568553 IMP P laminin, alpha 5 [a]5 gene taxon:10090 20050823 MGI relationship(CL:0000001) MGI MGI:105382 Lama5 GO:0001738 MGI:MGI:3623696|PMID:16365040 IMP MGI:1934917 P laminin, alpha 5 [a]5 gene taxon:10090 20060706 MGI relationship(CL:0000146) MGI MGI:105382 Lama5 GO:0001755 MGI:MGI:3611396|PMID:16316641 IMP MGI:1934917 P laminin, alpha 5 [a]5 gene taxon:10090 20060228 MGI relationship(CL:0000008) MGI MGI:105382 Lama5 GO:0001755 MGI:MGI:3611396|PMID:16316641 IMP MGI:1934917 P laminin, alpha 5 [a]5 gene taxon:10090 20060228 MGI relationship(CL:0000011) MGI MGI:105382 Lama5 GO:0007431 MGI:MGI:2678847|PMID:14568553 IMP P laminin, alpha 5 [a]5 gene taxon:10090 20050823 MGI relationship(CL:0000001) MGI MGI:105382 Lama5 GO:0007517 MGI:MGI:2670559|PMID:12921739 IMP MGI:1934917 P laminin, alpha 5 [a]5 gene taxon:10090 20050823 MGI relationship(CL:0000192) MGI MGI:105382 Lama5 GO:0016331 MGI:MGI:3623696|PMID:16365040 IMP MGI:1934917 P laminin, alpha 5 [a]5 gene taxon:10090 20060706 MGI relationship(CL:0000066) MGI MGI:105382 Lama5 GO:0030324 MGI:MGI:2181263|PMID:12051813 IMP MGI:1934917 P laminin, alpha 5 [a]5 gene taxon:10090 20051003 MGI relationship(CL:0000001) MGI MGI:105382 Lama5 GO:0042127 MGI:MGI:3623696|PMID:16365040 IMP MGI:1934917 P laminin, alpha 5 [a]5 gene taxon:10090 20060706 MGI relationship(CL:0000066) MGI MGI:105382 Lama5 GO:0042475 MGI:MGI:3623696|PMID:16365040 IMP MGI:1934917 P laminin, alpha 5 [a]5 gene taxon:10090 20060706 MGI relationship(CL:0000066) MGI MGI:105382 Lama5 GO:0048754 MGI:MGI:2678847|PMID:14568553 IMP P laminin, alpha 5 [a]5 gene taxon:10090 20051212 MGI relationship(CL:0000001) MGI MGI:96745 Lamp1 GO:0005764 MGI:MGI:3527911|PMID:15588329 IDA C lysosomal membrane glycoprotein 1 CD107a gene taxon:10090 20060913 MGI relationship(CL:0000002) MGI MGI:96745 Lamp1 GO:0005764 MGI:MGI:3615690|PMID:16415873 IDA C lysosomal membrane glycoprotein 1 CD107a gene taxon:10090 20060413 MGI relationship(CL:0000002) MGI MGI:96745 Lamp1 GO:0005764 MGI:MGI:3654230|PMID:16542649 IDA C lysosomal membrane glycoprotein 1 CD107a gene taxon:10090 20060925 MGI relationship(CL:0000001) MGI MGI:96745 Lamp1 GO:0005770 MGI:MGI:3615690|PMID:16415873 IDA C lysosomal membrane glycoprotein 1 CD107a gene taxon:10090 20060413 MGI relationship(CL:0000002) MGI MGI:96748 Lamp2 GO:0005764 MGI:MGI:2679144|PMID:14557411 IDA C lysosomal membrane glycoprotein 2 CD107b gene taxon:10090 20041008 MGI relationship(CL:0000002) MGI MGI:104867 Lbx1 GO:0045665 MGI:MGI:3607682|PMID:16234809 IMP MGI:2182635 P ladybird homeobox homolog 1 (Drosophila) Lbx1h gene taxon:10090 20060413 MGI relationship(CL:0000679) MGI MGI:104867 Lbx1 GO:0048664 MGI:MGI:3607682|PMID:16234809 IGI MGI:1351209 P ladybird homeobox homolog 1 (Drosophila) Lbx1h gene taxon:10090 20060413 MGI relationship(CL:0000617) MGI MGI:104867 Lbx1 GO:0048664 MGI:MGI:3607682|PMID:16234809 IGI MGI:1351209 P ladybird homeobox homolog 1 (Drosophila) Lbx1h gene taxon:10090 20060413 MGI relationship(CL:0000679) MGI MGI:104867 Lbx1 GO:0048664 MGI:MGI:3607682|PMID:16234809 IMP MGI:2182635 P ladybird homeobox homolog 1 (Drosophila) Lbx1h gene taxon:10090 20060413 MGI relationship(CL:0000617) MGI MGI:104808 Lcp1 GO:0005515 MGI:MGI:3042556|PMID:14756805 IPI UniProt:O70200 F lymphocyte cytosolic protein 1 D14Ertd310e|L-fimbrin|Pls2 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1344412 Ldb3 GO:0030018 MGI:MGI:3656458|PMID:16481394 IDA C LIM domain binding 3 cypher 1|cypher 2|PDLIM6|ZASP gene taxon:10090 20070312 MGI relationship(CL:0000746) MGI MGI:96770 Lef1 GO:0003705 MGI:MGI:3530428|PMID:15729346 IGI MGI:88276,MGI:97487,MGI:104633 F lymphoid enhancer binding factor 1 Lef-1|lymphoid enhancer factor 1 gene taxon:10090 20050513 MGI relationship(CL:0000002) MGI MGI:96770 Lef1 GO:0005634 MGI:MGI:2681050|PMID:14623238 IDA C lymphoid enhancer binding factor 1 Lef-1|lymphoid enhancer factor 1 gene taxon:10090 20041006 MGI relationship(CL:0000066) MGI MGI:96770 Lef1 GO:0005737 MGI:MGI:2681050|PMID:14623238 IDA C lymphoid enhancer binding factor 1 Lef-1|lymphoid enhancer factor 1 gene taxon:10090 20041006 MGI relationship(CL:0000066) MGI MGI:96770 Lef1 GO:0016055 MGI:MGI:3640895|PMID:16678815 IMP MGI:1926601 P lymphoid enhancer binding factor 1 Lef-1|lymphoid enhancer factor 1 gene taxon:10090 20060921 MGI relationship(CL:0000070) MGI MGI:107405 Lefty1 GO:0008285 MGI:MGI:3042338|PMID:15004567 IGI MGI:1201414 P left right determination factor 1 Leftb|lefty-1|Stra3 gene taxon:10090 20060125 MGI relationship(CL:0000223) MGI MGI:96778 Lgals3 GO:0005634 MGI:MGI:1355019|PMID:10745073 IDA C lectin, galactose binding, soluble 3 gal3|galectin-3|L-34|Mac-2 gene taxon:10090 20041228 MGI relationship(CL:0000002) MGI MGI:96778 Lgals3 GO:0005737 MGI:MGI:1355019|PMID:10745073 IDA C lectin, galactose binding, soluble 3 gal3|galectin-3|L-34|Mac-2 gene taxon:10090 20041228 MGI relationship(CL:0000002) MGI MGI:107536 Lgals4 GO:0005515 MGI:MGI:3041925|PMID:14961764 IPI UniProt:Q8CGB3 F lectin, galactose binding, soluble 4 galectin-4 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:99783 Lhx1 GO:0001706 MGI:MGI:3487194|PMID:15355796 IMP MGI:1857848 P LIM homeobox protein 1 Lim1 gene taxon:10090 20050131 MGI relationship(CL:0000223) MGI MGI:99783 Lhx1 GO:0010003 MGI:MGI:3487194|PMID:15355796 IMP MGI:1857848 P LIM homeobox protein 1 Lim1 gene taxon:10090 20050131 MGI relationship(CL:0000223) MGI MGI:102673 Lhx3 GO:0008045 MGI:MGI:1316601|PMID:9865699 IGI MGI:101776 P LIM homeobox protein 3 Lim3|mLim-3|P-LIM gene taxon:10090 20070226 MGI relationship(CL:0000100) MGI MGI:102673 Lhx3 GO:0021526 MGI:MGI:1316601|PMID:9865699 IGI MGI:101776 P LIM homeobox protein 3 Lim3|mLim-3|P-LIM gene taxon:10090 20070226 MGI relationship(CL:0000100) MGI MGI:101776 Lhx4 GO:0008045 MGI:MGI:1316601|PMID:9865699 IGI MGI:102673 P LIM homeobox protein 4 Gsh-4|Gsh4 gene taxon:10090 20070226 MGI relationship(CL:0000100) MGI MGI:101776 Lhx4 GO:0021526 MGI:MGI:1316601|PMID:9865699 IGI MGI:102673 P LIM homeobox protein 4 Gsh-4|Gsh4 gene taxon:10090 20070226 MGI relationship(CL:0000100) MGI MGI:104572 Limk1 GO:0005634 MGI:MGI:3624072|PMID:16399995 IDA C LIM-domain containing, protein kinase gene taxon:10090 20060706 MGI relationship(CL:0000017) MGI MGI:104572 Limk1 GO:0005634 MGI:MGI:3624072|PMID:16399995 IDA C LIM-domain containing, protein kinase gene taxon:10090 20060706 MGI relationship(CL:0000018) MGI MGI:104572 Limk1 GO:0005634 MGI:MGI:3624072|PMID:16399995 IDA C LIM-domain containing, protein kinase gene taxon:10090 20060706 MGI relationship(CL:0000216) MGI MGI:104572 Limk1 GO:0005737 MGI:MGI:3624072|PMID:16399995 IDA C LIM-domain containing, protein kinase gene taxon:10090 20060706 MGI relationship(CL:0000017) MGI MGI:104572 Limk1 GO:0005737 MGI:MGI:3624072|PMID:16399995 IDA C LIM-domain containing, protein kinase gene taxon:10090 20060706 MGI relationship(CL:0000018) MGI MGI:104572 Limk1 GO:0005737 MGI:MGI:3624072|PMID:16399995 IDA C LIM-domain containing, protein kinase gene taxon:10090 20060706 MGI relationship(CL:0000216) MGI MGI:104572 Limk1 GO:0005925 MGI:MGI:3624072|PMID:16399995 IDA C LIM-domain containing, protein kinase gene taxon:10090 20060706 MGI relationship(CL:0000002) MGI MGI:104572 Limk1 GO:0045773 MGI:MGI:3603857|PMID:16204183 IGI MGI:1921382 P LIM-domain containing, protein kinase gene taxon:10090 20060112 MGI relationship(CL:0000001) MGI MGI:1197517 Limk2 GO:0005737 MGI:MGI:3624072|PMID:16399995 IDA C LIM motif-containing protein kinase 2 LIM kinase 2|Limk2a|Limk2b gene taxon:10090 20060706 MGI relationship(CL:0000002) MGI MGI:1197517 Limk2 GO:0005801 MGI:MGI:3624072|PMID:16399995 IDA C LIM motif-containing protein kinase 2 LIM kinase 2|Limk2a|Limk2b gene taxon:10090 20060706 MGI relationship(CL:0000002) MGI MGI:1195263 Lims1 GO:0007160 MGI:MGI:3583852|PMID:15976450 IMP MGI:3584173|MGI:3584172 P LIM and senescent cell antigen-like domains 1 Lims1l|PINCH1 gene taxon:10090 20050825 MGI relationship(CL:0000002) MGI MGI:1195263 Lims1 GO:0007163 MGI:MGI:3583852|PMID:15976450 IMP MGI:3584173|MGI:3584172 P LIM and senescent cell antigen-like domains 1 Lims1l|PINCH1 gene taxon:10090 20050825 MGI relationship(CL:0000002) MGI MGI:1195263 Lims1 GO:0016337 MGI:MGI:3583852|PMID:15976450 IMP MGI:3584173|MGI:3584172 P LIM and senescent cell antigen-like domains 1 Lims1l|PINCH1 gene taxon:10090 20050825 MGI relationship(CL:0000002) MGI MGI:2135609 Lin7a GO:0048489 MGI:MGI:2680876|PMID:14622577 IMP P lin-7 homolog A (C. elegans) LIN-7A|MALS-1|TIP-33|Veli gene taxon:10090 20050721 MGI relationship(CL:0000001) MGI MGI:102682 Llgl1 GO:0005737 MGI:MGI:3037622|PMID:15037549 IDA C lethal giant larvae homolog 1 (Drosophila) gene taxon:10090 20040630 MGI relationship(CL:0000117) MGI MGI:102682 Llgl1 GO:0035090 MGI:MGI:3037622|PMID:15037549 IMP MGI:3039269 P lethal giant larvae homolog 1 (Drosophila) gene taxon:10090 20040630 MGI relationship(CL:0000117) MGI MGI:1353635 Lmcd1 GO:0000122 MGI:MGI:3603876|PMID:16199866 IGI MGI:107516 P LIM and cysteine-rich domains 1 dyxin gene taxon:10090 20051201 MGI relationship(CL:0000002) MGI MGI:1353635 Lmcd1 GO:0005634 MGI:MGI:3603876|PMID:16199866 IDA C LIM and cysteine-rich domains 1 dyxin gene taxon:10090 20051201 MGI relationship(CL:0000082) MGI MGI:1353635 Lmcd1 GO:0005634 MGI:MGI:3603876|PMID:16199866 IDA C LIM and cysteine-rich domains 1 dyxin gene taxon:10090 20051201 MGI relationship(CL:0000193) MGI MGI:1888519 Lmx1a GO:0007411 MGI:MGI:3051929|PMID:15183721 IMP MGI:1888413 P LIM homeobox transcription factor 1 alpha Lmx1.1|shaker short-tail|sst gene taxon:10090 20040929 MGI relationship(CL:0000099) MGI MGI:1888519 Lmx1a GO:0007417 MGI:MGI:3050905|PMID:15148302 IMP MGI:1888413 P LIM homeobox transcription factor 1 alpha Lmx1.1|shaker short-tail|sst gene taxon:10090 20041116 MGI relationship(CL:0000117) MGI MGI:1888519 Lmx1a GO:0030182 MGI:MGI:3051929|PMID:15183721 IMP MGI:1888413 P LIM homeobox transcription factor 1 alpha Lmx1.1|shaker short-tail|sst gene taxon:10090 20040929 MGI relationship(CL:0000099) MGI MGI:1888519 Lmx1a GO:0045665 MGI:MGI:3050905|PMID:15148302 IMP MGI:1888413 P LIM homeobox transcription factor 1 alpha Lmx1.1|shaker short-tail|sst gene taxon:10090 20041116 MGI relationship(CL:0000402) MGI MGI:1100513 Lmx1b GO:0001764 MGI:MGI:3051709|PMID:15229182 IMP MGI:2158463 P LIM homeobox transcription factor 1 beta LMX1.2 gene taxon:10090 20041005 MGI relationship(CL:0000117) MGI MGI:1100513 Lmx1b GO:0030182 MGI:MGI:3051709|PMID:15229182 IMP MGI:2158463 P LIM homeobox transcription factor 1 beta LMX1.2 gene taxon:10090 20041005 MGI relationship(CL:0000117) MGI MGI:96817 Lox GO:0004720 MGI:MGI:3604822|PMID:16192629 IDA F lysyl oxidase ras recision gene (rrg)|TSC-160 gene taxon:10090 20061107 MGI relationship(CL:0000001) MGI MGI:96817 Lox GO:0048251 MGI:MGI:3609311|PMID:12417550 IMP MGI:3610732 P lysyl oxidase ras recision gene (rrg)|TSC-160 gene taxon:10090 20061107 MGI relationship(CL:0000001) MGI MGI:1891340 Lpin1 GO:0045598 MGI:MGI:1929047|PMID:11138012 IMP MGI:1857584|MGI:1856603 P lipin 1 gene taxon:10090 20050721 MGI relationship(CL:0000136) MGI MGI:1917193 Lrch4 GO:0005737 MGI:MGI:3615854|PMID:16449650 IDA C leucine-rich repeats and calponin homology (CH) domain containing 4 LRN|LRRN4|SAP25 gene taxon:10090 20060517 MGI relationship(CL:0000002) MGI MGI:96828 Lrp1 GO:0030178 MGI:MGI:3619629|PMID:16207730 IDA P low density lipoprotein receptor-related protein 1 A2mr|CD91 gene taxon:10090 20060607 MGI relationship(CL:0000002) MGI MGI:95794 Lrp2 GO:0005783 MGI:MGI:3577702|PMID:15616221 IDA C low density lipoprotein receptor-related protein 2 Gp330|Megalin gene taxon:10090 20050609 MGI relationship(CL:0000007) MGI MGI:95794 Lrp2 GO:0005783 MGI:MGI:3577702|PMID:15616221 IDA C low density lipoprotein receptor-related protein 2 Gp330|Megalin gene taxon:10090 20050609 MGI relationship(CL:0000223) MGI MGI:95794 Lrp2 GO:0005794 MGI:MGI:3577702|PMID:15616221 IDA C low density lipoprotein receptor-related protein 2 Gp330|Megalin gene taxon:10090 20050609 MGI relationship(CL:0000223) MGI MGI:95794 Lrp2 GO:0005905 MGI:MGI:3577702|PMID:15616221 IDA C low density lipoprotein receptor-related protein 2 Gp330|Megalin gene taxon:10090 20050609 MGI relationship(CL:0000223) MGI MGI:95794 Lrp2 GO:0016324 MGI:MGI:3577702|PMID:15616221 IDA C low density lipoprotein receptor-related protein 2 Gp330|Megalin gene taxon:10090 20050609 MGI relationship(CL:0000223) MGI MGI:95794 Lrp2 GO:0016324 MGI:MGI:3577702|PMID:15616221 IDA C low density lipoprotein receptor-related protein 2 Gp330|Megalin gene taxon:10090 20050609 MGI relationship(CL:1000274) MGI MGI:95794 Lrp2 GO:0030139 MGI:MGI:3577702|PMID:15616221 IDA C low density lipoprotein receptor-related protein 2 Gp330|Megalin gene taxon:10090 20050609 MGI relationship(CL:0000223) MGI MGI:95794 Lrp2 GO:0045177 MGI:MGI:3577702|PMID:15616221 IDA C low density lipoprotein receptor-related protein 2 Gp330|Megalin gene taxon:10090 20050609 MGI relationship(CL:0000710) MGI MGI:95794 Lrp2 GO:0045177 MGI:MGI:3578036|PMID:15342463 IDA C low density lipoprotein receptor-related protein 2 Gp330|Megalin gene taxon:10090 20050607 MGI relationship(CL:0000223) MGI MGI:2442252 Lrp4 GO:0030178 MGI:MGI:3619629|PMID:16207730 IDA P low density lipoprotein receptor-related protein 4 mdig|Megf7 gene taxon:10090 20060607 MGI relationship(CL:0000002) MGI MGI:1278315 Lrp5 GO:0010003 MGI:MGI:3045836|PMID:15142971 IGI MGI:1298218 P low density lipoprotein receptor-related protein 5 BMND1|LR3|LRP7 gene taxon:10090 20040811 MGI relationship(CL:0000222) MGI MGI:1278315 Lrp5 GO:0016055 MGI:MGI:3581375|PMID:15923619 IGI MGI:2136761,MGI:1196625,MGI:98961 P low density lipoprotein receptor-related protein 5 BMND1|LR3|LRP7 gene taxon:10090 20050816 MGI relationship(CL:0000002) MGI MGI:1278315 Lrp5 GO:0042074 MGI:MGI:3045836|PMID:15142971 IGI MGI:1298218 P low density lipoprotein receptor-related protein 5 BMND1|LR3|LRP7 gene taxon:10090 20040811 MGI relationship(CL:0000222) MGI MGI:1298218 Lrp6 GO:0005624 MGI:MGI:3603992|PMID:16126904 IDA C low density lipoprotein receptor-related protein 6 Cd gene taxon:10090 20060119 MGI relationship(CL:0000002) MGI MGI:1298218 Lrp6 GO:0009952 MGI:MGI:3045836|PMID:15142971 IGI MGI:1278315 P low density lipoprotein receptor-related protein 6 Cd gene taxon:10090 20040811 MGI relationship(CL:0000222) MGI MGI:1298218 Lrp6 GO:0010003 MGI:MGI:3045836|PMID:15142971 IGI MGI:1278315 P low density lipoprotein receptor-related protein 6 Cd gene taxon:10090 20040811 MGI relationship(CL:0000222) MGI MGI:1298218 Lrp6 GO:0042074 MGI:MGI:3045836|PMID:15142971 IGI MGI:1278315 P low density lipoprotein receptor-related protein 6 Cd gene taxon:10090 20040811 MGI relationship(CL:0000222) MGI MGI:1340044 Lrp8 GO:0045860 MGI:MGI:3629864|PMID:12526740 IGI MGI:98935,MGI:103022 P low density lipoprotein receptor-related protein 8, apolipoprotein e receptor apoER2|Lr8b gene taxon:10090 20060807 MGI relationship(CL:0000001) MGI MGI:1914228 Luc7l GO:0005634 MGI:MGI:3055693|PMID:15474286 IDA C Luc7 homolog (S. cerevisiae)-like gene taxon:10090 20041207 MGI relationship(CL:0000002) MGI MGI:1914228 Luc7l GO:0045843 MGI:MGI:3055693|PMID:15474286 IDA P Luc7 homolog (S. cerevisiae)-like gene taxon:10090 20041207 MGI relationship(CL:0000002) MGI MGI:107629 Luzp1 GO:0005634 MGI:MGI:81707|PMID:8812416 IDA C leucine zipper protein 1 Luzp gene taxon:10090 20060727 MGI relationship(CL:0000540) MGI MGI:109440 Ly6g GO:0009897 MGI:MGI:1860996|PMID:10943842 IDA C lymphocyte antigen 6 complex, locus G Gr-1|Gr1|Ly-6G gene taxon:10090 20050617 MGI relationship(CL:0000081) MGI MGI:106910 Ly76 GO:0009897 MGI:MGI:1860996|PMID:10943842 IDA C lymphocyte antigen 76 TER-119|Ter119 gene taxon:10090 20050617 MGI relationship(CL:0000081) MGI MGI:96892 Lyn GO:0004713 MGI:MGI:1859033|PMID:10872802 IDA F Yamaguchi sarcoma viral (v-yes-1) oncogene homolog Hck-2 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:96892 Lyn GO:0018108 MGI:MGI:1859033|PMID:10872802 IDA P Yamaguchi sarcoma viral (v-yes-1) oncogene homolog Hck-2 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1345180 Lynx1 GO:0005886 MGI:MGI:2176631|PMID:11906696 IDA C Ly6/neurotoxin 1 gene taxon:10090 20041028 MGI relationship(CL:0000117) MGI MGI:1345180 Lynx1 GO:0005886 MGI:MGI:2176631|PMID:11906696 IDA C Ly6/neurotoxin 1 gene taxon:10090 20041028 MGI relationship(CL:0000598) MGI MGI:1333773 Mab21l1 GO:0008284 MGI:MGI:2652201|PMID:12642482 IMP MGI:2654257 P mab-21-like 1 (C. elegans) gene taxon:10090 20050721 MGI relationship(CL:0000306) MGI MGI:108559 Macf1 GO:0006620 MGI:MGI:3640889|PMID:16815997 IMP P microtubule-actin crosslinking factor 1 Acf7|Aclp7|trabeculin alpha gene taxon:10090 20060921 MGI relationship(CL:0000001) MGI MGI:108559 Macf1 GO:0016055 MGI:MGI:3640889|PMID:16815997 IGI MGI:1861437 P microtubule-actin crosslinking factor 1 Acf7|Aclp7|trabeculin alpha gene taxon:10090 20060921 MGI relationship(CL:0000001) MGI MGI:108559 Macf1 GO:0016055 MGI:MGI:3640889|PMID:16815997 IMP P microtubule-actin crosslinking factor 1 Acf7|Aclp7|trabeculin alpha gene taxon:10090 20060921 MGI relationship(CL:0000001) MGI MGI:1346866 Map2k1 GO:0030182 MGI:MGI:3050703|PMID:15145949 IMP P mitogen activated protein kinase kinase 1 MAP kinase kinase 1|Mek1|MEKK1|Prkmk1 gene taxon:10090 20040930 MGI relationship(CL:0000117) MGI MGI:1346872 Map3k1 GO:0008637 MGI:MGI:3577836|PMID:15882989 IMP P mitogen activated protein kinase kinase kinase 1 Mekk|MEKK1 gene taxon:10090 20051208 MGI relationship(CL:0000001) MGI MGI:1346877 Map3k7 GO:0001525 MGI:MGI:3621089|PMID:16556914 IMP MGI:3608889 P mitogen activated protein kinase kinase kinase 7 Tak1|TGF-beta activated kinase 1|transforming growth factor-beta-activated kinase 1 gene taxon:10090 20060522 MGI relationship(CL:0000359) MGI MGI:1346858 Mapk1 GO:0000165 MGI:MGI:79455|PMID:8626447 IDA P mitogen activated protein kinase 1 Erk2|MAPK2|p42mapk|Prkm1 gene taxon:10090 20050121 MGI relationship(CL:0000002) MGI MGI:1346858 Mapk1 GO:0004707 MGI:MGI:79455|PMID:8626447 IDA F mitogen activated protein kinase 1 Erk2|MAPK2|p42mapk|Prkm1 gene taxon:10090 20050121 MGI relationship(CL:0000002) MGI MGI:1346865 Mapk14 GO:0007519 MGI:MGI:3581988|PMID:15890335 IMP P mitogen activated protein kinase 14 Crk1|Csbp1|CSBP2|Mxi2|p38|p38 MAP Kinase|p38-alpha|p38MAPK|tRNA synthetase cofactor p38 gene taxon:10090 20050812 MGI relationship(CL:0000187) MGI MGI:1354946 Mapk6 GO:0005737 MGI:MGI:3521520|PMID:15538386 IDA C mitogen-activated protein kinase 6 Erk-3 related|ERK3|Mapk4|Mapk63|Prkm4|Prkm6 gene taxon:10090 20050316 MGI relationship(CL:0000002) MGI MGI:1353598 Mapk8ip3 GO:0005790 MGI:MGI:3629289|PMID:16606357 IDA C mitogen-activated protein kinase 8 interacting protein 3 c-Jun NH2-terminal kinase (JNK)/stress-activated protein kinase-associated protein 1|D17Wsu15e|Jip3|JNK-interacting protein 3|JSAP1|JSAP1a|JSAP1b|JSAP1c|JSAP1d|JUN/SAPK-associated protein 1|sunday driver 2|Syd2 gene taxon:10090 20060807 MGI relationship(CL:0000121) MGI MGI:1353598 Mapk8ip3 GO:0005886 MGI:MGI:3629289|PMID:16606357 IDA C mitogen-activated protein kinase 8 interacting protein 3 c-Jun NH2-terminal kinase (JNK)/stress-activated protein kinase-associated protein 1|D17Wsu15e|Jip3|JNK-interacting protein 3|JSAP1|JSAP1a|JSAP1b|JSAP1c|JSAP1d|JUN/SAPK-associated protein 1|sunday driver 2|Syd2 gene taxon:10090 20060807 MGI relationship(CL:0000121) MGI MGI:1353598 Mapk8ip3 GO:0007411 MGI:MGI:3527288|PMID:15572149 IMP MGI:3527900 P mitogen-activated protein kinase 8 interacting protein 3 c-Jun NH2-terminal kinase (JNK)/stress-activated protein kinase-associated protein 1|D17Wsu15e|Jip3|JNK-interacting protein 3|JSAP1|JSAP1a|JSAP1b|JSAP1c|JSAP1d|JUN/SAPK-associated protein 1|sunday driver 2|Syd2 gene taxon:10090 20050314 MGI relationship(CL:0000117) MGI MGI:1353598 Mapk8ip3 GO:0008104 MGI:MGI:3527288|PMID:15572149 IMP MGI:3527900 P mitogen-activated protein kinase 8 interacting protein 3 c-Jun NH2-terminal kinase (JNK)/stress-activated protein kinase-associated protein 1|D17Wsu15e|Jip3|JNK-interacting protein 3|JSAP1|JSAP1a|JSAP1b|JSAP1c|JSAP1d|JUN/SAPK-associated protein 1|sunday driver 2|Syd2 gene taxon:10090 20050314 MGI relationship(CL:0000117) MGI MGI:1353598 Mapk8ip3 GO:0030425 MGI:MGI:3629289|PMID:16606357 IDA C mitogen-activated protein kinase 8 interacting protein 3 c-Jun NH2-terminal kinase (JNK)/stress-activated protein kinase-associated protein 1|D17Wsu15e|Jip3|JNK-interacting protein 3|JSAP1|JSAP1a|JSAP1b|JSAP1c|JSAP1d|JUN/SAPK-associated protein 1|sunday driver 2|Syd2 gene taxon:10090 20060807 MGI relationship(CL:0000121) MGI MGI:1353598 Mapk8ip3 GO:0030673 MGI:MGI:3629289|PMID:16606357 IDA C mitogen-activated protein kinase 8 interacting protein 3 c-Jun NH2-terminal kinase (JNK)/stress-activated protein kinase-associated protein 1|D17Wsu15e|Jip3|JNK-interacting protein 3|JSAP1|JSAP1a|JSAP1b|JSAP1c|JSAP1d|JUN/SAPK-associated protein 1|sunday driver 2|Syd2 gene taxon:10090 20060807 MGI relationship(CL:0000117) MGI MGI:109298 Mapkapk2 GO:0005634 MGI:MGI:3521520|PMID:15538386 IDA C MAP kinase-activated protein kinase 2 MAPKAP kinase 2|MK2|Rps6kc1 gene taxon:10090 20050316 MGI relationship(CL:0000002) MGI MGI:109298 Mapkapk2 GO:0005737 MGI:MGI:3521520|PMID:15538386 IDA C MAP kinase-activated protein kinase 2 MAPKAP kinase 2|MK2|Rps6kc1 gene taxon:10090 20050316 MGI relationship(CL:0000002) MGI MGI:1333110 Mapkapk5 GO:0005634 MGI:MGI:3521520|PMID:15538386 IDA C MAP kinase-activated protein kinase 5 MK5|PRAK gene taxon:10090 20050316 MGI relationship(CL:0000002) MGI MGI:1333110 Mapkapk5 GO:0005737 MGI:MGI:3521520|PMID:15538386 IDA C MAP kinase-activated protein kinase 5 MK5|PRAK gene taxon:10090 20050316 MGI relationship(CL:0000002) MGI MGI:1333813 Mbd2 GO:0000792 MGI:MGI:2682503|PMID:14643676 IDA C methyl-CpG binding domain protein 2 MBD2a gene taxon:10090 20060724 MGI relationship(CL:0000007) MGI MGI:1333813 Mbd2 GO:0000792 MGI:MGI:2682503|PMID:14643676 IDA C methyl-CpG binding domain protein 2 MBD2a gene taxon:10090 20060724 MGI relationship(CL:1000274) MGI MGI:1333812 Mbd3 GO:0000792 MGI:MGI:2682503|PMID:14643676 IDA C methyl-CpG binding domain protein 3 gene taxon:10090 20060724 MGI relationship(CL:0000007) MGI MGI:1333812 Mbd3 GO:0000792 MGI:MGI:2682503|PMID:14643676 IDA C methyl-CpG binding domain protein 3 gene taxon:10090 20060724 MGI relationship(CL:1000274) MGI MGI:1333812 Mbd3 GO:0000792 MGI:MGI:3611125|PMID:16322236 IDA C methyl-CpG binding domain protein 3 gene taxon:10090 20060724 MGI relationship(CL:0000002) MGI MGI:1928482 Mbnl1 GO:0005634 MGI:MGI:3655436|PMID:16717059 IDA C muscleblind-like 1 (Drosophila) gene taxon:10090 20061016 MGI relationship(CL:0000188) MGI MGI:1928482 Mbnl1 GO:0005737 MGI:MGI:3655436|PMID:16717059 IDA C muscleblind-like 1 (Drosophila) gene taxon:10090 20061016 MGI relationship(CL:0000188) MGI MGI:1927235 Mbtps1 GO:0004175 MGI:MGI:3611598|PMID:15938716 IDA F membrane-bound transcription factor peptidase, site 1 S1P|site-1 protease|SKI-1|subtilisin/kexin isozyme-1 gene taxon:10090 20060309 MGI relationship(CL:0000002) MGI MGI:1927235 Mbtps1 GO:0005795 MGI:MGI:1331252|PMID:9990022 IDA C membrane-bound transcription factor peptidase, site 1 S1P|site-1 protease|SKI-1|subtilisin/kexin isozyme-1 gene taxon:10090 20060313 MGI relationship(CL:0000002) MGI MGI:1927235 Mbtps1 GO:0042990 MGI:MGI:3611598|PMID:15938716 IDA P membrane-bound transcription factor peptidase, site 1 S1P|site-1 protease|SKI-1|subtilisin/kexin isozyme-1 gene taxon:10090 20060309 MGI relationship(CL:0000002) MGI MGI:96956 mea GO:0021702 MGI:MGI:59633|PMID:2037292 IMP MGI:1856075 P meander tail gene taxon:10090 20070213 MGI relationship(CL:0000121) MGI MGI:96956 mea GO:0021707 MGI:MGI:59633|PMID:2037292 IMP MGI:1856075 P meander tail gene taxon:10090 20070213 MGI relationship(CL:0000120) MGI MGI:99918 Mecp2 GO:0005634 MGI:MGI:3612318|PMID:15939091 IDA C methyl CpG binding protein 2 Mbd5|WBP10 gene taxon:10090 20060411 MGI relationship(CL:0000127) MGI MGI:99918 Mecp2 GO:0005829 MGI:MGI:3612318|PMID:15939091 IDA C methyl CpG binding protein 2 Mbd5|WBP10 gene taxon:10090 20060411 MGI relationship(CL:0000127) MGI MGI:99918 Mecp2 GO:0008284 MGI:MGI:3612318|PMID:15939091 IMP P methyl CpG binding protein 2 Mbd5|WBP10 gene taxon:10090 20060411 MGI relationship(CL:0000127) MGI MGI:99918 Mecp2 GO:0016358 MGI:MGI:3512652|PMID:15519245 IMP MGI:2158354 P methyl CpG binding protein 2 Mbd5|WBP10 gene taxon:10090 20050121 MGI relationship(CL:0000598) MGI MGI:99918 Mecp2 GO:0042551 MGI:MGI:3512652|PMID:15519245 IMP MGI:2158354 P methyl CpG binding protein 2 Mbd5|WBP10 gene taxon:10090 20050121 MGI relationship(CL:0000598) MGI MGI:104717 Meis1 GO:0005634 MGI:MGI:3527920|PMID:15617687 IDA C myeloid ecotropic viral integration site 1 gene taxon:10090 20050412 MGI relationship(CL:0000134) MGI MGI:1096325 Mesp2 GO:0005634 MGI:MGI:3578712|PMID:15902259 IDA C mesoderm posterior 2 gene taxon:10090 20050818 MGI relationship(CL:0000222) MGI MGI:96969 Met GO:0051450 MGI:MGI:3618663|PMID:11061428 IMP MGI:1858021 P met proto-oncogene c-Met|HGF receptor|Par4 gene taxon:10090 20060606 MGI relationship(CL:0000515) MGI MGI:1917333 Metrn GO:0010001 MGI:MGI:3044244|PMID:15085178 IDA P meteorin, glial cell differentiation regulator gene taxon:10090 20040809 MGI relationship(CL:0000681) MGI MGI:1917333 Metrn GO:0050772 MGI:MGI:3044244|PMID:15085178 IDA P meteorin, glial cell differentiation regulator gene taxon:10090 20040809 MGI relationship(CL:0000117) MGI MGI:2442230 Mfn2 GO:0015630 MGI:MGI:3587532|PMID:16083859 IDA C mitofusin 2 Fzo|hypertension related protein 1 gene taxon:10090 20051017 MGI relationship(CL:0000007) MGI MGI:2442230 Mfn2 GO:0015630 MGI:MGI:3587532|PMID:16083859 IDA C mitofusin 2 Fzo|hypertension related protein 1 gene taxon:10090 20051017 MGI relationship(CL:0000023) MGI MGI:2443157 Mib1 GO:0031410 MGI:MGI:3603078|PMID:16000382 IDA C mindbomb homolog 1 (Drosophila) Mib gene taxon:10090 20051117 MGI relationship(CL:0000002) MGI MGI:2443157 Mib1 GO:0045665 MGI:MGI:3603078|PMID:16000382 IMP MGI:3603514 P mindbomb homolog 1 (Drosophila) Mib gene taxon:10090 20051117 MGI relationship(CL:0000117) MGI MGI:2443157 Mib1 GO:0045807 MGI:MGI:3603078|PMID:16000382 IDA P mindbomb homolog 1 (Drosophila) Mib gene taxon:10090 20051117 MGI relationship(CL:0000002) MGI MGI:2679684 Mib2 GO:0005769 MGI:MGI:3587544|PMID:15824097 IDA C mindbomb homolog 2 (Drosophila) Zzank1 gene taxon:10090 20051128 MGI relationship(CL:0000002) MGI MGI:1355329 Mink1 GO:0045060 MGI:MGI:3521627|PMID:15608642 IMP P misshapen-like kinase 1 (zebrafish) B55|Map4k6|MINK|Misshapen/NIKs-related kinase|Ysk2 gene taxon:10090 20050218 MGI relationship(CL:0000084) MGI MGI:104554 Mitf GO:0030154 MGI:MGI:893238|PMID:9199364 IMP MGI:1856094 P microphthalmia-associated transcription factor mi|wh gene taxon:10090 20050513 MGI relationship(CL:0000541) MGI MGI:106035 Mki67 GO:0005730 MGI:MGI:3047199|PMID:15237214 IDA C antigen identified by monoclonal antibody Ki 67 Ki-67 gene taxon:10090 20041006 MGI relationship(CL:0000007) MGI MGI:1891836 Mkks GO:0007608 MGI:MGI:3607949|PMID:16170314 IMP MGI:3608879 P McKusick-Kaufman syndrome protein Bbs6 gene taxon:10090 20060123 MGI relationship(CL:0000067) MGI MGI:1891836 Mkks GO:0035058 MGI:MGI:3607949|PMID:16170314 IGI MGI:2135272 P McKusick-Kaufman syndrome protein Bbs6 gene taxon:10090 20060123 MGI relationship(CL:0000601) MGI MGI:1891836 Mkks GO:0035058 MGI:MGI:3607949|PMID:16170314 IMP MGI:3608879 P McKusick-Kaufman syndrome protein Bbs6 gene taxon:10090 20060123 MGI relationship(CL:0000601) MGI MGI:1891836 Mkks GO:0045494 MGI:MGI:3607949|PMID:16170314 IMP MGI:3608879 P McKusick-Kaufman syndrome protein Bbs6 gene taxon:10090 20060123 MGI relationship(CL:0000287) MGI MGI:1891836 Mkks GO:0050910 MGI:MGI:3607949|PMID:16170314 IMP MGI:3608879 P McKusick-Kaufman syndrome protein Bbs6 gene taxon:10090 20060123 MGI relationship(CL:0000601) MGI MGI:3050795 Mkl2 GO:0051145 MGI:MGI:3607644|PMID:16204380 IMP MGI:3608959 P MKL/myocardin-like 2 MRTF-B gene taxon:10090 20060214 MGI relationship(CL:0000359) MGI MGI:101938 Mlh1 GO:0000795 MGI:MGI:3612193|PMID:16260499 IDA C mutL homolog 1 (E. coli) colon cancer, nonpolyposis type 2 gene taxon:10090 20060817 MGI relationship(CL:0000017) MGI MGI:1353455 Mlh3 GO:0000795 MGI:MGI:3612193|PMID:16260499 IDA C mutL homolog 3 (E coli) gene taxon:10090 20060817 MGI relationship(CL:0000017) MGI MGI:1353455 Mlh3 GO:0007130 MGI:MGI:3612193|PMID:16260499 IMP MGI:2384218 P mutL homolog 3 (E coli) gene taxon:10090 20060817 MGI relationship(CL:0000017) MGI MGI:1353455 Mlh3 GO:0007140 MGI:MGI:2183707|PMID:12091911 IMP MGI:2384218 P mutL homolog 3 (E coli) gene taxon:10090 20050721 MGI relationship(CL:0000017) MGI MGI:1353455 Mlh3 GO:0008104 MGI:MGI:3612193|PMID:16260499 IMP MGI:2384218 P mutL homolog 3 (E coli) gene taxon:10090 20060817 MGI relationship(CL:0000017) MGI MGI:1314653 Mllt4 GO:0005913 MGI:MGI:2154851|PMID:11731229 IDA C myeloid/lymphoid or mixed lineage-leukemia translocation to 4 homolog (Drosophila) AF6|Afadin|I-afadin|S-afadin gene taxon:10090 20060912 MGI relationship(CL:0000353) MGI MGI:97011 Mmp9 GO:0043065 MGI:MGI:3589495|PMID:15800063 IMP MGI:1932294 P matrix metallopeptidase 9 B/MMP9|Clg4b|Gel B|Gelatinase B|MMP-9 gene taxon:10090 20060306 MGI relationship(CL:0000743) MGI MGI:108511 Mobp GO:0005739 MGI:MGI:3573705|PMID:15625715 IDA C myelin-associated oligodendrocytic basic protein MOBP155 gene taxon:10090 20050823 MGI relationship(CL:0000002) MGI MGI:1096551 Morf4l1 GO:0008283 MGI:MGI:3575970|PMID:15798182 IMP MGI:3576922 P mortality factor 4 like 1 MORFRG15|MRG15|TEG-189|Tex189 gene taxon:10090 20050525 MGI relationship(CL:0000057) MGI MGI:97138 Mpv17 GO:0005777 MGI:MGI:69439|PMID:7957077 IDA C Mpv17 transgene, kidney disease mutant Tg.Mpv17 gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:97138 Mpv17 GO:0006800 MGI:MGI:69439|PMID:7957077 IDA P Mpv17 transgene, kidney disease mutant Tg.Mpv17 gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:2151839 Mreg GO:0042640 MGI:MGI:3513741|PMID:15550542 IMP MGI:1856847 P melanoregulin dsu|LOC381269|Wdt2 gene taxon:10090 20050207 MGI relationship(CL:0000148) MGI MGI:2151839 Mreg GO:0048066 MGI:MGI:3513741|PMID:15550542 IMP MGI:1856847 P melanoregulin dsu|LOC381269|Wdt2 gene taxon:10090 20050207 MGI relationship(CL:0000148) MGI MGI:108564 Mrg1 GO:0005634 MGI:MGI:3527920|PMID:15617687 IDA C myeloid ecotropic viral integration site-related gene 1 Meis2|Stra10 gene taxon:10090 20050412 MGI relationship(CL:0000134) MGI MGI:95495 Ms4a2 GO:0005887 MGI:MGI:78861|PMID:2527850 IDA C membrane-spanning 4-domains, subfamily A, member 2 Fce1b|Fcer1b|FcRB|Fcrbeta gene taxon:10090 20050214 MGI relationship(CL:0000002) MGI MGI:95495 Ms4a2 GO:0009897 MGI:MGI:78861|PMID:2527850 IDA C membrane-spanning 4-domains, subfamily A, member 2 Fce1b|Fcer1b|FcRB|Fcrbeta gene taxon:10090 20050214 MGI relationship(CL:0000002) MGI MGI:101816 Msh2 GO:0019237 MGI:MGI:3612193|PMID:16260499 IDA F mutS homolog 2 (E. coli) gene taxon:10090 20060817 MGI relationship(CL:0000017) MGI MGI:101816 Msh2 GO:0031573 MGI:MGI:3512823|PMID:15533840 IGI MGI:103557 P mutS homolog 2 (E. coli) gene taxon:10090 20060817 MGI relationship(CL:0000312) MGI MGI:109519 Msh3 GO:0019237 MGI:MGI:3612193|PMID:16260499 IDA F mutS homolog 3 (E. coli) D13Em1|Rep-3|Rep3 gene taxon:10090 20060817 MGI relationship(CL:0000017) MGI MGI:1860077 Msh4 GO:0000795 MGI:MGI:3612193|PMID:16260499 IDA C mutS homolog 4 (E. coli) mMsh4 gene taxon:10090 20060817 MGI relationship(CL:0000017) MGI MGI:1329021 Msh5 GO:0000795 MGI:MGI:3612193|PMID:16260499 IDA C mutS homolog 5 (E. coli) G7|Mut5 gene taxon:10090 20060817 MGI relationship(CL:0000017) MGI MGI:1343961 Msh6 GO:0000790 MGI:MGI:3641510|PMID:16618598 IDA C mutS homolog 6 (E. coli) GTBP|Msh6 gene taxon:10090 20061130 MGI relationship(CL:0000542) MGI MGI:1343961 Msh6 GO:0003682 MGI:MGI:3641510|PMID:16618598 IDA F mutS homolog 6 (E. coli) GTBP|Msh6 gene taxon:10090 20061130 MGI relationship(CL:0000542) MGI MGI:107376 Msi1 GO:0005634 MGI:MGI:3046455|PMID:15076722 IDA C Musashi homolog 1(Drosophila) m-Msi-1|Msi1|Msi1h|Musahi1 gene taxon:10090 20060726 MGI relationship(CL:0000098) MGI MGI:107376 Msi1 GO:0005634 MGI:MGI:3046455|PMID:15076722 IDA C Musashi homolog 1(Drosophila) m-Msi-1|Msi1|Msi1h|Musahi1 gene taxon:10090 20060726 MGI relationship(CL:0000633) MGI MGI:107376 Msi1 GO:0005634 MGI:MGI:3046455|PMID:15076722 IDA C Musashi homolog 1(Drosophila) m-Msi-1|Msi1|Msi1h|Musahi1 gene taxon:10090 20060726 MGI relationship(CL:0000634) MGI MGI:107376 Msi1 GO:0005634 MGI:MGI:3046455|PMID:15076722 IDA C Musashi homolog 1(Drosophila) m-Msi-1|Msi1|Msi1h|Musahi1 gene taxon:10090 20060726 MGI relationship(CL:0000635) MGI MGI:107376 Msi1 GO:0005737 MGI:MGI:3046455|PMID:15076722 IDA C Musashi homolog 1(Drosophila) m-Msi-1|Msi1|Msi1h|Musahi1 gene taxon:10090 20060726 MGI relationship(CL:0000098) MGI MGI:107376 Msi1 GO:0005737 MGI:MGI:3046455|PMID:15076722 IDA C Musashi homolog 1(Drosophila) m-Msi-1|Msi1|Msi1h|Musahi1 gene taxon:10090 20060726 MGI relationship(CL:0000633) MGI MGI:107376 Msi1 GO:0005737 MGI:MGI:3046455|PMID:15076722 IDA C Musashi homolog 1(Drosophila) m-Msi-1|Msi1|Msi1h|Musahi1 gene taxon:10090 20060726 MGI relationship(CL:0000634) MGI MGI:107376 Msi1 GO:0005737 MGI:MGI:3046455|PMID:15076722 IDA C Musashi homolog 1(Drosophila) m-Msi-1|Msi1|Msi1h|Musahi1 gene taxon:10090 20060726 MGI relationship(CL:0000635) MGI MGI:97168 Msx1 GO:0000122 MGI:MGI:3603095|PMID:16002402 IDA P homeo box, msh-like 1 Hox-7|Hox7|Hox7.1|msh|muscle-segment homeobox gene taxon:10090 20051104 MGI relationship(CL:0000002) MGI MGI:3043038 Mtu GO:0030154 MGI:MGI:3056222|PMID:15384171 IMP MGI:3043039 P montu gene taxon:10090 20050322 MGI relationship(CL:0000333) MGI MGI:1203527 Muc3 GO:0016324 MGI:MGI:3052756|PMID:11352827 IDA C mucin 3, intestinal gene taxon:10090 20040927 MGI relationship(CL:0000239) MGI MGI:103581 Musk GO:0005515 MGI:MGI:2384358|PMID:12165471 IPI UniProt:P51141|UniProt:O88643 F muscle, skeletal, receptor tyrosine kinase MDK4|Nsk1|Nsk2|Nsk3 gene taxon:10090 20070228 MGI relationship(CL:0000002) MGI MGI:103581 Musk GO:0007528 MGI:MGI:3630229|PMID:16794080 IGI MGI:3584043 P muscle, skeletal, receptor tyrosine kinase MDK4|Nsk1|Nsk2|Nsk3 gene taxon:10090 20060814 MGI relationship(CL:0000188) MGI MGI:103581 Musk GO:0043113 MGI:MGI:3630229|PMID:16794080 IGI MGI:3584043 P muscle, skeletal, receptor tyrosine kinase MDK4|Nsk1|Nsk2|Nsk3 gene taxon:10090 20060814 MGI relationship(CL:0000188) MGI MGI:97245 Mxi1 GO:0005634 MGI:MGI:3513728|PMID:15467743 IDA C Max interacting protein 1 Mad2 gene taxon:10090 20050120 MGI relationship(CL:0000002) MGI MGI:97357 Mycn GO:0005634 MGI:MGI:3574742|PMID:15716345 IDA C v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian) N-myc|Nmyc|Nmyc-1|Nmyc1 gene taxon:10090 20050513 MGI relationship(CL:0000002) MGI MGI:97357 Mycn GO:0008284 MGI:MGI:3574742|PMID:15716345 IMP MGI:2388717|MGI:3574949 P v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian) N-myc|Nmyc|Nmyc-1|Nmyc1 gene taxon:10090 20050513 MGI relationship(CL:0000082) MGI MGI:97252 Myf5 GO:0001952 MGI:MGI:3624056|PMID:16554364 IMP MGI:1857973 P myogenic factor 5 Myf-5 gene taxon:10090 20060707 MGI relationship(CL:0000056) MGI MGI:97252 Myf5 GO:0007519 MGI:MGI:64468|PMID:8269513 IGI MGI:97275 P myogenic factor 5 Myf-5 gene taxon:10090 20050722 MGI relationship(CL:0000056) MGI MGI:1930780 Myh10 GO:0000281 MGI:MGI:3052228|PMID:12893741 IMP MGI:2386445|MGI:3052104 P myosin, heavy polypeptide 10, non-muscle Myhn2|Myosin IIB|NMHC II-B|NMHC-B|nonmuscle myosin heavy chain II-B|nonmuscle myosin heavy chain IIB|SMemb gene taxon:10090 20061219 MGI relationship(CL:0000746) MGI MGI:1930780 Myh10 GO:0001701 MGI:MGI:3052228|PMID:12893741 IMP MGI:2386445|MGI:3052104 P myosin, heavy polypeptide 10, non-muscle Myhn2|Myosin IIB|NMHC II-B|NMHC-B|nonmuscle myosin heavy chain II-B|nonmuscle myosin heavy chain IIB|SMemb gene taxon:10090 20061219 MGI relationship(CL:0000746) MGI MGI:1930780 Myh10 GO:0001725 MGI:MGI:3042318|PMID:14617807 IMP C myosin, heavy polypeptide 10, non-muscle Myhn2|Myosin IIB|NMHC II-B|NMHC-B|nonmuscle myosin heavy chain II-B|nonmuscle myosin heavy chain IIB|SMemb gene taxon:10090 20040707 MGI relationship(CL:0000002) MGI MGI:1930780 Myh10 GO:0001764 MGI:MGI:3051726|PMID:15034141 IMP MGI:3052104 P myosin, heavy polypeptide 10, non-muscle Myhn2|Myosin IIB|NMHC II-B|NMHC-B|nonmuscle myosin heavy chain II-B|nonmuscle myosin heavy chain IIB|SMemb gene taxon:10090 20041001 MGI relationship(CL:0000117) MGI MGI:1930780 Myh10 GO:0001764 MGI:MGI:3051726|PMID:15034141 IMP MGI:3052104 P myosin, heavy polypeptide 10, non-muscle Myhn2|Myosin IIB|NMHC II-B|NMHC-B|nonmuscle myosin heavy chain II-B|nonmuscle myosin heavy chain IIB|SMemb gene taxon:10090 20041001 MGI relationship(CL:0000120) MGI MGI:1930780 Myh10 GO:0001778 MGI:MGI:3042318|PMID:14617807 IMP P myosin, heavy polypeptide 10, non-muscle Myhn2|Myosin IIB|NMHC II-B|NMHC-B|nonmuscle myosin heavy chain II-B|nonmuscle myosin heavy chain IIB|SMemb gene taxon:10090 20040707 MGI relationship(CL:0000002) MGI MGI:1930780 Myh10 GO:0006887 MGI:MGI:3042318|PMID:14617807 IMP P myosin, heavy polypeptide 10, non-muscle Myhn2|Myosin IIB|NMHC II-B|NMHC-B|nonmuscle myosin heavy chain II-B|nonmuscle myosin heavy chain IIB|SMemb gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1930780 Myh10 GO:0007512 MGI:MGI:3052228|PMID:12893741 IMP MGI:2386445|MGI:3052104 P myosin, heavy polypeptide 10, non-muscle Myhn2|Myosin IIB|NMHC II-B|NMHC-B|nonmuscle myosin heavy chain II-B|nonmuscle myosin heavy chain IIB|SMemb gene taxon:10090 20061219 MGI relationship(CL:0000746) MGI MGI:1930780 Myh10 GO:0008283 MGI:MGI:3052228|PMID:12893741 IMP MGI:2386445 P myosin, heavy polypeptide 10, non-muscle Myhn2|Myosin IIB|NMHC II-B|NMHC-B|nonmuscle myosin heavy chain II-B|nonmuscle myosin heavy chain IIB|SMemb gene taxon:10090 20061219 MGI relationship(CL:0000746) MGI MGI:1930780 Myh10 GO:0030239 MGI:MGI:1354135|PMID:10712438 IMP MGI:2386439|MGI:2386445 P myosin, heavy polypeptide 10, non-muscle Myhn2|Myosin IIB|NMHC II-B|NMHC-B|nonmuscle myosin heavy chain II-B|nonmuscle myosin heavy chain IIB|SMemb gene taxon:10090 20061110 MGI relationship(CL:0000746) MGI MGI:1930780 Myh10 GO:0043005 MGI:MGI:3656460|PMID:16481398 IDA C myosin, heavy polypeptide 10, non-muscle Myhn2|Myosin IIB|NMHC II-B|NMHC-B|nonmuscle myosin heavy chain II-B|nonmuscle myosin heavy chain IIB|SMemb gene taxon:10090 20061219 MGI relationship(CL:0000121) MGI MGI:1930780 Myh10 GO:0043025 MGI:MGI:3656460|PMID:16481398 IDA C myosin, heavy polypeptide 10, non-muscle Myhn2|Myosin IIB|NMHC II-B|NMHC-B|nonmuscle myosin heavy chain II-B|nonmuscle myosin heavy chain IIB|SMemb gene taxon:10090 20061219 MGI relationship(CL:0000121) MGI MGI:1930780 Myh10 GO:0043197 MGI:MGI:3656460|PMID:16481398 IDA C myosin, heavy polypeptide 10, non-muscle Myhn2|Myosin IIB|NMHC II-B|NMHC-B|nonmuscle myosin heavy chain II-B|nonmuscle myosin heavy chain IIB|SMemb gene taxon:10090 20061219 MGI relationship(CL:0000121) MGI MGI:1930780 Myh10 GO:0055003 MGI:MGI:1099556|PMID:9356462 IMP MGI:2386445 P myosin, heavy polypeptide 10, non-muscle Myhn2|Myosin IIB|NMHC II-B|NMHC-B|nonmuscle myosin heavy chain II-B|nonmuscle myosin heavy chain IIB|SMemb gene taxon:10090 20061110 MGI relationship(CL:0000746) MGI MGI:1930780 Myh10 GO:0055015 MGI:MGI:3052228|PMID:12893741 IMP MGI:2386445|MGI:3052104 P myosin, heavy polypeptide 10, non-muscle Myhn2|Myosin IIB|NMHC II-B|NMHC-B|nonmuscle myosin heavy chain II-B|nonmuscle myosin heavy chain IIB|SMemb gene taxon:10090 20061219 MGI relationship(CL:0000746) MGI MGI:102643 Myh11 GO:0001725 MGI:MGI:87235|PMID:8593698 IDA C myosin, heavy polypeptide 11, smooth muscle SM1|SM2|smMHC gene taxon:10090 20061222 MGI relationship(CL:0000002) MGI MGI:102643 Myh11 GO:0005859 MGI:MGI:3576700|PMID:11715025 IDA C myosin, heavy polypeptide 11, smooth muscle SM1|SM2|smMHC gene taxon:10090 20061222 MGI relationship(CL:0000192) MGI MGI:102643 Myh11 GO:0006939 MGI:MGI:3576700|PMID:11715025 IDA P myosin, heavy polypeptide 11, smooth muscle SM1|SM2|smMHC gene taxon:10090 20061222 MGI relationship(CL:0000192) MGI MGI:102643 Myh11 GO:0016459 MGI:MGI:87235|PMID:8593698 IDA C myosin, heavy polypeptide 11, smooth muscle SM1|SM2|smMHC gene taxon:10090 20061222 MGI relationship(CL:0000002) MGI MGI:102643 Myh11 GO:0030485 MGI:MGI:3576700|PMID:11715025 IDA C myosin, heavy polypeptide 11, smooth muscle SM1|SM2|smMHC gene taxon:10090 20061222 MGI relationship(CL:0000192) MGI MGI:1919210 Myh14 GO:0001725 MGI:MGI:3582121|PMID:15774463 IDA C myosin, heavy polypeptide 14 NMHC II-C gene taxon:10090 20061220 MGI relationship(CL:0000002) MGI MGI:1339710 Myh2 GO:0001778 MGI:MGI:3042318|PMID:14617807 IMP P myosin, heavy polypeptide 2, skeletal muscle, adult MHC2A|MyHC-IIa|Myhs-f|Myhs-f1|Myhsf1 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1339710 Myh2 GO:0005794 MGI:MGI:3042318|PMID:14617807 IMP C myosin, heavy polypeptide 2, skeletal muscle, adult MHC2A|MyHC-IIa|Myhs-f|Myhs-f1|Myhsf1 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1339709 Myh3 GO:0016459 MGI:MGI:79691|PMID:1728586 IDA C myosin, heavy polypeptide 3, skeletal muscle, embryonic MyHC-emb|Myhs-e|Myhse gene taxon:10090 20061024 MGI relationship(CL:0000188) MGI MGI:97255 Myh6 GO:0006941 MGI:MGI:1332374|PMID:10074482 IMP MGI:2182704 P myosin, heavy polypeptide 6, cardiac muscle, alpha alpha cardiac MHC|alpha myosin|cardiomyopathy, hypertrophic 1|Myhc-a|Myhca gene taxon:10090 20061018 MGI relationship(CL:0000746) MGI MGI:97255 Myh6 GO:0006941 MGI:MGI:3689292|PMID:16983074 IMP MGI:3690299|MGI:3690300 P myosin, heavy polypeptide 6, cardiac muscle, alpha alpha cardiac MHC|alpha myosin|cardiomyopathy, hypertrophic 1|Myhc-a|Myhca gene taxon:10090 20061212 MGI relationship(CL:0000746) MGI MGI:97255 Myh6 GO:0007512 MGI:MGI:1333559|PMID:10066683 IMP MGI:2182704 P myosin, heavy polypeptide 6, cardiac muscle, alpha alpha cardiac MHC|alpha myosin|cardiomyopathy, hypertrophic 1|Myhc-a|Myhca gene taxon:10090 20061020 MGI relationship(CL:0000746) MGI MGI:97255 Myh6 GO:0007512 MGI:MGI:83539|PMID:8878443 IMP MGI:3652543 P myosin, heavy polypeptide 6, cardiac muscle, alpha alpha cardiac MHC|alpha myosin|cardiomyopathy, hypertrophic 1|Myhc-a|Myhca gene taxon:10090 20060922 MGI relationship(CL:0000746) MGI MGI:97255 Myh6 GO:0008016 MGI:MGI:1332374|PMID:10074482 IMP MGI:2182704 P myosin, heavy polypeptide 6, cardiac muscle, alpha alpha cardiac MHC|alpha myosin|cardiomyopathy, hypertrophic 1|Myhc-a|Myhca gene taxon:10090 20061018 MGI relationship(CL:0000746) MGI MGI:97255 Myh6 GO:0030239 MGI:MGI:1333559|PMID:10066683 IMP MGI:2182704 P myosin, heavy polypeptide 6, cardiac muscle, alpha alpha cardiac MHC|alpha myosin|cardiomyopathy, hypertrophic 1|Myhc-a|Myhca gene taxon:10090 20061020 MGI relationship(CL:0000746) MGI MGI:97255 Myh6 GO:0045214 MGI:MGI:83539|PMID:8878443 IMP MGI:3652543 P myosin, heavy polypeptide 6, cardiac muscle, alpha alpha cardiac MHC|alpha myosin|cardiomyopathy, hypertrophic 1|Myhc-a|Myhca gene taxon:10090 20060922 MGI relationship(CL:0000746) MGI MGI:97255 Myh6 GO:0048739 MGI:MGI:1333559|PMID:10066683 IMP MGI:2182704 P myosin, heavy polypeptide 6, cardiac muscle, alpha alpha cardiac MHC|alpha myosin|cardiomyopathy, hypertrophic 1|Myhc-a|Myhca gene taxon:10090 20061020 MGI relationship(CL:0000746) MGI MGI:97255 Myh6 GO:0048739 MGI:MGI:83539|PMID:8878443 IMP MGI:3652543 P myosin, heavy polypeptide 6, cardiac muscle, alpha alpha cardiac MHC|alpha myosin|cardiomyopathy, hypertrophic 1|Myhc-a|Myhca gene taxon:10090 20060922 MGI relationship(CL:0000746) MGI MGI:1339712 Myh8 GO:0016459 MGI:MGI:79691|PMID:1728586 IDA C myosin, heavy polypeptide 8, skeletal muscle, perinatal MyHC-pn|Myhs-p|Myhsp gene taxon:10090 20061024 MGI relationship(CL:0000188) MGI MGI:107717 Myh9 GO:0000904 MGI:MGI:3522322|PMID:15292239 IMP MGI:3522434 P myosin, heavy polypeptide 9, non-muscle D0Jmb2|NMHC II-A gene taxon:10090 20050303 MGI relationship(CL:0000223) MGI MGI:107494 Mylc2b GO:0045177 MGI:MGI:3037622|PMID:15037549 IDA C myosin light chain, regulatory B RLC-B gene taxon:10090 20040630 MGI relationship(CL:0000066) MGI MGI:2139434 Mylk2 GO:0007274 MGI:MGI:3625625|PMID:16606832 IGI MGI:88323 P myosin, light polypeptide kinase 2, skeletal muscle gene taxon:10090 20060808 MGI relationship(CL:0000108) MGI MGI:2139434 Mylk2 GO:0007274 MGI:MGI:3625625|PMID:16606832 IMP P myosin, light polypeptide kinase 2, skeletal muscle gene taxon:10090 20060808 MGI relationship(CL:0000108) MGI MGI:106612 Myo1c GO:0032420 MGI:MGI:3686545|PMID:17050716 IDA C myosin IC C80397|mm1beta|myosin-Ibeta|myr2 gene taxon:10090 20070322 MGI relationship(CL:0000589) MGI MGI:106612 Myo1c GO:0032420 MGI:MGI:3686545|PMID:17050716 IDA C myosin IC C80397|mm1beta|myosin-Ibeta|myr2 gene taxon:10090 20070322 MGI relationship(CL:0000601) MGI MGI:105976 Myo5a GO:0042640 MGI:MGI:3513741|PMID:15550542 IMP MGI:1856004 P myosin Va flail|MVa|Myo5|MyoVA gene taxon:10090 20050207 MGI relationship(CL:0000148) MGI MGI:105976 Myo5a GO:0048066 MGI:MGI:3513741|PMID:15550542 IMP MGI:1856004 P myosin Va flail|MVa|Myo5|MyoVA gene taxon:10090 20050207 MGI relationship(CL:0000148) MGI MGI:104510 Myo7a GO:0060088 MGI:MGI:3686545|PMID:17050716 IMP P myosin VIIa Myo7|nmf371|USH1B gene taxon:10090 20070322 MGI relationship(CL:0000589) MGI MGI:104510 Myo7a GO:0060088 MGI:MGI:3686545|PMID:17050716 IMP P myosin VIIa Myo7|nmf371|USH1B gene taxon:10090 20070322 MGI relationship(CL:0000601) MGI MGI:2137495 Myocd GO:0001570 MGI:MGI:2670236|PMID:12867591 IMP MGI:3052940 P myocardin Srfcp gene taxon:10090 20050721 MGI relationship(CL:0000192) MGI MGI:2137495 Myocd GO:0042692 MGI:MGI:2670236|PMID:12867591 IMP MGI:3052940 P myocardin Srfcp gene taxon:10090 20050721 MGI relationship(CL:0000192) MGI MGI:97275 Myod1 GO:0007519 MGI:MGI:64468|PMID:8269513 IGI MGI:97252 P myogenic differentiation 1 MYF3|MyoD|Myod-1 gene taxon:10090 20050722 MGI relationship(CL:0000056) MGI MGI:2442415 Myst3 GO:0035019 MGI:MGI:3624570|PMID:16702405 IMP P MYST histone acetyltransferase (monocytic leukemia) 3 MOZ|Zfp220 gene taxon:10090 20060629 MGI relationship(CL:0000037) MGI MGI:1919200 Nanog GO:0005634 MGI:MGI:3527362|PMID:15582778 IDA C Nanog homeobox ecat4|ENK gene taxon:10090 20050308 MGI relationship(CL:0000001) MGI MGI:1919200 Nanog GO:0005634 MGI:MGI:3578587|PMID:15788452 IDA C Nanog homeobox ecat4|ENK gene taxon:10090 20050727 MGI relationship(CL:0000007) MGI MGI:2676627 Nanos2 GO:0007283 MGI:MGI:2680516|PMID:12947200 IMP MGI:2682606 P nanos homolog 2 (Drosophila) nos2 gene taxon:10090 20050721 MGI relationship(CL:0000015) MGI MGI:2675387 Nanos3 GO:0007283 MGI:MGI:2680516|PMID:12947200 IMP MGI:2682607 P nanos homolog 3 (Drosophila) nos3 gene taxon:10090 20050721 MGI relationship(CL:0000015) MGI MGI:2675387 Nanos3 GO:0048157 MGI:MGI:2680516|PMID:12947200 IMP MGI:2682607 P nanos homolog 3 (Drosophila) nos3 gene taxon:10090 20050721 MGI relationship(CL:0000021) MGI MGI:2183683 Nav1 GO:0001578 MGI:MGI:3574000|PMID:15797708 IDA P neuron navigator 1 POMFIL3|steerin-1|unc53H1 gene taxon:10090 20050504 MGI relationship(CL:0000002) MGI MGI:2183683 Nav1 GO:0001764 MGI:MGI:3574000|PMID:15797708 IMP P neuron navigator 1 POMFIL3|steerin-1|unc53H1 gene taxon:10090 20050504 MGI relationship(CL:0000117) MGI MGI:2183683 Nav1 GO:0015630 MGI:MGI:3574000|PMID:15797708 IDA C neuron navigator 1 POMFIL3|steerin-1|unc53H1 gene taxon:10090 20050504 MGI relationship(CL:0000002) MGI MGI:1351625 Nbn GO:0008283 MGI:MGI:3577830|PMID:15821748 IMP MGI:3578646 P nibrin Nbs1 gene taxon:10090 20050620 MGI relationship(CL:0000337) MGI MGI:1915548 Ncapd2 GO:0000793 MGI:MGI:3512088|PMID:12082153 IDA C non-SMC condensin I complex, subunit D2 CAP-D2|CNAP1 gene taxon:10090 20041230 MGI relationship(CL:0000007) MGI MGI:1915548 Ncapd2 GO:0000793 MGI:MGI:3512088|PMID:12082153 IDA C non-SMC condensin I complex, subunit D2 CAP-D2|CNAP1 gene taxon:10090 20041230 MGI relationship(CL:0000023) MGI MGI:1914453 Nde1 GO:0005813 MGI:MGI:3513966|PMID:15473967 IDA C nuclear distribution gene E homolog 1 (A nidulans) mNudE gene taxon:10090 20050208 MGI relationship(CL:0000002) MGI MGI:1914453 Nde1 GO:0005819 MGI:MGI:3513966|PMID:15473967 IDA C nuclear distribution gene E homolog 1 (A nidulans) mNudE gene taxon:10090 20050208 MGI relationship(CL:0000002) MGI MGI:1914453 Nde1 GO:0007405 MGI:MGI:3513966|PMID:15473967 IMP MGI:3514026 P nuclear distribution gene E homolog 1 (A nidulans) mNudE gene taxon:10090 20050208 MGI relationship(CL:0000031) MGI MGI:1914453 Nde1 GO:0030900 MGI:MGI:3513966|PMID:15473967 IMP MGI:3514026 P nuclear distribution gene E homolog 1 (A nidulans) mNudE gene taxon:10090 20050208 MGI relationship(CL:0000031) MGI MGI:1932915 Ndel1 GO:0000226 MGI:MGI:3588829|PMID:16107726 IGI MGI:109520 P nuclear distribution gene E-like homolog 1 (A. nidulans) MITAP1 gene taxon:10090 20051014 MGI relationship(CL:0000117) MGI MGI:1932915 Ndel1 GO:0001764 MGI:MGI:3588829|PMID:16107726 IGI MGI:109520 P nuclear distribution gene E-like homolog 1 (A. nidulans) MITAP1 gene taxon:10090 20051014 MGI relationship(CL:0000598) MGI MGI:1932915 Ndel1 GO:0001833 MGI:MGI:3588829|PMID:16107726 IMP MGI:3589467 P nuclear distribution gene E-like homolog 1 (A. nidulans) MITAP1 gene taxon:10090 20051014 MGI relationship(CL:0000001) MGI MGI:1932915 Ndel1 GO:0005813 MGI:MGI:3608033|PMID:16203747 IDA C nuclear distribution gene E-like homolog 1 (A. nidulans) MITAP1 gene taxon:10090 20060118 MGI relationship(CL:0000002) MGI MGI:1932915 Ndel1 GO:0021955 MGI:MGI:3047464|PMID:15208636 IMP P nuclear distribution gene E-like homolog 1 (A. nidulans) MITAP1 gene taxon:10090 20070306 MGI relationship(CL:0000001) MGI MGI:97290 Ndn GO:0001764 MGI:MGI:3582873|PMID:15972963 IMP MGI:2653048 P necdin Peg6 gene taxon:10090 20050824 MGI relationship(CL:0000117) MGI MGI:97290 Ndn GO:0005634 MGI:MGI:3027170|PMID:14593116 IDA C necdin Peg6 gene taxon:10090 20050424 MGI relationship(CL:0000002) MGI MGI:97290 Ndn GO:0005737 MGI:MGI:3027170|PMID:14593116 IDA C necdin Peg6 gene taxon:10090 20050424 MGI relationship(CL:0000002) MGI MGI:97290 Ndn GO:0005813 MGI:MGI:3530392|PMID:15649943 IDA C necdin Peg6 gene taxon:10090 20050424 MGI relationship(CL:0000002) MGI MGI:97290 Ndn GO:0007409 MGI:MGI:3582873|PMID:15972963 IMP MGI:2653048 P necdin Peg6 gene taxon:10090 20050824 MGI relationship(CL:0000117) MGI MGI:97290 Ndn GO:0007413 MGI:MGI:3582873|PMID:15972963 IMP MGI:2653048 P necdin Peg6 gene taxon:10090 20050824 MGI relationship(CL:0000540) MGI MGI:97290 Ndn GO:0007417 MGI:MGI:3530392|PMID:15649943 IMP MGI:2653048 P necdin Peg6 gene taxon:10090 20050424 MGI relationship(CL:0000117) MGI MGI:97290 Ndn GO:0008347 MGI:MGI:3582873|PMID:15972963 IMP MGI:2653048 P necdin Peg6 gene taxon:10090 20050824 MGI relationship(CL:0000681) MGI MGI:97290 Ndn GO:0019233 MGI:MGI:3586399|PMID:16049186 IMP MGI:3586988 P necdin Peg6 gene taxon:10090 20051213 MGI relationship(CL:0000101) MGI MGI:97290 Ndn GO:0043015 MGI:MGI:3530392|PMID:15649943 IDA F necdin Peg6 gene taxon:10090 20050424 MGI relationship(CL:0000002) MGI MGI:97290 Ndn GO:0048011 MGI:MGI:3586399|PMID:16049186 IMP MGI:3586988 P necdin Peg6 gene taxon:10090 20051213 MGI relationship(CL:0000540) MGI MGI:97290 Ndn GO:0048666 MGI:MGI:3586399|PMID:16049186 IMP MGI:3586988 P necdin Peg6 gene taxon:10090 20051213 MGI relationship(CL:0000101) MGI MGI:97290 Ndn GO:0048676 MGI:MGI:3582873|PMID:15972963 IMP MGI:2653048 P necdin Peg6 gene taxon:10090 20050824 MGI relationship(CL:0000540) MGI MGI:104719 Ndst1 GO:0000165 MGI:MGI:3588476|PMID:16020517 IMP MGI:3589383 P N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1 glucosaminyl N-deacetylase/N-sulfotransferase 1|Hsst|Ndst-1 gene taxon:10090 20051118 MGI relationship(CL:0000002) MGI MGI:104719 Ndst1 GO:0008543 MGI:MGI:3588476|PMID:16020517 IMP MGI:3589383 P N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1 glucosaminyl N-deacetylase/N-sulfotransferase 1|Hsst|Ndst-1 gene taxon:10090 20051118 MGI relationship(CL:0000002) MGI MGI:97309 Nefh GO:0000226 MGI:MGI:1342909|PMID:10461886 IGI MGI:97314 P neurofilament, heavy polypeptide NEFH|NF-H|NF200|Nfh gene taxon:10090 20070302 MGI relationship(CL:0000540) MGI MGI:97309 Nefh GO:0005883 MGI:MGI:1336062|PMID:10221457 IDA C neurofilament, heavy polypeptide NEFH|NF-H|NF200|Nfh gene taxon:10090 20070226 MGI relationship(CL:0000029) MGI MGI:97309 Nefh GO:0045110 MGI:MGI:1342909|PMID:10461886 IGI MGI:97313|MGI:97314 P neurofilament, heavy polypeptide NEFH|NF-H|NF200|Nfh gene taxon:10090 20070302 MGI relationship(CL:0000540) MGI MGI:97309 Nefh GO:0060052 MGI:MGI:1342909|PMID:10461886 IGI MGI:97313|MGI:97314 P neurofilament, heavy polypeptide NEFH|NF-H|NF200|Nfh gene taxon:10090 20070302 MGI relationship(CL:0000540) MGI MGI:97313 Nefl GO:0000226 MGI:MGI:2148377|PMID:11487626 IMP MGI:2180095 P neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070305 MGI relationship(CL:0000540) MGI MGI:97313 Nefl GO:0005883 MGI:MGI:1336062|PMID:10221457 IDA C neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070226 MGI relationship(CL:0000029) MGI MGI:97313 Nefl GO:0005883 MGI:MGI:81460|PMID:8821035 IDA C neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070222 MGI relationship(CL:0000111) MGI MGI:97313 Nefl GO:0014012 MGI:MGI:1100197|PMID:9398473 IMP MGI:2180095 P neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070222 MGI relationship(CL:0000111) MGI MGI:97313 Nefl GO:0030424 MGI:MGI:81460|PMID:8821035 IDA C neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070222 MGI relationship(CL:0000111) MGI MGI:97313 Nefl GO:0031133 MGI:MGI:1100197|PMID:9398473 IMP MGI:2180095 P neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070222 MGI relationship(CL:0000111) MGI MGI:97313 Nefl GO:0031133 MGI:MGI:1934092|PMID:11343650 IMP MGI:2180095 P neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070305 MGI relationship(CL:0000100) MGI MGI:97313 Nefl GO:0043524 MGI:MGI:1096547|PMID:7946341 IMP P neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070222 MGI relationship(CL:0000100) MGI MGI:97313 Nefl GO:0043524 MGI:MGI:1861055|PMID:10884316 IMP MGI:2180095 P neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070302 MGI relationship(CL:0000100) MGI MGI:97313 Nefl GO:0045109 MGI:MGI:1096547|PMID:7946341 IMP P neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070222 MGI relationship(CL:0000100) MGI MGI:97313 Nefl GO:0045110 MGI:MGI:1342909|PMID:10461886 IGI MGI:97314|MGI:97309 P neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070302 MGI relationship(CL:0000540) MGI MGI:97313 Nefl GO:0048812 MGI:MGI:1861055|PMID:10884316 IMP MGI:2180095 P neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070302 MGI relationship(CL:0000540) MGI MGI:97313 Nefl GO:0050772 MGI:MGI:1096547|PMID:7946341 IMP P neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070222 MGI relationship(CL:0000100) MGI MGI:97313 Nefl GO:0060052 MGI:MGI:1100197|PMID:9398473 IMP MGI:2180095 P neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070227 MGI relationship(CL:0000111) MGI MGI:97313 Nefl GO:0060052 MGI:MGI:1339419|PMID:10350642 IGI MGI:96568 P neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070302 MGI relationship(CL:0000540) MGI MGI:97313 Nefl GO:0060052 MGI:MGI:1342909|PMID:10461886 IGI MGI:97314|MGI:97309 P neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070302 MGI relationship(CL:0000540) MGI MGI:97313 Nefl GO:0060052 MGI:MGI:1347434|PMID:15132161 IMP MGI:2180095 P neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070302 MGI relationship(CL:0000540) MGI MGI:97313 Nefl GO:0060052 MGI:MGI:1934092|PMID:11343650 IGI MGI:98351 P neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070305 MGI relationship(CL:0000100) MGI MGI:97313 Nefl GO:0060052 MGI:MGI:2148377|PMID:11487626 IMP MGI:2180095 P neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070305 MGI relationship(CL:0000540) MGI MGI:97313 Nefl GO:0060052 MGI:MGI:3664358|PMID:16920084 IMP MGI:2180095 P neurofilament, light polypeptide CMT2E|NF-L|NF68|Nfl gene taxon:10090 20070309 MGI relationship(CL:0000540) MGI MGI:97314 Nefm GO:0000226 MGI:MGI:1342909|PMID:10461886 IGI MGI:97309 P neurofilament, medium polypeptide Nef3|NF-M|NF160|NF165|Nfm gene taxon:10090 20070302 MGI relationship(CL:0000540) MGI MGI:97314 Nefm GO:0005883 MGI:MGI:1336062|PMID:10221457 IDA C neurofilament, medium polypeptide Nef3|NF-M|NF160|NF165|Nfm gene taxon:10090 20070226 MGI relationship(CL:0000029) MGI MGI:97314 Nefm GO:0008088 MGI:MGI:1342909|PMID:10461886 IMP MGI:2180106 P neurofilament, medium polypeptide Nef3|NF-M|NF160|NF165|Nfm gene taxon:10090 20070302 MGI relationship(CL:0000540) MGI MGI:97314 Nefm GO:0031133 MGI:MGI:1203441|PMID:9566972 IMP MGI:2180135 P neurofilament, medium polypeptide Nef3|NF-M|NF160|NF165|Nfm gene taxon:10090 20070226 MGI relationship(CL:0000111) MGI MGI:97314 Nefm GO:0031133 MGI:MGI:1203441|PMID:9566972 IMP MGI:2180135 P neurofilament, medium polypeptide Nef3|NF-M|NF160|NF165|Nfm gene taxon:10090 20070226 MGI relationship(CL:0000117) MGI MGI:97314 Nefm GO:0031133 MGI:MGI:1342909|PMID:10461886 IMP MGI:2180106 P neurofilament, medium polypeptide Nef3|NF-M|NF160|NF165|Nfm gene taxon:10090 20070302 MGI relationship(CL:0000540) MGI MGI:97314 Nefm GO:0045110 MGI:MGI:1342909|PMID:10461886 IGI MGI:97313|MGI:97309 P neurofilament, medium polypeptide Nef3|NF-M|NF160|NF165|Nfm gene taxon:10090 20070302 MGI relationship(CL:0000540) MGI MGI:97314 Nefm GO:0060052 MGI:MGI:1203441|PMID:9566972 IMP MGI:2180135 P neurofilament, medium polypeptide Nef3|NF-M|NF160|NF165|Nfm gene taxon:10090 20070227 MGI relationship(CL:0000111) MGI MGI:97314 Nefm GO:0060052 MGI:MGI:1203441|PMID:9566972 IMP MGI:2180135 P neurofilament, medium polypeptide Nef3|NF-M|NF160|NF165|Nfm gene taxon:10090 20070227 MGI relationship(CL:0000117) MGI MGI:97314 Nefm GO:0060052 MGI:MGI:1342909|PMID:10461886 IGI MGI:97313|MGI:97309 P neurofilament, medium polypeptide Nef3|NF-M|NF160|NF165|Nfm gene taxon:10090 20070302 MGI relationship(CL:0000540) MGI MGI:109359 Nek2 GO:0000070 MGI:MGI:3057231|PMID:15479717 IMP P NIMA (never in mitosis gene a)-related expressed kinase 2 gene taxon:10090 20041130 MGI relationship(CL:0000007) MGI MGI:109359 Nek2 GO:0000794 MGI:MGI:3057231|PMID:15479717 IDA C NIMA (never in mitosis gene a)-related expressed kinase 2 gene taxon:10090 20041130 MGI relationship(CL:0000007) MGI MGI:109359 Nek2 GO:0000922 MGI:MGI:3057231|PMID:15479717 IDA C NIMA (never in mitosis gene a)-related expressed kinase 2 gene taxon:10090 20041130 MGI relationship(CL:0000007) MGI MGI:109359 Nek2 GO:0030496 MGI:MGI:3057231|PMID:15479717 IDA C NIMA (never in mitosis gene a)-related expressed kinase 2 gene taxon:10090 20041130 MGI relationship(CL:0000007) MGI MGI:1913458 Nenf GO:0008083 MGI:MGI:3573712|PMID:15605373 IDA F neuron derived neurotrophic factor neudesin gene taxon:10090 20050805 MGI relationship(CL:0000001) MGI MGI:1913458 Nenf GO:0043410 MGI:MGI:3573712|PMID:15605373 IDA P neuron derived neurotrophic factor neudesin gene taxon:10090 20050805 MGI relationship(CL:0000001) MGI MGI:101784 Nes GO:0005737 MGI:MGI:2686772|PMID:14706696 IDA C nestin ESTM46 gene taxon:10090 20041006 MGI relationship(CL:0000066) MGI MGI:1339708 Neurod1 GO:0005634 MGI:MGI:2159597|PMID:11891657 IDA C neurogenic differentiation 1 BETA2|BHF-1|Neurod gene taxon:10090 20041007 MGI relationship(CL:0000066) MGI MGI:1339708 Neurod1 GO:0043010 MGI:MGI:2158684|PMID:11861467 IGI MGI:108055 P neurogenic differentiation 1 BETA2|BHF-1|Neurod gene taxon:10090 20050721 MGI relationship(CL:0000561) MGI MGI:1339708 Neurod1 GO:0045165 MGI:MGI:2158684|PMID:11861467 IGI MGI:108055 P neurogenic differentiation 1 BETA2|BHF-1|Neurod gene taxon:10090 20050721 MGI relationship(CL:0000561) MGI MGI:108055 Neurod4 GO:0001764 MGI:MGI:3581944|PMID:15976074 IGI MGI:96919 P neurogenic differentiation 4 Atoh3|MATH-3|Math3 gene taxon:10090 20050822 MGI relationship(CL:0000100) MGI MGI:108055 Neurod4 GO:0001764 MGI:MGI:3581944|PMID:15976074 IMP MGI:2158737 P neurogenic differentiation 4 Atoh3|MATH-3|Math3 gene taxon:10090 20050822 MGI relationship(CL:0000100) MGI MGI:108055 Neurod4 GO:0007405 MGI:MGI:3581944|PMID:15976074 IGI MGI:96919 P neurogenic differentiation 4 Atoh3|MATH-3|Math3 gene taxon:10090 20050822 MGI relationship(CL:0000031) MGI MGI:108055 Neurod4 GO:0010001 MGI:MGI:3581944|PMID:15976074 IGI MGI:96919 P neurogenic differentiation 4 Atoh3|MATH-3|Math3 gene taxon:10090 20050822 MGI relationship(CL:0000128) MGI MGI:108055 Neurod4 GO:0043010 MGI:MGI:2158684|PMID:11861467 IGI MGI:1339708 P neurogenic differentiation 4 Atoh3|MATH-3|Math3 gene taxon:10090 20050721 MGI relationship(CL:0000561) MGI MGI:108055 Neurod4 GO:0045165 MGI:MGI:1926546|PMID:11032813 IGI MGI:1339708 P neurogenic differentiation 4 Atoh3|MATH-3|Math3 gene taxon:10090 20050721 MGI relationship(CL:0000561) MGI MGI:108055 Neurod4 GO:0048666 MGI:MGI:3581944|PMID:15976074 IMP MGI:2158737 P neurogenic differentiation 4 Atoh3|MATH-3|Math3 gene taxon:10090 20050822 MGI relationship(CL:0000100) MGI MGI:107754 Neurog1 GO:0030182 MGI:MGI:3607238|PMID:16145671 IMP MGI:2183171 P neurogenin 1 Math4C|Neurod3|neurogenin|neurogenin 1|ngn1 gene taxon:10090 20060221 MGI relationship(CL:0000101) MGI MGI:107754 Neurog1 GO:0031536 MGI:MGI:3607238|PMID:16145671 IMP P neurogenin 1 Math4C|Neurod3|neurogenin|neurogenin 1|ngn1 gene taxon:10090 20060221 MGI relationship(CL:0000337) MGI MGI:107754 Neurog1 GO:0045165 MGI:MGI:3055655|PMID:15229646 IGI MGI:109619 P neurogenin 1 Math4C|Neurod3|neurogenin|neurogenin 1|ngn1 gene taxon:10090 20041110 MGI relationship(CL:0000107) MGI MGI:107754 Neurog1 GO:0045165 MGI:MGI:3055655|PMID:15229646 IGI MGI:109619 P neurogenin 1 Math4C|Neurod3|neurogenin|neurogenin 1|ngn1 gene taxon:10090 20041110 MGI relationship(CL:0000617) MGI MGI:109619 Neurog2 GO:0001764 MGI:MGI:3612225|PMID:16396906 IMP MGI:2673381 P neurogenin 2 Atoh4|Math4A|ngn2 gene taxon:10090 20060324 MGI relationship(CL:0000700) MGI MGI:109619 Neurog2 GO:0007411 MGI:MGI:2670323|PMID:12895419 IMP MGI:2159010 P neurogenin 2 Atoh4|Math4A|ngn2 gene taxon:10090 20050721 MGI relationship(CL:0000117) MGI MGI:109619 Neurog2 GO:0030182 MGI:MGI:3612225|PMID:16396906 IMP MGI:2673381 P neurogenin 2 Atoh4|Math4A|ngn2 gene taxon:10090 20060324 MGI relationship(CL:0000700) MGI MGI:109619 Neurog2 GO:0045165 MGI:MGI:3055655|PMID:15229646 IGI MGI:107754 P neurogenin 2 Atoh4|Math4A|ngn2 gene taxon:10090 20041110 MGI relationship(CL:0000107) MGI MGI:109619 Neurog2 GO:0045165 MGI:MGI:3055655|PMID:15229646 IGI MGI:107754 P neurogenin 2 Atoh4|Math4A|ngn2 gene taxon:10090 20041110 MGI relationship(CL:0000617) MGI MGI:97306 Nf1 GO:0000165 MGI:MGI:3032882|PMID:14724565 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070208 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0001938 MGI:MGI:3629249|PMID:16644864 IGI MGI:97528 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000359) MGI MGI:97306 Nf1 GO:0001952 MGI:MGI:3613255|PMID:16405917 IMP MGI:1857478 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0005096 MGI:MGI:2149663|PMID:11435472 IMP MGI:1857478 F neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0005096 MGI:MGI:3526457|PMID:15665300 IGI MGI:96680 F neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0005096 MGI:MGI:79054|PMID:8563750 IMP MGI:1857444 F neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070125 MGI relationship(CL:0000002) MGI MGI:97306 Nf1 GO:0007265 MGI:MGI:1345870|PMID:10498620 IMP MGI:1857478 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070129 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0007265 MGI:MGI:1861510|PMID:10845775 IGI MGI:96680,MGI:96224 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070130 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0007265 MGI:MGI:2149663|PMID:11435472 IMP MGI:1857478 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0007265 MGI:MGI:2445662|PMID:12469121 IMP MGI:2176057|MGI:2450311 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070208 MGI relationship(CL:0000115) MGI MGI:97306 Nf1 GO:0007265 MGI:MGI:79054|PMID:8563750 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070125 MGI relationship(CL:0000002) MGI MGI:97306 Nf1 GO:0007265 MGI:MGI:85825|PMID:9001241 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070125 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0007406 MGI:MGI:66069|PMID:7926784 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070125 MGI relationship(CL:0000029) MGI MGI:97306 Nf1 GO:0008285 MGI:MGI:1339276|PMID:10383727 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070126 MGI relationship(CL:0000057) MGI MGI:97306 Nf1 GO:0008285 MGI:MGI:1342880|PMID:10442636 IMP MGI:1857478 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070126 MGI relationship(CL:0000127) MGI MGI:97306 Nf1 GO:0008285 MGI:MGI:1345870|PMID:10498620 IMP MGI:1857478 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070129 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0008285 MGI:MGI:1351242|PMID:10620616 IGI MGI:96677,MGI:96974 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070130 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0008285 MGI:MGI:1889141|PMID:10973261 IGI MGI:98834 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070130 MGI relationship(CL:0000125) MGI MGI:97306 Nf1 GO:0008285 MGI:MGI:1934508|PMID:11401406 IGI MGI:96974 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0008285 MGI:MGI:1934508|PMID:11401406 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0008285 MGI:MGI:2149663|PMID:11435472 IGI MGI:96974,MGI:97846 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0008285 MGI:MGI:3045579|PMID:14982883 IMP MGI:2176057|MGI:2176073 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070208 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0008285 MGI:MGI:3526457|PMID:15665300 IGI MGI:96680 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0008285 MGI:MGI:3579920|PMID:15944386 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0008285 MGI:MGI:3579920|PMID:15944386 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000031) MGI MGI:97306 Nf1 GO:0008285 MGI:MGI:79054|PMID:8563750 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070125 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0008285 MGI:MGI:85825|PMID:9001241 IGI UniProt:Q02297 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070130 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0008285 MGI:MGI:85825|PMID:9001241 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070125 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0014044 MGI:MGI:85825|PMID:9001241 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070125 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0014065 MGI:MGI:3032882|PMID:14724565 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070208 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0016525 MGI:MGI:3629251|PMID:16648142 IGI MGI:95516 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0021510 MGI:MGI:3689139|PMID:16906226 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20061205 MGI relationship(CL:0000029) MGI MGI:97306 Nf1 GO:0021897 MGI:MGI:3579920|PMID:15944386 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0022011 MGI:MGI:1352220|PMID:10586246 IMP P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070130 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0030036 MGI:MGI:3526457|PMID:15665300 IGI MGI:96680 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0030036 MGI:MGI:3613255|PMID:16405917 IMP MGI:1857478 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0030199 MGI:MGI:1339276|PMID:10383727 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070126 MGI relationship(CL:0000057) MGI MGI:97306 Nf1 GO:0030336 MGI:MGI:3032882|PMID:14724565 IGI MGI:1914172|MGI:98179 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070208 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0030336 MGI:MGI:3032882|PMID:14724565 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070208 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0030336 MGI:MGI:3629249|PMID:16644864 IGI MGI:97528 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000359) MGI MGI:97306 Nf1 GO:0032228 MGI:MGI:2157992|PMID:11793011 IGI MGI:96680 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0032320 MGI:MGI:2149663|PMID:11435472 IMP MGI:1857478 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070208 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0032320 MGI:MGI:79054|PMID:8563750 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070208 MGI relationship(CL:0000002) MGI MGI:97306 Nf1 GO:0035021 MGI:MGI:3526457|PMID:15665300 IGI MGI:96680 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0042060 MGI:MGI:1339276|PMID:10383727 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070126 MGI relationship(CL:0000057) MGI MGI:97306 Nf1 GO:0042992 MGI:MGI:2445662|PMID:12469121 IMP MGI:2176057|MGI:2450311 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070208 MGI relationship(CL:0000115) MGI MGI:97306 Nf1 GO:0043065 MGI:MGI:3038547|PMID:15039234 IGI MGI:99255,MGI:97583,MGI:96974 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0043065 MGI:MGI:3579920|PMID:15944386 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0043065 MGI:MGI:3579920|PMID:15944386 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000031) MGI MGI:97306 Nf1 GO:0043407 MGI:MGI:1351242|PMID:10620616 IGI MGI:96677,MGI:96974 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070130 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0043407 MGI:MGI:1932841|PMID:11297510 IMP MGI:2176057|MGI:2176055 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070130 MGI relationship(CL:0000117) MGI MGI:97306 Nf1 GO:0043409 MGI:MGI:3629249|PMID:16644864 IMP MGI:1857478 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000359) MGI MGI:97306 Nf1 GO:0043525 MGI:MGI:1861510|PMID:10845775 IGI MGI:96680,MGI:96224 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070130 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0043525 MGI:MGI:1932841|PMID:11297510 IMP MGI:2176057|MGI:2176055 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070130 MGI relationship(CL:0000540) MGI MGI:97306 Nf1 GO:0043525 MGI:MGI:1933752|PMID:7671302 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070130 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0045124 MGI:MGI:3689489|PMID:17053831 IMP MGI:1857478 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0045762 MGI:MGI:3628716|PMID:11788835 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0046580 MGI:MGI:3526457|PMID:15665300 IGI MGI:96680 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0046580 MGI:MGI:3526457|PMID:15665300 IMP MGI:2176057 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0046580 MGI:MGI:3579920|PMID:15944386 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0046580 MGI:MGI:3690406|PMID:16893911 IMP MGI:1857478 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000335) MGI MGI:97306 Nf1 GO:0046929 MGI:MGI:3612345|PMID:16298082 IGI MGI:97321 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000101) MGI MGI:97306 Nf1 GO:0046929 MGI:MGI:3612345|PMID:16298082 IMP MGI:1857478 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000101) MGI MGI:97306 Nf1 GO:0048169 MGI:MGI:2157992|PMID:11793011 IGI MGI:96680 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0048169 MGI:MGI:2157992|PMID:11793011 IMP MGI:1857478 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0048485 MGI:MGI:3689139|PMID:16906226 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20061205 MGI relationship(CL:0000029) MGI MGI:97306 Nf1 GO:0048712 MGI:MGI:1327500|PMID:9878702 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070126 MGI relationship(CL:0000127) MGI MGI:97306 Nf1 GO:0048712 MGI:MGI:1932841|PMID:11297510 IMP MGI:2176057|MGI:2176055 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070130 MGI relationship(CL:0000127) MGI MGI:97306 Nf1 GO:0048715 MGI:MGI:3579920|PMID:15944386 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:97306 Nf1 GO:0048745 MGI:MGI:66069|PMID:7926784 IMP MGI:1857444 P neurofibromatosis 1 neurofibromin|Nf-1 gene taxon:10090 20070125 MGI relationship(CL:0000192) MGI MGI:97307 Nf2 GO:0001726 MGI:MGI:1202233|PMID:9563848 IDA C neurofibromatosis 2 merlin|moesin-ezrin-radixin-like protein|schwannomin gene taxon:10090 20070119 MGI relationship(CL:0000002) MGI MGI:97307 Nf2 GO:0005515 MGI:MGI:3613261|PMID:16405865 IPI UniProt:Q60631 F neurofibromatosis 2 merlin|moesin-ezrin-radixin-like protein|schwannomin gene taxon:10090 20070119 MGI relationship(CL:0000002) MGI MGI:97307 Nf2 GO:0005737 MGI:MGI:79149|PMID:8547603 IDA C neurofibromatosis 2 merlin|moesin-ezrin-radixin-like protein|schwannomin gene taxon:10090 20070119 MGI relationship(CL:0000100) MGI MGI:97307 Nf2 GO:0005737 MGI:MGI:79149|PMID:8547603 IDA C neurofibromatosis 2 merlin|moesin-ezrin-radixin-like protein|schwannomin gene taxon:10090 20070119 MGI relationship(CL:0000121) MGI MGI:97307 Nf2 GO:0005737 MGI:MGI:79149|PMID:8547603 IDA C neurofibromatosis 2 merlin|moesin-ezrin-radixin-like protein|schwannomin gene taxon:10090 20070119 MGI relationship(CL:0000160) MGI MGI:97307 Nf2 GO:0030027 MGI:MGI:1202233|PMID:9563848 IDA C neurofibromatosis 2 merlin|moesin-ezrin-radixin-like protein|schwannomin gene taxon:10090 20070119 MGI relationship(CL:0000002) MGI MGI:97307 Nf2 GO:0030175 MGI:MGI:1202233|PMID:9563848 IDA C neurofibromatosis 2 merlin|moesin-ezrin-radixin-like protein|schwannomin gene taxon:10090 20070119 MGI relationship(CL:0000002) MGI MGI:97307 Nf2 GO:0032154 MGI:MGI:1197341|PMID:9631655 IDA C neurofibromatosis 2 merlin|moesin-ezrin-radixin-like protein|schwannomin gene taxon:10090 20070119 MGI relationship(CL:0000002) MGI MGI:1921289 Nfam1 GO:0045121 MGI:MGI:3044463|PMID:15143214 IDA C Nfat activating molecule with ITAM motif 1 Nfam1 gene taxon:10090 20050113 MGI relationship(CL:0000002) MGI MGI:102469 Nfatc1 GO:0001837 MGI:MGI:3053252|PMID:15339668 IMP MGI:2181762 P nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1 NF-ATc|NFAT2|NFATc gene taxon:10090 20060726 MGI relationship(CL:0000115) MGI MGI:102469 Nfatc1 GO:0001837 MGI:MGI:3053252|PMID:15339668 IMP MGI:2181762 P nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1 NF-ATc|NFAT2|NFATc gene taxon:10090 20060726 MGI relationship(CL:0000134) MGI MGI:102469 Nfatc1 GO:0005737 MGI:MGI:2445662|PMID:12469121 IDA C nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1 NF-ATc|NFAT2|NFATc gene taxon:10090 20070208 MGI relationship(CL:0000115) MGI MGI:102469 Nfatc1 GO:0007507 MGI:MGI:3053252|PMID:15339668 IMP MGI:2181762 P nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1 NF-ATc|NFAT2|NFATc gene taxon:10090 20060726 MGI relationship(CL:0000115) MGI MGI:102469 Nfatc1 GO:0007507 MGI:MGI:3053252|PMID:15339668 IMP MGI:2181762 P nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1 NF-ATc|NFAT2|NFATc gene taxon:10090 20060726 MGI relationship(CL:0000134) MGI MGI:103188 Nfib GO:0008285 MGI:MGI:3528545|PMID:15632069 IMP MGI:3530139 P nuclear factor I/B gene taxon:10090 20050322 MGI relationship(CL:0000134) MGI MGI:1099800 Nfkb2 GO:0002268 MGI:MGI:3655550|PMID:10586052 IMP MGI:2179705 P nuclear factor of kappa light polypeptide gene enhancer in B-cells 2, p49/p100 NF kappaB2|p52 gene taxon:10090 20061229 MGI relationship(CL:0000442) MGI MGI:97321 Ngfb GO:0045773 MGI:MGI:80051|PMID:8861722 IMP P nerve growth factor, beta gene taxon:10090 20070222 MGI relationship(CL:0000001) MGI MGI:97321 Ngfb GO:0046928 MGI:MGI:3612345|PMID:16298082 IGI MGI:97306 P nerve growth factor, beta gene taxon:10090 20070212 MGI relationship(CL:0000101) MGI MGI:97323 Ngfr GO:0021675 MGI:MGI:1098517|PMID:1317267 IMP MGI:1857226 P nerve growth factor receptor (TNFR superfamily, member 16) LNGFR|p75|p75 neurotrophin receptor|p75NGFR|p75NTR|Tnfrsf16 gene taxon:10090 20061116 MGI relationship(CL:0000101) MGI MGI:97347 Nkx2-2 GO:0005634 MGI:MGI:3611650|PMID:16306355 IDA C NK2 transcription factor related, locus 2 (Drosophila) Nkx-2.2|Nkx2.2|tinman gene taxon:10090 20060501 MGI relationship(CL:0000001) MGI MGI:97347 Nkx2-2 GO:0014003 MGI:MGI:3574147|PMID:11526078 IMP MGI:1932100 P NK2 transcription factor related, locus 2 (Drosophila) Nkx-2.2|Nkx2.2|tinman gene taxon:10090 20070301 MGI relationship(CL:0000128) MGI MGI:97347 Nkx2-2 GO:0021529 MGI:MGI:3574147|PMID:11526078 IMP MGI:1932100 P NK2 transcription factor related, locus 2 (Drosophila) Nkx-2.2|Nkx2.2|tinman gene taxon:10090 20070301 MGI relationship(CL:0000128) MGI MGI:97347 Nkx2-2 GO:0045944 MGI:MGI:3574147|PMID:11526078 IDA P NK2 transcription factor related, locus 2 (Drosophila) Nkx-2.2|Nkx2.2|tinman gene taxon:10090 20050509 MGI relationship(CL:0000002) MGI MGI:97347 Nkx2-2 GO:0045944 MGI:MGI:3574147|PMID:11526078 IDA P NK2 transcription factor related, locus 2 (Drosophila) Nkx-2.2|Nkx2.2|tinman gene taxon:10090 20070301 MGI relationship(CL:0000002) MGI MGI:97347 Nkx2-2 GO:0048468 MGI:MGI:3574147|PMID:11526078 IMP MGI:1932100 P NK2 transcription factor related, locus 2 (Drosophila) Nkx-2.2|Nkx2.2|tinman gene taxon:10090 20050509 MGI relationship(CL:0000128) MGI MGI:97347 Nkx2-2 GO:0048665 MGI:MGI:3611719|PMID:16339193 IGI MGI:97451 P NK2 transcription factor related, locus 2 (Drosophila) Nkx-2.2|Nkx2.2|tinman gene taxon:10090 20060227 MGI relationship(CL:0000403) MGI MGI:97350 Nkx2-5 GO:0007507 MGI:MGI:3039161|PMID:15085192 IMP MGI:1857618 P NK2 transcription factor related, locus 5 (Drosophila) Csx|Nkx-2.5|Nkx2.5|tinman gene taxon:10090 20060726 MGI relationship(CL:0000466) MGI MGI:97350 Nkx2-5 GO:0045944 MGI:MGI:3607868|PMID:12392994 IGI MGI:103580 P NK2 transcription factor related, locus 5 (Drosophila) Csx|Nkx-2.5|Nkx2.5|tinman gene taxon:10090 20060119 MGI relationship(CL:0000002) MGI MGI:1270158 Nkx2-9 GO:0007409 MGI:MGI:3607408|PMID:16267219 IMP MGI:2655862 P NK2 transcription factor related, locus 9 (Drosophila) Nkx-2.9|Nkx2.9|tinman gene taxon:10090 20060209 MGI relationship(CL:0000741) MGI MGI:97352 Nkx3-1 GO:0003700 MGI:MGI:1928182|PMID:10993896 IDA F NK-3 transcription factor, locus 1 (Drosophila) bagpipe|Bax|Nkx-3.1|NKX3.1|NKX3A gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:97352 Nkx3-1 GO:0006355 MGI:MGI:1928182|PMID:10993896 IDA P NK-3 transcription factor, locus 1 (Drosophila) bagpipe|Bax|Nkx-3.1|NKX3.1|NKX3A gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:97352 Nkx3-1 GO:0016563 MGI:MGI:1928182|PMID:10993896 IDA F NK-3 transcription factor, locus 1 (Drosophila) bagpipe|Bax|Nkx-3.1|NKX3.1|NKX3A gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:97352 Nkx3-1 GO:0050680 MGI:MGI:1891543|PMID:11002344 IMP MGI:1928655 P NK-3 transcription factor, locus 1 (Drosophila) bagpipe|Bax|Nkx-3.1|NKX3.1|NKX3A gene taxon:10090 20070305 MGI relationship(CL:0000066) MGI MGI:1206039 Nkx6-1 GO:0005634 MGI:MGI:3611650|PMID:16306355 IDA C NK6 transcription factor related, locus 1 (Drosophila) Nkx6.1|NKX6A gene taxon:10090 20060501 MGI relationship(CL:0000001) MGI MGI:1206039 Nkx6-1 GO:0030154 MGI:MGI:3579924|PMID:15944193 IGI MGI:1352738 P NK6 transcription factor related, locus 1 (Drosophila) Nkx6.1|NKX6A gene taxon:10090 20050817 MGI relationship(CL:0000171) MGI MGI:1206039 Nkx6-1 GO:0030154 MGI:MGI:3579924|PMID:15944193 IMP MGI:2386119 P NK6 transcription factor related, locus 1 (Drosophila) Nkx6.1|NKX6A gene taxon:10090 20050817 MGI relationship(CL:0000169) MGI MGI:1206039 Nkx6-1 GO:0045686 MGI:MGI:3578466|PMID:15629702 IGI MGI:1352738 P NK6 transcription factor related, locus 1 (Drosophila) Nkx6.1|NKX6A gene taxon:10090 20050615 MGI relationship(CL:0000128) MGI MGI:1206039 Nkx6-1 GO:0045687 MGI:MGI:3578466|PMID:15629702 IGI MGI:1352738 P NK6 transcription factor related, locus 1 (Drosophila) Nkx6.1|NKX6A gene taxon:10090 20050817 MGI relationship(CL:0000128) MGI MGI:1352738 Nkx6-2 GO:0030154 MGI:MGI:3579924|PMID:15944193 IGI MGI:1206039 P NK6 transcription factor related, locus 2 (Drosophila) Gtx|Nkx6.2 gene taxon:10090 20050817 MGI relationship(CL:0000171) MGI MGI:1352738 Nkx6-2 GO:0045686 MGI:MGI:3578466|PMID:15629702 IGI MGI:1206039 P NK6 transcription factor related, locus 2 (Drosophila) Gtx|Nkx6.2 gene taxon:10090 20050615 MGI relationship(CL:0000128) MGI MGI:1352738 Nkx6-2 GO:0045687 MGI:MGI:3578466|PMID:15629702 IGI MGI:1206039 P NK6 transcription factor related, locus 2 (Drosophila) Gtx|Nkx6.2 gene taxon:10090 20050817 MGI relationship(CL:0000128) MGI MGI:97359 Nodal GO:0008284 MGI:MGI:3042338|PMID:15004567 IMP MGI:2180793 P nodal Tg.413d gene taxon:10090 20060125 MGI relationship(CL:0000223) MGI MGI:97359 Nodal GO:0019827 MGI:MGI:3057068|PMID:15505202 IGI MGI:95518 P nodal Tg.413d gene taxon:10090 20041209 MGI relationship(CL:0000351) MGI MGI:97359 Nodal GO:0019827 MGI:MGI:3640721|PMID:16678814 IMP MGI:2180793 P nodal Tg.413d gene taxon:10090 20060927 MGI relationship(CL:0000352) MGI MGI:2146285 Nol12 GO:0005730 MGI:MGI:3622495|PMID:16430885 IDA C nucleolar protein 12 C78541|Nop25 gene taxon:10090 20060607 MGI relationship(CL:0000002) MGI MGI:97360 Nos1 GO:0002028 MGI:MGI:3686929|PMID:12074580 IMP MGI:1857227 P nitric oxide synthase 1, neuronal bNOS|nNOS|NO|Nos-1 gene taxon:10090 20061130 MGI relationship(CL:0000746) MGI MGI:97360 Nos1 GO:0043267 MGI:MGI:3686929|PMID:12074580 IMP MGI:1857227 P nitric oxide synthase 1, neuronal bNOS|nNOS|NO|Nos-1 gene taxon:10090 20061130 MGI relationship(CL:0000746) MGI MGI:97360 Nos1 GO:0051346 MGI:MGI:3686929|PMID:12074580 IMP MGI:1857227 P nitric oxide synthase 1, neuronal bNOS|nNOS|NO|Nos-1 gene taxon:10090 20061130 MGI relationship(CL:0000746) MGI MGI:97360 Nos1 GO:0051926 MGI:MGI:3686929|PMID:12074580 IMP MGI:1857227 P nitric oxide synthase 1, neuronal bNOS|nNOS|NO|Nos-1 gene taxon:10090 20061130 MGI relationship(CL:0000746) MGI MGI:97362 Nos3 GO:0002028 MGI:MGI:3686929|PMID:12074580 IMP MGI:2150145 P nitric oxide synthase 3, endothelial cell ecNOS|eNOS|Nos-3 gene taxon:10090 20061130 MGI relationship(CL:0000746) MGI MGI:97362 Nos3 GO:0043267 MGI:MGI:3686929|PMID:12074580 IMP MGI:2150145 P nitric oxide synthase 3, endothelial cell ecNOS|eNOS|Nos-3 gene taxon:10090 20061130 MGI relationship(CL:0000746) MGI MGI:97362 Nos3 GO:0051346 MGI:MGI:3686929|PMID:12074580 IMP MGI:2150145 P nitric oxide synthase 3, endothelial cell ecNOS|eNOS|Nos-3 gene taxon:10090 20061130 MGI relationship(CL:0000746) MGI MGI:97362 Nos3 GO:0051926 MGI:MGI:3686929|PMID:12074580 IMP MGI:2150145 P nitric oxide synthase 3, endothelial cell ecNOS|eNOS|Nos-3 gene taxon:10090 20061130 MGI relationship(CL:0000746) MGI MGI:97363 Notch1 GO:0001708 MGI:MGI:3042356|PMID:15068794 IMP MGI:2178778 P Notch gene homolog 1 (Drosophila) lin-12|Mis6|Tan1 gene taxon:10090 20050721 MGI relationship(CL:0000312) MGI MGI:97363 Notch1 GO:0005634 MGI:MGI:3624929|PMID:16607638 IDA C Notch gene homolog 1 (Drosophila) lin-12|Mis6|Tan1 gene taxon:10090 20060705 MGI relationship(CL:0000066) MGI MGI:97363 Notch1 GO:0007409 MGI:MGI:3604921|PMID:16120638 IMP MGI:1933835|MGI:1932522 P Notch gene homolog 1 (Drosophila) lin-12|Mis6|Tan1 gene taxon:10090 20051130 MGI relationship(CL:0000700) MGI MGI:97363 Notch1 GO:0008284 MGI:MGI:3521553|PMID:15509736 IGI MGI:95516 P Notch gene homolog 1 (Drosophila) lin-12|Mis6|Tan1 gene taxon:10090 20050309 MGI relationship(CL:0000710) MGI MGI:97363 Notch1 GO:0030154 MGI:MGI:2385995|PMID:12186854 IMP MGI:1933835 P Notch gene homolog 1 (Drosophila) lin-12|Mis6|Tan1 gene taxon:10090 20050721 MGI relationship(CL:0000128) MGI MGI:97363 Notch1 GO:0030216 MGI:MGI:3042356|PMID:15068794 IMP MGI:2178778 P Notch gene homolog 1 (Drosophila) lin-12|Mis6|Tan1 gene taxon:10090 20050721 MGI relationship(CL:0000312) MGI MGI:97363 Notch1 GO:0043065 MGI:MGI:3043471|PMID:15081359 IDA P Notch gene homolog 1 (Drosophila) lin-12|Mis6|Tan1 gene taxon:10090 20040811 MGI relationship(CL:0000031) MGI MGI:97363 Notch1 GO:0043066 MGI:MGI:3608163|PMID:16245338 IMP MGI:1933835|MGI:2158470 P Notch gene homolog 1 (Drosophila) lin-12|Mis6|Tan1 gene taxon:10090 20060118 MGI relationship(CL:0000221) MGI MGI:97363 Notch1 GO:0045165 MGI:MGI:3603059|PMID:16107537 IMP MGI:2684314|MGI:2447212 P Notch gene homolog 1 (Drosophila) lin-12|Mis6|Tan1 gene taxon:10090 20060308 MGI relationship(CL:0000584) MGI MGI:97363 Notch1 GO:0045596 MGI:MGI:3529381|PMID:15064243 IMP P Notch gene homolog 1 (Drosophila) lin-12|Mis6|Tan1 gene taxon:10090 20050322 MGI relationship(CL:0000165) MGI MGI:97363 Notch1 GO:0045665 MGI:MGI:3604921|PMID:16120638 IMP MGI:1933835|MGI:1932522 P Notch gene homolog 1 (Drosophila) lin-12|Mis6|Tan1 gene taxon:10090 20051130 MGI relationship(CL:0000117) MGI MGI:97363 Notch1 GO:0045944 MGI:MGI:3607225|PMID:16145673 IDA P Notch gene homolog 1 (Drosophila) lin-12|Mis6|Tan1 gene taxon:10090 20060113 MGI relationship(CL:0000002) MGI MGI:97363 Notch1 GO:0046533 MGI:MGI:3617079|PMID:16452096 IMP MGI:1933835|MGI:3052237 P Notch gene homolog 1 (Drosophila) lin-12|Mis6|Tan1 gene taxon:10090 20070309 MGI relationship(CL:0000573) MGI MGI:97363 Notch1 GO:0048103 MGI:MGI:3521553|PMID:15509736 IGI MGI:95516 P Notch gene homolog 1 (Drosophila) lin-12|Mis6|Tan1 gene taxon:10090 20050309 MGI relationship(CL:0000710) MGI MGI:97363 Notch1 GO:0048663 MGI:MGI:3604921|PMID:16120638 IGI MGI:99460 P Notch gene homolog 1 (Drosophila) lin-12|Mis6|Tan1 gene taxon:10090 20051130 MGI relationship(CL:0000117) MGI MGI:97363 Notch1 GO:0050678 MGI:MGI:3603059|PMID:16107537 IMP MGI:2684314|MGI:2684317 P Notch gene homolog 1 (Drosophila) lin-12|Mis6|Tan1 gene taxon:10090 20060308 MGI relationship(CL:0000034) MGI MGI:99460 Notch3 GO:0045596 MGI:MGI:3529381|PMID:15064243 IMP P Notch gene homolog 3 (Drosophila) gene taxon:10090 20050322 MGI relationship(CL:0000031) MGI MGI:99460 Notch3 GO:0045665 MGI:MGI:3529381|PMID:15064243 IMP P Notch gene homolog 3 (Drosophila) gene taxon:10090 20050322 MGI relationship(CL:0000540) MGI MGI:99460 Notch3 GO:0048663 MGI:MGI:3604921|PMID:16120638 IGI MGI:97363 P Notch gene homolog 3 (Drosophila) gene taxon:10090 20051130 MGI relationship(CL:0000117) MGI MGI:109205 Npas1 GO:0000122 MGI:MGI:3583927|PMID:15635607 IDA P neuronal PAS domain protein 1 MOP5 gene taxon:10090 20050921 MGI relationship(CL:0000002) MGI MGI:109205 Npas1 GO:0005634 MGI:MGI:3583927|PMID:15635607 IDA C neuronal PAS domain protein 1 MOP5 gene taxon:10090 20050921 MGI relationship(CL:0000117) MGI MGI:2664186 Npas4 GO:0005634 MGI:MGI:3056229|PMID:15363889 IDA C neuronal PAS domain protein 4 LE-PAS gene taxon:10090 20050310 MGI relationship(CL:0000002) MGI MGI:106184 Npm1 GO:0005730 MGI:MGI:3608543|PMID:16027046 IDA C nucleophosmin 1 B23|NO38|nucleolar protein NO38 gene taxon:10090 20060523 MGI relationship(CL:0000075) MGI MGI:97375 nr GO:0043524 MGI:MGI:3606364|PMID:15370195 IMP MGI:1856971 P nervous gene taxon:10090 20070118 MGI relationship(CL:0000540) MGI MGI:1352460 Nr0b1 GO:0030154 MGI:MGI:3578602|PMID:15829514 IGI MGI:1346833 P nuclear receptor subfamily 0, group B, member 1 Ahc|Ahch|AHX|DAX-1|Dax1 gene taxon:10090 20050812 MGI relationship(CL:0000178) MGI MGI:1352460 Nr0b1 GO:0030154 MGI:MGI:3578602|PMID:15829514 IGI MGI:1346833 P nuclear receptor subfamily 0, group B, member 1 Ahc|Ahch|AHX|DAX-1|Dax1 gene taxon:10090 20050812 MGI relationship(CL:0000216) MGI MGI:1100526 Nr2e1 GO:0008284 MGI:MGI:3624573|PMID:16702404 IMP MGI:2176560 P nuclear receptor subfamily 2, group E, member 1 Mtll|Nr2e1|Tlx gene taxon:10090 20060705 MGI relationship(CL:0000031) MGI MGI:1100526 Nr2e1 GO:0008347 MGI:MGI:3054148|PMID:15371513 IMP MGI:2176560 P nuclear receptor subfamily 2, group E, member 1 Mtll|Nr2e1|Tlx gene taxon:10090 20050215 MGI relationship(CL:0000127) MGI MGI:1100526 Nr2e1 GO:0043010 MGI:MGI:3054148|PMID:15371513 IMP MGI:2176560 P nuclear receptor subfamily 2, group E, member 1 Mtll|Nr2e1|Tlx gene taxon:10090 20050215 MGI relationship(CL:0000127) MGI MGI:1100526 Nr2e1 GO:0045165 MGI:MGI:3055655|PMID:15229646 IGI MGI:97490 P nuclear receptor subfamily 2, group E, member 1 Mtll|Nr2e1|Tlx gene taxon:10090 20041110 MGI relationship(CL:0000107) MGI MGI:1100526 Nr2e1 GO:0045165 MGI:MGI:3055655|PMID:15229646 IGI MGI:97490 P nuclear receptor subfamily 2, group E, member 1 Mtll|Nr2e1|Tlx gene taxon:10090 20041110 MGI relationship(CL:0000617) MGI MGI:1346317 Nr2e3 GO:0008285 MGI:MGI:3624051|PMID:12407160 IMP MGI:1346317 P nuclear receptor subfamily 2, group E, member 3 photoreceptor-specific nuclear receptor|Pnr|RNR gene taxon:10090 20060628 MGI relationship(CL:0000573) MGI MGI:1352451 Nr2f1 GO:0001764 MGI:MGI:3512834|PMID:15548577 IDA P nuclear receptor subfamily 2, group F, member 1 COUP-TF1|COUP-TFI|Erbal3|Tcfcoup1 gene taxon:10090 20050204 MGI relationship(CL:0000617) MGI MGI:1352451 Nr2f1 GO:0005634 MGI:MGI:3512834|PMID:15548577 IDA C nuclear receptor subfamily 2, group F, member 1 COUP-TF1|COUP-TFI|Erbal3|Tcfcoup1 gene taxon:10090 20050204 MGI relationship(CL:0000617) MGI MGI:1352451 Nr2f1 GO:0030900 MGI:MGI:3512834|PMID:15548577 IDA P nuclear receptor subfamily 2, group F, member 1 COUP-TF1|COUP-TFI|Erbal3|Tcfcoup1 gene taxon:10090 20050204 MGI relationship(CL:0000617) MGI MGI:1352452 Nr2f2 GO:0001764 MGI:MGI:3512834|PMID:15548577 IDA P nuclear receptor subfamily 2, group F, member 2 Aporp1|ARP-1|COUP-TF2|COUP-TFII|EAR3|Tcfcoup2 gene taxon:10090 20050204 MGI relationship(CL:0000117) MGI MGI:1352452 Nr2f2 GO:0005634 MGI:MGI:3512834|PMID:15548577 IDA C nuclear receptor subfamily 2, group F, member 2 Aporp1|ARP-1|COUP-TF2|COUP-TFII|EAR3|Tcfcoup2 gene taxon:10090 20050204 MGI relationship(CL:0000617) MGI MGI:1352452 Nr2f2 GO:0009956 MGI:MGI:3578605|PMID:15829524 IMP MGI:3579117|MGI:3579118 P nuclear receptor subfamily 2, group F, member 2 Aporp1|ARP-1|COUP-TF2|COUP-TFII|EAR3|Tcfcoup2 gene taxon:10090 20050617 MGI relationship(CL:0000192) MGI MGI:1352452 Nr2f2 GO:0030900 MGI:MGI:3512834|PMID:15548577 IDA P nuclear receptor subfamily 2, group F, member 2 Aporp1|ARP-1|COUP-TF2|COUP-TFII|EAR3|Tcfcoup2 gene taxon:10090 20050204 MGI relationship(CL:0000117) MGI MGI:1352452 Nr2f2 GO:0048514 MGI:MGI:3577693|PMID:15875024 IMP MGI:3579116 P nuclear receptor subfamily 2, group F, member 2 Aporp1|ARP-1|COUP-TF2|COUP-TFII|EAR3|Tcfcoup2 gene taxon:10090 20060213 MGI relationship(CL:0000071) MGI MGI:1352452 Nr2f2 GO:0048514 MGI:MGI:3577693|PMID:15875024 IMP MGI:3579116 P nuclear receptor subfamily 2, group F, member 2 Aporp1|ARP-1|COUP-TF2|COUP-TFII|EAR3|Tcfcoup2 gene taxon:10090 20060213 MGI relationship(CL:0000359) MGI MGI:1352456 Nr4a2 GO:0030182 MGI:MGI:1202150|PMID:9520484 IMP MGI:3043985 P nuclear receptor subfamily 4, group A, member 2 HZF-3|Nurr1|RNR-1 gene taxon:10090 20050218 MGI relationship(CL:0000117) MGI MGI:1352456 Nr4a2 GO:0030182 MGI:MGI:3041641|PMID:14622207 IMP MGI:3043985 P nuclear receptor subfamily 4, group A, member 2 HZF-3|Nurr1|RNR-1 gene taxon:10090 20050218 MGI relationship(CL:0000117) MGI MGI:1352457 Nr4a3 GO:0001707 MGI:MGI:3042044|PMID:13129926 IMP MGI:3043761 P nuclear receptor subfamily 4, group A, member 3 NOR-1|Nor1|TEC gene taxon:10090 20040707 MGI relationship(CL:0000222) MGI MGI:1346833 Nr5a1 GO:0030154 MGI:MGI:3578602|PMID:15829514 IGI MGI:1352460 P nuclear receptor subfamily 5, group A, member 1 Ad4BP|adrenal 4-binding protein|ELP|Ftz-F1|Ftzf1|SF-1|SF1|steroidogenic factor 1 gene taxon:10090 20050812 MGI relationship(CL:0000178) MGI MGI:1346833 Nr5a1 GO:0030154 MGI:MGI:3578602|PMID:15829514 IGI MGI:1352460 P nuclear receptor subfamily 5, group A, member 1 Ad4BP|adrenal 4-binding protein|ELP|Ftz-F1|Ftzf1|SF-1|SF1|steroidogenic factor 1 gene taxon:10090 20050812 MGI relationship(CL:0000216) MGI MGI:96083 Nrg1 GO:0010001 MGI:MGI:3625625|PMID:16606832 IMP MGI:2447761|MGI:2447758 P neuregulin 1 ARIA|GGF|GGFII|heregulin|HGL|HRG|HRGalpha|NDF|SMDF gene taxon:10090 20060808 MGI relationship(CL:0000218) MGI MGI:106206 Nrp1 GO:0007411 MGI:MGI:3505728|PMID:12852851 IMP MGI:3512099 P neuropilin 1 Neuropilin-1|NP-1|NPN-1|Npn1 gene taxon:10090 20050121 MGI relationship(CL:0000101) MGI MGI:106206 Nrp1 GO:0007411 MGI:MGI:3505728|PMID:12852851 IMP MGI:3512099 P neuropilin 1 Neuropilin-1|NP-1|NPN-1|Npn1 gene taxon:10090 20050121 MGI relationship(CL:0000540) MGI MGI:106206 Nrp1 GO:0007411 MGI:MGI:3525900|PMID:15604101 IMP MGI:1857853 P neuropilin 1 Neuropilin-1|NP-1|NPN-1|Npn1 gene taxon:10090 20050316 MGI relationship(CL:0000540) MGI MGI:106206 Nrp1 GO:0016358 MGI:MGI:3505728|PMID:12852851 IMP MGI:3512099 P neuropilin 1 Neuropilin-1|NP-1|NPN-1|Npn1 gene taxon:10090 20050121 MGI relationship(CL:0000598) MGI MGI:106206 Nrp1 GO:0016477 MGI:MGI:3505797|PMID:15376331 IMP MGI:1857853 P neuropilin 1 Neuropilin-1|NP-1|NPN-1|Npn1 gene taxon:10090 20050218 MGI relationship(CL:0000704) MGI MGI:106206 Nrp1 GO:0030517 MGI:MGI:3505728|PMID:12852851 IGI MGI:107558 P neuropilin 1 Neuropilin-1|NP-1|NPN-1|Npn1 gene taxon:10090 20050121 MGI relationship(CL:0000001) MGI MGI:1100492 Nrp2 GO:0001755 MGI:MGI:3613099|PMID:16319111 IMP MGI:2137037 P neuropilin 2 NP-2|NP2|Npn-2|Npn2 gene taxon:10090 20060501 MGI relationship(CL:0000011) MGI MGI:1100492 Nrp2 GO:0050919 MGI:MGI:3613099|PMID:16319111 IGI MGI:1096347 P neuropilin 2 NP-2|NP2|Npn-2|Npn2 gene taxon:10090 20060501 MGI relationship(CL:0000001) MGI MGI:894662 Nrsn1 GO:0016023 MGI:MGI:3623043|PMID:16527258 IDA C neurensin 1 Neurensin-1|Neuro-p24|Vmp gene taxon:10090 20060627 MGI relationship(CL:0000002) MGI MGI:894662 Nrsn1 GO:0016023 MGI:MGI:3623043|PMID:16527258 IDA C neurensin 1 Neurensin-1|Neuro-p24|Vmp gene taxon:10090 20060627 MGI relationship(CL:0000117) MGI MGI:894662 Nrsn1 GO:0016023 MGI:MGI:87837|PMID:9191101 IDA C neurensin 1 Neurensin-1|Neuro-p24|Vmp gene taxon:10090 20060627 MGI relationship(CL:0000002) MGI MGI:894662 Nrsn1 GO:0030426 MGI:MGI:3623043|PMID:16527258 IDA C neurensin 1 Neurensin-1|Neuro-p24|Vmp gene taxon:10090 20060627 MGI relationship(CL:0000002) MGI MGI:894662 Nrsn1 GO:0043025 MGI:MGI:87837|PMID:9191101 IDA C neurensin 1 Neurensin-1|Neuro-p24|Vmp gene taxon:10090 20060627 MGI relationship(CL:0000121) MGI MGI:2684969 Nrsn2 GO:0016023 MGI:MGI:3623043|PMID:16527258 IDA C neurensin 2 LOC228777|Neurensin-2 gene taxon:10090 20060627 MGI relationship(CL:0000002) MGI MGI:2684969 Nrsn2 GO:0016023 MGI:MGI:3623043|PMID:16527258 IDA C neurensin 2 LOC228777|Neurensin-2 gene taxon:10090 20060627 MGI relationship(CL:0000117) MGI MGI:2684969 Nrsn2 GO:0043025 MGI:MGI:3623043|PMID:16527258 IDA C neurensin 2 LOC228777|Neurensin-2 gene taxon:10090 20060627 MGI relationship(CL:0000002) MGI MGI:2684969 Nrsn2 GO:0043025 MGI:MGI:3623043|PMID:16527258 IDA C neurensin 2 LOC228777|Neurensin-2 gene taxon:10090 20060627 MGI relationship(CL:0000117) MGI MGI:97380 Ntf3 GO:0007411 MGI:MGI:3576404|PMID:15550985 IDA P neurotrophin 3 NT-3|NT3|Ntf-3 gene taxon:10090 20050526 MGI relationship(CL:0000101) MGI MGI:97380 Ntf3 GO:0007411 MGI:MGI:3576404|PMID:15550985 IMP MGI:1933844 P neurotrophin 3 NT-3|NT3|Ntf-3 gene taxon:10090 20050526 MGI relationship(CL:0000101) MGI MGI:97380 Ntf3 GO:0007411 MGI:MGI:80051|PMID:8861722 IMP P neurotrophin 3 NT-3|NT3|Ntf-3 gene taxon:10090 20070222 MGI relationship(CL:0000001) MGI MGI:97380 Ntf3 GO:0042490 MGI:MGI:3505841|PMID:15376326 IGI MGI:1857233,MGI:1857136 P neurotrophin 3 NT-3|NT3|Ntf-3 gene taxon:10090 20041221 MGI relationship(CL:0000199) MGI MGI:97380 Ntf3 GO:0048666 MGI:MGI:85958|PMID:8809809 IMP MGI:2388319 P neurotrophin 3 NT-3|NT3|Ntf-3 gene taxon:10090 20061115 MGI relationship(CL:0000531) MGI MGI:97380 Ntf3 GO:0048699 MGI:MGI:3604840|PMID:16142215 IGI MGI:97385 P neurotrophin 3 NT-3|NT3|Ntf-3 gene taxon:10090 20060112 MGI relationship(CL:0000540) MGI MGI:97381 Ntf5 GO:0042490 MGI:MGI:3505841|PMID:15376326 IGI MGI:1857136,MGI:1857232 P neurotrophin 5 neurotrophin-4|NT-4|NT4|NT4/5|Ntf-5|Ntf4 gene taxon:10090 20041221 MGI relationship(CL:0000199) MGI MGI:105088 Ntn1 GO:0001764 MGI:MGI:3041654|PMID:14750959 IMP MGI:1927548 P netrin 1 Netrin-1 gene taxon:10090 20041007 MGI relationship(CL:0000110) MGI MGI:105088 Ntn1 GO:0001764 MGI:MGI:3607408|PMID:16267219 IMP MGI:1927548 P netrin 1 Netrin-1 gene taxon:10090 20060209 MGI relationship(CL:0000741) MGI MGI:105088 Ntn1 GO:0007409 MGI:MGI:1861288|PMID:10908620 IDA P netrin 1 Netrin-1 gene taxon:10090 20040707 MGI relationship(CL:0000117) MGI MGI:105088 Ntn1 GO:0007411 MGI:MGI:3616408|PMID:16481423 IMP MGI:1927548 P netrin 1 Netrin-1 gene taxon:10090 20060406 MGI relationship(CL:0000678) MGI MGI:105088 Ntn1 GO:0008284 MGI:MGI:3616408|PMID:16481423 IMP MGI:1927548 P netrin 1 Netrin-1 gene taxon:10090 20060406 MGI relationship(CL:0000128) MGI MGI:105088 Ntn1 GO:0030334 MGI:MGI:3616408|PMID:16481423 IMP MGI:1927548 P netrin 1 Netrin-1 gene taxon:10090 20060406 MGI relationship(CL:0000128) MGI MGI:97383 Ntrk1 GO:0005737 MGI:MGI:1334487|PMID:10207144 IDA C neurotrophic tyrosine kinase, receptor, type 1 Tkr|TrkA gene taxon:10090 20060718 MGI relationship(CL:0000117) MGI MGI:97383 Ntrk1 GO:0042490 MGI:MGI:3505841|PMID:15376326 IMP MGI:1888374 P neurotrophic tyrosine kinase, receptor, type 1 Tkr|TrkA gene taxon:10090 20041221 MGI relationship(CL:0000199) MGI MGI:97384 Ntrk2 GO:0042490 MGI:MGI:3505841|PMID:15376326 IMP MGI:1857814 P neurotrophic tyrosine kinase, receptor, type 2 trkB gene taxon:10090 20041221 MGI relationship(CL:0000199) MGI MGI:97385 Ntrk3 GO:0005737 MGI:MGI:1334487|PMID:10207144 IDA C neurotrophic tyrosine kinase, receptor, type 3 TrkC gene taxon:10090 20060718 MGI relationship(CL:0000117) MGI MGI:97385 Ntrk3 GO:0042490 MGI:MGI:3505841|PMID:15376326 IMP MGI:1888375 P neurotrophic tyrosine kinase, receptor, type 3 TrkC gene taxon:10090 20041221 MGI relationship(CL:0000199) MGI MGI:97385 Ntrk3 GO:0048691 MGI:MGI:3604840|PMID:16142215 IGI MGI:97380 P neurotrophic tyrosine kinase, receptor, type 3 TrkC gene taxon:10090 20060112 MGI relationship(CL:0000540) MGI MGI:107423 Numb GO:0007405 MGI:MGI:2389562|PMID:12410312 IGI MGI:894702 P numb gene homolog (Drosophila) m-numb|mnb gene taxon:10090 20050722 MGI relationship(CL:0000031) MGI MGI:894702 Numbl GO:0007405 MGI:MGI:2389562|PMID:12410312 IGI MGI:107423 P numb-like nbl gene taxon:10090 20050722 MGI relationship(CL:0000031) MGI MGI:109404 Nup98 GO:0005634 MGI:MGI:3522382|PMID:15615787 IDA C nucleoporin 98 gene taxon:10090 20050512 MGI relationship(CL:0000002) MGI MGI:1858330 Nxf1 GO:0042405 MGI:MGI:3522382|PMID:15615787 IDA C nuclear RNA export factor 1 homolog (S. cerevisiae) Mex67|Mvb1|TAP|Tip associated protein gene taxon:10090 20050512 MGI relationship(CL:0000002) MGI MGI:2140770 Oas1d GO:0005737 MGI:MGI:3581331|PMID:15899864 IDA C 2'-5' oligoadenylate synthetase 1D gene taxon:10090 20060727 MGI relationship(CL:0000023) MGI MGI:2140770 Oas1d GO:0009790 MGI:MGI:3581331|PMID:15899864 IMP MGI:3581976 P 2'-5' oligoadenylate synthetase 1D gene taxon:10090 20060727 MGI relationship(CL:0000365) MGI MGI:1858170 Oaz3 GO:0005634 MGI:MGI:3529646|PMID:15642376 IDA C ornithine decarboxylase antizyme 3 antizyme 3|AZ-3|Oaz t|Oaz-t|ornithine decarboxylase antizyme in testis gene taxon:10090 20050325 MGI relationship(CL:0000002) MGI MGI:1858170 Oaz3 GO:0005737 MGI:MGI:3529646|PMID:15642376 IDA C ornithine decarboxylase antizyme 3 antizyme 3|AZ-3|Oaz t|Oaz-t|ornithine decarboxylase antizyme in testis gene taxon:10090 20050325 MGI relationship(CL:0000002) MGI MGI:1355331 Olig2 GO:0048709 MGI:MGI:3613362|PMID:16436615 IMP MGI:3614399|MGI:2179048 P oligodendrocyte transcription factor 2 Bhlhb1|Olg-2|RK17 gene taxon:10090 20060307 MGI relationship(CL:0000128) MGI MGI:1196423 Onecut1 GO:0005634 MGI:MGI:3512831|PMID:15548585 IDA C one cut domain, family member 1 D9Ertd423e|Hfh12|HNF6|Oc1 gene taxon:10090 20050315 MGI relationship(CL:0000066) MGI MGI:1196423 Onecut1 GO:0005634 MGI:MGI:3512831|PMID:15548585 IDA C one cut domain, family member 1 D9Ertd423e|Hfh12|HNF6|Oc1 gene taxon:10090 20050315 MGI relationship(CL:0000622) MGI MGI:104749 Osm GO:0007422 MGI:MGI:3574134|PMID:14985435 IMP MGI:3574987 P oncostatin M gene taxon:10090 20050504 MGI relationship(CL:0000101) MGI MGI:1930813 Osr2 GO:0008284 MGI:MGI:3513962|PMID:15175245 IMP MGI:3033240 P odd-skipped related 2 (Drosophila) gene taxon:10090 20060303 MGI relationship(CL:0000134) MGI MGI:97451 Otx2 GO:0001708 MGI:MGI:3578035|PMID:15888661 IMP MGI:2661065|MGI:2176222 P orthodenticle homolog 2 (Drosophila) gene taxon:10090 20050803 MGI relationship(CL:0000117) MGI MGI:97451 Otx2 GO:0005634 MGI:MGI:1861314|PMID:10891582 IDA C orthodenticle homolog 2 (Drosophila) gene taxon:10090 20070302 MGI relationship(CL:0000740) MGI MGI:97451 Otx2 GO:0005634 MGI:MGI:1861314|PMID:10891582 IDA C orthodenticle homolog 2 (Drosophila) gene taxon:10090 20070302 MGI relationship(CL:0000748) MGI MGI:97451 Otx2 GO:0009887 MGI:MGI:2680889|PMID:14625556 IMP MGI:2178753 P orthodenticle homolog 2 (Drosophila) gene taxon:10090 20050803 MGI relationship(CL:0000652) MGI MGI:97451 Otx2 GO:0030154 MGI:MGI:2680889|PMID:14625556 IMP MGI:2178753 P orthodenticle homolog 2 (Drosophila) gene taxon:10090 20050803 MGI relationship(CL:0000652) MGI MGI:97451 Otx2 GO:0030182 MGI:MGI:3578035|PMID:15888661 IMP MGI:2661065|MGI:2176222 P orthodenticle homolog 2 (Drosophila) gene taxon:10090 20050803 MGI relationship(CL:0000700) MGI MGI:97451 Otx2 GO:0030900 MGI:MGI:2680889|PMID:14625556 IMP MGI:2178753 P orthodenticle homolog 2 (Drosophila) gene taxon:10090 20050803 MGI relationship(CL:0000652) MGI MGI:97451 Otx2 GO:0045165 MGI:MGI:3039992|PMID:15105370 IMP MGI:2661065 P orthodenticle homolog 2 (Drosophila) gene taxon:10090 20040701 MGI relationship(CL:0000117) MGI MGI:97451 Otx2 GO:0048663 MGI:MGI:3611719|PMID:16339193 IMP MGI:2661065|MGI:2446434 P orthodenticle homolog 2 (Drosophila) gene taxon:10090 20060227 MGI relationship(CL:0000700) MGI MGI:1330290 Ovol1 GO:0000239 MGI:MGI:3604837|PMID:15716349 IMP MGI:1926599 P OVO homolog-like 1 (Drosophila) movo1|Ovo1 gene taxon:10090 20051130 MGI relationship(CL:0000017) MGI MGI:1330290 Ovol1 GO:0007283 MGI:MGI:3604837|PMID:15716349 IMP MGI:1926599 P OVO homolog-like 1 (Drosophila) movo1|Ovo1 gene taxon:10090 20051130 MGI relationship(CL:0000017) MGI MGI:1338039 Ovol2 GO:0001755 MGI:MGI:3618450|PMID:16423343 IMP MGI:3522498 P ovo-like 2 (Drosophila) M-OVO|M-OVO-A|M-OVO-B|movo2|Ovol2|Zfp339 gene taxon:10090 20060606 MGI relationship(CL:0000008) MGI MGI:1338039 Ovol2 GO:0008285 MGI:MGI:3618450|PMID:16423343 IMP MGI:3522498 P ovo-like 2 (Drosophila) M-OVO|M-OVO-A|M-OVO-B|movo2|Ovol2|Zfp339 gene taxon:10090 20060606 MGI relationship(CL:0000133) MGI MGI:1338039 Ovol2 GO:0048558 MGI:MGI:3618450|PMID:16423343 IMP MGI:3522498 P ovo-like 2 (Drosophila) M-OVO|M-OVO-A|M-OVO-B|movo2|Ovol2|Zfp339 gene taxon:10090 20060606 MGI relationship(CL:0000131) MGI MGI:2446472 P42pop GO:0005634 MGI:MGI:3526474|PMID:15615774 IDA C Myb protein P42POP gene taxon:10090 20050314 MGI relationship(CL:0000002) MGI MGI:109520 Pafah1b1 GO:0000226 MGI:MGI:3588829|PMID:16107726 IGI MGI:1932915 P platelet-activating factor acetylhydrolase, isoform 1b, beta1 subunit LIS-1|Lis1|lissencephaly-1 protein|Mdsh|Pafaha gene taxon:10090 20051014 MGI relationship(CL:0000117) MGI MGI:109520 Pafah1b1 GO:0001764 MGI:MGI:3052388|PMID:15331402 IMP MGI:2384054 P platelet-activating factor acetylhydrolase, isoform 1b, beta1 subunit LIS-1|Lis1|lissencephaly-1 protein|Mdsh|Pafaha gene taxon:10090 20050505 MGI relationship(CL:0000498) MGI MGI:109520 Pafah1b1 GO:0001764 MGI:MGI:3588829|PMID:16107726 IGI MGI:1932915 P platelet-activating factor acetylhydrolase, isoform 1b, beta1 subunit LIS-1|Lis1|lissencephaly-1 protein|Mdsh|Pafaha gene taxon:10090 20051014 MGI relationship(CL:0000598) MGI MGI:1339975 Pak1 GO:0007528 MGI:MGI:2384358|PMID:12165471 IGI MGI:87961|MGI:94941 P p21 (CDKN1A)-activated kinase 1 PAK-1|Paka gene taxon:10090 20070228 MGI relationship(CL:0000002) MGI MGI:1339975 Pak1 GO:0043113 MGI:MGI:2384358|PMID:12165471 IGI MGI:87961|MGI:94941 P p21 (CDKN1A)-activated kinase 1 PAK-1|Paka gene taxon:10090 20070228 MGI relationship(CL:0000002) MGI MGI:1261814 Palm GO:0005737 MGI:MGI:1861443|PMID:9813098 IDA C paralemmin gene taxon:10090 20050802 MGI relationship(CL:0000002) MGI MGI:1261814 Palm GO:0005886 MGI:MGI:1861443|PMID:9813098 IDA C paralemmin gene taxon:10090 20050802 MGI relationship(CL:0000002) MGI MGI:1261814 Palm GO:0007010 MGI:MGI:1861443|PMID:9813098 IDA P paralemmin gene taxon:10090 20050802 MGI relationship(CL:0000002) MGI MGI:1261814 Palm GO:0008360 MGI:MGI:1861443|PMID:9813098 IDA P paralemmin gene taxon:10090 20050802 MGI relationship(CL:0000002) MGI MGI:2135605 Pard6b GO:0005634 MGI:MGI:3582101|PMID:15950600 IDA C par-6 (partitioning defective 6) homolog beta (C. elegans) gene taxon:10090 20050822 MGI relationship(CL:0000007) MGI MGI:2135605 Pard6b GO:0005923 MGI:MGI:3582101|PMID:15950600 IDA C par-6 (partitioning defective 6) homolog beta (C. elegans) gene taxon:10090 20050822 MGI relationship(CL:0000007) MGI MGI:2135605 Pard6b GO:0005923 MGI:MGI:3582101|PMID:15950600 IDA C par-6 (partitioning defective 6) homolog beta (C. elegans) gene taxon:10090 20050822 MGI relationship(CL:1000274) MGI MGI:2135605 Pard6b GO:0005938 MGI:MGI:3582101|PMID:15950600 IDA C par-6 (partitioning defective 6) homolog beta (C. elegans) gene taxon:10090 20050822 MGI relationship(CL:0000007) MGI MGI:2135605 Pard6b GO:0045177 MGI:MGI:3582101|PMID:15950600 IDA C par-6 (partitioning defective 6) homolog beta (C. elegans) gene taxon:10090 20050822 MGI relationship(CL:0000007) MGI MGI:2135605 Pard6b GO:0045177 MGI:MGI:3582101|PMID:15950600 IDA C par-6 (partitioning defective 6) homolog beta (C. elegans) gene taxon:10090 20050822 MGI relationship(CL:1000274) MGI MGI:1355296 Park2 GO:0001963 MGI:MGI:2675710|PMID:12915482 IMP MGI:2678247 P parkin PRKN gene taxon:10090 20050915 MGI relationship(CL:0000700) MGI MGI:1355296 Park2 GO:0035249 MGI:MGI:2675710|PMID:12915482 IMP MGI:2678247 P parkin PRKN gene taxon:10090 20050914 MGI relationship(CL:0000001) MGI MGI:1355296 Park2 GO:0043005 MGI:MGI:2154577|PMID:11675120 IDA C parkin PRKN gene taxon:10090 20050914 MGI relationship(CL:0000117) MGI MGI:1355296 Park2 GO:0046928 MGI:MGI:2679747|PMID:12930822 IMP MGI:2681404 P parkin PRKN gene taxon:10090 20050912 MGI relationship(CL:0000700) MGI MGI:1355296 Park2 GO:0050804 MGI:MGI:2679747|PMID:12930822 IMP MGI:2681404 P parkin PRKN gene taxon:10090 20050912 MGI relationship(CL:0000117) MGI MGI:1355296 Park2 GO:0051583 MGI:MGI:2675710|PMID:12915482 IMP MGI:2678247 P parkin PRKN gene taxon:10090 20050914 MGI relationship(CL:0000001) MGI MGI:2135637 Park7 GO:0001963 MGI:MGI:3584207|PMID:15799973 IMP MGI:3586448 P Parkinson disease (autosomal recessive, early onset) 7 DJ-1|Dj1 gene taxon:10090 20050915 MGI relationship(CL:0000700) MGI MGI:2135637 Park7 GO:0042542 MGI:MGI:3575338|PMID:15784737 IDA P Parkinson disease (autosomal recessive, early onset) 7 DJ-1|Dj1 gene taxon:10090 20050916 MGI relationship(CL:0000001) MGI MGI:2135637 Park7 GO:0042542 MGI:MGI:3575338|PMID:15784737 IMP MGI:3576227 P Parkinson disease (autosomal recessive, early onset) 7 DJ-1|Dj1 gene taxon:10090 20050916 MGI relationship(CL:0000001) MGI MGI:97485 Pax1 GO:0043367 MGI:MGI:3590033|PMID:16093716 IMP MGI:3603176 P paired box gene 1 hbs|hunchback|Pax-1|wavy tail|wt gene taxon:10090 20051128 MGI relationship(CL:0000624) MGI MGI:97485 Pax1 GO:0043374 MGI:MGI:3590033|PMID:16093716 IMP MGI:3603176 P paired box gene 1 hbs|hunchback|Pax-1|wavy tail|wt gene taxon:10090 20051128 MGI relationship(CL:0000625) MGI MGI:97486 Pax2 GO:0001709 MGI:MGI:2662558|PMID:12756174 IMP MGI:1857673 P paired box gene 2 Pax-2 gene taxon:10090 20050722 MGI relationship(CL:0000529) MGI MGI:97486 Pax2 GO:0043010 MGI:MGI:2662558|PMID:12756174 IMP MGI:1857673 P paired box gene 2 Pax-2 gene taxon:10090 20050722 MGI relationship(CL:0000529) MGI MGI:97487 Pax3 GO:0001755 MGI:MGI:3056222|PMID:15384171 IMP MGI:3043030 P paired box gene 3 Pax-3 gene taxon:10090 20050322 MGI relationship(CL:0000333) MGI MGI:97487 Pax3 GO:0003705 MGI:MGI:3530428|PMID:15729346 IGI MGI:104633,MGI:96770,MGI:88276 F paired box gene 3 Pax-3 gene taxon:10090 20050513 MGI relationship(CL:0000002) MGI MGI:97487 Pax3 GO:0007517 MGI:MGI:3044235|PMID:15132998 IMP MGI:3047631|MGI:3047632|MGI:2687297|MGI:1856173 P paired box gene 3 Pax-3 gene taxon:10090 20050722 MGI relationship(CL:0000056) MGI MGI:97487 Pax3 GO:0008283 MGI:MGI:3044235|PMID:15132998 IMP MGI:3047631|MGI:3047632|MGI:2687297|MGI:1856173 P paired box gene 3 Pax-3 gene taxon:10090 20050722 MGI relationship(CL:0000056) MGI MGI:97487 Pax3 GO:0008284 MGI:MGI:3608103|PMID:10946068 IMP MGI:1856293 P paired box gene 3 Pax-3 gene taxon:10090 20060123 MGI relationship(CL:0000333) MGI MGI:97487 Pax3 GO:0016477 MGI:MGI:3044235|PMID:15132998 IMP MGI:3047631|MGI:3047632|MGI:2687297|MGI:1856173 P paired box gene 3 Pax-3 gene taxon:10090 20050722 MGI relationship(CL:0000056) MGI MGI:97487 Pax3 GO:0016563 MGI:MGI:3610892|PMID:16300735 IDA F paired box gene 3 Pax-3 gene taxon:10090 20060201 MGI relationship(CL:0000002) MGI MGI:97487 Pax3 GO:0045944 MGI:MGI:3610892|PMID:16300735 IDA P paired box gene 3 Pax-3 gene taxon:10090 20060201 MGI relationship(CL:0000002) MGI MGI:97490 Pax6 GO:0001709 MGI:MGI:2662558|PMID:12756174 IMP MGI:1934347 P paired box gene 6 AEY11|Dey|Dickie's small eye|Gsfaey11|Pax-6 gene taxon:10090 20050214 MGI relationship(CL:0000529) MGI MGI:97490 Pax6 GO:0007409 MGI:MGI:3513567|PMID:15514979 IMP MGI:1856158 P paired box gene 6 AEY11|Dey|Dickie's small eye|Gsfaey11|Pax-6 gene taxon:10090 20050218 MGI relationship(CL:0000117) MGI MGI:97490 Pax6 GO:0008285 MGI:MGI:3512833|PMID:15548580 IMP MGI:3521718 P paired box gene 6 AEY11|Dey|Dickie's small eye|Gsfaey11|Pax-6 gene taxon:10090 20050131 MGI relationship(CL:0000031) MGI MGI:97490 Pax6 GO:0030154 MGI:MGI:3051914|PMID:15031110 IMP MGI:1856155 P paired box gene 6 AEY11|Dey|Dickie's small eye|Gsfaey11|Pax-6 gene taxon:10090 20050725 MGI relationship(CL:0000170) MGI MGI:97490 Pax6 GO:0030900 MGI:MGI:3512833|PMID:15548580 IMP MGI:3521718 P paired box gene 6 AEY11|Dey|Dickie's small eye|Gsfaey11|Pax-6 gene taxon:10090 20050131 MGI relationship(CL:0000117) MGI MGI:97490 Pax6 GO:0045165 MGI:MGI:3055655|PMID:15229646 IGI MGI:1100526 P paired box gene 6 AEY11|Dey|Dickie's small eye|Gsfaey11|Pax-6 gene taxon:10090 20041110 MGI relationship(CL:0000107) MGI MGI:97490 Pax6 GO:0045165 MGI:MGI:3055655|PMID:15229646 IGI MGI:1100526 P paired box gene 6 AEY11|Dey|Dickie's small eye|Gsfaey11|Pax-6 gene taxon:10090 20041110 MGI relationship(CL:0000617) MGI MGI:97490 Pax6 GO:0045165 MGI:MGI:3581509|PMID:15878992 IMP MGI:1856155 P paired box gene 6 AEY11|Dey|Dickie's small eye|Gsfaey11|Pax-6 gene taxon:10090 20050816 MGI relationship(CL:0000679) MGI MGI:97490 Pax6 GO:0045665 MGI:MGI:3663573|PMID:16950124 IGI MGI:95728 P paired box gene 6 AEY11|Dey|Dickie's small eye|Gsfaey11|Pax-6 gene taxon:10090 20061221 MGI relationship(CL:0000540) MGI MGI:97490 Pax6 GO:0050767 MGI:MGI:3512833|PMID:15548580 IMP MGI:3521718 P paired box gene 6 AEY11|Dey|Dickie's small eye|Gsfaey11|Pax-6 gene taxon:10090 20050131 MGI relationship(CL:0000117) MGI MGI:97492 Pax8 GO:0030154 MGI:MGI:1203285|PMID:9590297 IMP MGI:2156985 P paired box gene 8 Pax-8 gene taxon:10090 20061116 MGI relationship(CL:0000477) MGI MGI:97492 Pax8 GO:0030878 MGI:MGI:1203285|PMID:9590297 IMP MGI:2156985 P paired box gene 8 Pax-8 gene taxon:10090 20061116 MGI relationship(CL:0000477) MGI MGI:97495 Pbx1 GO:0008284 MGI:MGI:3581070|PMID:15944191 IMP MGI:2155612 P pre B-cell leukemia transcription factor 1 Pbx-1 gene taxon:10090 20050816 MGI relationship(CL:0000134) MGI MGI:97495 Pbx1 GO:0045944 MGI:MGI:3581070|PMID:15944191 IDA P pre B-cell leukemia transcription factor 1 Pbx-1 gene taxon:10090 20050816 MGI relationship(CL:0000001) MGI MGI:97496 Pbx3 GO:0005634 MGI:MGI:3505657|PMID:15466398 IDA C pre B-cell leukemia transcription factor 3 gene taxon:10090 20050131 MGI relationship(CL:0000117) MGI MGI:97496 Pbx3 GO:0005634 MGI:MGI:3505657|PMID:15466398 IDA C pre B-cell leukemia transcription factor 3 gene taxon:10090 20050131 MGI relationship(CL:0000192) MGI MGI:97496 Pbx3 GO:0005634 MGI:MGI:3505657|PMID:15466398 IDA C pre B-cell leukemia transcription factor 3 gene taxon:10090 20050131 MGI relationship(CL:0000540) MGI MGI:1891428 Pcdh15 GO:0002009 MGI:MGI:1929046|PMID:11138007 IMP MGI:2151877 P protocadherin 15 nmf19|Ush1f gene taxon:10090 20070320 MGI relationship(CL:0000710) MGI MGI:1891428 Pcdh15 GO:0007015 MGI:MGI:3619110|PMID:11124469 IMP MGI:1856396,MGI:1856394,MGI:1855958 P protocadherin 15 nmf19|Ush1f gene taxon:10090 20070320 MGI relationship(CL:0000589) MGI MGI:1891428 Pcdh15 GO:0007015 MGI:MGI:3619110|PMID:11124469 IMP MGI:1856396,MGI:1856394,MGI:1855958 P protocadherin 15 nmf19|Ush1f gene taxon:10090 20070320 MGI relationship(CL:0000601) MGI MGI:1891428 Pcdh15 GO:0007015 MGI:MGI:3619110|PMID:11124469 IMP MGI:1856396,MGI:1856394,MGI:1855958 P protocadherin 15 nmf19|Ush1f gene taxon:10090 20070320 MGI relationship(CL:0000609) MGI MGI:1891428 Pcdh15 GO:0048839 MGI:MGI:3574187|PMID:15811708 IMP MGI:2183469 P protocadherin 15 nmf19|Ush1f gene taxon:10090 20070320 MGI relationship(CL:0000202) MGI MGI:1891428 Pcdh15 GO:0060088 MGI:MGI:1928787|PMID:10978835 IMP MGI:2151877 P protocadherin 15 nmf19|Ush1f gene taxon:10090 20070322 MGI relationship(CL:0000589) MGI MGI:1891428 Pcdh15 GO:0060088 MGI:MGI:1928787|PMID:10978835 IMP MGI:2151877 P protocadherin 15 nmf19|Ush1f gene taxon:10090 20070322 MGI relationship(CL:0000601) MGI MGI:1891428 Pcdh15 GO:0060088 MGI:MGI:3526751|PMID:15537665 IGI MGI:1890219 P protocadherin 15 nmf19|Ush1f gene taxon:10090 20070322 MGI relationship(CL:0000589) MGI MGI:1891428 Pcdh15 GO:0060088 MGI:MGI:3526751|PMID:15537665 IGI MGI:1890219 P protocadherin 15 nmf19|Ush1f gene taxon:10090 20070322 MGI relationship(CL:0000601) MGI MGI:1891428 Pcdh15 GO:0060088 MGI:MGI:3619110|PMID:11124469 IMP MGI:1856396,MGI:1856394,MGI:1855958 P protocadherin 15 nmf19|Ush1f gene taxon:10090 20070322 MGI relationship(CL:0000589) MGI MGI:1891428 Pcdh15 GO:0060088 MGI:MGI:3619110|PMID:11124469 IMP MGI:1856396,MGI:1856394,MGI:1855958 P protocadherin 15 nmf19|Ush1f gene taxon:10090 20070322 MGI relationship(CL:0000601) MGI MGI:1891428 Pcdh15 GO:0060088 MGI:MGI:3654702|PMID:16887306 IMP MGI:3505691 P protocadherin 15 nmf19|Ush1f gene taxon:10090 20070322 MGI relationship(CL:0000601) MGI MGI:2157782 Pcdh21 GO:0005887 MGI:MGI:2154844|PMID:11738025 IDA C protocadherin 21 Prcad gene taxon:10090 20050725 MGI relationship(CL:0000573) MGI MGI:2157782 Pcdh21 GO:0005887 MGI:MGI:2154844|PMID:11738025 IDA C protocadherin 21 Prcad gene taxon:10090 20050725 MGI relationship(CL:0000604) MGI MGI:2157782 Pcdh21 GO:0009987 MGI:MGI:2154844|PMID:11738025 IMP MGI:3046299 P protocadherin 21 Prcad gene taxon:10090 20050725 MGI relationship(CL:0000573) MGI MGI:2157782 Pcdh21 GO:0009987 MGI:MGI:2154844|PMID:11738025 IMP MGI:3046299 P protocadherin 21 Prcad gene taxon:10090 20050725 MGI relationship(CL:0000604) MGI MGI:2157782 Pcdh21 GO:0045494 MGI:MGI:2154844|PMID:11738025 IMP MGI:3046299 P protocadherin 21 Prcad gene taxon:10090 20050725 MGI relationship(CL:0000573) MGI MGI:2157782 Pcdh21 GO:0045494 MGI:MGI:2154844|PMID:11738025 IMP MGI:3046299 P protocadherin 21 Prcad gene taxon:10090 20050725 MGI relationship(CL:0000604) MGI MGI:1935169 Pcdhgb1 GO:0030426 MGI:MGI:3513228|PMID:15581637 IDA C protocadherin gamma subfamily B, 1 gene taxon:10090 20050121 MGI relationship(CL:0000001) MGI MGI:97503 Pcna GO:0005634 MGI:MGI:2651980|PMID:12638230 IDA C proliferating cell nuclear antigen gene taxon:10090 20050921 MGI relationship(CL:0000020) MGI MGI:97503 Pcna GO:0005634 MGI:MGI:2651980|PMID:12638230 IDA C proliferating cell nuclear antigen gene taxon:10090 20050921 MGI relationship(CL:0000656) MGI MGI:102722 Pcnt GO:0005813 MGI:MGI:3057091|PMID:15280373 IDA C pericentrin (kendrin) Pcnt2 gene taxon:10090 20050111 MGI relationship(CL:0000656) MGI MGI:102722 Pcnt GO:0005814 MGI:MGI:3037622|PMID:15037549 IDA C pericentrin (kendrin) Pcnt2 gene taxon:10090 20040630 MGI relationship(CL:0000066) MGI MGI:102722 Pcnt GO:0005814 MGI:MGI:3053250|PMID:15337773 IDA C pericentrin (kendrin) Pcnt2 gene taxon:10090 20041223 MGI relationship(CL:0000067) MGI MGI:88557 Pcyt1a GO:0005789 MGI:MGI:3603489|PMID:15169678 IDA C phosphate cytidylyltransferase 1, choline, alpha isoform CTalpha|CTP:phosphocholine cytidylyltransferase alpha|Ctpct|Cttalpha gene taxon:10090 20060119 MGI relationship(CL:0000326) MGI MGI:88557 Pcyt1a GO:0042587 MGI:MGI:3603489|PMID:15169678 IDA C phosphate cytidylyltransferase 1, choline, alpha isoform CTalpha|CTP:phosphocholine cytidylyltransferase alpha|Ctpct|Cttalpha gene taxon:10090 20060119 MGI relationship(CL:0000326) MGI MGI:104879 Pdcd1 GO:0009897 MGI:MGI:3521631|PMID:15568026 IDA C programmed cell death 1 PD-1|Pdc1 gene taxon:10090 20070104 MGI relationship(CL:0000002) MGI MGI:97528 Pdgfb GO:0001938 MGI:MGI:3629249|PMID:16644864 IGI MGI:97306 P platelet derived growth factor, B polypeptide PDGF-B|Sis gene taxon:10090 20070212 MGI relationship(CL:0000359) MGI MGI:97528 Pdgfb GO:0030336 MGI:MGI:3629249|PMID:16644864 IGI MGI:97306 P platelet derived growth factor, B polypeptide PDGF-B|Sis gene taxon:10090 20070212 MGI relationship(CL:0000359) MGI MGI:97530 Pdgfra GO:0009653 MGI:MGI:3525374|PMID:15543606 IMP MGI:1926728 P platelet derived growth factor receptor, alpha polypeptide CD140a gene taxon:10090 20050317 MGI relationship(CL:0000001) MGI MGI:97530 Pdgfra GO:0030198 MGI:MGI:3525374|PMID:15543606 IMP MGI:1926728 P platelet derived growth factor receptor, alpha polypeptide CD140a gene taxon:10090 20050317 MGI relationship(CL:0000008) MGI MGI:97530 Pdgfra GO:0042475 MGI:MGI:3525374|PMID:15543606 IMP MGI:1926728 P platelet derived growth factor receptor, alpha polypeptide CD140a gene taxon:10090 20050317 MGI relationship(CL:0000001) MGI MGI:95834 Pdia3 GO:0043065 MGI:MGI:3578073|PMID:15858817 IMP P protein disulfide isomerase associated 3 Erp|ERp57|ERp60|ERp61|Grp58|PDI|PDI-Q2|Plca gene taxon:10090 20050607 MGI relationship(CL:0000134) MGI MGI:102851 Pdx1 GO:0005634 MGI:MGI:2686820|PMID:14702043 IDA C pancreatic and duodenal homeobox 1 IDX-1|IPF-1|Ipf1|Mody4|pdx-1|STF-1 gene taxon:10090 20041006 MGI relationship(CL:0000066) MGI MGI:102851 Pdx1 GO:0005634 MGI:MGI:2686820|PMID:14702043 IDA C pancreatic and duodenal homeobox 1 IDX-1|IPF-1|Ipf1|Mody4|pdx-1|STF-1 gene taxon:10090 20041006 MGI relationship(CL:0000169) MGI MGI:102851 Pdx1 GO:0030154 MGI:MGI:3612374|PMID:16418487 IMP MGI:2181362 P pancreatic and duodenal homeobox 1 IDX-1|IPF-1|Ipf1|Mody4|pdx-1|STF-1 gene taxon:10090 20060324 MGI relationship(CL:0000164) MGI MGI:102851 Pdx1 GO:0030154 MGI:MGI:3612374|PMID:16418487 IMP MGI:2181362 P pancreatic and duodenal homeobox 1 IDX-1|IPF-1|Ipf1|Mody4|pdx-1|STF-1 gene taxon:10090 20060324 MGI relationship(CL:0000169) MGI MGI:894318 Pftk1 GO:0005634 MGI:MGI:893308|PMID:9202329 IDA C PFTAIRE protein kinase 1 gene taxon:10090 20070222 MGI relationship(CL:0000100) MGI MGI:894318 Pftk1 GO:0005737 MGI:MGI:893308|PMID:9202329 IDA C PFTAIRE protein kinase 1 gene taxon:10090 20070222 MGI relationship(CL:0000100) MGI MGI:97567 Pgr GO:0002070 MGI:MGI:3028786|PMID:14765981 IMP MGI:1857933 P progesterone receptor NR3C3|PR|PR-A|PR-B gene taxon:10090 20061117 MGI relationship(CL:0000070) MGI MGI:97567 Pgr GO:0030879 MGI:MGI:3028786|PMID:14765981 IMP MGI:1857933 P progesterone receptor NR3C3|PR|PR-A|PR-B gene taxon:10090 20061117 MGI relationship(CL:0000070) MGI MGI:2384756 Phf21a GO:0005634 MGI:MGI:3051428|PMID:15325272 IDA C PHD finger protein 21A 80kDa|Bhc80|Braf35/HDAC complex (Bhc)|PFTF1 gene taxon:10090 20060725 MGI relationship(CL:0000017) MGI MGI:2384756 Phf21a GO:0005634 MGI:MGI:3051428|PMID:15325272 IDA C PHD finger protein 21A 80kDa|Bhc80|Braf35/HDAC complex (Bhc)|PFTF1 gene taxon:10090 20060725 MGI relationship(CL:0000018) MGI MGI:2384756 Phf21a GO:0005634 MGI:MGI:3051428|PMID:15325272 IDA C PHD finger protein 21A 80kDa|Bhc80|Braf35/HDAC complex (Bhc)|PFTF1 gene taxon:10090 20060725 MGI relationship(CL:0000020) MGI MGI:2384756 Phf21a GO:0005634 MGI:MGI:3051428|PMID:15325272 IDA C PHD finger protein 21A 80kDa|Bhc80|Braf35/HDAC complex (Bhc)|PFTF1 gene taxon:10090 20060725 MGI relationship(CL:0000117) MGI MGI:1100882 Phox2b GO:0048468 MGI:MGI:3530939|PMID:15733675 IMP MGI:1926861 P paired-like homeobox 2b Dilp1|GENA 269|NBPhox|Phox2b|Pmx2b gene taxon:10090 20050509 MGI relationship(CL:0000166) MGI MGI:1913126 Pias3 GO:0005634 MGI:MGI:2679778|PMID:14596924 IDA C protein inhibitor of activated STAT 3 Pias3L gene taxon:10090 20050422 MGI relationship(CL:0000002) MGI MGI:97583 Pik3r1 GO:0043066 MGI:MGI:3038547|PMID:15039234 IGI MGI:97306,MGI:99255 P phosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha) p50alpha|p55alpha|p85alpha|PI3K gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:1298224 Pip5k1c GO:0007409 MGI:MGI:3037391|PMID:14741049 IDA P phosphatidylinositol-4-phosphate 5-kinase, type 1 gamma gene taxon:10090 20040504 MGI relationship(CL:0000120) MGI MGI:109340 Pitx2 GO:0030334 MGI:MGI:2389284|PMID:12397115 IMP MGI:2445428 P paired-like homeodomain transcription factor 2 Brx1|Brx1a|Brx1b|Munc30|Otlx2|Pitx2a|Pitx2b|Pitx2c|Ptx2|solurshin gene taxon:10090 20050725 MGI relationship(CL:0000056) MGI MGI:1100498 Pitx3 GO:0030901 MGI:MGI:3035846|PMID:14973278 IMP MGI:1856667 P paired-like homeodomain transcription factor 3 Ptx3 gene taxon:10090 20050908 MGI relationship(CL:0000700) MGI MGI:1100498 Pitx3 GO:0048666 MGI:MGI:3035846|PMID:14973278 IMP MGI:1856667 P paired-like homeodomain transcription factor 3 Ptx3 gene taxon:10090 20050908 MGI relationship(CL:0000700) MGI MGI:97603 Pkd1 GO:0005634 MGI:MGI:3512725|PMID:15545994 IDA C polycystic kidney disease 1 homolog PC-1|PC1|polycystin-1 gene taxon:10090 20050214 MGI relationship(CL:0000066) MGI MGI:97603 Pkd1 GO:0005634 MGI:MGI:3512725|PMID:15545994 IDA C polycystic kidney disease 1 homolog PC-1|PC1|polycystin-1 gene taxon:10090 20050214 MGI relationship(CL:0000134) MGI MGI:97603 Pkd1 GO:0005929 MGI:MGI:2449360|PMID:12514735 IDA C polycystic kidney disease 1 homolog PC-1|PC1|polycystin-1 gene taxon:10090 20050214 MGI relationship(CL:0000066) MGI MGI:97603 Pkd1 GO:0050982 MGI:MGI:3512725|PMID:15545994 IDA P polycystic kidney disease 1 homolog PC-1|PC1|polycystin-1 gene taxon:10090 20050214 MGI relationship(CL:0000066) MGI MGI:1099818 Pkd2 GO:0005929 MGI:MGI:2449360|PMID:12514735 IDA C polycystic kidney disease 2 polycystin-2|TRPP2 gene taxon:10090 20041223 MGI relationship(CL:0000067) MGI MGI:1099818 Pkd2 GO:0005929 MGI:MGI:3609104|PMID:16316413 IDA C polycystic kidney disease 2 polycystin-2|TRPP2 gene taxon:10090 20060221 MGI relationship(CL:0000064) MGI MGI:1099818 Pkd2 GO:0006816 MGI:MGI:2449360|PMID:12514735 IMP P polycystic kidney disease 2 polycystin-2|TRPP2 gene taxon:10090 20050725 MGI relationship(CL:0000067) MGI MGI:1099818 Pkd2 GO:0050974 MGI:MGI:2449360|PMID:12514735 IMP P polycystic kidney disease 2 polycystin-2|TRPP2 gene taxon:10090 20050725 MGI relationship(CL:0000067) MGI MGI:2445415 Pknox2 GO:0005634 MGI:MGI:3522406|PMID:15339927 IDA C Pbx/knotted 1 homeobox 2 Prep2 gene taxon:10090 20050214 MGI relationship(CL:0000134) MGI MGI:2445415 Pknox2 GO:0015629 MGI:MGI:3522406|PMID:15339927 IDA C Pbx/knotted 1 homeobox 2 Prep2 gene taxon:10090 20050214 MGI relationship(CL:0000002) MGI MGI:2445415 Pknox2 GO:0015630 MGI:MGI:3522406|PMID:15339927 IDA C Pbx/knotted 1 homeobox 2 Prep2 gene taxon:10090 20050214 MGI relationship(CL:0000002) MGI MGI:1914701 Pkp2 GO:0005912 MGI:MGI:3056846|PMID:15479741 IMP MGI:3487374 C plakophilin 2 gene taxon:10090 20050725 MGI relationship(CL:0000193) MGI MGI:1914701 Pkp2 GO:0016337 MGI:MGI:3056846|PMID:15479741 IMP MGI:3487374 P plakophilin 2 gene taxon:10090 20050725 MGI relationship(CL:0000193) MGI MGI:97610 Plat GO:0030141 MGI:MGI:3584304|PMID:15978259 IDA C plasminogen activator, tissue D8Ertd2e|t-PA|tPA gene taxon:10090 20051128 MGI relationship(CL:0000066) MGI MGI:97610 Plat GO:0045177 MGI:MGI:3584304|PMID:15978259 IDA C plasminogen activator, tissue D8Ertd2e|t-PA|tPA gene taxon:10090 20051128 MGI relationship(CL:0000066) MGI MGI:97614 Plcd1 GO:0005829 MGI:MGI:3590438|PMID:15899900 IDA C phospholipase C, delta 1 PLC-delta 1 gene taxon:10090 20051215 MGI relationship(CL:0000002) MGI MGI:2443078 Plch2 GO:0005886 MGI:MGI:3590438|PMID:15899900 IDA C phospholipase C, eta 2 PLCeta2|Plcl4 gene taxon:10090 20051215 MGI relationship(CL:0000002) MGI MGI:97620 Plg GO:0045445 MGI:MGI:2178512|PMID:11929773 IMP P plasminogen Pg gene taxon:10090 20050725 MGI relationship(CL:0000002) MGI MGI:1890505 Plin GO:0005811 MGI:MGI:3057082|PMID:15292255 IDA C perilipin Peri|perilipin A|perilipin B gene taxon:10090 20060726 MGI relationship(CL:0000057) MGI MGI:97622 Pln GO:0002026 MGI:MGI:1347184|PMID:10555147 IGI MGI:1330824,MGI:88110 P phospholamban PLB gene taxon:10090 20061016 MGI relationship(CL:0000746) MGI MGI:97622 Pln GO:0006874 MGI:MGI:1347184|PMID:10555147 IGI MGI:88110 P phospholamban PLB gene taxon:10090 20061016 MGI relationship(CL:0000746) MGI MGI:97622 Pln GO:0016529 MGI:MGI:85770|PMID:9038922 IDA C phospholamban PLB gene taxon:10090 20061010 MGI relationship(CL:0000746) MGI MGI:97622 Pln GO:0045822 MGI:MGI:1347184|PMID:10555147 IGI MGI:88110 P phospholamban PLB gene taxon:10090 20061016 MGI relationship(CL:0000746) MGI MGI:97622 Pln GO:0048738 MGI:MGI:1347184|PMID:10555147 IGI MGI:1330824 P phospholamban PLB gene taxon:10090 20061013 MGI relationship(CL:0000746) MGI MGI:97623 Plp1 GO:0022010 MGI:MGI:59023|PMID:1694232 IMP MGI:1856067 P proteolipid protein (myelin) 1 DM20|Plp gene taxon:10090 20061109 MGI relationship(CL:0000128) MGI MGI:97623 Plp1 GO:0048469 MGI:MGI:3614301|PMID:11746780 IMP P proteolipid protein (myelin) 1 DM20|Plp gene taxon:10090 20060309 MGI relationship(CL:0000128) MGI MGI:107683 Plxna3 GO:0007411 MGI:MGI:2152659|PMID:11683995 IMP MGI:2386961 P plexin A3 Plxn3|Plxn4|SEX gene taxon:10090 20061116 MGI relationship(CL:0000120) MGI MGI:107683 Plxna3 GO:0007411 MGI:MGI:2152659|PMID:11683995 IMP MGI:2386961 P plexin A3 Plxn3|Plxn4|SEX gene taxon:10090 20061116 MGI relationship(CL:0000540) MGI MGI:107683 Plxna3 GO:0007411 MGI:MGI:2152659|PMID:11683995 IMP MGI:2386961 P plexin A3 Plxn3|Plxn4|SEX gene taxon:10090 20061116 MGI relationship(CL:0000598) MGI MGI:107683 Plxna3 GO:0021766 MGI:MGI:2152659|PMID:11683995 IMP MGI:2386961 P plexin A3 Plxn3|Plxn4|SEX gene taxon:10090 20061116 MGI relationship(CL:0000120) MGI MGI:107683 Plxna3 GO:0021766 MGI:MGI:2152659|PMID:11683995 IMP MGI:2386961 P plexin A3 Plxn3|Plxn4|SEX gene taxon:10090 20061116 MGI relationship(CL:0000598) MGI MGI:107683 Plxna3 GO:0021860 MGI:MGI:2152659|PMID:11683995 IMP MGI:2386961 P plexin A3 Plxn3|Plxn4|SEX gene taxon:10090 20061116 MGI relationship(CL:0000598) MGI MGI:107683 Plxna3 GO:0048843 MGI:MGI:2152659|PMID:11683995 IGI MGI:1096347,MGI:107558 P plexin A3 Plxn3|Plxn4|SEX gene taxon:10090 20061116 MGI relationship(CL:0000001) MGI MGI:107683 Plxna3 GO:0050919 MGI:MGI:2152659|PMID:11683995 IGI MGI:1096347,MGI:107558 P plexin A3 Plxn3|Plxn4|SEX gene taxon:10090 20061116 MGI relationship(CL:0000001) MGI MGI:2154238 Plxnb1 GO:0050772 MGI:MGI:3531372|PMID:15330859 IGI MGI:109244 P plexin B1 gene taxon:10090 20050506 MGI relationship(CL:0000002) MGI MGI:2154239 Plxnb2 GO:0050772 MGI:MGI:3531372|PMID:15330859 IGI MGI:109244 P plexin B2 Debt gene taxon:10090 20050506 MGI relationship(CL:0000002) MGI MGI:2154244 Plxnd1 GO:0001569 MGI:MGI:3050159|PMID:15239958 IMP MGI:3050678 P plexin D1 gene taxon:10090 20041006 MGI relationship(CL:0000071) MGI MGI:1100514 Pnn GO:0005737 MGI:MGI:3626022|PMID:16427813 IDA C pinin D12Ertd512e gene taxon:10090 20060724 MGI relationship(CL:0000604) MGI MGI:1100514 Pnn GO:0016607 MGI:MGI:3626022|PMID:16427813 IDA C pinin D12Ertd512e gene taxon:10090 20060724 MGI relationship(CL:0000007) MGI MGI:1351317 Podxl GO:0050900 MGI:MGI:3580935|PMID:15701716 IMP MGI:1351317 P podocalyxin-like Ly102|PC|Pclp1|podocalyxin gene taxon:10090 20050805 MGI relationship(CL:0000738) MGI MGI:99660 Pola1 GO:0005634 MGI:MGI:1203906|PMID:9584195 IDA C polymerase (DNA directed), alpha 1 Pola gene taxon:10090 20060817 MGI relationship(CL:0000002) MGI MGI:99690 Pola2 GO:0005634 MGI:MGI:1203906|PMID:9584195 IDA C polymerase (DNA directed), alpha 2 gene taxon:10090 20060817 MGI relationship(CL:0000002) MGI MGI:97743 Poo GO:0007292 MGI:MGI:65716|PMID:8157170 IMP MGI:3040786 P primary oocyte ovulation gene taxon:10090 20050725 MGI relationship(CL:0000654) MGI MGI:101898 Pou2f1 GO:0045944 MGI:MGI:3603095|PMID:16002402 IDA P POU domain, class 2, transcription factor 1 oct-1|Oct-1A|Oct-1B|Oct-1C|Oct-1z|Otf-1|Otf1 gene taxon:10090 20051104 MGI relationship(CL:0000002) MGI MGI:101895 Pou3f2 GO:0045595 MGI:MGI:87235|PMID:8593698 IMP P POU domain, class 3, transcription factor 2 Brn-2|Brn2|Otf7 gene taxon:10090 20061222 MGI relationship(CL:0000002) MGI MGI:102525 Pou4f1 GO:0021535 MGI:MGI:84546|PMID:8955272 IMP MGI:3512302 P POU domain, class 4, transcription factor 1 Brn-3|Brn-3.0|Brn3|Brn3a gene taxon:10090 20061115 MGI relationship(CL:0000117) MGI MGI:102525 Pou4f1 GO:0021953 MGI:MGI:83320|PMID:8876243 IMP MGI:2387665 P POU domain, class 4, transcription factor 1 Brn-3|Brn-3.0|Brn3|Brn3a gene taxon:10090 20061115 MGI relationship(CL:0000117) MGI MGI:102525 Pou4f1 GO:0021953 MGI:MGI:84546|PMID:8955272 IMP MGI:3512302 P POU domain, class 4, transcription factor 1 Brn-3|Brn-3.0|Brn3|Brn3a gene taxon:10090 20061115 MGI relationship(CL:0000117) MGI MGI:102525 Pou4f1 GO:0030182 MGI:MGI:3587126|PMID:16040009 IMP MGI:2387665 P POU domain, class 4, transcription factor 1 Brn-3|Brn-3.0|Brn3|Brn3a gene taxon:10090 20060202 MGI relationship(CL:0000101) MGI MGI:102525 Pou4f1 GO:0048934 MGI:MGI:83320|PMID:8876243 IMP MGI:2387665 P POU domain, class 4, transcription factor 1 Brn-3|Brn-3.0|Brn3|Brn3a gene taxon:10090 20061115 MGI relationship(CL:0000101) MGI MGI:102525 Pou4f1 GO:0048934 MGI:MGI:84546|PMID:8955272 IMP MGI:3512302 P POU domain, class 4, transcription factor 1 Brn-3|Brn-3.0|Brn3|Brn3a gene taxon:10090 20061115 MGI relationship(CL:0000101) MGI MGI:102524 Pou4f2 GO:0007409 MGI:MGI:2429619|PMID:10357904 IMP MGI:2429632|MGI:2429634 P POU domain, class 4, transcription factor 2 Brn-3.2|Brn-3b|Brn3b|mBrn3-3R|Pou4f-rs1 gene taxon:10090 20050825 MGI relationship(CL:0000740) MGI MGI:102524 Pou4f2 GO:0007411 MGI:MGI:1928568|PMID:11163266 IMP MGI:3582493 P POU domain, class 4, transcription factor 2 Brn-3.2|Brn-3b|Brn3b|mBrn3-3R|Pou4f-rs1 gene taxon:10090 20050725 MGI relationship(CL:0000117) MGI MGI:102524 Pou4f2 GO:0030182 MGI:MGI:3621691|PMID:9630743 IMP MGI:2176272 P POU domain, class 4, transcription factor 2 Brn-3.2|Brn-3b|Brn3b|mBrn3-3R|Pou4f-rs1 gene taxon:10090 20060810 MGI relationship(CL:0000740) MGI MGI:102524 Pou4f2 GO:0030182 MGI:MGI:80981|PMID:8637595 IMP MGI:3582493 P POU domain, class 4, transcription factor 2 Brn-3.2|Brn-3b|Brn3b|mBrn3-3R|Pou4f-rs1 gene taxon:10090 20061115 MGI relationship(CL:0000740) MGI MGI:102524 Pou4f2 GO:0031290 MGI:MGI:2156641|PMID:11807038 IGI MGI:102523 P POU domain, class 4, transcription factor 2 Brn-3.2|Brn-3b|Brn3b|mBrn3-3R|Pou4f-rs1 gene taxon:10090 20070305 MGI relationship(CL:0000740) MGI MGI:102524 Pou4f2 GO:0048676 MGI:MGI:2156641|PMID:11807038 IGI MGI:102523 P POU domain, class 4, transcription factor 2 Brn-3.2|Brn-3b|Brn3b|mBrn3-3R|Pou4f-rs1 gene taxon:10090 20070305 MGI relationship(CL:0000001) MGI MGI:102524 Pou4f2 GO:0060041 MGI:MGI:3621691|PMID:9630743 IMP MGI:2176272 P POU domain, class 4, transcription factor 2 Brn-3.2|Brn-3b|Brn3b|mBrn3-3R|Pou4f-rs1 gene taxon:10090 20060810 MGI relationship(CL:0000740) MGI MGI:102523 Pou4f3 GO:0031290 MGI:MGI:2156641|PMID:11807038 IGI MGI:102524 P POU domain, class 4, transcription factor 3 Brn-3.1|Brn3.1|Brn3c gene taxon:10090 20070305 MGI relationship(CL:0000740) MGI MGI:102523 Pou4f3 GO:0042491 MGI:MGI:80981|PMID:8637595 IMP MGI:2176270 P POU domain, class 4, transcription factor 3 Brn-3.1|Brn3.1|Brn3c gene taxon:10090 20061115 MGI relationship(CL:0000202) MGI MGI:102523 Pou4f3 GO:0048676 MGI:MGI:2156641|PMID:11807038 IGI MGI:102524 P POU domain, class 4, transcription factor 3 Brn-3.1|Brn3.1|Brn3c gene taxon:10090 20070305 MGI relationship(CL:0000001) MGI MGI:101884 Ppard GO:0006629 MGI:MGI:3621068|PMID:16581799 IMP MGI:3623147 P peroxisome proliferator activator receptor delta mPPAR(delta)|Nr1c2|NUC-1|NUC1|Peroxisome proliferator-activated receptor beta|PPAR-beta|PPAR-delta|PPAR[b]|Pparb|Pparb/d|PPARdelta/beta gene taxon:10090 20060609 MGI relationship(CL:0000351) MGI MGI:101884 Ppard GO:0014068 MGI:MGI:3621068|PMID:16581799 IDA P peroxisome proliferator activator receptor delta mPPAR(delta)|Nr1c2|NUC-1|NUC1|Peroxisome proliferator-activated receptor beta|PPAR-beta|PPAR-delta|PPAR[b]|Pparb|Pparb/d|PPARdelta/beta gene taxon:10090 20060609 MGI relationship(CL:0000351) MGI MGI:97747 Pparg GO:0045944 MGI:MGI:3587162|PMID:16099986 IDA P peroxisome proliferator activated receptor gamma Nr1c3|PPAR-gamma|Ppar-gamma2 gene taxon:10090 20060201 MGI relationship(CL:0000002) MGI MGI:103016 Ppp1ca GO:0005654 MGI:MGI:3039057|PMID:15042703 IDA C protein phosphatase 1, catalytic subunit, alpha isoform dism2|Ppp1c gene taxon:10090 20040520 MGI relationship(CL:0000082) MGI MGI:103016 Ppp1ca GO:0005737 MGI:MGI:3039057|PMID:15042703 IDA C protein phosphatase 1, catalytic subunit, alpha isoform dism2|Ppp1c gene taxon:10090 20060726 MGI relationship(CL:0000066) MGI MGI:103016 Ppp1ca GO:0005737 MGI:MGI:3039057|PMID:15042703 IDA C protein phosphatase 1, catalytic subunit, alpha isoform dism2|Ppp1c gene taxon:10090 20060726 MGI relationship(CL:0000134) MGI MGI:2140494 Ppp1r8 GO:0008283 MGI:MGI:3047517|PMID:15199142 IMP MGI:3050545 P protein phosphatase 1, regulatory (inhibitor) subunit 8 NIPP1 gene taxon:10090 20060726 MGI relationship(CL:0000221) MGI MGI:107172 Ppp3r1 GO:0001837 MGI:MGI:3053252|PMID:15339668 IMP MGI:3044031 P protein phosphatase 3, regulatory subunit B, alpha isoform (calcineurin B, type I) Cnb1|PP2B beta 1 gene taxon:10090 20060726 MGI relationship(CL:0000115) MGI MGI:107172 Ppp3r1 GO:0001837 MGI:MGI:3053252|PMID:15339668 IMP MGI:3044031 P protein phosphatase 3, regulatory subunit B, alpha isoform (calcineurin B, type I) Cnb1|PP2B beta 1 gene taxon:10090 20060726 MGI relationship(CL:0000134) MGI MGI:107172 Ppp3r1 GO:0007507 MGI:MGI:3053252|PMID:15339668 IMP MGI:3044031 P protein phosphatase 3, regulatory subunit B, alpha isoform (calcineurin B, type I) Cnb1|PP2B beta 1 gene taxon:10090 20060726 MGI relationship(CL:0000115) MGI MGI:107172 Ppp3r1 GO:0007507 MGI:MGI:3053252|PMID:15339668 IMP MGI:3044031 P protein phosphatase 3, regulatory subunit B, alpha isoform (calcineurin B, type I) Cnb1|PP2B beta 1 gene taxon:10090 20060726 MGI relationship(CL:0000134) MGI MGI:1298204 Ppt1 GO:0005615 MGI:MGI:1276629|PMID:9685319 IDA C palmitoyl-protein thioesterase 1 CLN1|D4Ertd184e gene taxon:10090 20060913 MGI relationship(CL:0000002) MGI MGI:1298204 Ppt1 GO:0005764 MGI:MGI:1276629|PMID:9685319 IDA C palmitoyl-protein thioesterase 1 CLN1|D4Ertd184e gene taxon:10090 20060913 MGI relationship(CL:0000002) MGI MGI:1298204 Ppt1 GO:0005764 MGI:MGI:3608104|PMID:16242638 IMP MGI:2176390 C palmitoyl-protein thioesterase 1 CLN1|D4Ertd184e gene taxon:10090 20060913 MGI relationship(CL:0000001) MGI MGI:1298204 Ppt1 GO:0007040 MGI:MGI:3654230|PMID:16542649 IMP MGI:3527191 P palmitoyl-protein thioesterase 1 CLN1|D4Ertd184e gene taxon:10090 20060925 MGI relationship(CL:0000001) MGI MGI:1298204 Ppt1 GO:0007269 MGI:MGI:3608104|PMID:16242638 IMP MGI:2176390 P palmitoyl-protein thioesterase 1 CLN1|D4Ertd184e gene taxon:10090 20060913 MGI relationship(CL:0000001) MGI MGI:1298204 Ppt1 GO:0008474 MGI:MGI:3655641|PMID:12483688 IDA F palmitoyl-protein thioesterase 1 CLN1|D4Ertd184e gene taxon:10090 20060925 MGI relationship(CL:0000001) MGI MGI:1298204 Ppt1 GO:0030424 MGI:MGI:3655641|PMID:12483688 IDA C palmitoyl-protein thioesterase 1 CLN1|D4Ertd184e gene taxon:10090 20060925 MGI relationship(CL:0000001) MGI MGI:1298204 Ppt1 GO:0030425 MGI:MGI:1351142|PMID:10611498 IDA C palmitoyl-protein thioesterase 1 CLN1|D4Ertd184e gene taxon:10090 20060913 MGI relationship(CL:0000598) MGI MGI:1298204 Ppt1 GO:0043025 MGI:MGI:1351142|PMID:10611498 IDA C palmitoyl-protein thioesterase 1 CLN1|D4Ertd184e gene taxon:10090 20060913 MGI relationship(CL:0000598) MGI MGI:99655 Prdm1 GO:0001701 MGI:MGI:3604853|PMID:15750184 IMP MGI:3605483 P PR domain containing 1, with ZNF domain Blimp1|PRDI-BF1 gene taxon:10090 20051130 MGI relationship(CL:0000134) MGI MGI:99655 Prdm1 GO:0045165 MGI:MGI:3584335|PMID:15937476 IMP MGI:3586884 P PR domain containing 1, with ZNF domain Blimp1|PRDI-BF1 gene taxon:10090 20060202 MGI relationship(CL:0000670) MGI MGI:99655 Prdm1 GO:0045165 MGI:MGI:3604853|PMID:15750184 IMP MGI:3605483 P PR domain containing 1, with ZNF domain Blimp1|PRDI-BF1 gene taxon:10090 20051130 MGI relationship(CL:0000670) MGI MGI:2384854 Prdm9 GO:0007128 MGI:MGI:3608186|PMID:16292313 IMP P PR domain containing 9 Meisetz gene taxon:10090 20060131 MGI relationship(CL:0000017) MGI MGI:2384854 Prdm9 GO:0007128 MGI:MGI:3608186|PMID:16292313 IMP P PR domain containing 9 Meisetz gene taxon:10090 20060131 MGI relationship(CL:0000024) MGI MGI:99523 Prdx1 GO:0006979 MGI:MGI:3578073|PMID:15858817 IMP P peroxiredoxin 1 macrophage 23kDa stress protein|macrophase stress protein 22kDa|MSP23|OSF-3|osteoblast specific factor 3|PAG|Paga|Prx I|PrxI|Tdpx2|TDX2|thioredoxin dependent peroxide reductase 2|Trx dependent peroxide reductase 2 gene taxon:10090 20050607 MGI relationship(CL:0000134) MGI MGI:99523 Prdx1 GO:0042345 MGI:MGI:3578073|PMID:15858817 IMP P peroxiredoxin 1 macrophage 23kDa stress protein|macrophase stress protein 22kDa|MSP23|OSF-3|osteoblast specific factor 3|PAG|Paga|Prx I|PrxI|Tdpx2|TDX2|thioredoxin dependent peroxide reductase 2|Trx dependent peroxide reductase 2 gene taxon:10090 20050607 MGI relationship(CL:0000134) MGI MGI:97595 Prkca GO:0006874 MGI:MGI:3033566|PMID:14966518 IMP MGI:3037088 P protein kinase C, alpha Pkca gene taxon:10090 20051228 MGI relationship(CL:0000746) MGI MGI:99260 Prkci GO:0035089 MGI:MGI:3607414|PMID:16267237 IMP MGI:3526850|MGI:3608904 P protein kinase C, iota aPKClambda|Pkci|Pkcl|PKClambda|Prkcl gene taxon:10090 20060413 MGI relationship(CL:0000287) MGI MGI:99260 Prkci GO:0042462 MGI:MGI:3607414|PMID:16267237 IMP MGI:3526850|MGI:3608904 P protein kinase C, iota aPKClambda|Pkci|Pkcl|PKClambda|Prkcl gene taxon:10090 20060413 MGI relationship(CL:0000287) MGI MGI:99260 Prkci GO:0045177 MGI:MGI:3033551|PMID:14758363 IDA C protein kinase C, iota aPKClambda|Pkci|Pkcl|PKClambda|Prkcl gene taxon:10090 20040421 MGI relationship(CL:0000066) MGI MGI:97602 Prkcz GO:0005923 MGI:MGI:3582101|PMID:15950600 IDA C protein kinase C, zeta Pkcz|zetaPKC gene taxon:10090 20050822 MGI relationship(CL:0000007) MGI MGI:97602 Prkcz GO:0005923 MGI:MGI:3582101|PMID:15950600 IDA C protein kinase C, zeta Pkcz|zetaPKC gene taxon:10090 20050822 MGI relationship(CL:1000274) MGI MGI:97602 Prkcz GO:0005938 MGI:MGI:3582101|PMID:15950600 IDA C protein kinase C, zeta Pkcz|zetaPKC gene taxon:10090 20050822 MGI relationship(CL:0000007) MGI MGI:97602 Prkcz GO:0045179 MGI:MGI:3582101|PMID:15950600 IDA C protein kinase C, zeta Pkcz|zetaPKC gene taxon:10090 20050822 MGI relationship(CL:1000274) MGI MGI:108174 Prkg1 GO:0001764 MGI:MGI:3608256|PMID:16154207 IMP MGI:2181586 P protein kinase, cGMP-dependent, type I Prkg1b|Prkgr1b gene taxon:10090 20060131 MGI relationship(CL:0000117) MGI MGI:108174 Prkg1 GO:0016358 MGI:MGI:3608256|PMID:16154207 IMP MGI:2181586 P protein kinase, cGMP-dependent, type I Prkg1b|Prkgr1b gene taxon:10090 20060131 MGI relationship(CL:0000598) MGI MGI:1344375 Prkra GO:0005622 MGI:MGI:3623660|PMID:16571658 IDA C protein kinase, interferon inducible double stranded RNA dependent activator Pact|RAX gene taxon:10090 20060707 MGI relationship(CL:0000002) MGI MGI:1344375 Prkra GO:0006917 MGI:MGI:2386461|PMID:12181197 IDA P protein kinase, interferon inducible double stranded RNA dependent activator Pact|RAX gene taxon:10090 20060707 MGI relationship(CL:0000002) MGI MGI:97765 Prm1 GO:0006997 MGI:MGI:1934083|PMID:11326282 IMP MGI:3039794 P protamine 1 Prm-1 gene taxon:10090 20050725 MGI relationship(CL:0000018) MGI MGI:97765 Prm1 GO:0007286 MGI:MGI:1934083|PMID:11326282 IMP MGI:3039794 P protamine 1 Prm-1 gene taxon:10090 20050725 MGI relationship(CL:0000018) MGI MGI:97766 Prm2 GO:0006997 MGI:MGI:1934083|PMID:11326282 IMP MGI:3039800 P protamine 2 Prm-2 gene taxon:10090 20050725 MGI relationship(CL:0000018) MGI MGI:97766 Prm2 GO:0007286 MGI:MGI:1934083|PMID:11326282 IMP MGI:3039800 P protamine 2 Prm-2 gene taxon:10090 20050725 MGI relationship(CL:0000018) MGI MGI:1100886 Prom1 GO:0005902 MGI:MGI:3584059|PMID:15976444 IDA C prominin 1 AC133|CD133|Prom gene taxon:10090 20050906 MGI relationship(CL:0000133) MGI MGI:97772 Prox1 GO:0001709 MGI:MGI:2658694|PMID:12692551 IMP MGI:2386336 P prospero-related homeobox 1 gene taxon:10090 20060118 MGI relationship(CL:0000745) MGI MGI:97772 Prox1 GO:0008285 MGI:MGI:2658694|PMID:12692551 IMP MGI:2386336 P prospero-related homeobox 1 gene taxon:10090 20060118 MGI relationship(CL:0000031) MGI MGI:97772 Prox1 GO:0045446 MGI:MGI:2177970|PMID:11927535 IMP MGI:2386336 P prospero-related homeobox 1 gene taxon:10090 20040326 MGI relationship(CL:0000071) MGI MGI:97774 Prph1 GO:0005882 MGI:MGI:2653435|PMID:12642616 IDA C peripherin 1 gene taxon:10090 20070306 MGI relationship(CL:0000002) MGI MGI:97774 Prph1 GO:0005883 MGI:MGI:1336062|PMID:10221457 IDA C peripherin 1 gene taxon:10090 20070226 MGI relationship(CL:0000029) MGI MGI:97774 Prph1 GO:0030424 MGI:MGI:2447001|PMID:12107488 IDA C peripherin 1 gene taxon:10090 20050921 MGI relationship(CL:0000111) MGI MGI:97774 Prph1 GO:0045104 MGI:MGI:2653435|PMID:12642616 IDA P peripherin 1 gene taxon:10090 20070306 MGI relationship(CL:0000002) MGI MGI:2148204 Prrxl1 GO:0001764 MGI:MGI:3051709|PMID:15229182 IMP MGI:2182636 P paired related homeobox protein-like 1 Drg11 gene taxon:10090 20040929 MGI relationship(CL:0000540) MGI MGI:1921252 Psd2 GO:0030425 MGI:MGI:3577582|PMID:15836626 IDA C pleckstrin and Sec7 domain containing 2 EFA6C gene taxon:10090 20050805 MGI relationship(CL:0000121) MGI MGI:1921252 Psd2 GO:0043025 MGI:MGI:3577582|PMID:15836626 IDA C pleckstrin and Sec7 domain containing 2 EFA6C gene taxon:10090 20050805 MGI relationship(CL:0000121) MGI MGI:1202717 Psen1 GO:0001764 MGI:MGI:3045838|PMID:15163631 IMP MGI:1930934 P presenilin 1 Ad3h|presenilin-1|PS-1|PS1|S182 gene taxon:10090 20040818 MGI relationship(CL:0000117) MGI MGI:1202717 Psen1 GO:0001764 MGI:MGI:3526759|PMID:10421573 IMP MGI:2149116 P presenilin 1 Ad3h|presenilin-1|PS-1|PS1|S182 gene taxon:10090 20050502 MGI relationship(CL:0000117) MGI MGI:1202717 Psen1 GO:0005622 MGI:MGI:3526759|PMID:10421573 IDA C presenilin 1 Ad3h|presenilin-1|PS-1|PS1|S182 gene taxon:10090 20050502 MGI relationship(CL:0000001) MGI MGI:1202717 Psen1 GO:0006874 MGI:MGI:2449878|PMID:12431992 IMP MGI:2684616|MGI:2684620 P presenilin 1 Ad3h|presenilin-1|PS-1|PS1|S182 gene taxon:10090 20051206 MGI relationship(CL:0000001) MGI MGI:1202717 Psen1 GO:0030424 MGI:MGI:2154812|PMID:11740561 IDA C presenilin 1 Ad3h|presenilin-1|PS-1|PS1|S182 gene taxon:10090 20051005 MGI relationship(CL:0000540) MGI MGI:1202717 Psen1 GO:0030425 MGI:MGI:84297|PMID:8922407 IDA C presenilin 1 Ad3h|presenilin-1|PS-1|PS1|S182 gene taxon:10090 20051206 MGI relationship(CL:0000120) MGI MGI:1202717 Psen1 GO:0030425 MGI:MGI:84297|PMID:8922407 IDA C presenilin 1 Ad3h|presenilin-1|PS-1|PS1|S182 gene taxon:10090 20051206 MGI relationship(CL:0000598) MGI MGI:1202717 Psen1 GO:0031410 MGI:MGI:2154812|PMID:11740561 IDA C presenilin 1 Ad3h|presenilin-1|PS-1|PS1|S182 gene taxon:10090 20051005 MGI relationship(CL:0000540) MGI MGI:1202717 Psen1 GO:0043025 MGI:MGI:84297|PMID:8922407 IDA C presenilin 1 Ad3h|presenilin-1|PS-1|PS1|S182 gene taxon:10090 20051206 MGI relationship(CL:0000120) MGI MGI:1202717 Psen1 GO:0043025 MGI:MGI:84297|PMID:8922407 IDA C presenilin 1 Ad3h|presenilin-1|PS-1|PS1|S182 gene taxon:10090 20051206 MGI relationship(CL:0000598) MGI MGI:1202717 Psen1 GO:0051563 MGI:MGI:2449878|PMID:12431992 IGI MGI:88059 P presenilin 1 Ad3h|presenilin-1|PS-1|PS1|S182 gene taxon:10090 20051206 MGI relationship(CL:0000001) MGI MGI:1202717 Psen1 GO:0051604 MGI:MGI:3051716|PMID:15280425 IGI MGI:109284 P presenilin 1 Ad3h|presenilin-1|PS-1|PS1|S182 gene taxon:10090 20051207 MGI relationship(CL:0000002) MGI MGI:109284 Psen2 GO:0051605 MGI:MGI:3051716|PMID:15280425 IGI MGI:1202717 P presenilin 2 Ad4h|ALG-3|PS-2|PS2 gene taxon:10090 20051207 MGI relationship(CL:0000002) MGI MGI:105373 Ptch1 GO:0009953 MGI:MGI:3511726|PMID:15576403 IGI MGI:1341847 P patched homolog 1 Patched 1|Ptc|Ptc1 gene taxon:10090 20050110 MGI relationship(CL:0000117) MGI MGI:105373 Ptch1 GO:0030879 MGI:MGI:1346456|PMID:10529434 IMP MGI:1857447 P patched homolog 1 Patched 1|Ptc|Ptc1 gene taxon:10090 20061215 MGI relationship(CL:0000150) MGI MGI:1328312 Ptf1a GO:0048663 MGI:MGI:3590363|PMID:16039563 IDA P pancreas specific transcription factor, 1a PTF1-p48 gene taxon:10090 20060125 MGI relationship(CL:0000617) MGI MGI:97798 Ptgs2 GO:0042640 MGI:MGI:3531621|PMID:15713628 IMP P prostaglandin-endoperoxide synthase 2 Cox-2|COX2|cyclooxygenase 2|cyclooxygenase-2|PGHS-2|Pghs2|PHS-2|prostaglandin G/H synthase|Tis10 gene taxon:10090 20050511 MGI relationship(CL:0000001) MGI MGI:97800 Pthlh GO:0002076 MGI:MGI:3624906|PMID:9832460 IMP MGI:2154515 P parathyroid hormone-like peptide parathyroid hormone-like hormone|parathyroid hormone-related peptide|parathyroid hormone-related protein|PTH-like|PTH-related peptide|Pthrp gene taxon:10090 20060727 MGI relationship(CL:0000062) MGI MGI:97800 Pthlh GO:0030855 MGI:MGI:3042805|PMID:15162506 IMP MGI:2154515 P parathyroid hormone-like peptide parathyroid hormone-like hormone|parathyroid hormone-related peptide|parathyroid hormone-related protein|PTH-like|PTH-related peptide|Pthrp gene taxon:10090 20040715 MGI relationship(CL:0000082) MGI MGI:97800 Pthlh GO:0043129 MGI:MGI:3042805|PMID:15162506 IMP MGI:2154515 P parathyroid hormone-like peptide parathyroid hormone-like hormone|parathyroid hormone-related peptide|parathyroid hormone-related protein|PTH-like|PTH-related peptide|Pthrp gene taxon:10090 20040715 MGI relationship(CL:0000082) MGI MGI:97800 Pthlh GO:0048286 MGI:MGI:3042805|PMID:15162506 IMP MGI:2154515 P parathyroid hormone-like peptide parathyroid hormone-like hormone|parathyroid hormone-related peptide|parathyroid hormone-related protein|PTH-like|PTH-related peptide|Pthrp gene taxon:10090 20040715 MGI relationship(CL:0000082) MGI MGI:97801 Pthr1 GO:0002062 MGI:MGI:3620436|PMID:16476422 IGI MGI:99829 P parathyroid hormone receptor 1 PPR|PTH-related peptide receptor|PTH/PTHrP receptor|PTH1R gene taxon:10090 20060608 MGI relationship(CL:0000743) MGI MGI:97801 Pthr1 GO:0002062 MGI:MGI:3624906|PMID:9832460 IMP MGI:2154519 P parathyroid hormone receptor 1 PPR|PTH-related peptide receptor|PTH/PTHrP receptor|PTH1R gene taxon:10090 20060721 MGI relationship(CL:0000138) MGI MGI:97801 Pthr1 GO:0002076 MGI:MGI:3624906|PMID:9832460 IMP MGI:2154519 P parathyroid hormone receptor 1 PPR|PTH-related peptide receptor|PTH/PTHrP receptor|PTH1R gene taxon:10090 20060727 MGI relationship(CL:0000062) MGI MGI:97801 Pthr1 GO:0008284 MGI:MGI:3620436|PMID:16476422 IGI MGI:99829 P parathyroid hormone receptor 1 PPR|PTH-related peptide receptor|PTH/PTHrP receptor|PTH1R gene taxon:10090 20060608 MGI relationship(CL:0000138) MGI MGI:97801 Pthr1 GO:0008285 MGI:MGI:3625556|PMID:12194850 IMP MGI:3628795 P parathyroid hormone receptor 1 PPR|PTH-related peptide receptor|PTH/PTHrP receptor|PTH1R gene taxon:10090 20060725 MGI relationship(CL:0000744) MGI MGI:97801 Pthr1 GO:0048469 MGI:MGI:3625556|PMID:12194850 IMP MGI:3628795 P parathyroid hormone receptor 1 PPR|PTH-related peptide receptor|PTH/PTHrP receptor|PTH1R gene taxon:10090 20060725 MGI relationship(CL:0000743) MGI MGI:95481 Ptk2 GO:0005925 MGI:MGI:3613255|PMID:16405917 IDA C PTK2 protein tyrosine kinase 2 Fadk|FAK|FRNK gene taxon:10090 20070212 MGI relationship(CL:0000001) MGI MGI:1918711 Ptk7 GO:0045198 MGI:MGI:3046397|PMID:15229603 IMP MGI:3046905 P PTK7 protein tyrosine kinase 7 mPTK7/CCK4 gene taxon:10090 20040831 MGI relationship(CL:0000202) MGI MGI:99511 Ptpn11 GO:0005515 MGI:MGI:3521631|PMID:15568026 IPI UniProt:Q7TSA3 F protein tyrosine phosphatase, non-receptor type 11 PTP1D|PTP2C|SAP-2|SH-PTP2|SH-PTP3|SH2 domain-containing protein tyrosine phosphatase-2|SHP-2|Shp2|Syp gene taxon:10090 20070105 MGI relationship(CL:0000002) MGI MGI:103293 Ptpn13 GO:0005634 MGI:MGI:1349753|PMID:10526152 IDA C protein tyrosine phosphatase, non-receptor type 13 PTP-BL|Ptpri gene taxon:10090 20040409 MGI relationship(CL:0000002) MGI MGI:103293 Ptpn13 GO:0005737 MGI:MGI:1349753|PMID:10526152 IDA C protein tyrosine phosphatase, non-receptor type 13 PTP-BL|Ptpri gene taxon:10090 20040409 MGI relationship(CL:0000002) MGI MGI:97810 Ptprc GO:0009897 MGI:MGI:1860996|PMID:10943842 IDA C protein tyrosine phosphatase, receptor type, C B220|CD45|Ly-5|Lyt-4|T200 gene taxon:10090 20050617 MGI relationship(CL:0000081) MGI MGI:97810 Ptprc GO:0009897 MGI:MGI:75253|PMID:7630421 IDA C protein tyrosine phosphatase, receptor type, C B220|CD45|Ly-5|Lyt-4|T200 gene taxon:10090 20050117 MGI relationship(CL:0000236) MGI MGI:97810 Ptprc GO:0009897 MGI:MGI:77314|PMID:7477352 IDA C protein tyrosine phosphatase, receptor type, C B220|CD45|Ly-5|Lyt-4|T200 gene taxon:10090 20050117 MGI relationship(CL:0000236) MGI MGI:97810 Ptprc GO:0009897 MGI:MGI:77315|PMID:7477353 IDA C protein tyrosine phosphatase, receptor type, C B220|CD45|Ly-5|Lyt-4|T200 gene taxon:10090 20060726 MGI relationship(CL:0000236) MGI MGI:1929237 Pus1 GO:0005634 MGI:MGI:3053242|PMID:15327771 IDA C pseudouridine synthase 1 MPUS1|mPus1p gene taxon:10090 20041018 MGI relationship(CL:0000002) MGI MGI:1929237 Pus1 GO:0005730 MGI:MGI:3053242|PMID:15327771 IDA C pseudouridine synthase 1 MPUS1|mPus1p gene taxon:10090 20041018 MGI relationship(CL:0000002) MGI MGI:97821 Pvalb GO:0005737 MGI:MGI:3587126|PMID:16040009 IDA C parvalbumin PV|Pva gene taxon:10090 20060202 MGI relationship(CL:0000101) MGI MGI:1926483 Pvrl1 GO:0005913 MGI:MGI:3056026|PMID:15328010 IDA C poliovirus receptor-related 1 Cd111|HIgR|HveC|nectin-1|PRR|PRR1 gene taxon:10090 20041119 MGI relationship(CL:0000678) MGI MGI:1930171 Pvrl3 GO:0005913 MGI:MGI:3056026|PMID:15328010 IDA C poliovirus receptor-related 3 nectin-3 gene taxon:10090 20041119 MGI relationship(CL:0000678) MGI MGI:108295 Pxn GO:0005925 MGI:MGI:3624072|PMID:16399995 IDA C paxillin gene taxon:10090 20060706 MGI relationship(CL:0000002) MGI MGI:105068 Rab7 GO:0005770 MGI:MGI:3527911|PMID:15588329 IDA C RAB7, member RAS oncogene family gene taxon:10090 20060913 MGI relationship(CL:0000002) MGI MGI:97846 Rac2 GO:0008284 MGI:MGI:2149663|PMID:11435472 IGI MGI:97306 P RAS-related C3 botulinum substrate 2 gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:97846 Rac2 GO:0008284 MGI:MGI:2149663|PMID:11435472 IMP MGI:1857701 P RAS-related C3 botulinum substrate 2 gene taxon:10090 20070202 MGI relationship(CL:0000001) MGI MGI:97847 Raf1 GO:0048011 MGI:MGI:1933753|PMID:9852579 IMP P v-raf-leukemia viral oncogene 1 c-Raf|Craf1|Raf-1|sarcoma 3611 oncogene|v-Raf gene taxon:10090 20070130 MGI relationship(CL:0000540) MGI MGI:97857 Rarb GO:0043065 MGI:MGI:3608158|PMID:16207763 IGI MGI:97858 P retinoic acid receptor, beta Hap|RAR beta 2|RARbeta2 gene taxon:10090 20060123 MGI relationship(CL:0000134) MGI MGI:97858 Rarg GO:0005634 MGI:MGI:3053242|PMID:15327771 IDA C retinoic acid receptor, gamma Nr1b3|RAR gamma 2|RARD|RARgamma2 gene taxon:10090 20041018 MGI relationship(CL:0000002) MGI MGI:97858 Rarg GO:0043065 MGI:MGI:3608158|PMID:16207763 IGI MGI:97857 P retinoic acid receptor, gamma Nr1b3|RAR gamma 2|RARD|RARgamma2 gene taxon:10090 20060123 MGI relationship(CL:0000134) MGI MGI:97858 Rarg GO:0045944 MGI:MGI:3579939|PMID:15734736 IDA P retinoic acid receptor, gamma Nr1b3|RAR gamma 2|RARD|RARgamma2 gene taxon:10090 20060328 MGI relationship(CL:0000002) MGI MGI:97860 Rasa1 GO:0001726 MGI:MGI:3576987|PMID:15860730 IDA C RAS p21 protein activator 1 Gap|p120-rasGAP gene taxon:10090 20061208 MGI relationship(CL:0000001) MGI MGI:97860 Rasa1 GO:0005886 MGI:MGI:3576987|PMID:15860730 IDA C RAS p21 protein activator 1 Gap|p120-rasGAP gene taxon:10090 20061208 MGI relationship(CL:0000001) MGI MGI:1917153 Rasip1 GO:0005794 MGI:MGI:3576835|PMID:15031288 ISS EMBL:AY378097 C Ras interacting protein 1 Rain gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:1917153 Rasip1 GO:0008284 MGI:MGI:3576835|PMID:15031288 ISS EMBL:AY378097 P Ras interacting protein 1 Rain gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:1917153 Rasip1 GO:0017016 MGI:MGI:3576835|PMID:15031288 ISS EMBL:AY378097 F Ras interacting protein 1 Rain gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:1917153 Rasip1 GO:0048471 MGI:MGI:3576835|PMID:15031288 ISS EMBL:AY378097 C Ras interacting protein 1 Rain gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:2443623 Raver2 GO:0005634 MGI:MGI:3587983|PMID:16051233 IDA C ribonucleoprotein, PTB-binding 2 gene taxon:10090 20060202 MGI relationship(CL:0000002) MGI MGI:97874 Rb1 GO:0000082 MGI:MGI:3575978|PMID:15831459 IMP P retinoblastoma 1 pRb|Rb|RB-1 gene taxon:10090 20050725 MGI relationship(CL:0000002) MGI MGI:97874 Rb1 GO:0005634 MGI:MGI:3525032|PMID:15616565 IDA C retinoblastoma 1 pRb|Rb|RB-1 gene taxon:10090 20070131 MGI relationship(CL:0000235) MGI MGI:97874 Rb1 GO:0005634 MGI:MGI:3579756|PMID:15701640 IDA C retinoblastoma 1 pRb|Rb|RB-1 gene taxon:10090 20050823 MGI relationship(CL:0000467) MGI MGI:97874 Rb1 GO:0007050 MGI:MGI:3575978|PMID:15831459 IMP P retinoblastoma 1 pRb|Rb|RB-1 gene taxon:10090 20050725 MGI relationship(CL:0000002) MGI MGI:97874 Rb1 GO:0008285 MGI:MGI:3578603|PMID:15843406 IMP MGI:1857242 P retinoblastoma 1 pRb|Rb|RB-1 gene taxon:10090 20050616 MGI relationship(CL:0000202) MGI MGI:97874 Rb1 GO:0051146 MGI:MGI:3511080|PMID:15542848 IGI MGI:96680 P retinoblastoma 1 pRb|Rb|RB-1 gene taxon:10090 20050121 MGI relationship(CL:0000188) MGI MGI:97874 Rb1 GO:0051301 MGI:MGI:3578603|PMID:15843406 IMP MGI:1857242 P retinoblastoma 1 pRb|Rb|RB-1 gene taxon:10090 20050616 MGI relationship(CL:0000202) MGI MGI:96522 Rbpj GO:0001525 MGI:MGI:3056004|PMID:15466160 IMP MGI:1857411|MGI:2387130 P recombination signal binding protein for immunoglobulin kappa J region CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBPjk|Rbpsuh gene taxon:10090 20041117 MGI relationship(CL:0000071) MGI MGI:96522 Rbpj GO:0008284 MGI:MGI:3521553|PMID:15509736 IGI MGI:95516,MGI:95290 P recombination signal binding protein for immunoglobulin kappa J region CBF1|Igkjrb|Igkrsbp|RBP-J|RBP-J kappa|RBPjk|Rbpsuh gene taxon:10090 20050309 MGI relationship(CL:0000710) MGI MGI:97887 Rdx GO:0001726 MGI:MGI:1202233|PMID:9563848 IDA C radixin gene taxon:10090 20070119 MGI relationship(CL:0000002) MGI MGI:97887 Rdx GO:0030027 MGI:MGI:1202233|PMID:9563848 IDA C radixin gene taxon:10090 20070119 MGI relationship(CL:0000002) MGI MGI:97887 Rdx GO:0030175 MGI:MGI:1202233|PMID:9563848 IDA C radixin gene taxon:10090 20070119 MGI relationship(CL:0000002) MGI MGI:1929645 Rec8L1 GO:0000800 MGI:MGI:3578071|PMID:15870106 IDA C REC8-like 1 (yeast) mrec gene taxon:10090 20050609 MGI relationship(CL:0000654) MGI MGI:103290 Rela GO:0005634 MGI:MGI:2154675|PMID:11567019 IDA C v-rel reticuloendotheliosis viral oncogene homolog A (avian) p65|p65 NF kappaB gene taxon:10090 20040930 MGI relationship(CL:0000001) MGI MGI:103290 Rela GO:0005737 MGI:MGI:2154675|PMID:11567019 IDA C v-rel reticuloendotheliosis viral oncogene homolog A (avian) p65|p65 NF kappaB gene taxon:10090 20040930 MGI relationship(CL:0000001) MGI MGI:103022 Reln GO:0001764 MGI:MGI:2662645|PMID:12724835 IMP MGI:1856398 P reelin gene taxon:10090 20050424 MGI relationship(CL:0000700) MGI MGI:103022 Reln GO:0001764 MGI:MGI:3042094|PMID:14980731 IMP MGI:1856398 P reelin gene taxon:10090 20040712 MGI relationship(CL:0000402) MGI MGI:103022 Reln GO:0001764 MGI:MGI:3574745|PMID:15703280 IMP MGI:1856416 P reelin gene taxon:10090 20050509 MGI relationship(CL:0000100) MGI MGI:103022 Reln GO:0005737 MGI:MGI:3530985|PMID:15525772 IDA C reelin gene taxon:10090 20050424 MGI relationship(CL:0000695) MGI MGI:103022 Reln GO:0007411 MGI:MGI:3611655|PMID:16324103 IMP MGI:1856398 P reelin gene taxon:10090 20060510 MGI relationship(CL:0000117) MGI MGI:103022 Reln GO:0018108 MGI:MGI:3629864|PMID:12526740 IDA P reelin gene taxon:10090 20060807 MGI relationship(CL:0000001) MGI MGI:103022 Reln GO:0021511 MGI:MGI:3625412|PMID:16580148 IMP MGI:1856398 P reelin gene taxon:10090 20061117 MGI relationship(CL:0000198) MGI MGI:103022 Reln GO:0045860 MGI:MGI:3629864|PMID:12526740 IDA P reelin gene taxon:10090 20060807 MGI relationship(CL:0000001) MGI MGI:103022 Reln GO:0045860 MGI:MGI:3629864|PMID:12526740 IGI MGI:108554,MGI:98935,MGI:1340044 P reelin gene taxon:10090 20060807 MGI relationship(CL:0000001) MGI MGI:97898 Ren1 GO:0005615 MGI:MGI:1336863|PMID:10318840 IDA C renin 1 structural Ren|Ren-1|Ren-A|Ren1c|Ren1d|Rn-1|Rnr gene taxon:10090 20051229 MGI relationship(CL:0000461) MGI MGI:97898 Ren1 GO:0048469 MGI:MGI:1351364|PMID:10617578 IMP MGI:2136642 P renin 1 structural Ren|Ren-1|Ren-A|Ren1c|Ren1d|Rn-1|Rnr gene taxon:10090 20051230 MGI relationship(CL:0000461) MGI MGI:97902 Ret GO:0001755 MGI:MGI:3617928|PMID:15242795 IMP MGI:2449909 P ret proto-oncogene RET51|RET9 gene taxon:10090 20060605 MGI relationship(CL:0000333) MGI MGI:97902 Ret GO:0001838 MGI:MGI:3513229|PMID:15569713 IDA P ret proto-oncogene RET51|RET9 gene taxon:10090 20050121 MGI relationship(CL:0000002) MGI MGI:97902 Ret GO:0005515 MGI:MGI:1195875|PMID:9452475 IPI UniProt:O35118 F ret proto-oncogene RET51|RET9 gene taxon:10090 20050609 MGI relationship(CL:0000002) MGI MGI:97902 Ret GO:0042551 MGI:MGI:3052425|PMID:15233745 IMP MGI:2136894 P ret proto-oncogene RET51|RET9 gene taxon:10090 20051209 MGI relationship(CL:0000108) MGI MGI:97902 Ret GO:0048484 MGI:MGI:1313212|PMID:9834195 IMP MGI:2136894 P ret proto-oncogene RET51|RET9 gene taxon:10090 20061116 MGI relationship(CL:0000001) MGI MGI:1916049 Rgmb GO:0005793 MGI:MGI:3027667|PMID:14749425 IDA C RGM domain family, member B DRAGON gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1916049 Rgmb GO:0046658 MGI:MGI:3042498|PMID:14985445 IDA C RGM domain family, member B DRAGON gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1346016 Rgnef GO:0060052 MGI:MGI:3619625|PMID:16236762 IMP P Rho-guanine nucleotide exchange factor D13Bwg1089e|p190RhoGEF|Rho specific exchange factor|RhoGEF|RIP2 gene taxon:10090 20070307 MGI relationship(CL:0000002) MGI MGI:1096342 Rhoa GO:0000902 MGI:MGI:3576987|PMID:15860730 IGI MGI:107187 P ras homolog gene family, member A Arha|Arha1|Arha2|RhoA gene taxon:10090 20061207 MGI relationship(CL:0000001) MGI MGI:1096342 Rhoa GO:0043524 MGI:MGI:3588743|PMID:15071095 IMP P ras homolog gene family, member A Arha|Arha1|Arha2|RhoA gene taxon:10090 20060116 MGI relationship(CL:0000100) MGI MGI:1098622 Rif1 GO:0005634 MGI:MGI:3039061|PMID:15042697 IDA C Rap1 interacting factor 1 homolog (yeast) D2Ertd145e gene taxon:10090 20060125 MGI relationship(CL:0000007) MGI MGI:1921382 Rnf6 GO:0005737 MGI:MGI:3603857|PMID:16204183 IDA C ring finger protein (C3H2C3 type) 6 gene taxon:10090 20060112 MGI relationship(CL:0000540) MGI MGI:1921382 Rnf6 GO:0030424 MGI:MGI:3603857|PMID:16204183 IDA C ring finger protein (C3H2C3 type) 6 gene taxon:10090 20060112 MGI relationship(CL:0000001) MGI MGI:1921382 Rnf6 GO:0030424 MGI:MGI:3603857|PMID:16204183 IDA C ring finger protein (C3H2C3 type) 6 gene taxon:10090 20060112 MGI relationship(CL:0000540) MGI MGI:1921382 Rnf6 GO:0030517 MGI:MGI:3603857|PMID:16204183 IGI MGI:104572 P ring finger protein (C3H2C3 type) 6 gene taxon:10090 20060112 MGI relationship(CL:0000001) MGI MGI:1921382 Rnf6 GO:0030517 MGI:MGI:3603857|PMID:16204183 IMP P ring finger protein (C3H2C3 type) 6 gene taxon:10090 20060112 MGI relationship(CL:0000001) MGI MGI:1274781 Robo1 GO:0007411 MGI:MGI:3040153|PMID:15084255 IMP P roundabout homolog 1 (Drosophila) DUTT1 gene taxon:10090 20050725 MGI relationship(CL:0000540) MGI MGI:1274781 Robo1 GO:0007411 MGI:MGI:3041390|PMID:15091338 IGI MGI:1343102 P roundabout homolog 1 (Drosophila) DUTT1 gene taxon:10090 20050725 MGI relationship(CL:0000678) MGI MGI:1274781 Robo1 GO:0030673 MGI:MGI:3040153|PMID:15084255 IDA C roundabout homolog 1 (Drosophila) DUTT1 gene taxon:10090 20050725 MGI relationship(CL:0000678) MGI MGI:1890110 Robo2 GO:0007411 MGI:MGI:3041390|PMID:15091338 IMP MGI:3043127 P roundabout homolog 2 (Drosophila) gene taxon:10090 20040706 MGI relationship(CL:0000678) MGI MGI:1890110 Robo2 GO:0030673 MGI:MGI:3040153|PMID:15084255 IDA C roundabout homolog 2 (Drosophila) gene taxon:10090 20050725 MGI relationship(CL:0000678) MGI MGI:1343102 Robo3 GO:0001764 MGI:MGI:3047174|PMID:15233918 IMP MGI:3043150 P roundabout homolog 3 (Drosophila) Rbig1|Rig-1|Robo3a|Robo3b gene taxon:10090 20041007 MGI relationship(CL:0000117) MGI MGI:1343102 Robo3 GO:0007411 MGI:MGI:3040153|PMID:15084255 IDA P roundabout homolog 3 (Drosophila) Rbig1|Rig-1|Robo3a|Robo3b gene taxon:10090 20050725 MGI relationship(CL:0000540) MGI MGI:1343102 Robo3 GO:0007411 MGI:MGI:3040153|PMID:15084255 IGI MGI:1274781 P roundabout homolog 3 (Drosophila) Rbig1|Rig-1|Robo3a|Robo3b gene taxon:10090 20050725 MGI relationship(CL:0000540) MGI MGI:1343102 Robo3 GO:0007411 MGI:MGI:3040153|PMID:15084255 IMP MGI:3043150 P roundabout homolog 3 (Drosophila) Rbig1|Rig-1|Robo3a|Robo3b gene taxon:10090 20050725 MGI relationship(CL:0000540) MGI MGI:1343102 Robo3 GO:0007411 MGI:MGI:3047174|PMID:15233918 IMP MGI:3043150 P roundabout homolog 3 (Drosophila) Rbig1|Rig-1|Robo3a|Robo3b gene taxon:10090 20040902 MGI relationship(CL:0000117) MGI MGI:107927 Rock1 GO:0043524 MGI:MGI:3588743|PMID:15071095 IMP P Rho-associated coiled-coil containing protein kinase 1 Rock-I gene taxon:10090 20060116 MGI relationship(CL:0000100) MGI MGI:1347521 Ror2 GO:0030154 MGI:MGI:3037488|PMID:14745966 IMP MGI:2183225 P receptor tyrosine kinase-like orphan receptor 2 Ntrkr2 gene taxon:10090 20040513 MGI relationship(CL:0000138) MGI MGI:1923492 Rph3al GO:0017158 MGI:MGI:3044444|PMID:15159548 IMP MGI:3051976 P rabphilin 3A-like (without C2 domains) LOC385671|Noc2 gene taxon:10090 20050725 MGI relationship(CL:0000169) MGI MGI:1923492 Rph3al GO:0045744 MGI:MGI:3044444|PMID:15159548 IMP MGI:3051976 P rabphilin 3A-like (without C2 domains) LOC385671|Noc2 gene taxon:10090 20050725 MGI relationship(CL:0000169) MGI MGI:98179 Rras GO:0030336 MGI:MGI:3032882|PMID:14724565 IGI MGI:97306 P Harvey rat sarcoma oncogene, subgroup R gene taxon:10090 20070208 MGI relationship(CL:0000001) MGI MGI:1914172 Rras2 GO:0030335 MGI:MGI:3032882|PMID:14724565 IGI MGI:97306 P related RAS viral (r-ras) oncogene homolog 2 TC21 gene taxon:10090 20070208 MGI relationship(CL:0000001) MGI MGI:1915835 Rtn4 GO:0042995 MGI:MGI:3045671|PMID:15121177 IDA C reticulon 4 NSP-CL gene taxon:10090 20040812 MGI relationship(CL:0000128) MGI MGI:1915835 Rtn4 GO:0043025 MGI:MGI:3045671|PMID:15121177 IDA C reticulon 4 NSP-CL gene taxon:10090 20040812 MGI relationship(CL:0000128) MGI MGI:99852 Runx1 GO:0001501 MGI:MGI:3528197|PMID:15389629 IMP MGI:2668479 P runt related transcription factor 1 AML1|Cbfa2|Pebp2a2|runt domain, alpha subunit 2 gene taxon:10090 20050511 MGI relationship(CL:0000062) MGI MGI:99852 Runx1 GO:0030182 MGI:MGI:3047175|PMID:15240886 IMP MGI:2668479 P runt related transcription factor 1 AML1|Cbfa2|Pebp2a2|runt domain, alpha subunit 2 gene taxon:10090 20060726 MGI relationship(CL:0000108) MGI MGI:99829 Runx2 GO:0001649 MGI:MGI:3528197|PMID:15389629 IMP MGI:2183833 P runt related transcription factor 2 AML3|Cbfa1|Osf2|PEBP2 alpha A|PEBP2aA|polyomavirus enhancer binding factor 2 (PEBP2)|SL3-3 enhancer factor 1 gene taxon:10090 20050511 MGI relationship(CL:0000062) MGI MGI:99829 Runx2 GO:0001649 MGI:MGI:3587162|PMID:16099986 IGI MGI:1917649 P runt related transcription factor 2 AML3|Cbfa1|Osf2|PEBP2 alpha A|PEBP2aA|polyomavirus enhancer binding factor 2 (PEBP2)|SL3-3 enhancer factor 1 gene taxon:10090 20060201 MGI relationship(CL:0000002) MGI MGI:99829 Runx2 GO:0002062 MGI:MGI:3620436|PMID:16476422 IGI MGI:97801 P runt related transcription factor 2 AML3|Cbfa1|Osf2|PEBP2 alpha A|PEBP2aA|polyomavirus enhancer binding factor 2 (PEBP2)|SL3-3 enhancer factor 1 gene taxon:10090 20060608 MGI relationship(CL:0000743) MGI MGI:99829 Runx2 GO:0008284 MGI:MGI:3620436|PMID:16476422 IGI MGI:97801 P runt related transcription factor 2 AML3|Cbfa1|Osf2|PEBP2 alpha A|PEBP2aA|polyomavirus enhancer binding factor 2 (PEBP2)|SL3-3 enhancer factor 1 gene taxon:10090 20060608 MGI relationship(CL:0000138) MGI MGI:99829 Runx2 GO:0008284 MGI:MGI:3656469|PMID:15668330 IMP MGI:2176465 P runt related transcription factor 2 AML3|Cbfa1|Osf2|PEBP2 alpha A|PEBP2aA|polyomavirus enhancer binding factor 2 (PEBP2)|SL3-3 enhancer factor 1 gene taxon:10090 20061221 MGI relationship(CL:0000066) MGI MGI:99829 Runx2 GO:0008284 MGI:MGI:3656469|PMID:15668330 IMP MGI:2176465 P runt related transcription factor 2 AML3|Cbfa1|Osf2|PEBP2 alpha A|PEBP2aA|polyomavirus enhancer binding factor 2 (PEBP2)|SL3-3 enhancer factor 1 gene taxon:10090 20061221 MGI relationship(CL:0000134) MGI MGI:99829 Runx2 GO:0040036 MGI:MGI:3051915|PMID:15136142 IMP P runt related transcription factor 2 AML3|Cbfa1|Osf2|PEBP2 alpha A|PEBP2aA|polyomavirus enhancer binding factor 2 (PEBP2)|SL3-3 enhancer factor 1 gene taxon:10090 20040928 MGI relationship(CL:0000134) MGI MGI:99829 Runx2 GO:0042475 MGI:MGI:3051915|PMID:15136142 IMP P runt related transcription factor 2 AML3|Cbfa1|Osf2|PEBP2 alpha A|PEBP2aA|polyomavirus enhancer binding factor 2 (PEBP2)|SL3-3 enhancer factor 1 gene taxon:10090 20040928 MGI relationship(CL:0000134) MGI MGI:99829 Runx2 GO:0045944 MGI:MGI:3587162|PMID:16099986 IGI MGI:1917649 P runt related transcription factor 2 AML3|Cbfa1|Osf2|PEBP2 alpha A|PEBP2aA|polyomavirus enhancer binding factor 2 (PEBP2)|SL3-3 enhancer factor 1 gene taxon:10090 20060201 MGI relationship(CL:0000002) MGI MGI:99829 Runx2 GO:0048469 MGI:MGI:3528197|PMID:15389629 IMP MGI:2183833 P runt related transcription factor 2 AML3|Cbfa1|Osf2|PEBP2 alpha A|PEBP2aA|polyomavirus enhancer binding factor 2 (PEBP2)|SL3-3 enhancer factor 1 gene taxon:10090 20050511 MGI relationship(CL:0000062) MGI MGI:102672 Runx3 GO:0005634 MGI:MGI:3056362|PMID:15514019 IDA C runt related transcription factor 3 AML2|Cbfa3|Pebp2a3|runt domain, alpha subunit 3 gene taxon:10090 20060125 MGI relationship(CL:0000738) MGI MGI:102672 Runx3 GO:0007411 MGI:MGI:2387717|PMID:12352981 IMP MGI:2179229 P runt related transcription factor 3 AML2|Cbfa3|Pebp2a3|runt domain, alpha subunit 3 gene taxon:10090 20050725 MGI relationship(CL:0000100) MGI MGI:102672 Runx3 GO:0007411 MGI:MGI:2387717|PMID:12352981 IMP MGI:2179229 P runt related transcription factor 3 AML2|Cbfa3|Pebp2a3|runt domain, alpha subunit 3 gene taxon:10090 20050725 MGI relationship(CL:0000526) MGI MGI:102672 Runx3 GO:0031175 MGI:MGI:2387717|PMID:12352981 IMP MGI:2179229 P runt related transcription factor 3 AML2|Cbfa3|Pebp2a3|runt domain, alpha subunit 3 gene taxon:10090 20050725 MGI relationship(CL:0000001) MGI MGI:2441827 Rxfp3 GO:0008528 MGI:MGI:3619839|PMID:16378626 IDA F relaxin family peptide receptor 3 Rln3r1|Salpr gene taxon:10090 20060607 MGI relationship(CL:0000002) MGI MGI:2441827 Rxfp3 GO:0051482 MGI:MGI:3619839|PMID:16378626 IDA P relaxin family peptide receptor 3 Rln3r1|Salpr gene taxon:10090 20060607 MGI relationship(CL:0000002) MGI MGI:101766 Ryk GO:0005886 MGI:MGI:70393|PMID:7822791 IDA C receptor-like tyrosine kinase ERK-3|Vik gene taxon:10090 20051012 MGI relationship(CL:0000001) MGI MGI:101766 Ryk GO:0007409 MGI:MGI:3510085|PMID:15454084 IGI MGI:98956 P receptor-like tyrosine kinase ERK-3|Vik gene taxon:10090 20050204 MGI relationship(CL:0000001) MGI MGI:99659 Ryr1 GO:0030314 MGI:MGI:1342891|PMID:10444070 IDA C ryanodine receptor 1, skeletal muscle calcium release channel isoform 1|Ryr|skrr gene taxon:10090 20061010 MGI relationship(CL:0000188) MGI MGI:99684 Ryr3 GO:0030314 MGI:MGI:1342891|PMID:10444070 IDA C ryanodine receptor 3 calcium release channel isoform 3 gene taxon:10090 20061010 MGI relationship(CL:0000188) MGI MGI:98217 S100b GO:0005634 MGI:MGI:3588119|PMID:15782413 IDA C S100 protein, beta polypeptide, neural gene taxon:10090 20060112 MGI relationship(CL:0000117) MGI MGI:1925230 Sbf1 GO:0007283 MGI:MGI:2179365|PMID:11994405 IMP MGI:2449174 P SET binding factor 1 Mtmr5 gene taxon:10090 20050114 MGI relationship(CL:0000017) MGI MGI:893578 Scarb1 GO:0000299 MGI:MGI:87776|PMID:9148942 IDA C scavenger receptor class B, member 1 Cd36l1|Cla-1|D5Ertd460e|SR-BI|Srb1|SRBI gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:893578 Scarb1 GO:0005887 MGI:MGI:87776|PMID:9148942 IDA C scavenger receptor class B, member 1 Cd36l1|Cla-1|D5Ertd460e|SR-BI|Srb1|SRBI gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:893578 Scarb1 GO:0016599 MGI:MGI:87776|PMID:9148942 IDA C scavenger receptor class B, member 1 Cd36l1|Cla-1|D5Ertd460e|SR-BI|Srb1|SRBI gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:2449455 Scarf1 GO:0016358 MGI:MGI:3056881|PMID:15247299 IDA P scavenger receptor class F, member 1 SREC|SREC-I gene taxon:10090 20050110 MGI relationship(CL:0000002) MGI MGI:1353557 Schip1 GO:0005737 MGI:MGI:1353085|PMID:10669747 ISS EMBL:AF145713 C schwannomin interacting protein 1 SCHIP-1 gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:2145950 Scrib GO:0008105 MGI:MGI:3624469|PMID:16687519 IMP MGI:1889322 P scribbled homolog (Drosophila) Crc|CRIB|Scrb1|SCRIB1|vartul gene taxon:10090 20060629 MGI relationship(CL:0000601) MGI MGI:1349635 Sec23a GO:0048471 MGI:MGI:3529646|PMID:15642376 IDA C SEC23A (S. cerevisiae) Msec23|Sec23r gene taxon:10090 20050325 MGI relationship(CL:0000002) MGI MGI:1350925 Sec23b GO:0048471 MGI:MGI:3529646|PMID:15642376 IDA C SEC23B (S. cerevisiae) gene taxon:10090 20050325 MGI relationship(CL:0000002) MGI MGI:106689 Selplg GO:0005515 MGI:MGI:3510695|PMID:11238599 IPI UniProt:Q62230 F selectin, platelet (p-selectin) ligand CD162|Psgl-1|Psgl1 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:107558 Sema3a GO:0007411 MGI:MGI:3525900|PMID:15604101 IMP MGI:2449920 P sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A collapsin-1|sema III|Semad|semaphorin III|SemD gene taxon:10090 20050316 MGI relationship(CL:0000540) MGI MGI:107558 Sema3a GO:0030517 MGI:MGI:3505728|PMID:12852851 IDA P sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A collapsin-1|sema III|Semad|semaphorin III|SemD gene taxon:10090 20050121 MGI relationship(CL:0000001) MGI MGI:107558 Sema3a GO:0030517 MGI:MGI:3505728|PMID:12852851 IGI MGI:106206 P sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A collapsin-1|sema III|Semad|semaphorin III|SemD gene taxon:10090 20050121 MGI relationship(CL:0000001) MGI MGI:107558 Sema3a GO:0045499 MGI:MGI:2152659|PMID:11683995 IDA F sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A collapsin-1|sema III|Semad|semaphorin III|SemD gene taxon:10090 20061116 MGI relationship(CL:0000001) MGI MGI:107558 Sema3a GO:0048843 MGI:MGI:2152659|PMID:11683995 IGI MGI:107683 P sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A collapsin-1|sema III|Semad|semaphorin III|SemD gene taxon:10090 20061116 MGI relationship(CL:0000001) MGI MGI:107558 Sema3a GO:0050919 MGI:MGI:2152659|PMID:11683995 IGI MGI:107683 P sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A collapsin-1|sema III|Semad|semaphorin III|SemD gene taxon:10090 20061116 MGI relationship(CL:0000001) MGI MGI:1096347 Sema3f GO:0001755 MGI:MGI:3613099|PMID:16319111 IMP MGI:2670663 P sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3 F Sema IV|Semak gene taxon:10090 20060501 MGI relationship(CL:0000011) MGI MGI:1096347 Sema3f GO:0045499 MGI:MGI:2152659|PMID:11683995 IDA F sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3 F Sema IV|Semak gene taxon:10090 20061116 MGI relationship(CL:0000001) MGI MGI:1096347 Sema3f GO:0045499 MGI:MGI:3613099|PMID:16319111 IDA F sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3 F Sema IV|Semak gene taxon:10090 20060501 MGI relationship(CL:0000001) MGI MGI:1096347 Sema3f GO:0048843 MGI:MGI:2152659|PMID:11683995 IGI MGI:107683 P sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3 F Sema IV|Semak gene taxon:10090 20061116 MGI relationship(CL:0000001) MGI MGI:1096347 Sema3f GO:0050919 MGI:MGI:2152659|PMID:11683995 IGI MGI:107683 P sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3 F Sema IV|Semak gene taxon:10090 20061116 MGI relationship(CL:0000001) MGI MGI:1096347 Sema3f GO:0050919 MGI:MGI:3613099|PMID:16319111 IDA P sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3 F Sema IV|Semak gene taxon:10090 20060501 MGI relationship(CL:0000001) MGI MGI:1096347 Sema3f GO:0050919 MGI:MGI:3613099|PMID:16319111 IGI MGI:1100492 P sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3 F Sema IV|Semak gene taxon:10090 20060501 MGI relationship(CL:0000001) MGI MGI:109244 Sema4d GO:0050772 MGI:MGI:3531372|PMID:15330859 IDA P sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D CD100|coll-4|M-sema G|Semacl2|Semaj|semaphorin H|Semcl2 gene taxon:10090 20050506 MGI relationship(CL:0000540) MGI MGI:109244 Sema4d GO:0050772 MGI:MGI:3531372|PMID:15330859 IGI MGI:97321,MGI:97383,MGI:2154239,MGI:2154238 P sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D CD100|coll-4|M-sema G|Semacl2|Semaj|semaphorin H|Semcl2 gene taxon:10090 20050506 MGI relationship(CL:0000540) MGI MGI:1340055 Sema4f GO:0000299 MGI:MGI:1332310|PMID:10051670 ISS UniProt:Q9Z143 C sema domain, immunoglobulin domain (Ig), TM domain, and short cytoplasmic domain Sema W gene taxon:10090 20060112 MGI relationship(CL:0000002) MGI MGI:1340055 Sema4f GO:0005515 MGI:MGI:2138004|PMID:11483650 IPI UniProt:Q62108 F sema domain, immunoglobulin domain (Ig), TM domain, and short cytoplasmic domain Sema W gene taxon:10090 20050429 MGI relationship(CL:0000002) MGI MGI:1340055 Sema4f GO:0005886 MGI:MGI:2138004|PMID:11483650 IDA C sema domain, immunoglobulin domain (Ig), TM domain, and short cytoplasmic domain Sema W gene taxon:10090 20050429 MGI relationship(CL:0000002) MGI MGI:1340055 Sema4f GO:0016021 MGI:MGI:1332310|PMID:10051670 ISS UniProt:Q9Z143 C sema domain, immunoglobulin domain (Ig), TM domain, and short cytoplasmic domain Sema W gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:1934229 Setdb1 GO:0005634 MGI:MGI:3038026|PMID:14993285 IDA C SET domain, bifurcated 1 ESET gene taxon:10090 20040525 MGI relationship(CL:0000007) MGI MGI:1891831 Sfn GO:0030216 MGI:MGI:3608244|PMID:16239341 IMP MGI:1861121 P stratifin 14-3-3 sigma|Er|MME1|Ywhas gene taxon:10090 20060214 MGI relationship(CL:0000312) MGI MGI:98283 Sfrs1 GO:0005634 MGI:MGI:3522382|PMID:15615787 IDA C splicing factor, arginine/serine-rich 1 (ASF/SF2) gene taxon:10090 20050512 MGI relationship(CL:0000002) MGI MGI:1345171 Sh2b2 GO:0005515 MGI:MGI:1859033|PMID:10872802 IPI UniProt:Q62120,UniProt:Q62137,UniProt:P48025,UniProt:P39688,UniProt:P05532 F SH2B adaptor protein 2 Aps gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:893598 Sh2b3 GO:0030154 MGI:MGI:3041996|PMID:14612394 IMP P SH2B adaptor protein 3 Lnk gene taxon:10090 20040630 MGI relationship(CL:0000037) MGI MGI:893598 Sh2b3 GO:0035162 MGI:MGI:3041996|PMID:14612394 IDA P SH2B adaptor protein 3 Lnk gene taxon:10090 20040630 MGI relationship(CL:0000037) MGI MGI:893598 Sh2b3 GO:0035162 MGI:MGI:3041996|PMID:14612394 IMP P SH2B adaptor protein 3 Lnk gene taxon:10090 20040630 MGI relationship(CL:0000037) MGI MGI:1859730 Sh3glb1 GO:0001844 MGI:MGI:3607027|PMID:16227588 IMP P SH3-domain GRB2-like B1 (endophilin) Bif-1 gene taxon:10090 20060413 MGI relationship(CL:0000002) MGI MGI:106179 Shc3 GO:0035249 MGI:MGI:3577673|PMID:15716419 IMP MGI:1933356 P src homology 2 domain-containing transforming protein C3 N-Shc|Rai|ShcC gene taxon:10090 20050620 MGI relationship(CL:0000117) MGI MGI:98297 Shh GO:0001525 MGI:MGI:3629544|PMID:16778080 IDA P sonic hedgehog Hhg1 gene taxon:10090 20060807 MGI relationship(CL:0000001) MGI MGI:98297 Shh GO:0001755 MGI:MGI:3583396|PMID:15936751 IMP MGI:1857796 P sonic hedgehog Hhg1 gene taxon:10090 20050826 MGI relationship(CL:0000333) MGI MGI:98297 Shh GO:0002052 MGI:MGI:2154469|PMID:11748155 IDA P sonic hedgehog Hhg1 gene taxon:10090 20061219 MGI relationship(CL:0000001) MGI MGI:98297 Shh GO:0002076 MGI:MGI:3653954|PMID:16880529 IDA P sonic hedgehog Hhg1 gene taxon:10090 20061221 MGI relationship(CL:0000002) MGI MGI:98297 Shh GO:0007228 MGI:MGI:3653954|PMID:16880529 IGI MGI:95728 P sonic hedgehog Hhg1 gene taxon:10090 20061221 MGI relationship(CL:0000002) MGI MGI:98297 Shh GO:0007267 MGI:MGI:3045497|PMID:15199404 IMP MGI:1934268 P sonic hedgehog Hhg1 gene taxon:10090 20041007 MGI relationship(CL:0000066) MGI MGI:98297 Shh GO:0007267 MGI:MGI:3045497|PMID:15199404 IMP MGI:1934268 P sonic hedgehog Hhg1 gene taxon:10090 20041007 MGI relationship(CL:0000134) MGI MGI:98297 Shh GO:0007267 MGI:MGI:3617552|PMID:16492970 IMP MGI:1857796 P sonic hedgehog Hhg1 gene taxon:10090 20060706 MGI relationship(CL:0000066) MGI MGI:98297 Shh GO:0007267 MGI:MGI:3617552|PMID:16492970 IMP MGI:1857796 P sonic hedgehog Hhg1 gene taxon:10090 20060706 MGI relationship(CL:0000134) MGI MGI:98297 Shh GO:0007405 MGI:MGI:3053236|PMID:15337776 IDA P sonic hedgehog Hhg1 gene taxon:10090 20041018 MGI relationship(CL:0000011) MGI MGI:98297 Shh GO:0007411 MGI:MGI:2654974|PMID:12679031 IDA P sonic hedgehog Hhg1 gene taxon:10090 20050826 MGI relationship(CL:0000678) MGI MGI:98297 Shh GO:0007411 MGI:MGI:2662556|PMID:12756179 IMP MGI:1934268 P sonic hedgehog Hhg1 gene taxon:10090 20050826 MGI relationship(CL:0000740) MGI MGI:98297 Shh GO:0008284 MGI:MGI:2154469|PMID:11748155 IDA P sonic hedgehog Hhg1 gene taxon:10090 20061219 MGI relationship(CL:0000001) MGI MGI:98297 Shh GO:0008284 MGI:MGI:3051930|PMID:15183722 IMP MGI:1934268|MGI:2387802 P sonic hedgehog Hhg1 gene taxon:10090 20040930 MGI relationship(CL:0000120) MGI MGI:98297 Shh GO:0008284 MGI:MGI:3512837|PMID:15496441 IGI MGI:95728 P sonic hedgehog Hhg1 gene taxon:10090 20050204 MGI relationship(CL:0000120) MGI MGI:98297 Shh GO:0008284 MGI:MGI:3589306|PMID:16054035 IGI MGI:95728 P sonic hedgehog Hhg1 gene taxon:10090 20061220 MGI relationship(CL:0000362) MGI MGI:98297 Shh GO:0008284 MGI:MGI:3589306|PMID:16054035 IMP MGI:1857796 P sonic hedgehog Hhg1 gene taxon:10090 20061220 MGI relationship(CL:0000362) MGI MGI:98297 Shh GO:0008284 MGI:MGI:3608482|PMID:16236765 IMP MGI:1934268|MGI:3052661 P sonic hedgehog Hhg1 gene taxon:10090 20060119 MGI relationship(CL:0000031) MGI MGI:98297 Shh GO:0009986 MGI:MGI:3511726|PMID:15576403 IDA C sonic hedgehog Hhg1 gene taxon:10090 20050110 MGI relationship(CL:0000002) MGI MGI:98297 Shh GO:0021938 MGI:MGI:1338342|PMID:10375501 IDA P sonic hedgehog Hhg1 gene taxon:10090 20061214 MGI relationship(CL:0000001) MGI MGI:98297 Shh GO:0021938 MGI:MGI:1338342|PMID:10375501 IMP P sonic hedgehog Hhg1 gene taxon:10090 20061214 MGI relationship(CL:0000001) MGI MGI:98297 Shh GO:0021940 MGI:MGI:1329746|PMID:10027293 IDA P sonic hedgehog Hhg1 gene taxon:10090 20061218 MGI relationship(CL:0000001) MGI MGI:98297 Shh GO:0030324 MGI:MGI:3050270|PMID:15305287 IMP MGI:1934268|MGI:2679524 P sonic hedgehog Hhg1 gene taxon:10090 20050505 MGI relationship(CL:0000115) MGI MGI:98297 Shh GO:0030336 MGI:MGI:3053236|PMID:15337776 IDA P sonic hedgehog Hhg1 gene taxon:10090 20041018 MGI relationship(CL:0000011) MGI MGI:98297 Shh GO:0030902 MGI:MGI:3051930|PMID:15183722 IMP MGI:1934268|MGI:2387802 P sonic hedgehog Hhg1 gene taxon:10090 20040930 MGI relationship(CL:0000120) MGI MGI:98297 Shh GO:0030902 MGI:MGI:3512837|PMID:15496441 IGI MGI:95728 P sonic hedgehog Hhg1 gene taxon:10090 20050204 MGI relationship(CL:0000120) MGI MGI:98297 Shh GO:0042127 MGI:MGI:2662556|PMID:12756179 IDA P sonic hedgehog Hhg1 gene taxon:10090 20050725 MGI relationship(CL:0000127) MGI MGI:98297 Shh GO:0042130 MGI:MGI:1888832|PMID:10981962 IMP P sonic hedgehog Hhg1 gene taxon:10090 20061219 MGI relationship(CL:0000001) MGI MGI:98297 Shh GO:0045596 MGI:MGI:3053236|PMID:15337776 IDA P sonic hedgehog Hhg1 gene taxon:10090 20041018 MGI relationship(CL:0000029) MGI MGI:98297 Shh GO:0045596 MGI:MGI:3608482|PMID:16236765 IMP MGI:1934268|MGI:3052661 P sonic hedgehog Hhg1 gene taxon:10090 20060119 MGI relationship(CL:0000740) MGI MGI:98297 Shh GO:0045944 MGI:MGI:3653954|PMID:16880529 IGI MGI:95728 P sonic hedgehog Hhg1 gene taxon:10090 20061221 MGI relationship(CL:0000002) MGI MGI:98297 Shh GO:0046639 MGI:MGI:1888832|PMID:10981962 IMP P sonic hedgehog Hhg1 gene taxon:10090 20061219 MGI relationship(CL:0000001) MGI MGI:98297 Shh GO:0048468 MGI:MGI:3051930|PMID:15183722 IMP MGI:1934268|MGI:2387802 P sonic hedgehog Hhg1 gene taxon:10090 20040930 MGI relationship(CL:0000121) MGI MGI:98297 Shh GO:0048468 MGI:MGI:3608482|PMID:16236765 IMP MGI:1934268|MGI:3052661 P sonic hedgehog Hhg1 gene taxon:10090 20060119 MGI relationship(CL:0000561) MGI MGI:98297 Shh GO:0048468 MGI:MGI:3608482|PMID:16236765 IMP MGI:1934268|MGI:3052661 P sonic hedgehog Hhg1 gene taxon:10090 20060119 MGI relationship(CL:0000573) MGI MGI:98297 Shh GO:0048468 MGI:MGI:3608482|PMID:16236765 IMP MGI:1934268|MGI:3052661 P sonic hedgehog Hhg1 gene taxon:10090 20060119 MGI relationship(CL:0000745) MGI MGI:98297 Shh GO:0048663 MGI:MGI:3608263|PMID:16221724 IMP MGI:1934268 P sonic hedgehog Hhg1 gene taxon:10090 20060411 MGI relationship(CL:0000099) MGI MGI:98297 Shh GO:0048754 MGI:MGI:3050270|PMID:15305287 IMP MGI:1934268|MGI:2679524 P sonic hedgehog Hhg1 gene taxon:10090 20051212 MGI relationship(CL:0000115) MGI MGI:98297 Shh GO:0051146 MGI:MGI:3621570|PMID:15238161 IMP MGI:1857796 P sonic hedgehog Hhg1 gene taxon:10090 20060519 MGI relationship(CL:0000189) MGI MGI:98297 Shh GO:0060020 MGI:MGI:1338342|PMID:10375501 IDA P sonic hedgehog Hhg1 gene taxon:10090 20061214 MGI relationship(CL:0000644) MGI MGI:3047697 Shmu GO:0007498 MGI:MGI:3056222|PMID:15384171 IMP MGI:3047738 P shamu gene taxon:10090 20050322 MGI relationship(CL:0000222) MGI MGI:1351655 Shroom3 GO:0016324 MGI:MGI:3037622|PMID:15037549 IDA C shroom family member 3 D5Ertd287e|Shrm gene taxon:10090 20040630 MGI relationship(CL:0000066) MGI MGI:99668 Siglec1 GO:0005515 MGI:MGI:3510695|PMID:11238599 IPI UniProt:P15702,UniProt:Q62170 F sialic acid binding Ig-like lectin 1, sialoadhesin CD169|Siglec-1|Sn gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:102780 Six1 GO:0030855 MGI:MGI:3624596|PMID:16530750 IMP MGI:2655195 P sine oculis-related homeobox 1 homolog (Drosophila) gene taxon:10090 20061117 MGI relationship(CL:0000066) MGI MGI:102780 Six1 GO:0045664 MGI:MGI:3512702|PMID:15496442 IMP MGI:2655195 P sine oculis-related homeobox 1 homolog (Drosophila) gene taxon:10090 20050315 MGI relationship(CL:0000101) MGI MGI:102780 Six1 GO:0051451 MGI:MGI:3578604|PMID:15788460 IGI MGI:106034 P sine oculis-related homeobox 1 homolog (Drosophila) gene taxon:10090 20060213 MGI relationship(CL:0000056) MGI MGI:106034 Six4 GO:0051451 MGI:MGI:3578604|PMID:15788460 IGI MGI:102780 P sine oculis-related homeobox 4 homolog (Drosophila) AREC3|TrexBF gene taxon:10090 20060213 MGI relationship(CL:0000056) MGI MGI:1345279 Slc11a2 GO:0005768 MGI:MGI:3609504|PMID:16227996 IDA C solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2 DCT1|DMT1|microcytic anemia, viable anaemia|Nramp2|van gene taxon:10090 20060411 MGI relationship(CL:0000002) MGI MGI:1345279 Slc11a2 GO:0005886 MGI:MGI:3609504|PMID:16227996 IDA C solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2 DCT1|DMT1|microcytic anemia, viable anaemia|Nramp2|van gene taxon:10090 20060411 MGI relationship(CL:0000002) MGI MGI:101924 Slc12a2 GO:0050910 MGI:MGI:3625390|PMID:16529873 IMP MGI:1935144 P solute carrier family 12, member 2 mBSC2|Nkcc1|sodium/potassium/chloride cotransporters|sy-ns gene taxon:10090 20061017 MGI relationship(CL:0000202) MGI MGI:1920211 Slc17a7 GO:0042137 MGI:MGI:3042058|PMID:15103023 IMP MGI:3051945 P solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 7 Vglut1 gene taxon:10090 20040915 MGI relationship(CL:0000679) MGI MGI:1101061 Slc18a3 GO:0043195 MGI:MGI:1306999|PMID:9853118 IDA C solute carrier family 18 (vesicular monoamine), member 3 VAChT|VAT gene taxon:10090 20061115 MGI relationship(CL:0000100) MGI MGI:95755 Slc2a1 GO:0005886 MGI:MGI:3042070|PMID:14562105 IDA C solute carrier family 2 (facilitated glucose transporter), member 1 Glut-1|Glut1 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:95758 Slc2a4 GO:0000299 MGI:MGI:3042070|PMID:14562105 IDA C solute carrier family 2 (facilitated glucose transporter), member 4 Glut-4|Glut4 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:95758 Slc2a4 GO:0005768 MGI:MGI:3056883|PMID:15247266 IDA C solute carrier family 2 (facilitated glucose transporter), member 4 Glut-4|Glut4 gene taxon:10090 20050310 MGI relationship(CL:0000136) MGI MGI:95758 Slc2a4 GO:0005792 MGI:MGI:3042070|PMID:14562105 IDA C solute carrier family 2 (facilitated glucose transporter), member 4 Glut-4|Glut4 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:95758 Slc2a4 GO:0005886 MGI:MGI:3055460|PMID:10444069 IDA C solute carrier family 2 (facilitated glucose transporter), member 4 Glut-4|Glut4 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:95758 Slc2a4 GO:0005886 MGI:MGI:3056883|PMID:15247266 IDA C solute carrier family 2 (facilitated glucose transporter), member 4 Glut-4|Glut4 gene taxon:10090 20050310 MGI relationship(CL:0000136) MGI MGI:95758 Slc2a4 GO:0005887 MGI:MGI:3042070|PMID:14562105 IDA C solute carrier family 2 (facilitated glucose transporter), member 4 Glut-4|Glut4 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:95758 Slc2a4 GO:0048471 MGI:MGI:3055460|PMID:10444069 IDA C solute carrier family 2 (facilitated glucose transporter), member 4 Glut-4|Glut4 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1345281 Slc30a1 GO:0009935 MGI:MGI:3056220|PMID:15452870 IMP MGI:3056498 P solute carrier family 30 (zinc transporter), member 1 Znt1 gene taxon:10090 20050111 MGI relationship(CL:0000351) MGI MGI:1919277 Slc39a4 GO:0016324 MGI:MGI:2684332|PMID:12801924 IDA C solute carrier family 39 (zinc transporter), member 4 AWMS2|zip4 gene taxon:10090 20040326 MGI relationship(CL:0000223) MGI MGI:1919277 Slc39a4 GO:0016324 MGI:MGI:2684332|PMID:12801924 IDA C solute carrier family 39 (zinc transporter), member 4 AWMS2|zip4 gene taxon:10090 20040326 MGI relationship(CL:0000584) MGI MGI:107956 Slc8a1 GO:0002026 MGI:MGI:3607962|PMID:12767889 IMP MGI:3609617 P solute carrier family 8 (sodium/calcium exchanger), member 1 Ncx1 gene taxon:10090 20060221 MGI relationship(CL:0000001) MGI MGI:107956 Slc8a1 GO:0005886 MGI:MGI:3607962|PMID:12767889 IDA C solute carrier family 8 (sodium/calcium exchanger), member 1 Ncx1 gene taxon:10090 20060221 MGI relationship(CL:0000001) MGI MGI:107956 Slc8a1 GO:0006816 MGI:MGI:3607962|PMID:12767889 IMP MGI:3609617 P solute carrier family 8 (sodium/calcium exchanger), member 1 Ncx1 gene taxon:10090 20060221 MGI relationship(CL:0000001) MGI MGI:1315203 Slit1 GO:0007411 MGI:MGI:3041390|PMID:15091338 IGI MGI:2179460,MGI:2662358 P slit homolog 1 (Drosophila) Slil1 gene taxon:10090 20040706 MGI relationship(CL:0000678) MGI MGI:1315203 Slit1 GO:0031290 MGI:MGI:2157173|PMID:11804570 IGI MGI:1315205 P slit homolog 1 (Drosophila) Slil1 gene taxon:10090 20070305 MGI relationship(CL:0000740) MGI MGI:1315205 Slit2 GO:0007411 MGI:MGI:3041390|PMID:15091338 IGI MGI:2179459,MGI:2662358 P slit homolog 2 (Drosophila) Drad-1|Slil3 gene taxon:10090 20040706 MGI relationship(CL:0000678) MGI MGI:1315205 Slit2 GO:0031290 MGI:MGI:2157173|PMID:11804570 IGI MGI:1315203 P slit homolog 2 (Drosophila) Drad-1|Slil3 gene taxon:10090 20070305 MGI relationship(CL:0000740) MGI MGI:1315202 Slit3 GO:0009887 MGI:MGI:3041390|PMID:15091338 IGI MGI:2179460,MGI:2179459 P slit homolog 3 (Drosophila) gene taxon:10090 20040706 MGI relationship(CL:0000678) MGI MGI:109452 Smad1 GO:0007276 MGI:MGI:3044557|PMID:15198985 IMP MGI:3045219 P MAD homolog 1 (Drosophila) Madh1|Madr1|Smad 1 gene taxon:10090 20040721 MGI relationship(CL:0000586) MGI MGI:109452 Smad1 GO:0042592 MGI:MGI:3044557|PMID:15198985 IMP MGI:3045218 P MAD homolog 1 (Drosophila) Madh1|Madr1|Smad 1 gene taxon:10090 20040721 MGI relationship(CL:0000066) MGI MGI:108051 Smad2 GO:0007179 MGI:MGI:3032478|PMID:14749725 IDA P MAD homolog 2 (Drosophila) Madh2|Madr2|Smad 2 gene taxon:10090 20050429 MGI relationship(CL:0000002) MGI MGI:108051 Smad2 GO:0007242 MGI:MGI:3032478|PMID:14749725 IDA P MAD homolog 2 (Drosophila) Madh2|Madr2|Smad 2 gene taxon:10090 20050429 MGI relationship(CL:0000002) MGI MGI:88192 Smarca4 GO:0000792 MGI:MGI:3611125|PMID:16322236 IDA C SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 Brg1|SNF2beta|SW1/SNF gene taxon:10090 20060724 MGI relationship(CL:0000002) MGI MGI:88192 Smarca4 GO:0007403 MGI:MGI:3611670|PMID:16330018 IMP MGI:3605892|MGI:2176173 P SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 Brg1|SNF2beta|SW1/SNF gene taxon:10090 20060522 MGI relationship(CL:0000030) MGI MGI:1328366 Smarcb1 GO:0001824 MGI:MGI:1932782|PMID:11263494 IMP MGI:2387974 P SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 Baf47|Ini1|integrase interactor 1|Snf5|SNF5/INI1 gene taxon:10090 20060130 MGI relationship(CL:0000001) MGI MGI:1328366 Smarcb1 GO:0030154 MGI:MGI:3610866|PMID:16138077 IMP MGI:2387974 P SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 Baf47|Ini1|integrase interactor 1|Snf5|SNF5/INI1 gene taxon:10090 20060130 MGI relationship(CL:0000182) MGI MGI:2154049 Smc1b GO:0000800 MGI:MGI:3578071|PMID:15870106 IDA C structural maintenace of chromosomes 1B SMC1beta|Smc1l2 gene taxon:10090 20050609 MGI relationship(CL:0000654) MGI MGI:1339795 Smc3 GO:0000800 MGI:MGI:3578071|PMID:15870106 IDA C structural maintenace of chromosomes 3 Bamacan|Cspg6|Mmip1|SmcD gene taxon:10090 20050609 MGI relationship(CL:0000654) MGI MGI:108075 Smo GO:0002052 MGI:MGI:3619284|PMID:16543460 IGI MGI:88274 P smoothened homolog (Drosophila) gene taxon:10090 20061220 MGI relationship(CL:0000337) MGI MGI:108075 Smo GO:0005929 MGI:MGI:3610248|PMID:16229832 IDA C smoothened homolog (Drosophila) gene taxon:10090 20060203 MGI relationship(CL:0000064) MGI MGI:108075 Smo GO:0008284 MGI:MGI:2429663|PMID:12403705 IMP MGI:2176256|MGI:2445832 P smoothened homolog (Drosophila) gene taxon:10090 20061219 MGI relationship(CL:0000059) MGI MGI:108075 Smo GO:0021938 MGI:MGI:3624180|PMID:16571625 IMP MGI:2176256|MGI:2176173 P smoothened homolog (Drosophila) gene taxon:10090 20061221 MGI relationship(CL:0000120) MGI MGI:108075 Smo GO:0021953 MGI:MGI:3624182|PMID:16571630 IMP MGI:2176256|MGI:2446434 P smoothened homolog (Drosophila) gene taxon:10090 20061221 MGI relationship(CL:0000117) MGI MGI:108075 Smo GO:0021953 MGI:MGI:3624182|PMID:16571630 IMP MGI:2176256|MGI:2446434 P smoothened homolog (Drosophila) gene taxon:10090 20061221 MGI relationship(CL:0000403) MGI MGI:108075 Smo GO:0021953 MGI:MGI:3624182|PMID:16571630 IMP MGI:2176256|MGI:2446434 P smoothened homolog (Drosophila) gene taxon:10090 20061221 MGI relationship(CL:0000700) MGI MGI:108075 Smo GO:0048468 MGI:MGI:2429663|PMID:12403705 IMP MGI:2176256|MGI:2445832 P smoothened homolog (Drosophila) gene taxon:10090 20061219 MGI relationship(CL:0000059) MGI MGI:98330 Snai1 GO:0005634 MGI:MGI:3576202|PMID:15630473 IDA C snail homolog 1 (Drosophila) Sna|Sna1|Snail|Snail1 gene taxon:10090 20050518 MGI relationship(CL:0000362) MGI MGI:1277151 Snca GO:0001956 MGI:MGI:3512696|PMID:15510220 IDA P synuclein, alpha alpha-synuclein|alphaSYN gene taxon:10090 20050908 MGI relationship(CL:0000001) MGI MGI:1277151 Snca GO:0001963 MGI:MGI:1352916|PMID:10707987 IMP MGI:1888382 P synuclein, alpha alpha-synuclein|alphaSYN gene taxon:10090 20050915 MGI relationship(CL:0000700) MGI MGI:1277151 Snca GO:0046928 MGI:MGI:1352916|PMID:10707987 IMP MGI:1888382 P synuclein, alpha alpha-synuclein|alphaSYN gene taxon:10090 20050908 MGI relationship(CL:0000700) MGI MGI:1277151 Snca GO:0046928 MGI:MGI:3512696|PMID:15510220 IMP MGI:2429773 P synuclein, alpha alpha-synuclein|alphaSYN gene taxon:10090 20050908 MGI relationship(CL:0000117) MGI MGI:1277151 Snca GO:0048169 MGI:MGI:3512696|PMID:15510220 IMP MGI:2429773 P synuclein, alpha alpha-synuclein|alphaSYN gene taxon:10090 20050908 MGI relationship(CL:0000117) MGI MGI:1277151 Snca GO:0048489 MGI:MGI:2388931|PMID:12388586 IMP MGI:2389489 P synuclein, alpha alpha-synuclein|alphaSYN gene taxon:10090 20050908 MGI relationship(CL:0000117) MGI MGI:1298397 Sncg GO:0005737 MGI:MGI:3051957|PMID:15147505 IDA C synuclein, gamma C79089|persyn gene taxon:10090 20050218 MGI relationship(CL:0000117) MGI MGI:1298397 Sncg GO:0030424 MGI:MGI:1289088|PMID:10195122 IDA C synuclein, gamma C79089|persyn gene taxon:10090 20051207 MGI relationship(CL:0000540) MGI MGI:1298397 Sncg GO:0030424 MGI:MGI:2679896|PMID:14585981 IDA C synuclein, gamma C79089|persyn gene taxon:10090 20051207 MGI relationship(CL:0000100) MGI MGI:1298397 Sncg GO:0030424 MGI:MGI:2679896|PMID:14585981 IDA C synuclein, gamma C79089|persyn gene taxon:10090 20051207 MGI relationship(CL:0000101) MGI MGI:1298397 Sncg GO:0043025 MGI:MGI:1289088|PMID:10195122 IDA C synuclein, gamma C79089|persyn gene taxon:10090 20051207 MGI relationship(CL:0000540) MGI MGI:1298397 Sncg GO:0043025 MGI:MGI:2679896|PMID:14585981 IDA C synuclein, gamma C79089|persyn gene taxon:10090 20051207 MGI relationship(CL:0000100) MGI MGI:1298397 Sncg GO:0043025 MGI:MGI:3051957|PMID:15147505 IDA C synuclein, gamma C79089|persyn gene taxon:10090 20050218 MGI relationship(CL:0000117) MGI MGI:98351 Sod1 GO:0060052 MGI:MGI:1934092|PMID:11343650 IGI MGI:97313 P superoxide dismutase 1, soluble Cu(2+)-Zn2+ superoxide dismutase|Cu/Zn-SOD|CuZnSOD|Ipo-1|Ipo1|Sod-1|SODC gene taxon:10090 20070305 MGI relationship(CL:0000100) MGI MGI:98351 Sod1 GO:0060052 MGI:MGI:1934092|PMID:11343650 IMP MGI:3574016 P superoxide dismutase 1, soluble Cu(2+)-Zn2+ superoxide dismutase|Cu/Zn-SOD|CuZnSOD|Ipo-1|Ipo1|Sod-1|SODC gene taxon:10090 20070305 MGI relationship(CL:0000100) MGI MGI:2684956 Sohlh1 GO:0005634 MGI:MGI:3628699|PMID:16564520 IDA C spermatogenesis and oogenesis specific basic helix-loop-helix 1 LOC227631|NOHLH gene taxon:10090 20060807 MGI relationship(CL:0000020) MGI MGI:2684956 Sohlh1 GO:0030154 MGI:MGI:3628699|PMID:16564520 IMP MGI:3629211 P spermatogenesis and oogenesis specific basic helix-loop-helix 1 LOC227631|NOHLH gene taxon:10090 20060807 MGI relationship(CL:0000017) MGI MGI:700013 Sorbs3 GO:0000122 MGI:MGI:3579939|PMID:15734736 IGI MGI:97858 P sorbin and SH3 domain containing 3 Sh3d4|SH3P3|vinexin alpha|vinexin beta gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:700013 Sorbs3 GO:0005515 MGI:MGI:3608171|PMID:15836771 IPI UniProt:Q99N57 F sorbin and SH3 domain containing 3 Sh3d4|SH3P3|vinexin alpha|vinexin beta gene taxon:10090 20060328 MGI relationship(CL:0000002) MGI MGI:700013 Sorbs3 GO:0005634 MGI:MGI:1349785|PMID:9885244 IDA C sorbin and SH3 domain containing 3 Sh3d4|SH3P3|vinexin alpha|vinexin beta gene taxon:10090 20060328 MGI relationship(CL:0000002) MGI MGI:700013 Sorbs3 GO:0005634 MGI:MGI:3579939|PMID:15734736 IDA C sorbin and SH3 domain containing 3 Sh3d4|SH3P3|vinexin alpha|vinexin beta gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:700013 Sorbs3 GO:0005737 MGI:MGI:1349785|PMID:9885244 IDA C sorbin and SH3 domain containing 3 Sh3d4|SH3P3|vinexin alpha|vinexin beta gene taxon:10090 20060328 MGI relationship(CL:0000002) MGI MGI:700013 Sorbs3 GO:0005737 MGI:MGI:3579939|PMID:15734736 IDA C sorbin and SH3 domain containing 3 Sh3d4|SH3P3|vinexin alpha|vinexin beta gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:700013 Sorbs3 GO:0005737 MGI:MGI:3608171|PMID:15836771 IDA C sorbin and SH3 domain containing 3 Sh3d4|SH3P3|vinexin alpha|vinexin beta gene taxon:10090 20060328 MGI relationship(CL:0000216) MGI MGI:700013 Sorbs3 GO:0005925 MGI:MGI:1349785|PMID:9885244 IDA C sorbin and SH3 domain containing 3 Sh3d4|SH3P3|vinexin alpha|vinexin beta gene taxon:10090 20060328 MGI relationship(CL:0000002) MGI MGI:700013 Sorbs3 GO:0031589 MGI:MGI:1349785|PMID:9885244 IDA P sorbin and SH3 domain containing 3 Sh3d4|SH3P3|vinexin alpha|vinexin beta gene taxon:10090 20060328 MGI relationship(CL:0000002) MGI MGI:700013 Sorbs3 GO:0043410 MGI:MGI:3608171|PMID:15836771 IDA P sorbin and SH3 domain containing 3 Sh3d4|SH3P3|vinexin alpha|vinexin beta gene taxon:10090 20060328 MGI relationship(CL:0000002) MGI MGI:1913292 Sostdc1 GO:0030514 MGI:MGI:3603904|PMID:16179481 IDA P sclerostin domain containing 1 ectodin|Sostl|USAG-1|Wise gene taxon:10090 20051128 MGI relationship(CL:0000001) MGI MGI:1913292 Sostdc1 GO:0030514 MGI:MGI:3603904|PMID:16179481 IGI MGI:88180 P sclerostin domain containing 1 ectodin|Sostl|USAG-1|Wise gene taxon:10090 20051128 MGI relationship(CL:0000001) MGI MGI:1913292 Sostdc1 GO:0042475 MGI:MGI:3603904|PMID:16179481 IGI MGI:88180 P sclerostin domain containing 1 ectodin|Sostl|USAG-1|Wise gene taxon:10090 20051128 MGI relationship(CL:0000001) MGI MGI:1913292 Sostdc1 GO:0042475 MGI:MGI:3603904|PMID:16179481 IMP MGI:3604658 P sclerostin domain containing 1 ectodin|Sostl|USAG-1|Wise gene taxon:10090 20051128 MGI relationship(CL:0000001) MGI MGI:98358 Sox10 GO:0048469 MGI:MGI:3578469|PMID:15102707 IGI MGI:98370 P SRY-box containing gene 10 Sox21 gene taxon:10090 20050728 MGI relationship(CL:0000128) MGI MGI:98358 Sox10 GO:0048469 MGI:MGI:3578469|PMID:15102707 IMP MGI:2151173 P SRY-box containing gene 10 Sox21 gene taxon:10090 20050728 MGI relationship(CL:0000128) MGI MGI:98363 Sox15 GO:0005634 MGI:MGI:1858709|PMID:10821863 IDA C SRY-box containing gene 15 gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:98363 Sox15 GO:0045843 MGI:MGI:1858709|PMID:10821863 IDA P SRY-box containing gene 15 gene taxon:10090 20060725 MGI relationship(CL:0000002) MGI MGI:98364 Sox2 GO:0050910 MGI:MGI:3578496|PMID:15846349 IMP MGI:2447995 P SRY-box containing gene 2 lcc|Sox-2|ysb gene taxon:10090 20060214 MGI relationship(CL:0000202) MGI MGI:98364 Sox2 GO:0050973 MGI:MGI:3578496|PMID:15846349 IMP MGI:2447995 P SRY-box containing gene 2 lcc|Sox-2|ysb gene taxon:10090 20060214 MGI relationship(CL:0000202) MGI MGI:98365 Sox3 GO:0048515 MGI:MGI:3582097|PMID:15893302 IMP MGI:2682663 P SRY-box containing gene 3 Sox-3 gene taxon:10090 20050907 MGI relationship(CL:0000018) MGI MGI:98366 Sox4 GO:0031017 MGI:MGI:3611650|PMID:16306355 IMP MGI:2182092 P SRY-box containing gene 4 Sox-4 gene taxon:10090 20060501 MGI relationship(CL:0000001) MGI MGI:98367 Sox5 GO:0045165 MGI:MGI:3525903|PMID:15634692 IGI MGI:98368 P SRY-box containing gene 5 gene taxon:10090 20050314 MGI relationship(CL:0000058) MGI MGI:98368 Sox6 GO:0045165 MGI:MGI:3525903|PMID:15634692 IGI MGI:98367 P SRY-box containing gene 6 gene taxon:10090 20050314 MGI relationship(CL:0000058) MGI MGI:98370 Sox8 GO:0045165 MGI:MGI:3578716|PMID:15893981 IGI MGI:98371 P SRY-box containing gene 8 gene taxon:10090 20050812 MGI relationship(CL:0000128) MGI MGI:98370 Sox8 GO:0048469 MGI:MGI:3578469|PMID:15102707 IGI MGI:98358 P SRY-box containing gene 8 gene taxon:10090 20050728 MGI relationship(CL:0000128) MGI MGI:98370 Sox8 GO:0048469 MGI:MGI:3578469|PMID:15102707 IMP MGI:2154329 P SRY-box containing gene 8 gene taxon:10090 20050728 MGI relationship(CL:0000128) MGI MGI:98371 Sox9 GO:0005634 MGI:MGI:3051710|PMID:15229180 IDA C SRY-box containing gene 9 gene taxon:10090 20041001 MGI relationship(CL:0000216) MGI MGI:98371 Sox9 GO:0005634 MGI:MGI:3513641|PMID:15585950 IDA C SRY-box containing gene 9 gene taxon:10090 20050201 MGI relationship(CL:0000216) MGI MGI:98371 Sox9 GO:0005634 MGI:MGI:3573967|PMID:15590666 IDA C SRY-box containing gene 9 gene taxon:10090 20050531 MGI relationship(CL:0000216) MGI MGI:98371 Sox9 GO:0005634 MGI:MGI:3583842|PMID:15944199 IDA C SRY-box containing gene 9 gene taxon:10090 20060913 MGI relationship(CL:0000216) MGI MGI:98371 Sox9 GO:0014032 MGI:MGI:3613316|PMID:15691760 IMP MGI:3041881 P SRY-box containing gene 9 gene taxon:10090 20060307 MGI relationship(CL:0000011) MGI MGI:98371 Sox9 GO:0045165 MGI:MGI:3578716|PMID:15893981 IGI MGI:98370 P SRY-box containing gene 9 gene taxon:10090 20050812 MGI relationship(CL:0000128) MGI MGI:98372 Sp1 GO:0005634 MGI:MGI:1861311|PMID:11004506 IDA C trans-acting transcription factor 1 Sp1-1 gene taxon:10090 20060817 MGI relationship(CL:0000002) MGI MGI:1913972 Spag16 GO:0005634 MGI:MGI:3052627|PMID:15328412 IDA C sperm associated antigen 16 Pf20|Wdr29 gene taxon:10090 20041018 MGI relationship(CL:0000018) MGI MGI:1913972 Spag16 GO:0005737 MGI:MGI:3052627|PMID:15328412 IDA C sperm associated antigen 16 Pf20|Wdr29 gene taxon:10090 20041018 MGI relationship(CL:0000017) MGI MGI:1913972 Spag16 GO:0005737 MGI:MGI:3052627|PMID:15328412 IDA C sperm associated antigen 16 Pf20|Wdr29 gene taxon:10090 20041018 MGI relationship(CL:0000018) MGI MGI:1913972 Spag16 GO:0007283 MGI:MGI:3052627|PMID:15328412 IMP P sperm associated antigen 16 Pf20|Wdr29 gene taxon:10090 20050217 MGI relationship(CL:0000018) MGI MGI:1913972 Spag16 GO:0035086 MGI:MGI:3052627|PMID:15328412 IDA C sperm associated antigen 16 Pf20|Wdr29 gene taxon:10090 20041018 MGI relationship(CL:0000019) MGI MGI:1921531 Spatc1 GO:0005737 MGI:MGI:3057091|PMID:15280373 IDA C spermatogenesis and centriole associated 1 speriolin gene taxon:10090 20050111 MGI relationship(CL:0000018) MGI MGI:1921531 Spatc1 GO:0005813 MGI:MGI:3057091|PMID:15280373 IDA C spermatogenesis and centriole associated 1 speriolin gene taxon:10090 20050111 MGI relationship(CL:0000656) MGI MGI:1915416 Spire1 GO:0005794 MGI:MGI:3581973|PMID:11747823 IDA C spire homolog 1 (Drosophila) Spir-1 gene taxon:10090 20050719 MGI relationship(CL:0000002) MGI MGI:98384 Spn GO:0005515 MGI:MGI:3510695|PMID:11238599 IPI UniProt:Q62230 F sialophorin 3E8 antigen|Cd43|Galgp|leukosialin|Ly-48|Ly48 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:98384 Spn GO:0007162 MGI:MGI:3029938|PMID:11828253 IMP MGI:1857246 P sialophorin 3E8 antigen|Cd43|Galgp|leukosialin|Ly-48|Ly48 gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:98384 Spn GO:0009897 MGI:MGI:1860996|PMID:10943842 IDA C sialophorin 3E8 antigen|Cd43|Galgp|leukosialin|Ly-48|Ly48 gene taxon:10090 20050617 MGI relationship(CL:0000081) MGI MGI:98384 Spn GO:0009897 MGI:MGI:77315|PMID:7477353 IDA C sialophorin 3E8 antigen|Cd43|Galgp|leukosialin|Ly-48|Ly48 gene taxon:10090 20050117 MGI relationship(CL:0000236) MGI MGI:98386 Spna2 GO:0005916 MGI:MGI:3656458|PMID:16481394 IDA C spectrin alpha 2 alpha-fodrin|brain|Spna-2 gene taxon:10090 20070312 MGI relationship(CL:0000746) MGI MGI:1890574 Spnb4 GO:0019226 MGI:MGI:3057033|PMID:15381686 IMP MGI:3497744 P spectrin beta 4 dyn|neuroaxonal dystrophy|nmf261|ROSA62|SpbIV gene taxon:10090 20041130 MGI relationship(CL:0000117) MGI MGI:1890574 Spnb4 GO:0030424 MGI:MGI:3057033|PMID:15381686 IDA C spectrin beta 4 dyn|neuroaxonal dystrophy|nmf261|ROSA62|SpbIV gene taxon:10090 20041130 MGI relationship(CL:0000117) MGI MGI:1890574 Spnb4 GO:0043203 MGI:MGI:3057033|PMID:15381686 IDA C spectrin beta 4 dyn|neuroaxonal dystrophy|nmf261|ROSA62|SpbIV gene taxon:10090 20041130 MGI relationship(CL:0000117) MGI MGI:98389 Spp1 GO:0005737 MGI:MGI:3624396|PMID:16518820 IDA C secreted phosphoprotein 1 44kDa bone phosphoprotein|BNSP|bone sialoprotein|Bsp|BSPI|ETA-1|minopontin|OP|Opn|Opnl|osteopontin|Ric|Spp-1 gene taxon:10090 20060925 MGI relationship(CL:0000066) MGI MGI:98389 Spp1 GO:0045177 MGI:MGI:3624396|PMID:16518820 IDA C secreted phosphoprotein 1 44kDa bone phosphoprotein|BNSP|bone sialoprotein|Bsp|BSPI|ETA-1|minopontin|OP|Opn|Opnl|osteopontin|Ric|Spp-1 gene taxon:10090 20060814 MGI relationship(CL:0000068) MGI MGI:1345138 Spry2 GO:0045165 MGI:MGI:3577817|PMID:15809037 IGI MGI:99604 P sprouty homolog 2 (Drosophila) sprouty2 gene taxon:10090 20050608 MGI relationship(CL:0000635) MGI MGI:1345138 Spry2 GO:0045165 MGI:MGI:3577817|PMID:15809037 IMP MGI:3578633 P sprouty homolog 2 (Drosophila) sprouty2 gene taxon:10090 20050608 MGI relationship(CL:0000635) MGI MGI:1345138 Spry2 GO:0048754 MGI:MGI:1331548|PMID:10074434 IMP P sprouty homolog 2 (Drosophila) sprouty2 gene taxon:10090 20051212 MGI relationship(CL:0000001) MGI MGI:98397 Src GO:0018108 MGI:MGI:3629864|PMID:12526740 IDA P Rous sarcoma oncogene pp60c-src gene taxon:10090 20060807 MGI relationship(CL:0000002) MGI MGI:106658 Srf GO:0005634 MGI:MGI:3603734|PMID:15929941 IDA C serum response factor gene taxon:10090 20060123 MGI relationship(CL:0000746) MGI MGI:1891338 Srpk3 GO:0007519 MGI:MGI:3588628|PMID:16140986 IMP P serine/arginine-rich protein specific kinase 3 Mssk1|Stk23 gene taxon:10090 20060208 MGI relationship(CL:0000188) MGI MGI:1858303 Srrm1 GO:0016363 MGI:MGI:2148694|PMID:9531537 ISS EMBL:AF048977 C serine/arginine repetitive matrix 1 gene taxon:10090 20050216 MGI relationship(CL:0000002) MGI MGI:106011 St8sia1 GO:0008284 MGI:MGI:3575596|PMID:15748692 IDA P ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1 alpha-2,8-sialyltransferase|GD3 synthase|GD3S|Sia-T|Siat8|Siat8a|ST8Sia I gene taxon:10090 20050510 MGI relationship(CL:0000066) MGI MGI:1355311 Stag3 GO:0000802 MGI:MGI:3578071|PMID:15870106 IDA C stromal antigen 3 SA-2|stromalin 3 gene taxon:10090 20050609 MGI relationship(CL:0000654) MGI MGI:102760 Star GO:0008211 MGI:MGI:1098076|PMID:9326645 IMP MGI:2388706 P steroidogenic acute regulatory protein D8Ertd419e gene taxon:10090 20060809 MGI relationship(CL:0000174) MGI MGI:102760 Star GO:0008211 MGI:MGI:1098076|PMID:9326645 IMP MGI:2388706 P steroidogenic acute regulatory protein D8Ertd419e gene taxon:10090 20060809 MGI relationship(CL:0000178) MGI MGI:102760 Star GO:0044255 MGI:MGI:1098076|PMID:9326645 IMP MGI:2388706 P steroidogenic acute regulatory protein D8Ertd419e gene taxon:10090 20060809 MGI relationship(CL:0000174) MGI MGI:102760 Star GO:0044255 MGI:MGI:1098076|PMID:9326645 IMP MGI:2388706 P steroidogenic acute regulatory protein D8Ertd419e gene taxon:10090 20060809 MGI relationship(CL:0000178) MGI MGI:103038 Stat3 GO:0001754 MGI:MGI:3045481|PMID:15207851 IMP P signal transducer and activator of transcription 3 Aprf gene taxon:10090 20040818 MGI relationship(CL:0000604) MGI MGI:103038 Stat3 GO:0005737 MGI:MGI:3530170|PMID:15749075 IDA C signal transducer and activator of transcription 3 Aprf gene taxon:10090 20060726 MGI relationship(CL:0000039) MGI MGI:103036 Stat5a GO:0003677 MGI:MGI:3577956|PMID:10485657 IDA F signal transducer and activator of transcription 5A STAT5 gene taxon:10090 20050603 MGI relationship(CL:0000002) MGI MGI:103036 Stat5a GO:0045647 MGI:MGI:1332382|PMID:10072077 IGI MGI:103035 P signal transducer and activator of transcription 5A STAT5 gene taxon:10090 20050601 MGI relationship(CL:0000232) MGI MGI:103035 Stat5b GO:0003677 MGI:MGI:3577956|PMID:10485657 IDA F signal transducer and activator of transcription 5B gene taxon:10090 20050603 MGI relationship(CL:0000002) MGI MGI:103035 Stat5b GO:0045647 MGI:MGI:1332382|PMID:10072077 IGI MGI:103036 P signal transducer and activator of transcription 5B gene taxon:10090 20050602 MGI relationship(CL:0000232) MGI MGI:1889642 Statip1 GO:0008023 MGI:MGI:3583922|PMID:11714725 ISS NCBI_NM:018255 C signal transducer and activator of transcription interacting protein 1 Elp2|Stat3-interacting protein|StIP1 gene taxon:10090 20060112 MGI relationship(CL:0000002) MGI MGI:1915678 Steap3 GO:0005768 MGI:MGI:3609504|PMID:16227996 IDA C STEAP family member 3 pHyde gene taxon:10090 20060411 MGI relationship(CL:0000002) MGI MGI:1915678 Steap3 GO:0005886 MGI:MGI:3609504|PMID:16227996 IDA C STEAP family member 3 pHyde gene taxon:10090 20060411 MGI relationship(CL:0000002) MGI MGI:96739 Stmn1 GO:0005737 MGI:MGI:1337459|PMID:10369391 IDA C stathmin 1 19K|Lag|Lap18|leukemia associated phosphoprotein p18|metablastin|oncoprotein18|op18|p18|p19|pig|PP17|PP18|PR22|prosolin|SMN gene taxon:10090 20040420 MGI relationship(CL:0000007) MGI MGI:96739 Stmn1 GO:0051272 MGI:MGI:3529385|PMID:15652749 IGI MGI:104565 P stathmin 1 19K|Lag|Lap18|leukemia associated phosphoprotein p18|metablastin|oncoprotein18|op18|p18|p19|pig|PP17|PP18|PR22|prosolin|SMN gene taxon:10090 20050503 MGI relationship(CL:0000002) MGI MGI:98241 Stmn2 GO:0030426 MGI:MGI:3513228|PMID:15581637 IDA C stathmin-like 2 SCG10|Scgn10 gene taxon:10090 20050121 MGI relationship(CL:0000001) MGI MGI:108059 Stx2 GO:0030154 MGI:MGI:3577788|PMID:15685636 IDA P syntaxin 2 Epim gene taxon:10090 20050805 MGI relationship(CL:0000351) MGI MGI:1926235 Stx6 GO:0005802 MGI:MGI:3689271|PMID:17003121 IDA C syntaxin 6 gene taxon:10090 20061212 MGI relationship(CL:0000001) MGI MGI:107363 Stxbp1 GO:0007412 MGI:MGI:3046454|PMID:15182301 IMP MGI:2183278 P syntaxin binding protein 1 Munc-18a|Munc18-1|N-sec1|nsec1|Rb-sec1|Sxtbp1|Unc18h gene taxon:10090 20041222 MGI relationship(CL:0000117) MGI MGI:107363 Stxbp1 GO:0016188 MGI:MGI:3046625|PMID:15145078 IMP MGI:2183278 P syntaxin binding protein 1 Munc-18a|Munc18-1|N-sec1|nsec1|Rb-sec1|Sxtbp1|Unc18h gene taxon:10090 20040818 MGI relationship(CL:0000117) MGI MGI:1096399 Sybl1 GO:0045177 MGI:MGI:3033551|PMID:14758363 IDA C synaptobrevin like 1 VAMP-7 gene taxon:10090 20040421 MGI relationship(CL:0000066) MGI MGI:1921325 Syce1 GO:0000795 MGI:MGI:3581466|PMID:15944401 IDA C synaptonemal complex central element protein 1 gene taxon:10090 20060313 MGI relationship(CL:0000017) MGI MGI:1921325 Syce1 GO:0007130 MGI:MGI:3581466|PMID:15944401 IC GO:0000795 P synaptonemal complex central element protein 1 gene taxon:10090 20060313 MGI relationship(CL:0000017) MGI MGI:1919096 Syce2 GO:0000795 MGI:MGI:3581466|PMID:15944401 IDA C synaptonemal complex central element protein 2 gene taxon:10090 20060313 MGI relationship(CL:0000017) MGI MGI:1919096 Syce2 GO:0007130 MGI:MGI:3581466|PMID:15944401 IC GO:0000795 P synaptonemal complex central element protein 2 gene taxon:10090 20060313 MGI relationship(CL:0000017) MGI MGI:105931 Sycp1 GO:0000802 MGI:MGI:3578071|PMID:15870106 IDA C synaptonemal complex protein 1 SCP1 gene taxon:10090 20050609 MGI relationship(CL:0000654) MGI MGI:109542 Sycp3 GO:0000802 MGI:MGI:3578071|PMID:15870106 IDA C synaptonemal complex protein 3 Cor1|Scp3 gene taxon:10090 20050609 MGI relationship(CL:0000654) MGI MGI:109542 Sycp3 GO:0007129 MGI:MGI:3578071|PMID:15870106 IMP MGI:2179041 P synaptonemal complex protein 3 Cor1|Scp3 gene taxon:10090 20050609 MGI relationship(CL:0000654) MGI MGI:99515 Syk GO:0000187 MGI:MGI:79455|PMID:8626447 IDA P spleen tyrosine kinase gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:99515 Syk GO:0004713 MGI:MGI:1859033|PMID:10872802 IDA F spleen tyrosine kinase gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:99515 Syk GO:0004713 MGI:MGI:82860|PMID:8798454 IDA F spleen tyrosine kinase gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:99515 Syk GO:0004715 MGI:MGI:79455|PMID:8626447 IDA F spleen tyrosine kinase gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:99515 Syk GO:0004716 MGI:MGI:79455|PMID:8626447 IDA F spleen tyrosine kinase gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:99515 Syk GO:0007166 MGI:MGI:86952|PMID:9099676 IDA P spleen tyrosine kinase gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:99515 Syk GO:0007242 MGI:MGI:79455|PMID:8626447 IDA P spleen tyrosine kinase gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:99515 Syk GO:0018108 MGI:MGI:1859033|PMID:10872802 IDA P spleen tyrosine kinase gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:99515 Syk GO:0018108 MGI:MGI:82860|PMID:8798454 IDA P spleen tyrosine kinase gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:99515 Syk GO:0019815 MGI:MGI:79455|PMID:8626447 IDA C spleen tyrosine kinase gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:99515 Syk GO:0045579 MGI:MGI:77314|PMID:7477352 IMP MGI:2384078 P spleen tyrosine kinase gene taxon:10090 20050117 MGI relationship(CL:0000236) MGI MGI:99515 Syk GO:0045579 MGI:MGI:77315|PMID:7477353 IMP MGI:1857421 P spleen tyrosine kinase gene taxon:10090 20060726 MGI relationship(CL:0000236) MGI MGI:99515 Syk GO:0045588 MGI:MGI:77314|PMID:7477352 IMP MGI:2384078 P spleen tyrosine kinase gene taxon:10090 20050117 MGI relationship(CL:0000084) MGI MGI:99515 Syk GO:0045588 MGI:MGI:83585|PMID:8790395 IMP MGI:1857421 P spleen tyrosine kinase gene taxon:10090 20060726 MGI relationship(CL:0000084) MGI MGI:99515 Syk GO:0046777 MGI:MGI:79455|PMID:8626447 IDA P spleen tyrosine kinase gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:99515 Syk GO:0050853 MGI:MGI:79455|PMID:8626447 IDA P spleen tyrosine kinase gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:98460 Syn1 GO:0007269 MGI:MGI:74599|PMID:7777057 IGI MGI:103020 P synapsin I Syn-1|Synapsin Ia|Synapsin Ib gene taxon:10090 20060824 MGI relationship(CL:0000117) MGI MGI:98460 Syn1 GO:0007269 MGI:MGI:74599|PMID:7777057 IMP MGI:1857250 P synapsin I Syn-1|Synapsin Ia|Synapsin Ib gene taxon:10090 20060824 MGI relationship(CL:0000117) MGI MGI:98460 Syn1 GO:0045202 MGI:MGI:3653273|PMID:16818724 IDA C synapsin I Syn-1|Synapsin Ia|Synapsin Ib gene taxon:10090 20070228 MGI relationship(CL:0000117) MGI MGI:103020 Syn2 GO:0007269 MGI:MGI:74599|PMID:7777057 IGI MGI:98460 P synapsin II Synapsin IIa|Synapsin IIb gene taxon:10090 20060824 MGI relationship(CL:0000117) MGI MGI:103020 Syn2 GO:0007269 MGI:MGI:74599|PMID:7777057 IMP MGI:1857251 P synapsin II Synapsin IIa|Synapsin IIb gene taxon:10090 20060824 MGI relationship(CL:0000117) MGI MGI:3039785 Syngap1 GO:0016358 MGI:MGI:3510474|PMID:15470153 IMP MGI:3511175 P synaptic Ras GTPase activating protein 1 homolog (rat) Syngap gene taxon:10090 20060308 MGI relationship(CL:0000001) MGI MGI:3039785 Syngap1 GO:0043066 MGI:MGI:3590468|PMID:15733080 IMP MGI:3511175 P synaptic Ras GTPase activating protein 1 homolog (rat) Syngap gene taxon:10090 20060308 MGI relationship(CL:0000117) MGI MGI:3039785 Syngap1 GO:0043113 MGI:MGI:3575363|PMID:12598599 IMP MGI:3576223 P synaptic Ras GTPase activating protein 1 homolog (rat) Syngap gene taxon:10090 20060308 MGI relationship(CL:0000117) MGI MGI:3039785 Syngap1 GO:0043198 MGI:MGI:3614311|PMID:16452659 IDA C synaptic Ras GTPase activating protein 1 homolog (rat) Syngap gene taxon:10090 20060308 MGI relationship(CL:0000117) MGI MGI:3039785 Syngap1 GO:0043408 MGI:MGI:3580530|PMID:12427827 IMP MGI:3580631 P synaptic Ras GTPase activating protein 1 homolog (rat) Syngap gene taxon:10090 20060308 MGI relationship(CL:0000117) MGI MGI:3039785 Syngap1 GO:0048169 MGI:MGI:3576792|PMID:15781580 IMP MGI:3576223 P synaptic Ras GTPase activating protein 1 homolog (rat) Syngap gene taxon:10090 20060308 MGI relationship(CL:0000117) MGI MGI:3039785 Syngap1 GO:0048169 MGI:MGI:3580530|PMID:12427827 IGI MGI:1277959 P synaptic Ras GTPase activating protein 1 homolog (rat) Syngap gene taxon:10090 20060308 MGI relationship(CL:0000117) MGI MGI:3039785 Syngap1 GO:0048169 MGI:MGI:3580530|PMID:12427827 IMP MGI:3580631 P synaptic Ras GTPase activating protein 1 homolog (rat) Syngap gene taxon:10090 20060308 MGI relationship(CL:0000117) MGI MGI:3039785 Syngap1 GO:0050803 MGI:MGI:3510474|PMID:15470153 IMP MGI:3511175 P synaptic Ras GTPase activating protein 1 homolog (rat) Syngap gene taxon:10090 20060308 MGI relationship(CL:0000001) MGI MGI:98467 Syp GO:0042734 MGI:MGI:3052624|PMID:15328414 IDA C synaptophysin p38|Syn|Syp I gene taxon:10090 20070313 MGI relationship(CL:0000601) MGI MGI:98474 Tac1 GO:0030424 MGI:MGI:1098517|PMID:1317267 IDA C tachykinin 1 neurokinin 1|neurokinin A|NK-1|NK1|Nkna|PPT-A|preprotachykinin A|SP|substance P gene taxon:10090 20061116 MGI relationship(CL:0000101) MGI MGI:98474 Tac1 GO:0030424 MGI:MGI:67873|PMID:7521790 IDA C tachykinin 1 neurokinin 1|neurokinin A|NK-1|NK1|Nkna|PPT-A|preprotachykinin A|SP|substance P gene taxon:10090 20061114 MGI relationship(CL:0000101) MGI MGI:98474 Tac1 GO:0043025 MGI:MGI:1306999|PMID:9853118 IDA C tachykinin 1 neurokinin 1|neurokinin A|NK-1|NK1|Nkna|PPT-A|preprotachykinin A|SP|substance P gene taxon:10090 20061115 MGI relationship(CL:0000540) MGI MGI:107404 Tbr1 GO:0005634 MGI:MGI:3042553|PMID:14999075 IDA C T-box brain gene 1 gene taxon:10090 20040811 MGI relationship(CL:0000117) MGI MGI:98493 Tbx1 GO:0001708 MGI:MGI:3039048|PMID:15084464 IMP MGI:2179191 P T-box 1 gene taxon:10090 20040712 MGI relationship(CL:0000101) MGI MGI:98493 Tbx1 GO:0001708 MGI:MGI:3044254|PMID:15064766 IGI MGI:1351209 P T-box 1 gene taxon:10090 20040809 MGI relationship(CL:0000679) MGI MGI:98493 Tbx1 GO:0001755 MGI:MGI:3530686|PMID:15652707 IMP MGI:2179190 P T-box 1 gene taxon:10090 20050424 MGI relationship(CL:0000008) MGI MGI:98493 Tbx1 GO:0007389 MGI:MGI:3512717|PMID:15385444 IMP MGI:2179190 P T-box 1 gene taxon:10090 20050215 MGI relationship(CL:0000134) MGI MGI:98493 Tbx1 GO:0007517 MGI:MGI:3512717|PMID:15385444 IMP MGI:2179190 P T-box 1 gene taxon:10090 20050215 MGI relationship(CL:0000188) MGI MGI:1923615 Tbx18 GO:0002053 MGI:MGI:3618666|PMID:16511601 IMP MGI:3044914 P T-box18 gene taxon:10090 20060518 MGI relationship(CL:0000134) MGI MGI:1923615 Tbx18 GO:0016331 MGI:MGI:3618666|PMID:16511601 IMP MGI:3044914 P T-box18 gene taxon:10090 20060517 MGI relationship(CL:0000192) MGI MGI:1923615 Tbx18 GO:0050679 MGI:MGI:3618666|PMID:16511601 IMP MGI:3044914 P T-box18 gene taxon:10090 20060517 MGI relationship(CL:0000066) MGI MGI:1923615 Tbx18 GO:0051145 MGI:MGI:3618666|PMID:16511601 IMP MGI:3044914 P T-box18 gene taxon:10090 20060517 MGI relationship(CL:0000192) MGI MGI:102539 Tbx6 GO:0001708 MGI:MGI:2447720|PMID:9490412 IMP MGI:2447721 P T-box 6 gene taxon:10090 20050601 MGI relationship(CL:0000222) MGI MGI:102539 Tbx6 GO:0005634 MGI:MGI:3583044|PMID:15986483 IDA C T-box 6 gene taxon:10090 20050819 MGI relationship(CL:0000222) MGI MGI:98496 Tbxa2r GO:0045987 MGI:MGI:2672939|PMID:12925702 IDA P thromboxane A2 receptor TP|Tp receptor gene taxon:10090 20051227 MGI relationship(CL:0000192) MGI MGI:98505 Tcf2 GO:0005634 MGI:MGI:3521591|PMID:15280201 IDA C transcription factor 2 hepatocyte nuclear factor-1 beta|HNF-1Beta|Hnf1beta|Tcf-2|vHNF1 gene taxon:10090 20050314 MGI relationship(CL:0000055) MGI MGI:1202876 Tcf3 GO:0046022 MGI:MGI:3582095|PMID:15907834 IDA P transcription factor 3 gene taxon:10090 20050912 MGI relationship(CL:0000001) MGI MGI:1202879 Tcf7l2 GO:0005634 MGI:MGI:3579620|PMID:15778706 IDA C transcription factor 7-like 2, T-cell specific, HMG-box mTcf-4B|mTcf-4E|Tcf-4|Tcf4|TCF4B|TCF4E gene taxon:10090 20050824 MGI relationship(CL:0000510) MGI MGI:106032 Tcfap2c GO:0030154 MGI:MGI:2386497|PMID:11940672 IMP MGI:3040993 P transcription factor AP-2, gamma Ap-2.2 gene taxon:10090 20050726 MGI relationship(CL:0000066) MGI MGI:2672878 Tcfl5 GO:0001673 MGI:MGI:3513664|PMID:15585666 IDA C transcription factor-like 5 (basic helix-loop-helix) FIG beta|Figlb gene taxon:10090 20050201 MGI relationship(CL:0000656) MGI MGI:2672878 Tcfl5 GO:0001673 MGI:MGI:3513664|PMID:15585666 IDA C transcription factor-like 5 (basic helix-loop-helix) FIG beta|Figlb gene taxon:10090 20050201 MGI relationship(CL:0000657) MGI MGI:98579 Tcrb-C GO:0009897 MGI:MGI:83585|PMID:8790395 IDA C T-cell receptor beta, constant region gene taxon:10090 20070129 MGI relationship(CL:0000084) MGI MGI:98612 Tcrd-C GO:0009897 MGI:MGI:83585|PMID:8790395 IDA C T-cell receptor delta, constant region gene taxon:10090 20050124 MGI relationship(CL:0000084) MGI MGI:98633 Tcrg-V3 GO:0009897 MGI:MGI:77314|PMID:7477352 IDA C T-cell receptor gamma, variable 3 vgamma3 gene taxon:10090 20050117 MGI relationship(CL:0000084) MGI MGI:101876 Tead1 GO:0003677 MGI:MGI:1934000|PMID:11306707 IDA F TEA domain family member 1 Gtrgeo5|mTEF-1|Tcf13|TEAD-1|TEF-1 gene taxon:10090 20051220 MGI relationship(CL:0000193) MGI MGI:101876 Tead1 GO:0005667 MGI:MGI:3608264|PMID:16207754 IDA C TEA domain family member 1 Gtrgeo5|mTEF-1|Tcf13|TEAD-1|TEF-1 gene taxon:10090 20060317 MGI relationship(CL:0000002) MGI MGI:101876 Tead1 GO:0016563 MGI:MGI:3608264|PMID:16207754 IGI MGI:103262 F TEA domain family member 1 Gtrgeo5|mTEF-1|Tcf13|TEAD-1|TEF-1 gene taxon:10090 20060317 MGI relationship(CL:0000002) MGI MGI:101876 Tead1 GO:0045944 MGI:MGI:3608264|PMID:16207754 IGI MGI:103262 P TEA domain family member 1 Gtrgeo5|mTEF-1|Tcf13|TEAD-1|TEF-1 gene taxon:10090 20060317 MGI relationship(CL:0000002) MGI MGI:104904 Tead2 GO:0005667 MGI:MGI:3608264|PMID:16207754 IDA C TEA domain family member 2 TEAD-2|TEF-4 gene taxon:10090 20060317 MGI relationship(CL:0000002) MGI MGI:104904 Tead2 GO:0016563 MGI:MGI:3608264|PMID:16207754 IGI MGI:103262 F TEA domain family member 2 TEAD-2|TEF-4 gene taxon:10090 20060317 MGI relationship(CL:0000002) MGI MGI:104904 Tead2 GO:0045944 MGI:MGI:3608264|PMID:16207754 IGI MGI:103262 P TEA domain family member 2 TEAD-2|TEF-4 gene taxon:10090 20060317 MGI relationship(CL:0000002) MGI MGI:109241 Tead3 GO:0005667 MGI:MGI:3608264|PMID:16207754 IGI MGI:103262 C TEA domain family member 3 DTEF-1|ETFR-1|Tcf13r2|TEAD-3|TEF-5 gene taxon:10090 20060317 MGI relationship(CL:0000002) MGI MGI:109241 Tead3 GO:0016563 MGI:MGI:3608264|PMID:16207754 IGI MGI:103262 F TEA domain family member 3 DTEF-1|ETFR-1|Tcf13r2|TEAD-3|TEF-5 gene taxon:10090 20060317 MGI relationship(CL:0000002) MGI MGI:109241 Tead3 GO:0045944 MGI:MGI:3608264|PMID:16207754 IGI MGI:103262 P TEA domain family member 3 DTEF-1|ETFR-1|Tcf13r2|TEAD-3|TEF-5 gene taxon:10090 20060317 MGI relationship(CL:0000002) MGI MGI:106907 Tead4 GO:0005667 MGI:MGI:3608264|PMID:16207754 IDA C TEA domain family member 4 ETFR-2a|Tcf13r1|TEAD-4|TEF-3|Tefr1a gene taxon:10090 20060317 MGI relationship(CL:0000002) MGI MGI:106907 Tead4 GO:0016563 MGI:MGI:3608264|PMID:16207754 IGI MGI:103262 F TEA domain family member 4 ETFR-2a|Tcf13r1|TEAD-4|TEF-3|Tefr1a gene taxon:10090 20060317 MGI relationship(CL:0000002) MGI MGI:106907 Tead4 GO:0045944 MGI:MGI:3608264|PMID:16207754 IGI MGI:103262 P TEA domain family member 4 ETFR-2a|Tcf13r1|TEAD-4|TEF-3|Tefr1a gene taxon:10090 20060317 MGI relationship(CL:0000002) MGI MGI:104638 Tff3 GO:0030141 MGI:MGI:3528104|PMID:15645444 IDA C trefoil factor 3, intestinal ITF|mITF gene taxon:10090 20050308 MGI relationship(CL:0000160) MGI MGI:98822 Tfrc GO:0005768 MGI:MGI:3042070|PMID:14562105 IDA C transferrin receptor CD71|Mtvr-1|Mtvr1|p90|TfR1|Trfr gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:98822 Tfrc GO:0005768 MGI:MGI:3609504|PMID:16227996 IDA C transferrin receptor CD71|Mtvr-1|Mtvr1|p90|TfR1|Trfr gene taxon:10090 20060411 MGI relationship(CL:0000002) MGI MGI:98822 Tfrc GO:0005886 MGI:MGI:3042070|PMID:14562105 IDA C transferrin receptor CD71|Mtvr-1|Mtvr1|p90|TfR1|Trfr gene taxon:10090 20041028 MGI relationship(CL:0000002) MGI MGI:98822 Tfrc GO:0005886 MGI:MGI:3055460|PMID:10444069 IDA C transferrin receptor CD71|Mtvr-1|Mtvr1|p90|TfR1|Trfr gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:98822 Tfrc GO:0005886 MGI:MGI:3609504|PMID:16227996 IDA C transferrin receptor CD71|Mtvr-1|Mtvr1|p90|TfR1|Trfr gene taxon:10090 20060411 MGI relationship(CL:0000002) MGI MGI:98822 Tfrc GO:0048471 MGI:MGI:3055460|PMID:10444069 IDA C transferrin receptor CD71|Mtvr-1|Mtvr1|p90|TfR1|Trfr gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:98725 Tgfb1 GO:0008284 MGI:MGI:3525900|PMID:15604101 IDA P transforming growth factor, beta 1 TGF-beta 1|Tgfb|Tgfb-1 gene taxon:10090 20050316 MGI relationship(CL:0000134) MGI MGI:98726 Tgfb2 GO:0007411 MGI:MGI:3522686|PMID:15528466 IMP MGI:1888389 P transforming growth factor, beta 2 Tgf-beta2 gene taxon:10090 20050318 MGI relationship(CL:0000029) MGI MGI:98726 Tgfb2 GO:0042981 MGI:MGI:3608105|PMID:12393102 IMP MGI:1888389 P transforming growth factor, beta 2 Tgf-beta2 gene taxon:10090 20060221 MGI relationship(CL:0000134) MGI MGI:98726 Tgfb2 GO:0048663 MGI:MGI:3588127|PMID:15744664 IDA P transforming growth factor, beta 2 Tgf-beta2 gene taxon:10090 20060208 MGI relationship(CL:0000540) MGI MGI:98727 Tgfb3 GO:0008285 MGI:MGI:2667731|PMID:12815624 IDA P transforming growth factor, beta 3 gene taxon:10090 20041007 MGI relationship(CL:0000066) MGI MGI:98727 Tgfb3 GO:0009887 MGI:MGI:2686862|PMID:14697364 IMP MGI:1857259 P transforming growth factor, beta 3 gene taxon:10090 20041007 MGI relationship(CL:0000066) MGI MGI:98728 Tgfbr1 GO:0008354 MGI:MGI:3588906|PMID:15993878 IMP MGI:2388050 P transforming growth factor, beta receptor I Alk-5|ALK5|TbetaR-I|TbetaRI gene taxon:10090 20060209 MGI relationship(CL:0000670) MGI MGI:98728 Tgfbr1 GO:0048663 MGI:MGI:3588127|PMID:15744664 IMP P transforming growth factor, beta receptor I Alk-5|ALK5|TbetaR-I|TbetaRI gene taxon:10090 20060208 MGI relationship(CL:0000540) MGI MGI:98729 Tgfbr2 GO:0042127 MGI:MGI:2678274|PMID:12975342 IMP MGI:2384511 P transforming growth factor, beta receptor II DNIIR|TbetaR-II|TbetaRII gene taxon:10090 20060510 MGI relationship(CL:0000008) MGI MGI:105080 Tgoln1 GO:0005802 MGI:MGI:2449260|PMID:12488345 IDA C trans-golgi network protein D6Ertd384e|TGN38|TGN38A|Ttgn1 gene taxon:10090 20061101 MGI relationship(CL:0000001) MGI MGI:98735 Th GO:0005737 MGI:MGI:1352916|PMID:10707987 IDA C tyrosine hydroxylase gene taxon:10090 20050908 MGI relationship(CL:0000700) MGI MGI:107913 Tial1 GO:0005634 MGI:MGI:1197399|PMID:9482885 IDA C Tia1 cytotoxic granule-associated RNA binding protein-like 1 mTIAR gene taxon:10090 20061012 MGI relationship(CL:0000670) MGI MGI:1321393 Timeless GO:0005634 MGI:MGI:2675515|PMID:12950082 IDA C timeless homolog (Drosophila) tim gene taxon:10090 20050616 MGI relationship(CL:0000082) MGI MGI:1321393 Timeless GO:0005634 MGI:MGI:2675515|PMID:12950082 IDA C timeless homolog (Drosophila) tim gene taxon:10090 20050616 MGI relationship(CL:0000134) MGI MGI:98753 Timp2 GO:0005178 MGI:MGI:3578612|PMID:15901773 IDA F tissue inhibitor of metalloproteinase 2 D11Bwg1104e|TIMP-2 gene taxon:10090 20050722 MGI relationship(CL:0000002) MGI MGI:98753 Timp2 GO:0008285 MGI:MGI:3578612|PMID:15901773 IDA P tissue inhibitor of metalloproteinase 2 D11Bwg1104e|TIMP-2 gene taxon:10090 20050722 MGI relationship(CL:0000002) MGI MGI:98753 Timp2 GO:0009986 MGI:MGI:3578612|PMID:15901773 IDA C tissue inhibitor of metalloproteinase 2 D11Bwg1104e|TIMP-2 gene taxon:10090 20050722 MGI relationship(CL:0000002) MGI MGI:98753 Timp2 GO:0030814 MGI:MGI:3578612|PMID:15901773 IDA P tissue inhibitor of metalloproteinase 2 D11Bwg1104e|TIMP-2 gene taxon:10090 20050722 MGI relationship(CL:0000002) MGI MGI:98753 Timp2 GO:0043408 MGI:MGI:3578612|PMID:15901773 IDA P tissue inhibitor of metalloproteinase 2 D11Bwg1104e|TIMP-2 gene taxon:10090 20050722 MGI relationship(CL:0000002) MGI MGI:98753 Timp2 GO:0045664 MGI:MGI:3578612|PMID:15901773 IDA P tissue inhibitor of metalloproteinase 2 D11Bwg1104e|TIMP-2 gene taxon:10090 20050722 MGI relationship(CL:0000002) MGI MGI:98753 Timp2 GO:0045664 MGI:MGI:3578612|PMID:15901773 IMP P tissue inhibitor of metalloproteinase 2 D11Bwg1104e|TIMP-2 gene taxon:10090 20050722 MGI relationship(CL:0000117) MGI MGI:108067 Titf1 GO:0001764 MGI:MGI:3607390|PMID:12902388 IMP MGI:1857494 P thyroid transcription factor 1 Nkx2-1|Nkx2.1|T/EBP|thyroid-specific enhancer-binding protein|tinman|Ttf-1 gene taxon:10090 20060213 MGI relationship(CL:0000117) MGI MGI:108067 Titf1 GO:0005634 MGI:MGI:3511765|PMID:15576401 IDA C thyroid transcription factor 1 Nkx2-1|Nkx2.1|T/EBP|thyroid-specific enhancer-binding protein|tinman|Ttf-1 gene taxon:10090 20050105 MGI relationship(CL:0000223) MGI MGI:98759 Tjp1 GO:0005913 MGI:MGI:2154851|PMID:11731229 IDA C tight junction protein 1 ZO-1|ZO1 gene taxon:10090 20060912 MGI relationship(CL:0000353) MGI MGI:98759 Tjp1 GO:0005923 MGI:MGI:3582101|PMID:15950600 IDA C tight junction protein 1 ZO-1|ZO1 gene taxon:10090 20050822 MGI relationship(CL:0000007) MGI MGI:98759 Tjp1 GO:0005923 MGI:MGI:3582101|PMID:15950600 IDA C tight junction protein 1 ZO-1|ZO1 gene taxon:10090 20050822 MGI relationship(CL:1000274) MGI MGI:98759 Tjp1 GO:0016020 MGI:MGI:3578587|PMID:15788452 IDA C tight junction protein 1 ZO-1|ZO1 gene taxon:10090 20050727 MGI relationship(CL:1000274) MGI MGI:104636 Tle1 GO:0003682 MGI:MGI:3603095|PMID:16002402 IDA F transducin-like enhancer of split 1, homolog of Drosophila E(spl) Grg1 gene taxon:10090 20051104 MGI relationship(CL:0000002) MGI MGI:104633 Tle4 GO:0000122 MGI:MGI:3603095|PMID:16002402 IDA P transducin-like enhancer of split 4, homolog of Drosophila E(spl) Bce1|ESTM13|ESTM14|Grg4 gene taxon:10090 20051104 MGI relationship(CL:0000002) MGI MGI:104633 Tle4 GO:0003682 MGI:MGI:3603095|PMID:16002402 IDA F transducin-like enhancer of split 4, homolog of Drosophila E(spl) Bce1|ESTM13|ESTM14|Grg4 gene taxon:10090 20051104 MGI relationship(CL:0000002) MGI MGI:104633 Tle4 GO:0003705 MGI:MGI:3530428|PMID:15729346 IGI MGI:97487,MGI:96770,MGI:88276 F transducin-like enhancer of split 4, homolog of Drosophila E(spl) Bce1|ESTM13|ESTM14|Grg4 gene taxon:10090 20050513 MGI relationship(CL:0000002) MGI MGI:104633 Tle4 GO:0003714 MGI:MGI:3603095|PMID:16002402 IGI MGI:97168,MGI:101898 F transducin-like enhancer of split 4, homolog of Drosophila E(spl) Bce1|ESTM13|ESTM14|Grg4 gene taxon:10090 20060221 MGI relationship(CL:0000002) MGI MGI:1932389 Tlr9 GO:0005886 MGI:MGI:3615690|PMID:16415873 IDA C toll-like receptor 9 gene taxon:10090 20060413 MGI relationship(CL:0000002) MGI MGI:98769 Tlx1 GO:0008284 MGI:MGI:3581070|PMID:15944191 IMP MGI:1857260 P T-cell leukemia, homeobox 1 Hox-11|Hox11 gene taxon:10090 20050816 MGI relationship(CL:0000134) MGI MGI:98769 Tlx1 GO:0045944 MGI:MGI:3581070|PMID:15944191 IDA P T-cell leukemia, homeobox 1 Hox-11|Hox11 gene taxon:10090 20050816 MGI relationship(CL:0000001) MGI MGI:1351209 Tlx3 GO:0001708 MGI:MGI:3044254|PMID:15064766 IGI MGI:98769 P T-cell leukemia, homeobox 3 Hox11l2|Rnx|Tlx1l2 gene taxon:10090 20040809 MGI relationship(CL:0000617) MGI MGI:1351209 Tlx3 GO:0001708 MGI:MGI:3044254|PMID:15064766 IMP MGI:2180105 P T-cell leukemia, homeobox 3 Hox11l2|Rnx|Tlx1l2 gene taxon:10090 20040809 MGI relationship(CL:0000679) MGI MGI:1351209 Tlx3 GO:0001764 MGI:MGI:3051709|PMID:15229182 IMP MGI:2180105 P T-cell leukemia, homeobox 3 Hox11l2|Rnx|Tlx1l2 gene taxon:10090 20040929 MGI relationship(CL:0000540) MGI MGI:1351209 Tlx3 GO:0005634 MGI:MGI:3505657|PMID:15466398 IDA C T-cell leukemia, homeobox 3 Hox11l2|Rnx|Tlx1l2 gene taxon:10090 20050131 MGI relationship(CL:0000117) MGI MGI:1351209 Tlx3 GO:0045665 MGI:MGI:3607682|PMID:16234809 IGI MGI:104867 P T-cell leukemia, homeobox 3 Hox11l2|Rnx|Tlx1l2 gene taxon:10090 20060413 MGI relationship(CL:0000617) MGI MGI:1351209 Tlx3 GO:0048665 MGI:MGI:3607682|PMID:16234809 IGI MGI:104867 P T-cell leukemia, homeobox 3 Hox11l2|Rnx|Tlx1l2 gene taxon:10090 20060413 MGI relationship(CL:0000679) MGI MGI:99510 Tmsb4x GO:0030334 MGI:MGI:3511711|PMID:15565145 IDA P thymosin, beta 4, X chromosome Ptmb4 gene taxon:10090 20050103 MGI relationship(CL:0000193) MGI MGI:101922 Tnc GO:0005604 MGI:MGI:61475|PMID:7687262 IDA C tenascin C Hxb|tenascin-C|TN|TN-C gene taxon:10090 20051013 MGI relationship(CL:0000066) MGI MGI:104798 Tnf GO:0005886 MGI:MGI:3050738|PMID:15155767 IDA C tumor necrosis factor DIF|TNF alpha|TNF-alpha|TNFalpha|Tnfsf1a|tumor necrosis factor-alpha gene taxon:10090 20040930 MGI relationship(CL:0000001) MGI MGI:104798 Tnf GO:0008624 MGI:MGI:3525895|PMID:15629131 IDA P tumor necrosis factor DIF|TNF alpha|TNF-alpha|TNFalpha|Tnfsf1a|tumor necrosis factor-alpha gene taxon:10090 20060307 MGI relationship(CL:0000002) MGI MGI:104798 Tnf GO:0030316 MGI:MGI:3525391|PMID:15485831 IGI MGI:1100089,MGI:99484 P tumor necrosis factor DIF|TNF alpha|TNF-alpha|TNFalpha|Tnfsf1a|tumor necrosis factor-alpha gene taxon:10090 20050317 MGI relationship(CL:0000092) MGI MGI:104798 Tnf GO:0046325 MGI:MGI:2181851|PMID:12068289 IDA P tumor necrosis factor DIF|TNF alpha|TNF-alpha|TNFalpha|Tnfsf1a|tumor necrosis factor-alpha gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1100089 Tnfsf11 GO:0030316 MGI:MGI:3525391|PMID:15485831 IGI MGI:104798,MGI:99484 P tumor necrosis factor (ligand) superfamily, member 11 Ly109l|ODF|OPG|OPGL|osteoclast differentiation factor|RANKL|Trance gene taxon:10090 20050317 MGI relationship(CL:0000092) MGI MGI:1858308 Tnk2 GO:0030424 MGI:MGI:3590361|PMID:16052498 IDA C tyrosine kinase, non-receptor, 2 Ack|ACK1|activated p21cdc42Hs kinase|P21cdc42Hs kinase|Pyk1 gene taxon:10090 20051129 MGI relationship(CL:0000117) MGI MGI:1858308 Tnk2 GO:0030425 MGI:MGI:3590361|PMID:16052498 IDA C tyrosine kinase, non-receptor, 2 Ack|ACK1|activated p21cdc42Hs kinase|P21cdc42Hs kinase|Pyk1 gene taxon:10090 20051129 MGI relationship(CL:0000121) MGI MGI:1858308 Tnk2 GO:0030425 MGI:MGI:3590361|PMID:16052498 IDA C tyrosine kinase, non-receptor, 2 Ack|ACK1|activated p21cdc42Hs kinase|P21cdc42Hs kinase|Pyk1 gene taxon:10090 20051129 MGI relationship(CL:0000598) MGI MGI:1858308 Tnk2 GO:0030426 MGI:MGI:3590361|PMID:16052498 IDA C tyrosine kinase, non-receptor, 2 Ack|ACK1|activated p21cdc42Hs kinase|P21cdc42Hs kinase|Pyk1 gene taxon:10090 20051129 MGI relationship(CL:0000001) MGI MGI:1858308 Tnk2 GO:0043025 MGI:MGI:3590361|PMID:16052498 IDA C tyrosine kinase, non-receptor, 2 Ack|ACK1|activated p21cdc42Hs kinase|P21cdc42Hs kinase|Pyk1 gene taxon:10090 20051129 MGI relationship(CL:0000117) MGI MGI:98783 Tnni3 GO:0030017 MGI:MGI:3656458|PMID:16481394 IDA C troponin I, cardiac Tn1 gene taxon:10090 20070312 MGI relationship(CL:0000746) MGI MGI:2443012 Tns3 GO:0008284 MGI:MGI:3531231|PMID:15733665 IMP MGI:3574415 P tensin 3 TEM6|Tens1 gene taxon:10090 20050505 MGI relationship(CL:0000138) MGI MGI:2443012 Tns3 GO:0016477 MGI:MGI:3531231|PMID:15733665 IMP MGI:3574415 P tensin 3 TEM6|Tens1 gene taxon:10090 20050505 MGI relationship(CL:0000131) MGI MGI:98788 Top1 GO:0003917 MGI:MGI:86770|PMID:9094096 IDA F topoisomerase (DNA) I Top-1 gene taxon:10090 20060825 MGI relationship(CL:0000017) MGI MGI:98788 Top1 GO:0003917 MGI:MGI:86770|PMID:9094096 IDA F topoisomerase (DNA) I Top-1 gene taxon:10090 20060825 MGI relationship(CL:0000018) MGI MGI:98788 Top1 GO:0005634 MGI:MGI:3612364|PMID:16261531 IDA C topoisomerase (DNA) I Top-1 gene taxon:10090 20060825 MGI relationship(CL:0000117) MGI MGI:98788 Top1 GO:0005634 MGI:MGI:3612364|PMID:16261531 IDA C topoisomerase (DNA) I Top-1 gene taxon:10090 20060825 MGI relationship(CL:0000120) MGI MGI:98788 Top1 GO:0005634 MGI:MGI:3612364|PMID:16261531 IDA C topoisomerase (DNA) I Top-1 gene taxon:10090 20060825 MGI relationship(CL:0000121) MGI MGI:98788 Top1 GO:0005634 MGI:MGI:3612364|PMID:16261531 IDA C topoisomerase (DNA) I Top-1 gene taxon:10090 20060825 MGI relationship(CL:0000598) MGI MGI:98788 Top1 GO:0005634 MGI:MGI:83974|PMID:8943335 IDA C topoisomerase (DNA) I Top-1 gene taxon:10090 20060825 MGI relationship(CL:0000353) MGI MGI:98788 Top1 GO:0005634 MGI:MGI:86770|PMID:9094096 IDA C topoisomerase (DNA) I Top-1 gene taxon:10090 20060825 MGI relationship(CL:0000017) MGI MGI:98788 Top1 GO:0005634 MGI:MGI:86770|PMID:9094096 IDA C topoisomerase (DNA) I Top-1 gene taxon:10090 20060825 MGI relationship(CL:0000018) MGI MGI:98788 Top1 GO:0005737 MGI:MGI:3612364|PMID:16261531 IDA C topoisomerase (DNA) I Top-1 gene taxon:10090 20060825 MGI relationship(CL:0000117) MGI MGI:98788 Top1 GO:0005737 MGI:MGI:3612364|PMID:16261531 IDA C topoisomerase (DNA) I Top-1 gene taxon:10090 20060825 MGI relationship(CL:0000121) MGI MGI:98788 Top1 GO:0005737 MGI:MGI:3612364|PMID:16261531 IDA C topoisomerase (DNA) I Top-1 gene taxon:10090 20060825 MGI relationship(CL:0000598) MGI MGI:98788 Top1 GO:0040016 MGI:MGI:83974|PMID:8943335 IMP MGI:2678314 P topoisomerase (DNA) I Top-1 gene taxon:10090 20060825 MGI relationship(CL:0000353) MGI MGI:98788 Top1 GO:0043204 MGI:MGI:3612364|PMID:16261531 IDA C topoisomerase (DNA) I Top-1 gene taxon:10090 20060825 MGI relationship(CL:0000127) MGI MGI:98790 Top2a GO:0003918 MGI:MGI:86770|PMID:9094096 IDA F topoisomerase (DNA) II alpha DNA Topoisomerase II alpha|Top-2 gene taxon:10090 20060825 MGI relationship(CL:0000017) MGI MGI:98790 Top2a GO:0003918 MGI:MGI:86770|PMID:9094096 IDA F topoisomerase (DNA) II alpha DNA Topoisomerase II alpha|Top-2 gene taxon:10090 20060825 MGI relationship(CL:0000018) MGI MGI:98790 Top2a GO:0005634 MGI:MGI:86770|PMID:9094096 IDA C topoisomerase (DNA) II alpha DNA Topoisomerase II alpha|Top-2 gene taxon:10090 20060825 MGI relationship(CL:0000017) MGI MGI:98790 Top2a GO:0005634 MGI:MGI:86770|PMID:9094096 IDA C topoisomerase (DNA) II alpha DNA Topoisomerase II alpha|Top-2 gene taxon:10090 20060825 MGI relationship(CL:0000018) MGI MGI:98791 Top2b GO:0001764 MGI:MGI:3521808|PMID:12773624 IMP MGI:3521923 P topoisomerase (DNA) II beta Top-2 gene taxon:10090 20050214 MGI relationship(CL:0000117) MGI MGI:2146189 Topors GO:0045941 MGI:MGI:3578084|PMID:15735665 IGI MGI:98834 P topoisomerase I binding, arginine/serine-rich gene taxon:10090 20050729 MGI relationship(CL:0000002) MGI MGI:1336194 Tpp1 GO:0007040 MGI:MGI:3522013|PMID:15483130 IMP MGI:3521972 P tripeptidyl peptidase I Cln2 gene taxon:10090 20060912 MGI relationship(CL:0000100) MGI MGI:1336194 Tpp1 GO:0007040 MGI:MGI:3522013|PMID:15483130 IMP MGI:3521972 P tripeptidyl peptidase I Cln2 gene taxon:10090 20060912 MGI relationship(CL:0000101) MGI MGI:1336194 Tpp1 GO:0007040 MGI:MGI:3522013|PMID:15483130 IMP MGI:3521972 P tripeptidyl peptidase I Cln2 gene taxon:10090 20060912 MGI relationship(CL:0000117) MGI MGI:108072 Traf6 GO:0048468 MGI:MGI:3575245|PMID:15705807 IMP MGI:2675469 P Tnf receptor-associated factor 6 gene taxon:10090 20050510 MGI relationship(CL:0000066) MGI MGI:1924897 Trat1 GO:0001920 MGI:MGI:3047098|PMID:11390434 ISS UniProt:Q6PIZ9 P T cell receptor associated transmembrane adaptor 1 Tcrim|Trim gene taxon:10090 20060727 MGI relationship(CL:0000002) MGI MGI:1924897 Trat1 GO:0005886 MGI:MGI:3047098|PMID:11390434 ISS UniProt:Q6PIZ9 C T cell receptor associated transmembrane adaptor 1 Tcrim|Trim gene taxon:10090 20060112 MGI relationship(CL:0000002) MGI MGI:1924897 Trat1 GO:0042101 MGI:MGI:3047098|PMID:11390434 ISS UniProt:Q6PIZ9 C T cell receptor associated transmembrane adaptor 1 Tcrim|Trim gene taxon:10090 20060112 MGI relationship(CL:0000002) MGI MGI:1924897 Trat1 GO:0050850 MGI:MGI:3047098|PMID:11390434 ISS UniProt:Q6PIZ9 P T cell receptor associated transmembrane adaptor 1 Tcrim|Trim gene taxon:10090 20060112 MGI relationship(CL:0000002) MGI MGI:1924897 Trat1 GO:0050862 MGI:MGI:3047098|PMID:11390434 ISS UniProt:Q6PIZ9 P T cell receptor associated transmembrane adaptor 1 Tcrim|Trim gene taxon:10090 20060112 MGI relationship(CL:0000002) MGI MGI:1924897 Trat1 GO:0051051 MGI:MGI:3047098|PMID:11390434 ISS UniProt:Q6PIZ9 P T cell receptor associated transmembrane adaptor 1 Tcrim|Trim gene taxon:10090 20060112 MGI relationship(CL:0000002) MGI MGI:98821 Trf GO:0005768 MGI:MGI:3609504|PMID:16227996 IDA C transferrin Cd176|HP|Tfn gene taxon:10090 20060411 MGI relationship(CL:0000002) MGI MGI:1914104 Trim35 GO:0005634 MGI:MGI:3037567|PMID:14662771 IDA C tripartite motif-containing 35 Hls5|Mair gene taxon:10090 20060125 MGI relationship(CL:0000002) MGI MGI:1914104 Trim35 GO:0005737 MGI:MGI:3037567|PMID:14662771 IDA C tripartite motif-containing 35 Hls5|Mair gene taxon:10090 20060125 MGI relationship(CL:0000002) MGI MGI:1914104 Trim35 GO:0008285 MGI:MGI:3037567|PMID:14662771 IDA P tripartite motif-containing 35 Hls5|Mair gene taxon:10090 20060125 MGI relationship(CL:0000002) MGI MGI:1919276 Trmu GO:0005739 MGI:MGI:3028355|PMID:14746906 IDA C tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase Trmt1 gene taxon:10090 20050422 MGI relationship(CL:0000002) MGI MGI:98834 Trp53 GO:0006974 MGI:MGI:3032464|PMID:14744935 IDA P transformation related protein 53 p53 gene taxon:10090 20070314 MGI relationship(CL:0000002) MGI MGI:98834 Trp53 GO:0007406 MGI:MGI:1203920|PMID:9608530 IGI MGI:97306 P transformation related protein 53 p53 gene taxon:10090 20070126 MGI relationship(CL:0000001) MGI MGI:98834 Trp53 GO:0008285 MGI:MGI:1889141|PMID:10973261 IGI MGI:97306 P transformation related protein 53 p53 gene taxon:10090 20070130 MGI relationship(CL:0000125) MGI MGI:98834 Trp53 GO:0009411 MGI:MGI:3032464|PMID:14744935 IDA P transformation related protein 53 p53 gene taxon:10090 20070314 MGI relationship(CL:0000002) MGI MGI:98834 Trp53 GO:0010332 MGI:MGI:3032464|PMID:14744935 IDA P transformation related protein 53 p53 gene taxon:10090 20070314 MGI relationship(CL:0000002) MGI MGI:98834 Trp53 GO:0043525 MGI:MGI:1203920|PMID:9608530 IMP MGI:1857263 P transformation related protein 53 p53 gene taxon:10090 20070126 MGI relationship(CL:0000001) MGI MGI:98834 Trp53 GO:0045941 MGI:MGI:3578084|PMID:15735665 IDA P transformation related protein 53 p53 gene taxon:10090 20050729 MGI relationship(CL:0000002) MGI MGI:98834 Trp53 GO:0045941 MGI:MGI:3578084|PMID:15735665 IGI MGI:2146189 P transformation related protein 53 p53 gene taxon:10090 20050729 MGI relationship(CL:0000002) MGI MGI:1330810 Trp63 GO:0005634 MGI:MGI:3513641|PMID:15585950 IDA C transformation related protein 63 KET protein|p51/p63|p63|p73L|TAp63|Trp53rp1 gene taxon:10090 20050201 MGI relationship(CL:0000216) MGI MGI:1330810 Trp63 GO:0005634 MGI:MGI:3522396|PMID:15361520 IDA C transformation related protein 63 KET protein|p51/p63|p63|p73L|TAp63|Trp53rp1 gene taxon:10090 20050309 MGI relationship(CL:0000362) MGI MGI:1330810 Trp63 GO:0030154 MGI:MGI:3487217|PMID:15371309 IMP MGI:1934580 P transformation related protein 63 KET protein|p51/p63|p63|p73L|TAp63|Trp53rp1 gene taxon:10090 20050726 MGI relationship(CL:0000646) MGI MGI:1330810 Trp63 GO:0030859 MGI:MGI:3525891|PMID:15189821 IMP MGI:1934269 P transformation related protein 63 KET protein|p51/p63|p63|p73L|TAp63|Trp53rp1 gene taxon:10090 20050303 MGI relationship(CL:0000067) MGI MGI:1336991 Trp73 GO:0005634 MGI:MGI:3530985|PMID:15525772 IDA C transformation related protein 73 p73 gene taxon:10090 20050424 MGI relationship(CL:0000695) MGI MGI:2153272 Trrap GO:0007093 MGI:MGI:2151302|PMID:11544477 IMP MGI:2446468 P transformation/transcription domain-associated protein transactivation/transformation-domain associated protein gene taxon:10090 20050726 MGI relationship(CL:0000007) MGI MGI:2685063 Tsga10 GO:0043005 MGI:MGI:3625570|PMID:16643851 IDA C testis specific 10 Mtsga10 gene taxon:10090 20060705 MGI relationship(CL:0000001) MGI MGI:1916987 Ttl GO:0000226 MGI:MGI:3584093|PMID:15899979 IMP MGI:3584264 P tubulin tyrosine ligase gene taxon:10090 20060202 MGI relationship(CL:0000117) MGI MGI:1916987 Ttl GO:0000226 MGI:MGI:3584093|PMID:15899979 IMP MGI:3584264 P tubulin tyrosine ligase gene taxon:10090 20060202 MGI relationship(CL:0000128) MGI MGI:1916987 Ttl GO:0030516 MGI:MGI:3584093|PMID:15899979 IMP MGI:3584264 P tubulin tyrosine ligase gene taxon:10090 20060202 MGI relationship(CL:0000117) MGI MGI:98864 Ttn GO:0030018 MGI:MGI:3656458|PMID:16481394 IDA C titin connectin|mdm|shru gene taxon:10090 20070312 MGI relationship(CL:0000746) MGI MGI:98864 Ttn GO:0031672 MGI:MGI:3656458|PMID:16481394 IDA C titin connectin|mdm|shru gene taxon:10090 20070312 MGI relationship(CL:0000746) MGI MGI:98864 Ttn GO:0031674 MGI:MGI:3656458|PMID:16481394 IDA C titin connectin|mdm|shru gene taxon:10090 20070312 MGI relationship(CL:0000746) MGI MGI:107813 Tubb3 GO:0015630 MGI:MGI:3037230|PMID:15003631 IDA C tubulin, beta 3 gene taxon:10090 20050428 MGI relationship(CL:0000002) MGI MGI:98872 Twist1 GO:0001764 MGI:MGI:3042807|PMID:15162501 IMP MGI:1857265 P twist gene homolog 1 (Drosophila) charlie chaplin|M-Twist|pdt|Pluridigite|Ska|Ska10 gene taxon:10090 20040715 MGI relationship(CL:0000117) MGI MGI:98872 Twist1 GO:0030154 MGI:MGI:2384366|PMID:12142027 IMP MGI:1857265 P twist gene homolog 1 (Drosophila) charlie chaplin|M-Twist|pdt|Pluridigite|Ska|Ska10 gene taxon:10090 20040715 MGI relationship(CL:0000134) MGI MGI:2137520 Twsg1 GO:0001707 MGI:MGI:3578079|PMID:15843411 IGI MGI:103302 P twisted gastrulation homolog 1 (Drosophila) D17Ertd403e|Tsg gene taxon:10090 20050617 MGI relationship(CL:0000222) MGI MGI:2137520 Twsg1 GO:0005615 MGI:MGI:3577114|PMID:15780974 IDA C twisted gastrulation homolog 1 (Drosophila) D17Ertd403e|Tsg gene taxon:10090 20050928 MGI relationship(CL:0000002) MGI MGI:2137520 Twsg1 GO:0009790 MGI:MGI:3037153|PMID:15013800 IMP MGI:2655736 P twisted gastrulation homolog 1 (Drosophila) D17Ertd403e|Tsg gene taxon:10090 20040506 MGI relationship(CL:0000223) MGI MGI:2137520 Twsg1 GO:0030154 MGI:MGI:3043486|PMID:14681194 IMP MGI:3044357 P twisted gastrulation homolog 1 (Drosophila) D17Ertd403e|Tsg gene taxon:10090 20040730 MGI relationship(CL:0000138) MGI MGI:2137520 Twsg1 GO:0030514 MGI:MGI:3577114|PMID:15780974 IDA P twisted gastrulation homolog 1 (Drosophila) D17Ertd403e|Tsg gene taxon:10090 20050928 MGI relationship(CL:0000002) MGI MGI:2137520 Twsg1 GO:0045668 MGI:MGI:3577114|PMID:15780974 IDA P twisted gastrulation homolog 1 (Drosophila) D17Ertd403e|Tsg gene taxon:10090 20050928 MGI relationship(CL:0000002) MGI MGI:1347023 Txnrd2 GO:0007507 MGI:MGI:3511375|PMID:15485910 IMP MGI:3512409 P thioredoxin reductase 2 ESTM573010|TGR|TR beta|TR3 gene taxon:10090 20050214 MGI relationship(CL:0000193) MGI MGI:1347023 Txnrd2 GO:0030097 MGI:MGI:3511375|PMID:15485910 IMP MGI:3512409 P thioredoxin reductase 2 ESTM573010|TGR|TR beta|TR3 gene taxon:10090 20050214 MGI relationship(CL:0000081) MGI MGI:1919815 Uaca GO:0005515 MGI:MGI:3041925|PMID:14961764 IPI UniProt:Q8K419,UniProt:P17931 F uveal autoantigen with coiled-coil domains and ankyrin repeats nucling gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1919815 Uaca GO:0005624 MGI:MGI:2670459|PMID:12761289 IDA C uveal autoantigen with coiled-coil domains and ankyrin repeats nucling gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1919815 Uaca GO:0005625 MGI:MGI:2670459|PMID:12761289 IDA C uveal autoantigen with coiled-coil domains and ankyrin repeats nucling gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1919815 Uaca GO:0005635 MGI:MGI:2670459|PMID:12761289 IDA C uveal autoantigen with coiled-coil domains and ankyrin repeats nucling gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1919815 Uaca GO:0005635 MGI:MGI:3041925|PMID:14961764 IDA C uveal autoantigen with coiled-coil domains and ankyrin repeats nucling gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1919815 Uaca GO:0005737 MGI:MGI:2670459|PMID:12761289 IDA C uveal autoantigen with coiled-coil domains and ankyrin repeats nucling gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1919815 Uaca GO:0005737 MGI:MGI:3041925|PMID:14961764 IDA C uveal autoantigen with coiled-coil domains and ankyrin repeats nucling gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1919815 Uaca GO:0042307 MGI:MGI:3056865|PMID:15271982 IMP MGI:3043446 P uveal autoantigen with coiled-coil domains and ankyrin repeats nucling gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1919815 Uaca GO:0042307 MGI:MGI:3056865|PMID:15271982 IMP MGI:3043446 P uveal autoantigen with coiled-coil domains and ankyrin repeats nucling gene taxon:10090 20060726 MGI relationship(CL:0000057) MGI MGI:1919815 Uaca GO:0043065 MGI:MGI:3056865|PMID:15271982 IDA P uveal autoantigen with coiled-coil domains and ankyrin repeats nucling gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1919815 Uaca GO:0043280 MGI:MGI:3056865|PMID:15271982 IDA P uveal autoantigen with coiled-coil domains and ankyrin repeats nucling gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:1919815 Uaca GO:0048471 MGI:MGI:3056865|PMID:15271982 IDA C uveal autoantigen with coiled-coil domains and ankyrin repeats nucling gene taxon:10090 20060726 MGI relationship(CL:0000002) MGI MGI:103149 Uchl1 GO:0006512 MGI:MGI:2671638|PMID:12913066 IMP MGI:1856882 P ubiquitin carboxy-terminal hydrolase L1 PGP 9.5|PGP9.5 gene taxon:10090 20050921 MGI relationship(CL:0000117) MGI MGI:103149 Uchl1 GO:0007409 MGI:MGI:50250|PMID:1630580 IMP MGI:1856882 P ubiquitin carboxy-terminal hydrolase L1 PGP 9.5|PGP9.5 gene taxon:10090 20050921 MGI relationship(CL:0000101) MGI MGI:103149 Uchl1 GO:0008283 MGI:MGI:2651980|PMID:12638230 IMP MGI:1856882 P ubiquitin carboxy-terminal hydrolase L1 PGP 9.5|PGP9.5 gene taxon:10090 20050921 MGI relationship(CL:0000020) MGI MGI:103149 Uchl1 GO:0008283 MGI:MGI:2651980|PMID:12638230 IMP MGI:1856882 P ubiquitin carboxy-terminal hydrolase L1 PGP 9.5|PGP9.5 gene taxon:10090 20050921 MGI relationship(CL:0000656) MGI MGI:103149 Uchl1 GO:0019896 MGI:MGI:78216|PMID:2558488 IMP MGI:1856882 P ubiquitin carboxy-terminal hydrolase L1 PGP 9.5|PGP9.5 gene taxon:10090 20050921 MGI relationship(CL:0000101) MGI MGI:103149 Uchl1 GO:0030424 MGI:MGI:2182674|PMID:12074562 IDA C ubiquitin carboxy-terminal hydrolase L1 PGP 9.5|PGP9.5 gene taxon:10090 20050921 MGI relationship(CL:0000540) MGI MGI:103149 Uchl1 GO:0030424 MGI:MGI:2447001|PMID:12107488 IDA C ubiquitin carboxy-terminal hydrolase L1 PGP 9.5|PGP9.5 gene taxon:10090 20050921 MGI relationship(CL:0000111) MGI MGI:103149 Uchl1 GO:0030424 MGI:MGI:2669017|PMID:12866128 IDA C ubiquitin carboxy-terminal hydrolase L1 PGP 9.5|PGP9.5 gene taxon:10090 20050922 MGI relationship(CL:0000540) MGI MGI:103149 Uchl1 GO:0030424 MGI:MGI:3035850|PMID:14973275 IDA C ubiquitin carboxy-terminal hydrolase L1 PGP 9.5|PGP9.5 gene taxon:10090 20050916 MGI relationship(CL:0000111) MGI MGI:103149 Uchl1 GO:0030424 MGI:MGI:83949|PMID:8896700 IDA C ubiquitin carboxy-terminal hydrolase L1 PGP 9.5|PGP9.5 gene taxon:10090 20050926 MGI relationship(CL:0000540) MGI MGI:103149 Uchl1 GO:0043025 MGI:MGI:2150278|PMID:11549719 IDA C ubiquitin carboxy-terminal hydrolase L1 PGP 9.5|PGP9.5 gene taxon:10090 20050922 MGI relationship(CL:0000540) MGI MGI:1099787 Ucp3 GO:0005739 MGI:MGI:2157174|PMID:11707458 IMP MGI:2183204 C uncoupling protein 3 (mitochondrial, proton carrier) Slc25a9|UCP-3 gene taxon:10090 20050726 MGI relationship(CL:0000188) MGI MGI:3051532 Unc13a GO:0016188 MGI:MGI:1341485|PMID:10440375 IMP MGI:2449468 P unc-13 homolog A (C. elegans) Munc13-1 gene taxon:10090 20050726 MGI relationship(CL:0000679) MGI MGI:2149021 Unc13c GO:0007268 MGI:MGI:1929572|PMID:11150314 IMP MGI:2449467 P unc-13 homolog C (C. elegans) D9Ertd414e|Munc13-3|Unc13h3 gene taxon:10090 20050726 MGI relationship(CL:0000121) MGI MGI:1859307 Unc93b1 GO:0005783 MGI:MGI:3615690|PMID:16415873 IDA C unc-93 homolog B1 (C. elegans) gene taxon:10090 20060413 MGI relationship(CL:0000002) MGI MGI:1919338 Ush1c GO:0005886 MGI:MGI:2451048|PMID:15461667 IDA C Usher syndrome 1C homolog (human) harmonin gene taxon:10090 20050503 MGI relationship(CL:0000066) MGI MGI:1313277 Vamp2 GO:0008021 MGI:MGI:3046625|PMID:15145078 IDA C vesicle-associated membrane protein 2 Syb2|synaptobrevin II gene taxon:10090 20040818 MGI relationship(CL:0000117) MGI MGI:2135272 Vangl2 GO:0016324 MGI:MGI:3624469|PMID:16687519 IDA C vang-like 2 (van gogh, Drosophila) Lpp1|Ltap|strabismus gene taxon:10090 20060629 MGI relationship(CL:0000601) MGI MGI:2135272 Vangl2 GO:0035058 MGI:MGI:3607949|PMID:16170314 IGI MGI:1277215,MGI:1891836 P vang-like 2 (van gogh, Drosophila) Lpp1|Ltap|strabismus gene taxon:10090 20060123 MGI relationship(CL:0000601) MGI MGI:2135272 Vangl2 GO:0045176 MGI:MGI:3616416|PMID:16495441 IMP MGI:1857642 P vang-like 2 (van gogh, Drosophila) Lpp1|Ltap|strabismus gene taxon:10090 20060329 MGI relationship(CL:0000202) MGI MGI:2135272 Vangl2 GO:0045176 MGI:MGI:3624469|PMID:16687519 IMP MGI:1857642 P vang-like 2 (van gogh, Drosophila) Lpp1|Ltap|strabismus gene taxon:10090 20060629 MGI relationship(CL:0000601) MGI MGI:109268 Vasp GO:0007411 MGI:MGI:3054149|PMID:15371503 IGI MGI:108360 P vasodilator-stimulated phosphoprotein gene taxon:10090 20041026 MGI relationship(CL:0000117) MGI MGI:109268 Vasp GO:0030036 MGI:MGI:3054149|PMID:15371503 IGI MGI:108360 P vasodilator-stimulated phosphoprotein gene taxon:10090 20041026 MGI relationship(CL:0000075) MGI MGI:1277163 Vax1 GO:0001764 MGI:MGI:3051699|PMID:15280216 IMP MGI:1859863 P ventral anterior homeobox containing gene 1 gene taxon:10090 20040930 MGI relationship(CL:0000117) MGI MGI:1277163 Vax1 GO:0001764 MGI:MGI:3531600|PMID:15590934 IMP MGI:1859863 P ventral anterior homeobox containing gene 1 gene taxon:10090 20050505 MGI relationship(CL:0000117) MGI MGI:1277163 Vax1 GO:0007399 MGI:MGI:3051699|PMID:15280216 IMP MGI:1859863 P ventral anterior homeobox containing gene 1 gene taxon:10090 20040930 MGI relationship(CL:0000617) MGI MGI:1277163 Vax1 GO:0007406 MGI:MGI:3531600|PMID:15590934 IMP MGI:1859863 P ventral anterior homeobox containing gene 1 gene taxon:10090 20050505 MGI relationship(CL:0000031) MGI MGI:1277163 Vax1 GO:0030154 MGI:MGI:3531600|PMID:15590934 IMP MGI:1859863 P ventral anterior homeobox containing gene 1 gene taxon:10090 20050505 MGI relationship(CL:0000065) MGI MGI:1277163 Vax1 GO:0030154 MGI:MGI:3531600|PMID:15590934 IMP MGI:1859863 P ventral anterior homeobox containing gene 1 gene taxon:10090 20050505 MGI relationship(CL:0000127) MGI MGI:1277163 Vax1 GO:0043010 MGI:MGI:3578573|PMID:15905411 IGI MGI:1346018 P ventral anterior homeobox containing gene 1 gene taxon:10090 20050622 MGI relationship(CL:0000710) MGI MGI:1346018 Vax2 GO:0043010 MGI:MGI:3578573|PMID:15905411 IGI MGI:1277163 P ventral anterior homeobox containing gene 2 gene taxon:10090 20050622 MGI relationship(CL:0000710) MGI MGI:98927 Vcl GO:0005886 MGI:MGI:3656458|PMID:16481394 IDA C vinculin gene taxon:10090 20070312 MGI relationship(CL:0000746) MGI MGI:98927 Vcl GO:0005916 MGI:MGI:3656458|PMID:16481394 IDA C vinculin gene taxon:10090 20070312 MGI relationship(CL:0000746) MGI MGI:103178 Vegfa GO:0001525 MGI:MGI:3629544|PMID:16778080 IGI MGI:1202890 P vascular endothelial growth factor A Vegf|VEGF-A|VEGF120|VPF gene taxon:10090 20060807 MGI relationship(CL:0000001) MGI MGI:103178 Vegfa GO:0006916 MGI:MGI:3039988|PMID:15073147 IMP MGI:1931048 P vascular endothelial growth factor A Vegf|VEGF-A|VEGF120|VPF gene taxon:10090 20040811 MGI relationship(CL:0000138) MGI MGI:103178 Vegfa GO:0016477 MGI:MGI:3525930|PMID:15601856 IDA P vascular endothelial growth factor A Vegf|VEGF-A|VEGF120|VPF gene taxon:10090 20050303 MGI relationship(CL:0000007) MGI MGI:103178 Vegfa GO:0016477 MGI:MGI:3525930|PMID:15601856 IGI MGI:96683,MGI:95558 P vascular endothelial growth factor A Vegf|VEGF-A|VEGF120|VPF gene taxon:10090 20050303 MGI relationship(CL:0000007) MGI MGI:103178 Vegfa GO:0030324 MGI:MGI:3583398|PMID:15927453 IMP P vascular endothelial growth factor A Vegf|VEGF-A|VEGF120|VPF gene taxon:10090 20050826 MGI relationship(CL:0000082) MGI MGI:103178 Vegfa GO:0030855 MGI:MGI:3607459|PMID:16251428 IMP MGI:1931048|MGI:2387296 P vascular endothelial growth factor A Vegf|VEGF-A|VEGF120|VPF gene taxon:10090 20060727 MGI relationship(CL:0000066) MGI MGI:103178 Vegfa GO:0042462 MGI:MGI:3607459|PMID:16251428 IMP MGI:1931048|MGI:2387296 P vascular endothelial growth factor A Vegf|VEGF-A|VEGF120|VPF gene taxon:10090 20060214 MGI relationship(CL:0000210) MGI MGI:103178 Vegfa GO:0050679 MGI:MGI:3583398|PMID:15927453 IMP P vascular endothelial growth factor A Vegf|VEGF-A|VEGF120|VPF gene taxon:10090 20050826 MGI relationship(CL:0000082) MGI MGI:109124 Vegfc GO:0008284 MGI:MGI:3620294|PMID:16462734 IMP MGI:3026650 P vascular endothelial growth factor C VEGF-C gene taxon:10090 20060512 MGI relationship(CL:0000339) MGI MGI:1313291 Vezf1 GO:0001885 MGI:MGI:3581991|PMID:15882861 IMP MGI:3583268 P vascular endothelial zinc finger 1 db1 gene taxon:10090 20050822 MGI relationship(CL:0000071) MGI MGI:1313291 Vezf1 GO:0005634 MGI:MGI:3581991|PMID:15882861 IDA C vascular endothelial zinc finger 1 db1 gene taxon:10090 20050822 MGI relationship(CL:0000002) MGI MGI:103223 Vhlh GO:0001525 MGI:MGI:3619780|PMID:16537898 IMP MGI:2136645|MGI:2450311 P von Hippel-Lindau syndrome homolog VHL gene taxon:10090 20060607 MGI relationship(CL:0000071) MGI MGI:103223 Vhlh GO:0030198 MGI:MGI:3619780|PMID:16537898 IMP MGI:2136645|MGI:2450311 P von Hippel-Lindau syndrome homolog VHL gene taxon:10090 20060607 MGI relationship(CL:0000071) MGI MGI:103223 Vhlh GO:0043534 MGI:MGI:3619780|PMID:16537898 IMP MGI:2136645|MGI:2450311 P von Hippel-Lindau syndrome homolog VHL gene taxon:10090 20060607 MGI relationship(CL:0000071) MGI MGI:98931 Vil2 GO:0035088 MGI:MGI:3051954|PMID:15177033 IMP MGI:3052158 P villin 2 cytovillin|ezrin|p81 gene taxon:10090 20050726 MGI relationship(CL:0000131) MGI MGI:98935 Vldlr GO:0045860 MGI:MGI:3629864|PMID:12526740 IGI MGI:103022,MGI:1340044 P very low density lipoprotein receptor gene taxon:10090 20060807 MGI relationship(CL:0000001) MGI MGI:1917410 Vps36 GO:0005764 MGI:MGI:3582124|PMID:15755741 IDA C vacuolar protein sorting 36 (yeast) Eap45 gene taxon:10090 20050817 MGI relationship(CL:0000002) MGI MGI:1917410 Vps36 GO:0005770 MGI:MGI:3582124|PMID:15755741 IDA C vacuolar protein sorting 36 (yeast) Eap45 gene taxon:10090 20050817 MGI relationship(CL:0000002) MGI MGI:2178798 Vps54 GO:0060052 MGI:MGI:2149279|PMID:11493023 IMP MGI:1857091 P vacuolar protein sorting 54 (yeast) mSLP8|Vps54l|wr gene taxon:10090 20070305 MGI relationship(CL:0000100) MGI MGI:1096875 Wdfy3 GO:0005737 MGI:MGI:3522125|PMID:15342963 IDA C WD repeat and FYVE domain containing 3 Bwf1|D5Ertd66e|Ggtb3|ZFYVE25 gene taxon:10090 20060719 MGI relationship(CL:0000002) MGI MGI:2682003 Whrn GO:0005929 MGI:MGI:2682448|PMID:12833159 IDA C whirlin wi gene taxon:10090 20050726 MGI relationship(CL:0000202) MGI MGI:98953 Wnt1 GO:0016055 MGI:MGI:3619629|PMID:16207730 IDA P wingless-related MMTV integration site 1 Int-1|Wnt-1 gene taxon:10090 20060607 MGI relationship(CL:0000002) MGI MGI:98953 Wnt1 GO:0048663 MGI:MGI:3611719|PMID:16339193 IMP MGI:2153126 P wingless-related MMTV integration site 1 Int-1|Wnt-1 gene taxon:10090 20060227 MGI relationship(CL:0000700) MGI MGI:98956 Wnt3a GO:0007409 MGI:MGI:3510085|PMID:15454084 IDA P wingless-related MMTV integration site 3A Wnt-3a gene taxon:10090 20050204 MGI relationship(CL:0000001) MGI MGI:98956 Wnt3a GO:0007409 MGI:MGI:3510085|PMID:15454084 IGI MGI:101766 P wingless-related MMTV integration site 3A Wnt-3a gene taxon:10090 20050204 MGI relationship(CL:0000001) MGI MGI:98957 Wnt4 GO:0001838 MGI:MGI:3624584|PMID:16546160 IDA P wingless-related MMTV integration site 4 Wnt-4 gene taxon:10090 20060717 MGI relationship(CL:0000001) MGI MGI:98957 Wnt4 GO:0007276 MGI:MGI:3042808|PMID:15162500 IGI MGI:95586 P wingless-related MMTV integration site 4 Wnt-4 gene taxon:10090 20040715 MGI relationship(CL:0000021) MGI MGI:98957 Wnt4 GO:0030154 MGI:MGI:3618017|PMID:15581876 IMP MGI:1857453 P wingless-related MMTV integration site 4 Wnt-4 gene taxon:10090 20060606 MGI relationship(CL:0000216) MGI MGI:98957 Wnt4 GO:0045596 MGI:MGI:3618017|PMID:15581876 IMP MGI:1857453 P wingless-related MMTV integration site 4 Wnt-4 gene taxon:10090 20060606 MGI relationship(CL:0000174) MGI MGI:98957 Wnt4 GO:0048599 MGI:MGI:1329753|PMID:9989404 IMP MGI:1857453 P wingless-related MMTV integration site 4 Wnt-4 gene taxon:10090 20050726 MGI relationship(CL:0000023) MGI MGI:98957 Wnt4 GO:0051145 MGI:MGI:3624584|PMID:16546160 IDA P wingless-related MMTV integration site 4 Wnt-4 gene taxon:10090 20060717 MGI relationship(CL:0000001) MGI MGI:98957 Wnt4 GO:0051145 MGI:MGI:3624584|PMID:16546160 IMP MGI:1857453 P wingless-related MMTV integration site 4 Wnt-4 gene taxon:10090 20060717 MGI relationship(CL:0000192) MGI MGI:98961 Wnt7a GO:0007269 MGI:MGI:3653273|PMID:16818724 IGI MGI:94941 P wingless-related MMTV integration site 7A tw|Wnt-7a gene taxon:10090 20070228 MGI relationship(CL:0000117) MGI MGI:98961 Wnt7a GO:0021707 MGI:MGI:1195230|PMID:9405095 IDA P wingless-related MMTV integration site 7A tw|Wnt-7a gene taxon:10090 20061110 MGI relationship(CL:0000001) MGI MGI:98961 Wnt7a GO:0031133 MGI:MGI:1195230|PMID:9405095 IDA P wingless-related MMTV integration site 7A tw|Wnt-7a gene taxon:10090 20061110 MGI relationship(CL:0000001) MGI MGI:98961 Wnt7a GO:0050770 MGI:MGI:1195230|PMID:9405095 IDA P wingless-related MMTV integration site 7A tw|Wnt-7a gene taxon:10090 20061110 MGI relationship(CL:0000001) MGI MGI:98961 Wnt7a GO:0050808 MGI:MGI:3653273|PMID:16818724 IGI MGI:94941 P wingless-related MMTV integration site 7A tw|Wnt-7a gene taxon:10090 20070228 MGI relationship(CL:0000117) MGI MGI:98961 Wnt7a GO:0050808 MGI:MGI:3653273|PMID:16818724 IMP MGI:1857704 P wingless-related MMTV integration site 7A tw|Wnt-7a gene taxon:10090 20070228 MGI relationship(CL:0000117) MGI MGI:98961 Wnt7a GO:0051965 MGI:MGI:1195230|PMID:9405095 IDA P wingless-related MMTV integration site 7A tw|Wnt-7a gene taxon:10090 20061110 MGI relationship(CL:0000001) MGI MGI:98962 Wnt7b GO:0016055 MGI:MGI:3581375|PMID:15923619 IGI MGI:1278315,MGI:1196625,MGI:2136761 P wingless-related MMTV integration site 7B Wnt-7b gene taxon:10090 20050816 MGI relationship(CL:0000002) MGI MGI:98962 Wnt7b GO:0050808 MGI:MGI:3653273|PMID:16818724 IGI MGI:98961 P wingless-related MMTV integration site 7B Wnt-7b gene taxon:10090 20070228 MGI relationship(CL:0000117) MGI MGI:98968 Wt1 GO:0007281 MGI:MGI:3051942|PMID:15063178 IMP MGI:1857268 P Wilms tumor homolog Wt-1 gene taxon:10090 20040929 MGI relationship(CL:0000015) MGI MGI:98968 Wt1 GO:0030855 MGI:MGI:87728|PMID:9118800 IMP MGI:1857268 P Wilms tumor homolog Wt-1 gene taxon:10090 20041007 MGI relationship(CL:0000066) MGI MGI:1917649 Wwtr1 GO:0000122 MGI:MGI:3587162|PMID:16099986 IGI MGI:97747 P WW domain containing transcription regulator 1 TAZ|transcriptional coactivator with PDZ binding motif gene taxon:10090 20060201 MGI relationship(CL:0000002) MGI MGI:1917649 Wwtr1 GO:0003713 MGI:MGI:3587162|PMID:16099986 IGI MGI:99829 F WW domain containing transcription regulator 1 TAZ|transcriptional coactivator with PDZ binding motif gene taxon:10090 20060201 MGI relationship(CL:0000002) MGI MGI:1917649 Wwtr1 GO:0003713 MGI:MGI:3587162|PMID:16099986 IMP F WW domain containing transcription regulator 1 TAZ|transcriptional coactivator with PDZ binding motif gene taxon:10090 20060201 MGI relationship(CL:0000002) MGI MGI:1917649 Wwtr1 GO:0003713 MGI:MGI:3610892|PMID:16300735 IGI MGI:97487 F WW domain containing transcription regulator 1 TAZ|transcriptional coactivator with PDZ binding motif gene taxon:10090 20060201 MGI relationship(CL:0000002) MGI MGI:1917649 Wwtr1 GO:0003714 MGI:MGI:3587162|PMID:16099986 IGI MGI:97747 F WW domain containing transcription regulator 1 TAZ|transcriptional coactivator with PDZ binding motif gene taxon:10090 20060201 MGI relationship(CL:0000002) MGI MGI:1917649 Wwtr1 GO:0005634 MGI:MGI:3610892|PMID:16300735 IDA C WW domain containing transcription regulator 1 TAZ|transcriptional coactivator with PDZ binding motif gene taxon:10090 20060201 MGI relationship(CL:0000002) MGI MGI:1917649 Wwtr1 GO:0005737 MGI:MGI:3587162|PMID:16099986 IDA C WW domain containing transcription regulator 1 TAZ|transcriptional coactivator with PDZ binding motif gene taxon:10090 20060201 MGI relationship(CL:0000002) MGI MGI:1917649 Wwtr1 GO:0045599 MGI:MGI:3587162|PMID:16099986 IGI MGI:97747 P WW domain containing transcription regulator 1 TAZ|transcriptional coactivator with PDZ binding motif gene taxon:10090 20060201 MGI relationship(CL:0000002) MGI MGI:1917649 Wwtr1 GO:0045944 MGI:MGI:3587162|PMID:16099986 IGI MGI:99829 P WW domain containing transcription regulator 1 TAZ|transcriptional coactivator with PDZ binding motif gene taxon:10090 20060201 MGI relationship(CL:0000002) MGI MGI:1917649 Wwtr1 GO:0045944 MGI:MGI:3610892|PMID:16300735 IGI MGI:97487 P WW domain containing transcription regulator 1 TAZ|transcriptional coactivator with PDZ binding motif gene taxon:10090 20060201 MGI relationship(CL:0000002) MGI MGI:2144013 Xpo1 GO:0006611 MGI:MGI:2177366|PMID:11796723 IDA P exportin 1, CRM1 homolog (yeast) Crm1 gene taxon:10090 20050824 MGI relationship(CL:0000002) MGI MGI:103262 Yap1 GO:0005667 MGI:MGI:3608264|PMID:16207754 IGI MGI:101876,MGI:104904,MGI:106907,MGI:109241 C yes-associated protein 1 gene taxon:10090 20060317 MGI relationship(CL:0000002) MGI MGI:103262 Yap1 GO:0016563 MGI:MGI:3608264|PMID:16207754 IGI MGI:101876,MGI:104904,MGI:106907,MGI:109241 F yes-associated protein 1 gene taxon:10090 20060317 MGI relationship(CL:0000002) MGI MGI:103262 Yap1 GO:0045944 MGI:MGI:3608264|PMID:16207754 IGI MGI:101876,MGI:104904,MGI:106907,MGI:109241 P yes-associated protein 1 gene taxon:10090 20060317 MGI relationship(CL:0000002) MGI MGI:1096372 Ybx2 GO:0007286 MGI:MGI:3576442|PMID:15824319 IMP MGI:3576937 P Y box protein 2 MSY2 gene taxon:10090 20060821 MGI relationship(CL:0000018) MGI MGI:1096372 Ybx2 GO:0048157 MGI:MGI:3576442|PMID:15824319 IMP MGI:3576937 P Y box protein 2 MSY2 gene taxon:10090 20060821 MGI relationship(CL:0000023) MGI MGI:1914430 Yipf5 GO:0042175 MGI:MGI:3522558|PMID:15254263 IDA C Yip1 domain family, member 5 Yip1a gene taxon:10090 20050819 MGI relationship(CL:0000002) MGI MGI:109484 Ywhaz GO:0005634 MGI:MGI:3522382|PMID:15615787 IDA C tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide gene taxon:10090 20050512 MGI relationship(CL:0000002) MGI MGI:99613 Zap70 GO:0007242 MGI:MGI:75253|PMID:7630421 IMP MGI:2677447 P zeta-chain (TCR) associated protein kinase Srk|TZK|ZAP-70 gene taxon:10090 20050117 MGI relationship(CL:0000084) MGI MGI:99613 Zap70 GO:0042101 MGI:MGI:66058|PMID:8176201 ISS UniProt:P43403 C zeta-chain (TCR) associated protein kinase Srk|TZK|ZAP-70 gene taxon:10090 20060112 MGI relationship(CL:0000002) MGI MGI:99613 Zap70 GO:0045059 MGI:MGI:75253|PMID:7630421 IMP MGI:2677447 P zeta-chain (TCR) associated protein kinase Srk|TZK|ZAP-70 gene taxon:10090 20050117 MGI relationship(CL:0000084) MGI MGI:99613 Zap70 GO:0045060 MGI:MGI:75253|PMID:7630421 IMP MGI:2677447 P zeta-chain (TCR) associated protein kinase Srk|TZK|ZAP-70 gene taxon:10090 20050117 MGI relationship(CL:0000084) MGI MGI:99613 Zap70 GO:0046638 MGI:MGI:75253|PMID:7630421 IMP MGI:2677447 P zeta-chain (TCR) associated protein kinase Srk|TZK|ZAP-70 gene taxon:10090 20050117 MGI relationship(CL:0000084) MGI MGI:99613 Zap70 GO:0050850 MGI:MGI:75253|PMID:7630421 IMP MGI:2677447 P zeta-chain (TCR) associated protein kinase Srk|TZK|ZAP-70 gene taxon:10090 20050117 MGI relationship(CL:0000084) MGI MGI:103222 Zbtb16 GO:0005634 MGI:MGI:3628699|PMID:16564520 IDA C zinc finger and BTB domain containing 16 Green's luxoid|PLZF|Zfp145 gene taxon:10090 20060807 MGI relationship(CL:0000020) MGI MGI:1915336 Zdhhc15 GO:0016188 MGI:MGI:3521633|PMID:15603741 IGI MGI:1277959 P zinc finger, DHHC domain containing 15 gene taxon:10090 20050315 MGI relationship(CL:0000117) MGI MGI:1915336 Zdhhc15 GO:0016188 MGI:MGI:3521633|PMID:15603741 IMP P zinc finger, DHHC domain containing 15 gene taxon:10090 20050315 MGI relationship(CL:0000117) MGI MGI:1332234 Zfp148 GO:0007276 MGI:MGI:2449362|PMID:12524542 IMP MGI:3040891 P zinc finger protein 148 BERF-1|beta enolase repressor factor 1|BFCOL1|ZBP-89 gene taxon:10090 20050726 MGI relationship(CL:0000586) MGI MGI:1927246 Zfp326 GO:0005626 MGI:MGI:1355426|PMID:10798446 IDA C zinc finger protein 326 ZAN75 gene taxon:10090 20050818 MGI relationship(CL:0000002) MGI MGI:1927246 Zfp326 GO:0005634 MGI:MGI:1309638|PMID:9809746 IDA C zinc finger protein 326 ZAN75 gene taxon:10090 20050815 MGI relationship(CL:0000002) MGI MGI:1927246 Zfp326 GO:0005634 MGI:MGI:1355426|PMID:10798446 IDA C zinc finger protein 326 ZAN75 gene taxon:10090 20050818 MGI relationship(CL:0000002) MGI MGI:1927246 Zfp326 GO:0016363 MGI:MGI:1309638|PMID:9809746 IDA C zinc finger protein 326 ZAN75 gene taxon:10090 20050815 MGI relationship(CL:0000002) MGI MGI:1927246 Zfp326 GO:0016563 MGI:MGI:1355426|PMID:10798446 IDA F zinc finger protein 326 ZAN75 gene taxon:10090 20050818 MGI relationship(CL:0000002) MGI MGI:1927246 Zfp326 GO:0045941 MGI:MGI:1355426|PMID:10798446 IDA P zinc finger protein 326 ZAN75 gene taxon:10090 20070124 MGI relationship(CL:0000002) MGI MGI:99180 Zfp36 GO:0003729 MGI:MGI:1859531|PMID:10751406 IDA F zinc finger protein 36 Nup475|Tis11|Tristetraprolin|Zfp-36 gene taxon:10090 20050818 MGI relationship(CL:0000002) MGI MGI:99180 Zfp36 GO:0005634 MGI:MGI:2177366|PMID:11796723 IDA C zinc finger protein 36 Nup475|Tis11|Tristetraprolin|Zfp-36 gene taxon:10090 20050824 MGI relationship(CL:0000002) MGI MGI:99180 Zfp36 GO:0005737 MGI:MGI:2177366|PMID:11796723 IDA C zinc finger protein 36 Nup475|Tis11|Tristetraprolin|Zfp-36 gene taxon:10090 20050824 MGI relationship(CL:0000002) MGI MGI:99180 Zfp36 GO:0005829 MGI:MGI:1859531|PMID:10751406 IDA C zinc finger protein 36 Nup475|Tis11|Tristetraprolin|Zfp-36 gene taxon:10090 20050818 MGI relationship(CL:0000002) MGI MGI:99180 Zfp36 GO:0005829 MGI:MGI:1859531|PMID:10751406 ISS UniProt:P26651 C zinc finger protein 36 Nup475|Tis11|Tristetraprolin|Zfp-36 gene taxon:10090 20060112 MGI relationship(CL:0000002) MGI MGI:99180 Zfp36 GO:0006402 MGI:MGI:1859531|PMID:10751406 ISS UniProt:P26651 P zinc finger protein 36 Nup475|Tis11|Tristetraprolin|Zfp-36 gene taxon:10090 20060112 MGI relationship(CL:0000002) MGI MGI:99180 Zfp36 GO:0007243 MGI:MGI:73465|PMID:7768935 IDA P zinc finger protein 36 Nup475|Tis11|Tristetraprolin|Zfp-36 gene taxon:10090 20050810 MGI relationship(CL:0000002) MGI MGI:99180 Zfp36 GO:0045638 MGI:MGI:2152007|PMID:11588035 IMP MGI:2652418 P zinc finger protein 36 Nup475|Tis11|Tristetraprolin|Zfp-36 gene taxon:10090 20050823 MGI relationship(CL:0000037) MGI MGI:107946 Zfp36l1 GO:0003729 MGI:MGI:1859531|PMID:10751406 ISS UniProt:P17431 F zinc finger protein 36, C3H type-like 1 Berg36|Brf1|cMG1|ERF1|TIS11b gene taxon:10090 20060112 MGI relationship(CL:0000002) MGI MGI:107946 Zfp36l1 GO:0005634 MGI:MGI:2177366|PMID:11796723 IDA C zinc finger protein 36, C3H type-like 1 Berg36|Brf1|cMG1|ERF1|TIS11b gene taxon:10090 20050824 MGI relationship(CL:0000002) MGI MGI:107946 Zfp36l1 GO:0005737 MGI:MGI:2177366|PMID:11796723 IDA C zinc finger protein 36, C3H type-like 1 Berg36|Brf1|cMG1|ERF1|TIS11b gene taxon:10090 20050824 MGI relationship(CL:0000002) MGI MGI:107946 Zfp36l1 GO:0005829 MGI:MGI:1859531|PMID:10751406 ISS UniProt:P17431 C zinc finger protein 36, C3H type-like 1 Berg36|Brf1|cMG1|ERF1|TIS11b gene taxon:10090 20060112 MGI relationship(CL:0000002) MGI MGI:107946 Zfp36l1 GO:0006402 MGI:MGI:1859531|PMID:10751406 ISS UniProt:P17431 P zinc finger protein 36, C3H type-like 1 Berg36|Brf1|cMG1|ERF1|TIS11b gene taxon:10090 20060112 MGI relationship(CL:0000002) MGI MGI:107945 Zfp36l2 GO:0005634 MGI:MGI:2177366|PMID:11796723 IDA C zinc finger protein 36, C3H type-like 2 Brf2|ERF2|Tis11d gene taxon:10090 20050824 MGI relationship(CL:0000002) MGI MGI:107945 Zfp36l2 GO:0005737 MGI:MGI:2177366|PMID:11796723 IDA C zinc finger protein 36, C3H type-like 2 Brf2|ERF2|Tis11d gene taxon:10090 20050824 MGI relationship(CL:0000002) MGI MGI:1095400 Zfpm1 GO:0007507 MGI:MGI:3583527|PMID:14614148 IMP MGI:3583784|MGI:2450311 P zinc finger protein, multitype 1 Fog1|Friend of GATA-1 gene taxon:10090 20051017 MGI relationship(CL:0000115) MGI MGI:106679 Zic2 GO:0005634 MGI:MGI:3056015|PMID:15465018 IDA C Zic finger protein of the cerebellum 2 GENA 29|Ku|odd-paired homolog gene taxon:10090 20050509 MGI relationship(CL:0000002) MGI MGI:106679 Zic2 GO:0030154 MGI:MGI:3056222|PMID:15384171 IMP MGI:1862004 P Zic finger protein of the cerebellum 2 GENA 29|Ku|odd-paired homolog gene taxon:10090 20050322 MGI relationship(CL:0000333) MGI MGI:107201 Zic4 GO:0005634 MGI:MGI:3056015|PMID:15465018 IDA C zinc finger protein of the cerebellum 4 gene taxon:10090 20050509 MGI relationship(CL:0000002) MGI MGI:1929518 Zic5 GO:0005634 MGI:MGI:3056015|PMID:15465018 IDA C zinc finger protein of the cerebellum 5 odd-paired related|Opr gene taxon:10090 20050509 MGI relationship(CL:0000002) MGI MGI:1929518 Zic5 GO:0030154 MGI:MGI:3051968|PMID:15136147 IMP MGI:3052154 P zinc finger protein of the cerebellum 5 odd-paired related|Opr gene taxon:10090 20040929 MGI relationship(CL:0000008) MGI MGI:99215 Zp3 GO:0007339 MGI:MGI:1098917|PMID:9374408 IPI UniProt:P15535 P zona pellucida glycoprotein 3 Zp-3 gene taxon:10090 20070215 MGI relationship(CL:0000025) go-perl-0.15/t/data/generic.0208000644 000765 000024 00000013723 11615622157 016037 0ustar00cjmstaff000000 000000 !version: $Revision: 1.1 $ !date: $Date: 2004/06/09 00:21:15 $ !GO_slim_name: generic go_slim !GO_slim_version: 1.0 !GO_slim_date: 20020826 !GO_slim_authors: Suparna Mundodi and Amelia Ireland !GO_slim_contact: smundodi@acoma.stanford.edu !type: % is_a is a !type: < part_of Part of $Gene_Ontology ; GO:0003673 default-namespace: test [Term] id: A name: A is_a: B ! B relationship: part_of C {implied=true} ! C relationship: part_of D {implied=true} ! D relationship: part_of E {implied=true} ! E [Term] id: B name: B relationship: part_of C ! C relationship: part_of D {implied=true} ! D relationship: part_of E {implied=true} ! E [Term] id: C name: C is_a: D ! D is_a: E {implied=true} ! E [Term] id: D name: D is_a: E ! E [Term] id: E name: E [Typedef] id: part_of name: part_of go-perl-0.15/t/data/llm.obo000644 000765 000024 00000005775 11615622157 015405 0ustar00cjmstaff000000 000000 format-version: 1.2 date: 23:09:2005 14:37 saved-by: cjm auto-generated-by: Obol default-namespace: gene_ontology remark: cdefs for GO id-mapping: has_participant OBO_REL:has_participant id-mapping: located_in OBO_REL:located_in id-mapping: develops_from OBO_REL:derives_from id-mapping: sensu OBOL:sensu id-mapping: has_quality OBOL:has_quality id-mapping: during OBOL:during id-mapping: directly_involves_anatomical OBOL:directly_involves_anatomical [Term] id: GO:0008150 name: biological_process namespace: biological_process def: "A phenomenon marked by changes that lead to a particular result, mediated by one or more gene products." [] [Term] id: GO:0050896 name: response to stimulus namespace: biological_process def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0007610 name: behavior namespace: biological_process def: "The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions." [] synonym: "behavioral response to stimulus" [] exact synonym: "behaviour" [] exact synonym: "behavioural response to stimulus" [] exact is_a: GO:0050896 ! response to stimulus [Term] id: GO:0007626 name: locomotory behavior namespace: biological_process def: "The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions." [] synonym: "locomotion in response to stimulus" [] exact synonym: "locomotory behavioral response to stimulus" [] exact synonym: "locomotory behaviour" [] exact synonym: "locomotory behavioural response to stimulus" [] exact is_a: GO:0007610 ! behavior [Term] id: GO:0008345 name: larval locomotory behavior namespace: biological_process is_a: GO:0007626 ! locomotory behavior is_a: GO:0030537 ! larval behavior intersection_of: GO:0007626 {namespace=foo} intersection_of: during FBdv:00005336 {namespace=foo} [Term] id: GO:0030537 name: larval behavior namespace: biological_process def: "Behavior in a larval form of an organism, an immature organism that must undergo metamorphosis to assume adult characteristics." [] synonym: "larval behaviour" [] exact synonym: "larval behavior (sensu Drosophila)" [] narrow synonym: "larval behavior (sensu Insecta)" [] narrow is_a: GO:0007610 ! behavior comment: See also the biological process term 'behavior ; GO:0007610'. intersection_of: GO:0007610 {namespace=foo} intersection_of: during FBdv:00005336 {namespace=foo} [Typedef] id: OBO_REL:part_of name: part_of namespace: relationship [Typedef] id: bzz name: bzz [Typedef] id: foo name: foo namespace: gene_ontology [Typedef] id: X:Y name: XY [Typedef] id: Y:Z name: YZ namespace: yz go-perl-0.15/t/data/llm2.obo000644 000765 000024 00000006005 11615622157 015452 0ustar00cjmstaff000000 000000 format-version: 1.2 date: 23:09:2005 14:37 saved-by: cjm auto-generated-by: Obol default-namespace: gene_ontology remark: cdefs for GO id-mapping: has_participant OBO_REL:has_participant id-mapping: located_in OBO_REL:located_in id-mapping: develops_from OBO_REL:derives_from id-mapping: sensu OBOL:sensu id-mapping: has_quality OBOL:has_quality id-mapping: during OBOL:during id-mapping: directly_involves_anatomical OBOL:directly_involves_anatomical [Term] id: GO:0008150 name: biological_process namespace: biological_process def: "A phenomenon marked by changes that lead to a particular result, mediated by one or more gene products." [] [Term] id: GO:0050896 name: response to stimulus namespace: biological_process def: "A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0007610 name: behavior namespace: biological_process def: "The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions." [] synonym: "behavioral response to stimulus" [] exact synonym: "behaviour" [] exact synonym: "behavioural response to stimulus" [] exact is_a: GO:0050896 ! response to stimulus [Term] id: GO:0007626 name: locomotory behavior namespace: biological_process def: "The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions." [] synonym: "locomotion in response to stimulus" [] exact synonym: "locomotory behavioral response to stimulus" [] exact synonym: "locomotory behaviour" [] exact synonym: "locomotory behavioural response to stimulus" [] exact is_a: GO:0007610 ! behavior [Term] id: GO:0008345 name: larval locomotory behavior namespace: biological_process is_a: GO:0007626 ! locomotory behavior is_a: GO:0030537 ! larval behavior intersection_of: GO:0007626 {namespace=foo} intersection_of: during FBdv:00005336 {namespace=foo} [Term] id: GO:0030537 name: larval behavior namespace: biological_process def: "Behavior in a larval form of an organism, an immature organism that must undergo metamorphosis to assume adult characteristics." [] synonym: "larval behaviour" [] exact synonym: "larval behavior (sensu Drosophila)" [] narrow synonym: "larval behavior (sensu Insecta)" [] narrow is_a: GO:0007610 ! behavior comment: See also the biological process term 'behavior ; GO:0007610'. intersection_of: GO:0007610 {namespace=foo} intersection_of: during FBdv:00005336 {namespace=foo} [Typedef] id: part_of name: part_of xref: OBO_REL:part_of [Typedef] id: bzz name: bzz [Typedef] id: foo name: foo namespace: gene_ontology xref: OBO_REL:foo [Typedef] id: X:Y name: XY [Typedef] id: Y:Z name: YZ namespace: yz go-perl-0.15/t/data/mged.obo000644 000765 000024 00001321423 11615622157 015525 0ustar00cjmstaff000000 000000 format-version: 1.2 idspace: rdf http://www.w3.org/1999/02/22-rdf-syntax-ns# "" idspace: rdfs http://www.w3.org/2000/01/rdf-schema# "" idspace: owl http://www.w3.org/2002/07/owl# "" idspace: xsd http://www.w3.org/2001/XMLSchema# "" idspace: dc http://purl.org/dc/elements/1.1/ "" idspace: eor http://dublincore.org/2000/03/13/eor# "" idspace: serql http://www.openrdf.org/schema/serql# "" idspace: obd http://www.bioontology.org/obd/obd-ontology# "" idspace: oboInOwl http://www.bioontology.org/oboInOwl# "" idspace: ncithesaurus http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# "" idspace: biopax1 http://www.biopax.org/release/biopax-level1.owl# "" idspace: mged http://mged.sourceforge.net/ontologies/MGEDOntology.owl# "" idspace: bfo http://www.ifomis.org/bfo/1.0# "" idspace: snap http://www.ifomis.org/bfo/1.0/snap# "" idspace: span http://www.ifomis.org/bfo/1.0/span# "" idspace: oban http://www.berkeleybop.org/ontologies/oban/alpha# "" idspace: obi http://obi.sourceforge.net/ontology/OBI.owl# "" idspace: galen http://www.co-ode.org/ontologies/galen# "" idspace: propreo http://lsdis.cs.uga.edu/projects/glycomics/propreo# "" idspace: swrl http://www.w3.org/2003/11/swrl# "" idspace: p2 http://www.owl-ontologies.com/assert.owl# "" idspace: daml http://www.daml.org/2001/03/daml+oil# "" idspace: protege http://protege.stanford.edu/plugins/owl/protege# "" [Term] id: mged:Action comment: Procedures used during treatment. is_a: mged:BiologicalFactorCategory is_a: mged:BioMaterialPackage property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_193" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:Age comment: The time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting (e.g. 3 days post planting). is_a: mged:BioMaterialCharacteristics relationship: mged:has_initial_time_point mged:InitialTimePoint relationship: mged:has_measurement mged:Measurement relationship: mged:has_maximum_measurement mged:Measurement property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_178" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:Allele comment: One of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on phenotype or sequence. Polymorphisms are included in this definition. is_a: mged:IndividualGeneticCharacteristics property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_58" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:ArrayDesignPackage comment: MAGE package that describes the array layout and design. The array may be physical or virtual. is_a: mged:MGEDCoreOntology property_value: mged:unique_identifier "MO_33" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:ArrayGroup comment: An array group is a physical platform that contains one or more arrays that are separately addressable or a virtual grouping of arrays. is_a: mged:ArrayPackage relationship: mged:has_fiducials mged:Fiducial relationship: mged:has_type mged:SubstrateType property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_34" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:ArrayPackage comment: MAGE package for describing the process by which arrays were manufactured. is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_107" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:Atmosphere comment: The atmospheric conditions used to culture or grow an organism. is_a: mged:GrowthCondition relationship: mged:has_atmospheric_component mged:Compound property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_219" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:AtomicAction comment: An atomic action is a single step process on the biomaterial, e.g. mix by inversion, wait, add is_a: mged:Action property_value: mged:unique_identifier "MO_68" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:AuditAndSecurityPackage comment: MAGE package for contacts including organizations and people. is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_172" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:BarrierFacility comment: Rating of containment system for the protection of organisms from infectious agents. is_a: mged:GrowthCondition property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_97" xsd:string [Term] id: mged:Bedding comment: Refers to the bedding material present in an animals housing. is_a: mged:EnvironmentalHistory property_value: mged:unique_identifier "MO_154" xsd:string property_value: mged:class_role "place_holder" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:BibliographicReference comment: A bibliographic reference is a published citation in a journal, book, other format e.g. web resource is_a: mged:DescriptionPackage relationship: mged:has_volume xsd:string relationship: mged:has_issue xsd:string relationship: mged:has_type mged:PublicationType relationship: mged:has_pages xsd:string relationship: mged:has_publisher xsd:string relationship: mged:has_URI mged:URI relationship: mged:has_title xsd:string relationship: mged:has_editor xsd:string relationship: mged:has_year xsd:date relationship: mged:has_authors xsd:string relationship: mged:has_publication xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_201" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:BioAssay comment: A bioassay is an abstract class representing physical and computational groupings of biomaterials and arrays. is_a: mged:BioAssayPackage property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_56" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:BioAssayData comment: BioAssayData refers to the data files including images generated from one or more BioAssays. is_a: mged:BioAssayDataPackage property_value: mged:unique_identifier "MO_40" xsd:string [Term] id: mged:BioAssayDataCluster comment: A grouping of bioassay data that has been organized by one or more mathematical functions into nodes. is_a: mged:HigherLevelAnalysisPackage relationship: mged:has_nodes mged:Node property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_116" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:BioAssayDataPackage comment: MAGE package for BioAssayData. is_a: mged:MGEDExtendedOntology property_value: mged:unique_identifier "MO_186" xsd:string [Term] id: mged:BioAssayPackage comment: MAGE package for bioassay. is_a: mged:MGEDCoreOntology property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_0" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:BioMaterial comment: Description of the processing state of the biomaterial for use in the microarray hybridization. is_a: mged:BioMaterialPackage relationship: mged:has_type mged:MaterialType relationship: mged:has_biomaterial_characteristics mged:BioMaterialCharacteristics property_value: mged:unique_identifier "MO_226" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:BioMaterialCharacteristicCategory comment: General descriptor of a BioMaterialCharacteristic category. Such as strain or line where the name of the strain or line is encoded in the FactorValue. is_a: mged:BiologicalFactorCategory property_value: mged:unique_identifier "MO_100" xsd:string [Term] id: mged:BioMaterialCharacteristics comment: Properties of the biomaterial before treated in any manner for the purposes of the experiment. is_a: mged:BiologicalFactorCategory is_a: mged:BioMaterialPackage property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_5" xsd:string [Term] id: mged:BioMaterialPackage comment: Description of the source of the nucleic acid used to generate labeled material for the microarray experiment. is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_182" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:BioMaterialPurity comment: A measure of homogeneity of a biomaterial. For example, an expression of the percentage of a tumor biopsy that is tumor cells. is_a: mged:BioMaterialCharacteristics property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_20" xsd:string [Term] id: mged:BioMolecularAnnotation comment: BioMolecularAnnotation experiment design types are those which are designed to investigate functions, processes, locations and identity at the molecular level e.g. binding site identification, genotyping. is_a: mged:ExperimentDesignType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_213" xsd:string [Term] id: mged:BioSample comment: The BioSource after any treatment. is_a: mged:BioMaterial relationship: mged:has_been_treated mged:Treatment relationship: mged:has_type mged:BioSampleType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_93" xsd:string [Term] id: mged:BioSampleType comment: Used to tell when the BioSample is an extract or not. is_a: mged:BioMaterialPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_161" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:BioSequence comment: A representation of a DNA, RNA, or protein sequence. is_a: mged:BioSequencePackage relationship: mged:has_species mged:Organism relationship: mged:has_type mged:BioSequenceType relationship: mged:has_type mged:PolymerType property_value: mged:unique_identifier "MO_163" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:BioSequencePackage comment: MAGE package for biological sequences (biosequence). is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_191" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:BioSequenceType comment: Controlled terms for descriptors indicating the type of biosequence. Types may be physical (e.g. BAC, cDNA clone), or computational (e.g. unigene cluster, consensus). is_a: mged:BioSequencePackage property_value: mged:unique_identifier "MO_152" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:BioSource comment: The BioSource is the original source material before any treatment events. is_a: mged:BioMaterial property_value: mged:unique_identifier "MO_77" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:BioSourceProvider comment: The resource (e.g. company, hospital, geographical location) used to obtain or purchase the biomaterial. is_a: mged:BioMaterialCharacteristics relationship: mged:has_owner mged:Person relationship: mged:has_donor mged:Organization property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_230" xsd:string [Term] id: mged:BioSourceType comment: The form in which the BioMaterial was obtained/maintained e.g. frozen, fresh etc. Note can be used to describe BioSamples as well as BioSources. is_a: mged:BioMaterialCharacteristics property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_95" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:BiologicalFactorCategory comment: Factors that relate to properties of the biomaterial, its treatment, or \n its growth. is_a: mged:ExperimentalFactorCategory property_value: mged:unique_identifier "MO_190" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:BiologicalProperty comment: A biological property experiment design type is where an intrinsic characteristic of an organism(s) or biological system is examined. is_a: mged:ExperimentDesignType property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_224" xsd:string [Term] id: mged:Biometrics comment: Physical properties of the BioMaterial e. g. mass or height is_a: mged:BioMaterialCharacteristics relationship: mged:has_individual mged:Individual relationship: mged:has_length mged:Measurement relationship: mged:has_cubic_volume mged:Measurement relationship: mged:has_mass mged:Measurement relationship: mged:has_diameter mged:Measurement relationship: mged:has_height mged:Measurement relationship: mged:has_organism_part mged:OrganismPart property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_129" xsd:string [Term] id: mged:CancerSite comment: class to hold instances used as the filler for the property has_cancer_site is_a: mged:MGEDCoreOntology property_value: mged:unique_identifier "MO_26" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:CellLine comment: The identifier for the established culture of a metazoan cell if one was used as a biomaterial.\n is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry relationship: mged:has_database mged:CellLineDatabase property_value: mged:unique_identifier "MO_49" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:CellLineDatabase comment: Database of cell line information. is_a: mged:Database property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_145" xsd:string [Term] id: mged:CellType comment: CellType, the type of cell used in the experiment if non mixed, if mixed the TargetedCellType should be used, example of instances, epithelial, glial etc. is_a: mged:OntologyEntry is_a: mged:BioMaterialCharacteristics relationship: mged:has_database mged:CellTypeDatabase property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_135" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:CellTypeDatabase comment: Database of cell type information. is_a: mged:Database property_value: mged:unique_identifier "MO_141" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:ChromosomalAberration comment: An abnormality of a chromosome's number or structure, which excludes simple changes in sequence and is usually detectable by cytogenetic and microscopic techniques such as FISH. is_a: mged:DeprecatedTerms relationship: mged:has_chromosomal_aberration_classification mged:ChromosomalAberrationClassification property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_78" xsd:string property_value: mged:deprecation_in_version "1.1.7" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_old_restriction "some|has_chromosomal_aberration_classification|ChromosomalAberrationClassification" xsd:string [Term] id: mged:ChromosomalAberrationClassification comment: An irregularity in the number or structure of chromosomes, usually in the form of a gain (duplication), loss (deletion), exchange (translocation), or alteration in sequence (inversion) of genetic material. Excludes simple changes in sequence such as mutations, and is usually detectable by cytogenetic and microscopic techniques such as FISH. is_a: mged:BioMaterialCharacteristics property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_6" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:ClinicalHistory comment: The BioMaterial's (i.e., the patient's) medical record as background information relevant to the experiment. is_a: mged:EnvironmentalHistory relationship: mged:has_clinical_record mged:OntologyEntry relationship: mged:has_clinical_treatment mged:ClinicalTreatment relationship: mged:has_test_type mged:TestType relationship: mged:has_prior_disease_state mged:DiseaseState relationship: mged:has_clinical_finding mged:TestResult property_value: mged:unique_identifier "MO_189" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:ClinicalTreatment comment: The current clinical treatment(s) of the patient from which the biosource is derived. is_a: mged:OntologyEntry is_a: mged:BioMaterialCharacteristics relationship: mged:has_database mged:ClinicalTreatmentDatabase property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_69" xsd:string [Term] id: mged:ClinicalTreatmentDatabase comment: Database of clinical treatment information is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_114" xsd:string [Term] id: mged:ComplexAction comment: Complex actions are composed of multiple steps (as opposed to AtomicAction) e.g. mRNA labeling, protein purification. is_a: mged:Action property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_90" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:Compound comment: A drug, solvent, chemical, etc., with a property that can be measured such as concentration. is_a: mged:BiologicalFactorCategory is_a: mged:OntologyEntry relationship: mged:has_database mged:CompoundDatabase relationship: mged:is_solvent xsd:boolean property_value: mged:unique_identifier "MO_70" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:CompoundDatabase comment: Database of compound information. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_151" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:ConcentrationUnit comment: Units used for concentration measurements. is_a: mged:Unit property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_61" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:ConcentrationUnitOther comment: Concentration units not specified in MAGE. is_a: mged:ConcentrationUnit property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_86" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:Contact comment: Organizations or individuals that may be contacted. is_a: mged:AuditAndSecurityPackage relationship: mged:has_type mged:Roles relationship: mged:has_email xsd:string relationship: mged:has_toll_free_phone xsd:string relationship: mged:has_fax xsd:string relationship: mged:has_phone xsd:string relationship: mged:has_address xsd:string relationship: mged:has_URI mged:URI property_value: mged:unique_identifier "MO_147" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:ControlType comment: Controlled terms for descriptors for the type of control design element. is_a: mged:DesignElementPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_50" xsd:string [Term] id: mged:Cultivar comment: a plant variety obtained in agriculture in horticulture is_a: mged:StrainOrLine relationship: mged:has_database mged:StrainOrLineDatabase property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_124" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:DataTransformationProtocolType comment: The process by which derived BioAssays are created from measured BioAssays and/or derived BioAssays. is_a: mged:ProtocolType property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_165" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:DataType comment: Primitive data types found in computing languages such as float, boolean, etc. is_a: mged:MGEDCoreOntology property_value: mged:unique_identifier "MO_125" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:Database comment: Identifiable resource containing data or external ontologies or controlled vocabularies which has uniquely identifiable records. is_a: mged:DescriptionPackage relationship: mged:has_version xsd:string relationship: mged:has_URI mged:URI property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_118" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:DatabaseEntryType comment: Controlled set of descriptors for the type of database record such as a protein record (in SWISS-PROT) or a gene object (in SGD). is_a: mged:DescriptionPackage property_value: mged:unique_identifier "MO_157" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:DefectType comment: Defects associated with features or zones such as those that are missing or moved. is_a: mged:ArrayPackage property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_16" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:DeliveryMethod comment: Method used to deliver a compound for treatment. is_a: mged:MGEDExtendedOntology property_value: mged:unique_identifier "MO_223" xsd:string [Term] id: mged:DeprecatedTerms comment: Class to hold deprecated instances and classes. is_a: mged:MGEDCoreOntology relationship: mged:has_reason_for_deprecation mged:DeprecationReason property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_206" xsd:string [Term] id: mged:DeprecationReason comment: class to hold instances used as the filler for the property has_reason_for_deprecation is_a: mged:MGEDCoreOntology property_value: mged:unique_identifier "MO_94" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:DerivedBioAssay comment: A BioAssay that is created by the transformation of measured or derived BioAssays. is_a: mged:BioAssay relationship: mged:has_type mged:DerivedBioAssayType property_value: mged:unique_identifier "MO_209" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:DerivedBioAssayType comment: Controlled set of descriptors for the type of derivation of the BioAssay such as averaging features, taking ratios of signal QuantitationTypes, and normalizing BioAssay data. is_a: mged:BioAssayPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_111" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:DescriptionPackage comment: MAGE package for description of annotations and references to annotations. is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_167" xsd:string [Term] id: mged:DesignElement comment: Design elements are reporters, features, and composite elements as defined by MAGE. is_a: mged:DesignElementPackage relationship: mged:has_type mged:ControlType property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_173" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:DesignElementGroup comment: A DesignElementGroup holds information on Features, Reporters, or CompositeSequences. is_a: mged:ArrayDesignPackage relationship: mged:has_type mged:DesignElementGroupType relationship: mged:has_species mged:Organism property_value: mged:unique_identifier "MO_128" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:DesignElementGroupType comment: Controlled set of descriptors for indicating the specific type of a Feature, Reporter, or CompositeSequence. is_a: mged:ArrayDesignPackage property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_14" xsd:string [Term] id: mged:DesignElementPackage comment: The MAGE package for describing the elements located on the array. is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_15" xsd:string [Term] id: mged:DevelopmentalStage comment: The developmental stage of the organism's life cycle during which the biomaterial was extracted. is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry relationship: mged:has_database mged:DevelopmentalStageDatabase property_value: mged:unique_identifier "MO_120" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:DevelopmentalStageDatabase comment: Database of developmental stage information. is_a: mged:Database property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_215" xsd:string [Term] id: mged:DiseaseLocation comment: Anatomical location(s) of disease. is_a: mged:OrganismPart relationship: mged:has_cancer_site mged:CancerSite property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_37" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:DiseaseStaging comment: The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression. is_a: mged:OntologyEntry is_a: mged:BioMaterialCharacteristics relationship: mged:has_database mged:DiseaseStagingDatabase property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_133" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:DiseaseStagingDatabase comment: Database of disease staging information is_a: mged:Database property_value: mged:unique_identifier "MO_225" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:DiseaseState comment: The name of the pathology diagnosed in the organism from which the biomaterial was derived. The disease state is normal if no disease has been diagnosed. is_a: mged:OntologyEntry is_a: mged:BioMaterialCharacteristics relationship: mged:has_database mged:DiseaseStateDatabase relationship: mged:has_disease_staging mged:DiseaseStaging relationship: mged:has_disease_location mged:DiseaseLocation property_value: mged:unique_identifier "MO_126" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:DiseaseStateDatabase comment: Database of disease state information. is_a: mged:Database property_value: mged:unique_identifier "MO_181" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:DistanceUnit comment: Units used for distance measurements. is_a: mged:Unit property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_4" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:DistanceUnitOther comment: Distance units not specified in MAGE. is_a: mged:DistanceUnit property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "place_holder" xsd:string property_value: mged:unique_identifier "MO_143" xsd:string [Term] id: mged:Ecotype comment: a biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler is_a: mged:StrainOrLine relationship: mged:has_database mged:StrainOrLineDatabase property_value: mged:unique_identifier "MO_71" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:EnvironmentalFactorCategory comment: Factors that relate to properties of the environmental history of the biomaterial, its treatment, or its growth. is_a: mged:ExperimentalFactorCategory property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_117" xsd:string [Term] id: mged:EnvironmentalHistory comment: A description of the conditions the organism has been exposed to that are not one of the variables under study. is_a: mged:BioMaterialCharacteristics property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_55" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:EnvironmentalStress comment: Environmental stress is a treatment where some aspect of the environment is perturbed in order to stress the organism or culture, e.g. temperature shock, osmotic shock is_a: mged:MGEDExtendedOntology relationship: mged:has_measurement mged:Measurement property_value: mged:unique_identifier "MO_227" xsd:string [Term] id: mged:EpidemiologicalDesign comment: An epidemiological experiment design type is where the biosource history is studied e.g. environmental, clinical and family history. is_a: mged:ExperimentDesignType property_value: mged:unique_identifier "MO_142" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:Experiment comment: The complete set of bioassays (hybridizations) and their descriptions performed as an experiment for a common purpose. Here we take experiment to mean an observational or perturbing study. An experiment will be often equivalent to a publication. is_a: mged:ExperimentPackage relationship: mged:has_bioassays mged:BioAssay relationship: mged:has_citation mged:BibliographicReference relationship: mged:has_experiment_design mged:ExperimentDesign relationship: mged:has_providers mged:Contact relationship: mged:has_bioassay_data mged:BioAssayData property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_112" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:ExperimentDesign comment: ExperimentDesign refers to both observational and experimental (perturbational) studies. The organizing principles of the study including the relationships between assays and the steps taken to interpret the data. is_a: mged:ExperimentPackage relationship: mged:has_bioassays mged:BioAssay relationship: mged:has_description xsd:string relationship: mged:has_MAGE_description mged:ReplicateDescription relationship: mged:has_experiment_design_type mged:ExperimentDesignType relationship: mged:has_MAGE_description mged:NormalizationDescription relationship: mged:has_MAGE_description mged:QualityControlDescription relationship: mged:has_experiment_factors mged:ExperimentalFactor property_value: mged:unique_identifier "MO_170" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:ExperimentDesignType comment: The ExperimentDesignType is the high level description for studies such as \"time series\", \"dose response\", etc. is_a: mged:ExperimentPackage property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_158" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:ExperimentPackage comment: The descriptions associated with the Experiment package of MAGE is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_31" xsd:string [Term] id: mged:ExperimentalFactor comment: The factors in the study that are experimental parameters or regarded as influencing the experimental results. is_a: mged:ExperimentPackage relationship: mged:has_category mged:MethodologicalFactorCategory relationship: mged:has_factor_value mged:FactorValue relationship: mged:has_category mged:BiologicalFactorCategory property_value: mged:class_source "mage" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_10" xsd:string [Term] id: mged:ExperimentalFactorCategory comment: A factor category describes factors which are examined in the experiment, e.g. disease_state, where the factor values are ALL and AML. is_a: mged:ExperimentPackage property_value: mged:unique_identifier "MO_205" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:ExperimentalProtocolType comment: All protocols which involve treatment of a biomaterial or an array during the course of a microarray experiment. is_a: mged:ProtocolType property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_75" xsd:string [Term] id: mged:FactorValue comment: The value of an ExperimentFactor. is_a: mged:ExperimentPackage relationship: mged:has_factor_value_ontology_entry mged:ExperimentalFactorCategory relationship: mged:has_property_set mged:FactorValueSet relationship: mged:has_property_set mged:FactorValueDependency relationship: mged:has_measurement mged:Measurement property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_203" xsd:string [Term] id: mged:FactorValueDependency comment: A group of FactorValues which refer to the same condition used to treat or describe a BioMaterial, e.g. 10% glucose, 1 hour OR larval stage, age 24 hours. is_a: mged:ExperimentPackage is_a: mged:DeprecatedTerms relationship: mged:has_value xsd:string property_value: mged:deprecation_in_version "1.1.9" xsd:string property_value: mged:unique_identifier "MO_148" xsd:string property_value: mged:deprecation_old_restriction "some|has_value|string" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:class_role "place_holder" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:FactorValueSet comment: A super grouping of FactorValueDependencies or FactorValues which describes combinations of conditions used to treat or describe a BioMaterial applied to a BioAssay, typically separating things on the basis of channels or the concepts of measured and reference samples e.g. 10% glucose, 1 hour AND 10mm NaCl, 2 hours in channel 1. is_a: mged:ExperimentPackage is_a: mged:DeprecatedTerms relationship: mged:has_value xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:deprecation_old_restriction "some|has_value|string" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.1.9" xsd:string property_value: mged:class_role "place_holder" xsd:string property_value: mged:unique_identifier "MO_217" xsd:string [Term] id: mged:FailType comment: Controlled terms for descriptors of failures (as in PCR) associated with reporters. is_a: mged:DesignElementPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_98" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:FamilyHistory comment: Relevant aspects of genetic preconditions or family member's clinical history. is_a: mged:EnvironmentalHistory relationship: mged:has_family_member mged:FamilyMember property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_59" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:FamilyMember comment: Member of the biosource's family. is_a: mged:BioMaterialPackage relationship: mged:has_individual_genetic_characteristics mged:IndividualGeneticCharacteristics relationship: mged:has_clinical_record mged:OntologyEntry relationship: mged:has_disease_state mged:DiseaseState relationship: mged:has_family_relationship mged:FamilyRelationship property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_188" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:FamilyRelationship comment: A type of relationship applicable to mammals to describe the genetic relatedness of the individual under study. E.g. brother or mother. is_a: mged:BioMaterialPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_36" xsd:string [Term] id: mged:FeatureDefect comment: A technical manufacturer described defect for features. is_a: mged:ArrayPackage relationship: mged:has_type mged:DefectType property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_138" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:FeatureGroup comment: Technology-based grouping of features representing individual locations on the array. is_a: mged:DesignElementGroup relationship: mged:has_feature_shape mged:FeatureShape relationship: mged:has_type mged:TechnologyType property_value: mged:unique_identifier "MO_54" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:FeatureShape comment: The expected shape of the feature on the array. is_a: mged:ArrayDesignPackage property_value: mged:unique_identifier "MO_8" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:Fiducial comment: A marking on the surface of the array that can be used to identify the origin of the array. is_a: mged:ArrayPackage relationship: mged:has_type mged:FiducialType property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_136" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:FiducialType comment: A descriptor that indicates the type of the fiducial such as chrome border of an Affymetrix array or a laser ablation mark. is_a: mged:ArrayPackage property_value: mged:unique_identifier "MO_17" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:Generation comment: The number of cell passages if the organism or organism part that is cultured is unicellular or a cell culture otherwise the number of generations. is_a: mged:EnvironmentalHistory property_value: mged:class_role "place_holder" xsd:string property_value: mged:unique_identifier "MO_43" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:GeneticMaterial comment: Genetic material may be DNA or RNA and identifiable as an entry in a public external database such as EMBL/DDBJ/GenBank or one of the model organism databases. is_a: mged:MGEDExtendedOntology property_value: mged:unique_identifier "MO_137" xsd:string [Term] id: mged:GeneticModification comment: The genetic modification introduced into the organism from which the biomaterial was derived. Examples of genetic modification include specification of a transgene or the gene knocked-out or details of transient transfection. is_a: mged:BioMaterialCharacteristics property_value: mged:unique_identifier "MO_122" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:Genotype comment: The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism\neither prior to or during the experiment. is_a: mged:IndividualGeneticCharacteristics property_value: mged:unique_identifier "MO_51" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:GeographicLocation comment: A descriptor of the location from which a BioMaterial was obtained, e.g. country, region, grid reference. is_a: mged:OntologyEntry is_a: mged:EnvironmentalHistory relationship: mged:has_database mged:GeographicLocationDatabase property_value: mged:unique_identifier "MO_132" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:GeographicLocationDatabase comment: Database of geographic locations. is_a: mged:Database property_value: mged:unique_identifier "MO_35" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:GrowthCondition comment: A description of the conditions used to grow organisms or parts of the organism. This includes isolated environments such as cultures and open environments such as field studies. is_a: mged:EnvironmentalHistory relationship: mged:has_value xsd:string relationship: mged:has_maximum_measurement mged:Measurement relationship: mged:has_measurement mged:Measurement property_value: mged:unique_identifier "MO_183" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:Haplotype comment: The genotype of a single chromosome (i.e., the haploid genotype) that is known and relevant to the experiment being performed. is_a: mged:IndividualGeneticCharacteristics property_value: mged:unique_identifier "MO_146" xsd:string property_value: mged:class_role "place_holder" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:Hardware comment: The machine or instrument used. is_a: mged:ProtocolPackage relationship: mged:has_model xsd:string relationship: mged:has_type mged:HardwareType relationship: mged:has_manufacturer mged:Contact relationship: mged:has_software mged:Software relationship: mged:has_make xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_134" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:HardwareType comment: Controlled terms for descriptors of types of hardware. is_a: mged:ProtocolPackage property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_113" xsd:string [Term] id: mged:HardwareVariation comment: The effects of different hardware, types of hardware, or models of hardware on experimental results are studied. is_a: mged:MethodologicalFactorCategory property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_81" xsd:string property_value: mged:class_role "place_holder" xsd:string [Term] id: mged:HigherLevelAnalysisPackage comment: MAGE package for HigherLevelAnalysis is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_228" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:HigherLevelAnalysisProtocolType comment: A protocol which yields a dataset(s) from which biological conclusions can be derived. E.g. clustering (not normalization or averaging). is_a: mged:ProtocolType property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_47" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:Histology comment: Microscopic morphology of tissues. is_a: mged:OntologyEntry is_a: mged:BioMaterialCharacteristics relationship: mged:has_organism_part mged:OrganismPart relationship: mged:has_database mged:HistologyDatabase relationship: mged:has_performer mged:Contact property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_194" xsd:string [Term] id: mged:HistologyDatabase comment: Database of histology information. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_175" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:HistoryFactor comment: Factors that are measured or observed parts of the study but not induced or under the control of the experiment. These factors do not have protocols (e.g., epidemiology factors). is_a: mged:MGEDExtendedOntology property_value: mged:unique_identifier "MO_82" xsd:string [Term] id: mged:Host comment: Organisms or organism parts used as a designed part of the culture (e.g., red blood cells, stromal cells). is_a: mged:EnvironmentalHistory relationship: mged:has_host_part mged:OrganismPart relationship: mged:has_host mged:Organism property_value: mged:unique_identifier "MO_101" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:Humidity comment: The humidity that the biosource is exposed to. is_a: mged:GrowthCondition property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_29" xsd:string [Term] id: mged:Image is_a: mged:DescriptionPackage relationship: mged:has_image_format mged:ImageFormat relationship: mged:has_URI mged:URI relationship: mged:has_database mged:Database property_value: mged:unique_identifier "MO_22" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:ImageFormat comment: Controlled terms for descriptors of the image file format (TIFF, JPEG, GIF, etc.) is_a: mged:BioAssayPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_211" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:Individual comment: Identifier or name of the individual organism from which the biomaterial was derived. is_a: mged:BioMaterialCharacteristics property_value: mged:unique_identifier "MO_169" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "place_holder" xsd:string [Term] id: mged:IndividualChromosomalAbnormality comment: An abnormality in the number or structure of chromosomes in the biomaterial from an individual organism, detected by karyotyping or other methods. E.g., a B-cell lymphoma from a patient has an abnormal karyotype 48,XY,t(1;2)(p22;p11),+3,+12. is_a: mged:DeprecatedTerms is_a: mged:IndividualGeneticCharacteristics property_value: mged:unique_identifier "MO_185" xsd:string property_value: mged:class_role "place_holder" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:IndividualGeneticCharacteristics comment: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. is_a: mged:BioMaterialCharacteristics relationship: mged:has_value xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_66" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:InitialTimePoint comment: The point from which measurements of age were taken. is_a: mged:BioMaterialPackage property_value: mged:unique_identifier "MO_80" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:LabelCompound comment: Compounds that are used for labeling extracts. is_a: mged:Compound property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_13" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:LabeledExtract comment: The BioSample after labeling for detection of the nucleic acids. is_a: mged:BioMaterial relationship: mged:has_been_treated mged:Treatment relationship: mged:has_compound mged:LabelCompound property_value: mged:class_source "mage" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_221" xsd:string [Term] id: mged:Light comment: The photoperiod and type (e.g., natural, restricted wavelength) of light exposure. is_a: mged:GrowthCondition property_value: mged:unique_identifier "MO_60" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:LightUnit comment: Units for measuring the intensity of light. is_a: mged:OtherUnit property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_119" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:MGEDCoreOntology comment: An ontology developed by the Microarray Gene Expression Data (MGED) Society to provide descriptors required for MAGE v.1 documents. is_a: mged:MGEDOntology relationship: mged:has_ID xsd:string property_value: mged:unique_identifier "MO_57" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:MGEDExtendedOntology comment: Location for those classes that are not in the Core ontology as they do are not containable in MAGE. It is not yet structured to work with the Core ontology is_a: mged:MGEDOntology property_value: mged:unique_identifier "MO_196" xsd:string [Term] id: mged:MGEDOntology comment: The MGED Ontology is a top level container for the MGEDCoreOntology and the MGEDExtendedOntology. The MGED ontology describes microarray experiments and is split into the MGEDCoreOntology, which supports MAGE-OM v1.0 and is organized consistently with MAGE, and the MGEDExtendedOntology, which expands MAGE v1.0 and contains concepts and relationships which are not included in MAGE. relationship: mged:is_user_defined mged:Contact relationship: mged:is_user_defined mged:BibliographicReference property_value: mged:unique_identifier "MO_174" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:MGEDOntologyVersion comment: The version of the MGED Ontology. is_a: mged:MGEDCoreOntology property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_115" xsd:string [Term] id: mged:MassUnit comment: Units used for mass measurements. is_a: mged:Unit property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_149" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:MassUnitOther comment: Mass units not specified in MAGE. is_a: mged:MassUnit property_value: mged:unique_identifier "MO_11" xsd:string property_value: mged:class_role "place_holder" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:MaterialType comment: Controlled terms for the state of the BioMaterial. Each state (BioSource, different BioSamples, and LabeledExtract) have MaterialTypes. Examples are population of an organism, organism, organism part, cell, etc. is_a: mged:BioMaterialPackage property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_32" xsd:string [Term] id: mged:Measurement comment: Measured values and units. is_a: mged:MeasurementPackage relationship: mged:has_value xsd:string relationship: mged:has_units mged:Unit relationship: mged:has_measurement_type mged:MeasurementType property_value: mged:unique_identifier "MO_144" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:MeasurementPackage comment: MAGE package for measurement. is_a: mged:MGEDCoreOntology property_value: mged:unique_identifier "MO_89" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:MeasurementType comment: class to hold instances used as the filler for the property has_measurement_type is_a: mged:MGEDCoreOntology property_value: mged:unique_identifier "MO_72" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:Media comment: The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) . is_a: mged:GrowthCondition property_value: mged:unique_identifier "MO_19" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:MethodologicalDesign comment: A methodological experiment design type investigates differences caused by application of protocols, hardware, software and bioassay relationships, e.g. quality control, replicates, loop. is_a: mged:ExperimentDesignType property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_2" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:MethodologicalFactorCategory comment: The effects on results of changing protocols, hardware, software, or people performing the experiments are studied Examples are comparison of data across different labeling protocols, scanners, image quantification software, or laboratories. is_a: mged:ExperimentalFactorCategory property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_85" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:Node comment: A node is an individual component of BioAssayDataCluster that groups design elements, quantitation types, and BioAssays together. A node may contain other nodes. is_a: mged:HigherLevelAnalysisPackage relationship: mged:has_node_value mged:NodeValue property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_73" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:NodeValue comment: Node values allow the organization of the nodes in relation to other nodes produced by mathematical functions such as a clustering algorithm. is_a: mged:HigherLevelAnalysisPackage relationship: mged:has_node_value_type mged:NodeValueType relationship: mged:has_type mged:DataType relationship: mged:has_scale mged:Scale property_value: mged:unique_identifier "MO_104" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:NodeValueType comment: Controlled set of terms for describing the type of values (e.g., Euclidean distance). is_a: mged:HigherLevelAnalysisPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_160" xsd:string [Term] id: mged:NormalizationDescription comment: NormalizationDescription provides details of the normalization strategy for the experiment. is_a: mged:ExperimentPackage relationship: mged:has_type mged:NormalizationDescriptionType property_value: mged:unique_identifier "MO_131" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:NormalizationDescriptionType comment: Controlled descriptors for the normalization strategy used for the experiment. is_a: mged:ExperimentPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_27" xsd:string [Term] id: mged:Nutrients comment: The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.). is_a: mged:GrowthCondition relationship: mged:has_nutrient_component mged:Compound property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_127" xsd:string [Term] id: mged:Observation comment: Observation will record the macroscopic examination of the biomaterial. is_a: mged:BioMaterialCharacteristics relationship: mged:has_performer mged:Contact relationship: mged:has_database mged:ObservationDatabase property_value: mged:unique_identifier "MO_53" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:ObservationDatabase comment: Database of terms for observations such as 'abnormal coat', 'skin pigment abnormality' describing macroscopic examinations. is_a: mged:Database property_value: mged:unique_identifier "MO_91" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:OntologyEntry comment: External (to the MGED ontology) controlled vocabulary or ontology that can be referred such as ICD-9 or Gene Ontology. is_a: mged:DescriptionPackage relationship: mged:has_description xsd:string relationship: mged:has_accession xsd:string relationship: mged:has_value xsd:string relationship: mged:has_accession_version xsd:string relationship: mged:has_database_entry_type mged:DatabaseEntryType relationship: mged:has_database mged:Database property_value: mged:unique_identifier "MO_87" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:OperatorVariation comment: The effects of different investigators, laboratories, or organizations on experimental results are studied. is_a: mged:MethodologicalFactorCategory property_value: mged:unique_identifier "MO_38" xsd:string property_value: mged:class_role "place_holder" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:Organism comment: The genus and species (and subspecies) of the organism from which the biomaterial is derived from. is_a: mged:OntologyEntry is_a: mged:BioMaterialCharacteristics relationship: mged:has_database mged:OrganismDatabase property_value: mged:unique_identifier "MO_229" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:OrganismDatabase comment: Database of taxonomic information. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_64" xsd:string [Term] id: mged:OrganismPart comment: The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm). is_a: mged:OntologyEntry is_a: mged:BioMaterialCharacteristics relationship: mged:has_database mged:OrganismPartDatabase property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_1" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:OrganismPartDatabase comment: Database of organism part information. is_a: mged:Database property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_200" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:OrganismStatus comment: The stage premortem or postmortem at which the sample was processed for extraction of biomaterials. is_a: mged:BioMaterialCharacteristics property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_84" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:Organization comment: The organization (e.g. company, hospital) to contact to obtain or purchase something. is_a: mged:Contact relationship: mged:has_parent_organization mged:Organization relationship: mged:has_name xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_177" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:OtherUnit comment: Other units are those types not specified in MAGE such as lumens, radioactivity, etc. is_a: mged:Unit property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_199" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:Parameter comment: A parameter is a variable within a protocol. is_a: mged:ProtocolPackage relationship: mged:has_type mged:DataType relationship: mged:has_units mged:Unit property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_110" xsd:string [Term] id: mged:PathogenTest comment: Tests and results for pathogens infecting organism from which the biosource is derived is_a: mged:EnvironmentalHistory relationship: mged:was_tested_for mged:Organism relationship: mged:has_result mged:Result property_value: mged:unique_identifier "MO_184" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:Person comment: The individual to contact regarding something provided such as a biomaterial. is_a: mged:Contact relationship: mged:has_last_name xsd:string relationship: mged:has_mid_initials xsd:string relationship: mged:has_affiliation mged:Organization relationship: mged:has_first_name xsd:string property_value: mged:unique_identifier "MO_24" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:PerturbationalDesign comment: A perturbational design type is where the organism(s) are treated or manipulated or modified, for example a genetic modification, somatic modification is_a: mged:ExperimentDesignType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_106" xsd:string [Term] id: mged:Phenotype comment: The observable form taken by some character (or group of characters) in an individual or an organism, excluding pathology and disease. The detectable outward manifestations of a specific genotype. is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry relationship: mged:has_database mged:PhenotypeDatabase property_value: mged:unique_identifier "MO_192" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:PhenotypeDatabase comment: Database of phenotype information is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_39" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:PhysicalArrayDesign comment: Descriptions pertaining to the array. is_a: mged:ArrayDesignPackage relationship: mged:has_type mged:SurfaceType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_212" xsd:string [Term] id: mged:PhysicalBioAssay comment: A physical bioassay is the combination of arrays and biomaterials as in a hybridization. is_a: mged:BioAssay relationship: mged:has_image_format mged:ImageFormat property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_99" xsd:string property_value: mged:class_source "mage" xsd:string [Term] id: mged:PhysicalBioSequenceType comment: A physical biosequence type represents biological sequence that can be physically placed (spotted or synthesized) on an array e.g. BAC, PAC. is_a: mged:BioSequenceType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_92" xsd:string [Term] id: mged:Ploidy comment: The number of single sets of chromosomes in the cell or an organism e.g., haploid, diploid, triploid, etc. is_a: mged:IndividualGeneticCharacteristics property_value: mged:unique_identifier "MO_220" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:PolymerType comment: Controlled terms for descriptors of the type of polymer (RNA, DNA, protein) of the biosequence. is_a: mged:BioSequencePackage property_value: mged:unique_identifier "MO_102" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:PopulationDensity comment: The concentration range of the organism. is_a: mged:GrowthCondition property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_46" xsd:string [Term] id: mged:Preservation comment: Method and type of preserving the organism or biosource (i.e. keeping it in stasis). is_a: mged:MGEDExtendedOntology relationship: mged:has_type mged:PreservationType relationship: mged:has_protocol mged:Protocol property_value: mged:unique_identifier "MO_176" xsd:string [Term] id: mged:PreservationType comment: The type of method used to preserve (keep in stasis) the organism or biosource. is_a: mged:MGEDExtendedOntology property_value: mged:unique_identifier "MO_195" xsd:string [Term] id: mged:Protocol comment: Documentation of the set of steps taken in a procedure. is_a: mged:ProtocolPackage relationship: mged:has_URI mged:URI relationship: mged:has_software mged:Software relationship: mged:has_type mged:ProtocolType relationship: mged:has_citation mged:BibliographicReference relationship: mged:has_text xsd:string relationship: mged:has_hardware mged:Hardware relationship: mged:has_title xsd:string relationship: mged:has_description xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_214" xsd:string [Term] id: mged:ProtocolPackage comment: The MAGE package for protocols. is_a: mged:MGEDCoreOntology property_value: mged:class_source "mage" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_63" xsd:string [Term] id: mged:ProtocolParameterType comment: Descriptors for protocol parameter types, e.g. compound concentration, media type. is_a: mged:MGEDExtendedOntology property_value: mged:unique_identifier "MO_164" xsd:string [Term] id: mged:ProtocolType comment: A controlled set of terms to provide a descriptor for the type of protocol. is_a: mged:MethodologicalFactorCategory is_a: mged:ProtocolPackage property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_150" xsd:string [Term] id: mged:ProtocolVariation comment: The effects of different protocols or changes in protocols on experimental results are studied. is_a: mged:MGEDExtendedOntology property_value: mged:unique_identifier "MO_140" xsd:string [Term] id: mged:PublicationType comment: Controlled terms for descriptors of the type of publication such as those used by Medline (review, book, etc.). is_a: mged:DescriptionPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_208" xsd:string [Term] id: mged:QualityControlDescription comment: QualityControlDescription provides details of the quality control aspects of the experiment. is_a: mged:ExperimentPackage relationship: mged:has_type mged:QualityControlDescriptionType property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_88" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:QualityControlDescriptionType comment: Controlled descriptors for the quality control strategy for an experiment. is_a: mged:ExperimentPackage property_value: mged:unique_identifier "MO_121" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:QuantitationType comment: The QuantitationType provides a method for calculating a single datum of the BioAssayData matrix. is_a: mged:QuantitationTypePackage relationship: mged:has_scale mged:Scale relationship: mged:has_type mged:DataType property_value: mged:class_source "mage" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_67" xsd:string [Term] id: mged:QuantitationTypePackage comment: The MAGE package for defining classes for quantitation. is_a: mged:MGEDCoreOntology property_value: mged:class_source "mage" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_130" xsd:string [Term] id: mged:QuantityUnit comment: Units used for quantity measurements. is_a: mged:Unit property_value: mged:unique_identifier "MO_210" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:QuantityUnitOther comment: Quantity units not specified in MAGE. is_a: mged:QuantityUnit property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_156" xsd:string [Term] id: mged:RadiationUnit comment: Units for measuring decay of a radioactive isotope over time. is_a: mged:OtherUnit property_value: mged:unique_identifier "MO_204" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:ReplicateDescription comment: ReplicateDescription provides details about the type of replication used in the experiment. is_a: mged:ExperimentPackage relationship: mged:has_type mged:ReplicateDescriptionType property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_162" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:ReplicateDescriptionType comment: Controlled descriptors for the type of replication. is_a: mged:ExperimentPackage property_value: mged:unique_identifier "MO_52" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:Reporter comment: Description of the material placed on a feature (spot). is_a: mged:DesignElement relationship: mged:has_type mged:FailType relationship: mged:has_type mged:WarningType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_74" xsd:string [Term] id: mged:Result comment: class to hold instances used as the filler for the property has_result is_a: mged:MGEDCoreOntology property_value: mged:unique_identifier "MO_65" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:Roles comment: Controlled terms for descriptors of the role of contact, e.g. submitter, biosource_provider. is_a: mged:AuditAndSecurityPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_180" xsd:string [Term] id: mged:SamplingTimePoint comment: A descriptor of the time point that a sample was taken. Not to be used \n where the sample is part of a time course. SamplingTimePoint is not \n related to age. An instance could be summer, a date, a time, or a range \n value. is_a: mged:EnvironmentalHistory property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_139" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:Scale comment: The scale (linear, log10, ln, etc) used to represent the value. is_a: mged:MGEDCoreOntology property_value: mged:unique_identifier "MO_108" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:SeqFeatureBasis comment: Controlled terms for how the sequence features were determined (e.g., experimental, computational, etc.) is_a: mged:BioSequencePackage property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_207" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:SequenceOntologyBioSequenceType comment: Descriptors of biosequence based on the Sequence Ontology (SO) project. is_a: mged:TheoreticalBioSequenceType is_a: mged:PhysicalBioSequenceType is_a: mged:OntologyEntry relationship: mged:has_database mged:SequenceOntologyDatabase property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_25" xsd:string [Term] id: mged:SequenceOntologyDatabase comment: Database for sequence annotation information. is_a: mged:Database property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_83" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:Serotype comment: An antigenic property of a cell (e.g. bacteria, RBC) or virus identified by serological methods is_a: mged:BioMaterialCharacteristics property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_159" xsd:string property_value: mged:class_role "place_holder" xsd:string [Term] id: mged:Sex comment: Term applied to any organism able to undergo sexual reproduction in order to differentiate the individuals or types involved. Sexual reproduction is defined as the ability to exchange genetic material with the potential of recombinant progeny. is_a: mged:BioMaterialCharacteristics property_value: mged:unique_identifier "MO_168" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:Software comment: The software application used. is_a: mged:ProtocolPackage relationship: mged:has_software mged:Software relationship: mged:has_hardware mged:Hardware relationship: mged:has_manufacturer mged:Contact relationship: mged:has_type mged:SoftwareType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_109" xsd:string [Term] id: mged:SoftwareType comment: Controlled terms that provide descriptors for the type of software. is_a: mged:ProtocolPackage property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_202" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:SoftwareVariation comment: The effects of different software, software packages, or software versions on experimental results are studied. is_a: mged:MethodologicalFactorCategory property_value: mged:class_role "place_holder" xsd:string property_value: mged:unique_identifier "MO_222" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:SomaticModification comment: The organism has had non-genetic parts removed, added, or rearranged. is_a: mged:MGEDExtendedOntology relationship: mged:has_part_modified mged:OrganismPart property_value: mged:unique_identifier "MO_44" xsd:string [Term] id: mged:StrainOrLine comment: A strain or line is an animal or plant offspring that has a single ancestral breeding pair or parent as a result of brother x sister or parent x offspring matings. This class is extended to include F1 offspring and established breeding lines. For microbes, these are isolates derived from nature or in the laboratory. is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry relationship: mged:has_species mged:Organism relationship: mged:has_database mged:StrainOrLineDatabase property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_9" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:StrainOrLineDatabase comment: Database of strain, line, cultivar or ecotype information. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_30" xsd:string [Term] id: mged:StrandType comment: A descriptor of the strand type the sequence feature belongs to. e.g. forward, reverse is_a: mged:MGEDExtendedOntology property_value: mged:unique_identifier "MO_7" xsd:string [Term] id: mged:SubstrateType comment: Controlled terms for descriptors of types of array substrates. is_a: mged:ArrayPackage property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_79" xsd:string [Term] id: mged:SurfaceType comment: Controlled terms for descriptors for coating of the substrate. is_a: mged:ArrayDesignPackage property_value: mged:unique_identifier "MO_198" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:TargetedCellType comment: The target cell type is the cell of primary interest. The biomaterial may be derived from a mixed population of cells although only one cell type is of interest. is_a: mged:BioMaterialCharacteristics is_a: mged:OntologyEntry property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_123" xsd:string [Term] id: mged:TargetedCellTypeDatabase comment: Database of targeted cell type information. is_a: mged:Database property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_45" xsd:string [Term] id: mged:TechnologicalDesign comment: The purpose(s) for which the array is used within an experiment, e.g. to \n assess the transcriptome, the genomic content, or to identify \n transcription factor binding sites. is_a: mged:ExperimentDesignType property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_21" xsd:string [Term] id: mged:TechnologyType comment: The technology type or platform of the reporters on the array. is_a: mged:ArrayDesignPackage property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_18" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:Temperature comment: The temperature that a biosource is exposed to. is_a: mged:GrowthCondition property_value: mged:unique_identifier "MO_171" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:TemperatureUnit comment: Units used for temperature measurements. is_a: mged:Unit property_value: mged:unique_identifier "MO_48" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:Test comment: An assay performed on a biomaterial for the purposes of determining one or more biomaterial characteristics e.g. clinical chemistry. is_a: mged:BioMaterialCharacteristics relationship: mged:has_performer mged:Contact relationship: mged:has_test_type mged:TestType relationship: mged:has_test_result mged:TestResult property_value: mged:unique_identifier "MO_197" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:TestResult comment: TestResult is the recorded value of the test outcome. is_a: mged:BioMaterialCharacteristics relationship: mged:has_measurement mged:Measurement property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_96" xsd:string [Term] id: mged:TestType comment: Descriptor of the Test performed e.g. Leukocyte count is_a: mged:OntologyEntry is_a: mged:BioMaterialCharacteristics relationship: mged:has_database mged:TestTypeDatabase property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_218" xsd:string property_value: mged:class_role "abstract" xsd:string [Term] id: mged:TestTypeDatabase comment: Database of codes for clinical findings. is_a: mged:Database property_value: mged:unique_identifier "MO_76" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string [Term] id: mged:TheoreticalBioSequenceType comment: A theoretical biosequence type is an abstraction used for annotation design of elements, e.g. gene, intron. is_a: mged:BioSequenceType property_value: mged:unique_identifier "MO_42" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:TimeUnit comment: Units used for time measurements. is_a: mged:Unit property_value: mged:unique_identifier "MO_166" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:TimeUnitOther comment: Time units not specified in MAGE. is_a: mged:TimeUnit property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_103" xsd:string [Term] id: mged:Transformation comment: The process by which BioAssays (data, elements, quantitation types) are averaged normalized, selected, filtered, or otherwise changed into a new set of BioAssay data. is_a: mged:BioAssayDataPackage relationship: mged:has_protocol mged:Protocol property_value: mged:unique_identifier "MO_216" xsd:string [Term] id: mged:Treatment comment: A treatment is the process or action by which a biomaterial is created from an input biomaterial. is_a: mged:BioMaterialPackage relationship: mged:has_action mged:Action relationship: mged:has_protocol mged:Protocol relationship: mged:has_order xsd:int property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "mage" xsd:string property_value: mged:unique_identifier "MO_23" xsd:string [Term] id: mged:TumorGrading comment: A descriptor used in cancer biology to describe abnormalities of tumor cells. E.g. an instance from NCI Thesaurus. is_a: mged:OntologyEntry is_a: mged:BioMaterialCharacteristics relationship: mged:has_database mged:TumorGradingDatabase property_value: mged:unique_identifier "MO_28" xsd:string property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:TumorGradingDatabase comment: Database of tumor grading information is_a: mged:Database property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_187" xsd:string [Term] id: mged:URI comment: Uniform Resource Identifier is_a: mged:MGEDCoreOntology property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_12" xsd:string [Term] id: mged:Unit comment: Units of measure. is_a: mged:MeasurementPackage property_value: mged:class_role "abstract" xsd:string property_value: mged:class_source "ontology" xsd:string property_value: mged:unique_identifier "MO_3" xsd:string [Term] id: mged:User comment: User is a way to id a person in a database is_a: mged:MGEDExtendedOntology relationship: mged:has_ID xsd:string property_value: mged:unique_identifier "MO_62" xsd:string [Term] id: mged:VolumeUnit comment: Units used for volume measurements. is_a: mged:Unit property_value: mged:unique_identifier "MO_179" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:VolumeUnitOther comment: Volume units not specified in MAGE. is_a: mged:VolumeUnit property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "place_holder" xsd:string property_value: mged:unique_identifier "MO_155" xsd:string [Term] id: mged:WarningType comment: Controlled terms for descriptors of the warnings associated with reporters. is_a: mged:DesignElementPackage property_value: mged:class_source "ontology" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_41" xsd:string [Term] id: mged:Water comment: Water consumed by or enveloping the organism that the biosource is derived from. is_a: mged:GrowthCondition relationship: mged:has_additive mged:Compound relationship: mged:has_treatment mged:Protocol property_value: mged:class_role "abstract" xsd:string property_value: mged:unique_identifier "MO_153" xsd:string property_value: mged:class_source "ontology" xsd:string [Term] id: mged:ZoneDefect comment: A technical manufactured described defect for zones. is_a: mged:ArrayPackage relationship: mged:has_type mged:DefectType property_value: mged:class_source "mage" xsd:string property_value: mged:class_role "concrete" xsd:string property_value: mged:unique_identifier "MO_105" xsd:string [Typedef] id: mged:class_role comment: This property is used to identify the type of class of the term. The value \"abstract\" indicates that the class is used for organizational purposes. The value \"instantiated\" indicates that the class contains Individuals that can be used as annotation terms. The value \"abstract\" indicates that the class is used to provide organization within the MGED Ontology. The value \"place_holder\" indicates that this class represents the location in the ontology where terms of this class would be located. range: __file:///Users/cjm/obo-utils/obo-all/mged/mged.owl#__Description194 property_value: rdfs:comment "This property is used to identify the type of class of the term. The value \"abstract\" indicates that the class is used for organizational purposes. The value \"instantiated\" indicates that the class contains Individuals that can be used as annotation terms. The value \"abstract\" indicates that the class is used to provide organization within the MGED Ontology. The value \"place_holder\" indicates that this class represents the location in the ontology where terms of this class would be located." xsd:string property_value: mged:unique_identifier "MO_338" xsd:string [Typedef] id: mged:class_role comment: This property is used to identify the type of class of the term. The value \"abstract\" indicates that the class is used for organizational purposes. The value \"instantiated\" indicates that the class contains Individuals that can be used as annotation terms. The value \"abstract\" indicates that the class is used to provide organization within the MGED Ontology. The value \"place_holder\" indicates that this class represents the location in the ontology where terms of this class would be located. range: __file:///Users/cjm/obo-utils/obo-all/mged/mged.owl#__Description194 property_value: rdfs:comment "This property is used to identify the type of class of the term. The value \"abstract\" indicates that the class is used for organizational purposes. The value \"instantiated\" indicates that the class contains Individuals that can be used as annotation terms. The value \"abstract\" indicates that the class is used to provide organization within the MGED Ontology. The value \"place_holder\" indicates that this class represents the location in the ontology where terms of this class would be located." xsd:string property_value: mged:unique_identifier "MO_338" xsd:string [Typedef] id: mged:class_source comment: The property indicates the derivation of the class. A value of \"mage\" means that the class is derived from the MAGE-OM and the value \"ontology\" indicates that the class is derived from the ontology. This property is being added since the MGED Ontology was developed in such a way to include classes that exist in the MAGE-OM as well as classes that exist only in the MGED Ontology. range: __file:///Users/cjm/obo-utils/obo-all/mged/mged.owl#__Description198 property_value: mged:unique_identifier "MO_343" xsd:string property_value: rdfs:comment "The property indicates the derivation of the class. A value of \"mage\" means that the class is derived from the MAGE-OM and the value \"ontology\" indicates that the class is derived from the ontology. This property is being added since the MGED Ontology was developed in such a way to include classes that exist in the MAGE-OM as well as classes that exist only in the MGED Ontology." xsd:string [Typedef] id: mged:class_source comment: The property indicates the derivation of the class. A value of \"mage\" means that the class is derived from the MAGE-OM and the value \"ontology\" indicates that the class is derived from the ontology. This property is being added since the MGED Ontology was developed in such a way to include classes that exist in the MAGE-OM as well as classes that exist only in the MGED Ontology. range: __file:///Users/cjm/obo-utils/obo-all/mged/mged.owl#__Description198 property_value: mged:unique_identifier "MO_343" xsd:string property_value: rdfs:comment "The property indicates the derivation of the class. A value of \"mage\" means that the class is derived from the MAGE-OM and the value \"ontology\" indicates that the class is derived from the ontology. This property is being added since the MGED Ontology was developed in such a way to include classes that exist in the MAGE-OM as well as classes that exist only in the MGED Ontology." xsd:string [Typedef] id: mged:deprecated_from_version comment: property indicating the version of the MGED Ontology that the term was deprecated from property_value: mged:unique_identifier "MO_299" xsd:string property_value: rdfs:comment "property indicating the version of the MGED Ontology that the term was deprecated from" xsd:string [Typedef] id: mged:deprecation_in_version comment: The value of the property indicates what version of the ontology the term was deprecated from. range: __file:///Users/cjm/obo-utils/obo-all/mged/mged.owl#__Description188 property_value: rdfs:comment "The value of the property indicates what version of the ontology the term was deprecated from." xsd:string property_value: mged:unique_identifier "MO_1014" xsd:string [Typedef] id: mged:deprecation_in_version comment: The value of the property indicates what version of the ontology the term was deprecated from. range: __file:///Users/cjm/obo-utils/obo-all/mged/mged.owl#__Description188 property_value: rdfs:comment "The value of the property indicates what version of the ontology the term was deprecated from." xsd:string property_value: mged:unique_identifier "MO_1014" xsd:string [Typedef] id: mged:deprecation_old_parent comment: The value indicates the parent of the term before the term was deprecated. property_value: rdfs:comment "The value indicates the parent of the term before the term was deprecated." xsd:string property_value: mged:unique_identifier "MO_1016" xsd:string [Typedef] id: mged:deprecation_old_parent comment: The value indicates the parent of the term before the term was deprecated. property_value: rdfs:comment "The value indicates the parent of the term before the term was deprecated." xsd:string property_value: mged:unique_identifier "MO_1016" xsd:string [Typedef] id: mged:deprecation_old_restriction comment: The value of the property indicates the restriction that was applied to the class at the time it was deprecated. The value is in the form of: some|property|filler, e.g. some|has_species|Organism. property_value: rdfs:comment "The value of the property indicates the restriction that was applied to the class at the time it was deprecated. The value is in the form of: some|property|filler, e.g. some|has_species|Organism." xsd:string property_value: mged:unique_identifier "MO_1015" xsd:string [Typedef] id: mged:deprecation_old_restriction comment: The value of the property indicates the restriction that was applied to the class at the time it was deprecated. The value is in the form of: some|property|filler, e.g. some|has_species|Organism. property_value: rdfs:comment "The value of the property indicates the restriction that was applied to the class at the time it was deprecated. The value is in the form of: some|property|filler, e.g. some|has_species|Organism." xsd:string property_value: mged:unique_identifier "MO_1015" xsd:string [Typedef] id: mged:deprecation_reason comment: Indicates the why the term was deprecated. The possible values are: deleted_term, split_term, merged_term, replaced_term. range: __file:///Users/cjm/obo-utils/obo-all/mged/mged.owl#__Description202 property_value: rdfs:comment "Indicates the why the term was deprecated. The possible values are: deleted_term, split_term, merged_term, replaced_term." xsd:string property_value: mged:unique_identifier "MO_1013" xsd:string [Typedef] id: mged:deprecation_reason comment: Indicates the why the term was deprecated. The possible values are: deleted_term, split_term, merged_term, replaced_term. range: __file:///Users/cjm/obo-utils/obo-all/mged/mged.owl#__Description202 property_value: rdfs:comment "Indicates the why the term was deprecated. The possible values are: deleted_term, split_term, merged_term, replaced_term." xsd:string property_value: mged:unique_identifier "MO_1013" xsd:string [Typedef] id: mged:deprecation_replacement_term comment: The value of the property indicates the replacement term for the deprecated term. If the term is deprecated without replacement, the value of the property will be the same as the deprecated term itself. property_value: mged:unique_identifier "MO_1012" xsd:string property_value: rdfs:comment "The value of the property indicates the replacement term for the deprecated term. If the term is deprecated without replacement, the value of the property will be the same as the deprecated term itself." xsd:string [Typedef] id: mged:deprecation_replacement_term comment: The value of the property indicates the replacement term for the deprecated term. If the term is deprecated without replacement, the value of the property will be the same as the deprecated term itself. property_value: mged:unique_identifier "MO_1012" xsd:string property_value: rdfs:comment "The value of the property indicates the replacement term for the deprecated term. If the term is deprecated without replacement, the value of the property will be the same as the deprecated term itself." xsd:string [Typedef] id: mged:has_ID comment: property indicating that the class has an identifier property_value: mged:unique_identifier "MO_323" xsd:string property_value: rdfs:comment "property indicating that the class has an identifier" xsd:string [Typedef] id: mged:has_MAGE_description comment: property indicating that the class has an association to a MAGE description property_value: mged:unique_identifier "MO_260" xsd:string property_value: rdfs:comment "property indicating that the class has an association to a MAGE description" xsd:string [Typedef] id: mged:has_URI comment: property indicating that the class has a URI property_value: rdfs:comment "property indicating that the class has a URI" xsd:string property_value: mged:unique_identifier "MO_340" xsd:string [Typedef] id: mged:has_accession comment: property indicating that the class has an accession number property_value: mged:unique_identifier "MO_231" xsd:string property_value: rdfs:comment "property indicating that the class has an accession number" xsd:string [Typedef] id: mged:has_accession_version comment: property indicating that the class has an accession number version property_value: mged:unique_identifier "MO_339" xsd:string property_value: rdfs:comment "property indicating that the class has an accession number version" xsd:string [Typedef] id: mged:has_action comment: property indicating that the class has an action property_value: rdfs:comment "property indicating that the class has an action" xsd:string property_value: mged:unique_identifier "MO_312" xsd:string [Typedef] id: mged:has_additive comment: property indicating that the class has an additive property_value: rdfs:comment "property indicating that the class has an additive" xsd:string property_value: mged:unique_identifier "MO_314" xsd:string [Typedef] id: mged:has_address comment: property indicating that the class has an address property_value: rdfs:comment "property indicating that the class has an address" xsd:string property_value: mged:unique_identifier "MO_277" xsd:string [Typedef] id: mged:has_affiliation comment: property indicating that the class has an affiliation to an institution property_value: mged:unique_identifier "MO_309" xsd:string property_value: rdfs:comment "property indicating that the class has an affiliation to an institution" xsd:string [Typedef] id: mged:has_atmospheric_component comment: property indicating that the class has an atmospheric component property_value: rdfs:comment "property indicating that the class has an atmospheric component" xsd:string property_value: mged:unique_identifier "MO_259" xsd:string [Typedef] id: mged:has_authors comment: property indicating that the class has authors property_value: rdfs:comment "property indicating that the class has authors" xsd:string property_value: mged:unique_identifier "MO_318" xsd:string [Typedef] id: mged:has_been_treated comment: property indicating that the class has been treated property_value: mged:unique_identifier "MO_341" xsd:string property_value: rdfs:comment "property indicating that the class has been treated" xsd:string [Typedef] id: mged:has_bioassay_data comment: property indicating that the class has bioassaydata property_value: rdfs:comment "property indicating that the class has bioassaydata" xsd:string property_value: mged:unique_identifier "MO_252" xsd:string [Typedef] id: mged:has_bioassays comment: property indicating that the class has bioassays property_value: rdfs:comment "property indicating that the class has bioassays" xsd:string property_value: mged:unique_identifier "MO_238" xsd:string [Typedef] id: mged:has_biomaterial_characteristics comment: property indicating that the class has biomaterial characteristics property_value: rdfs:comment "property indicating that the class has biomaterial characteristics" xsd:string property_value: mged:unique_identifier "MO_272" xsd:string [Typedef] id: mged:has_biosource_type comment: property indicating that the class has a biosource type domain: mged:BioSourceProvider property_value: mged:unique_identifier "MO_315" xsd:string property_value: rdfs:comment "property indicating that the class has a biosource type" xsd:string [Typedef] id: mged:has_cancer_site comment: property indicating that the class has a cancer site property_value: mged:unique_identifier "MO_248" xsd:string property_value: rdfs:comment "property indicating that the class has a cancer site" xsd:string [Typedef] id: mged:has_category comment: property indicating that the class has a category property_value: rdfs:comment "property indicating that the class has a category" xsd:string property_value: mged:unique_identifier "MO_249" xsd:string [Typedef] id: mged:has_chromosomal_aberration_classification comment: property indicating that the class has a chromosomal aberration classification property_value: rdfs:comment "property indicating that the class has a chromosomal aberration classification" xsd:string property_value: mged:unique_identifier "MO_253" xsd:string [Typedef] id: mged:has_citation comment: property indicating that the class has a citation property_value: mged:unique_identifier "MO_274" xsd:string property_value: rdfs:comment "property indicating that the class has a citation" xsd:string [Typedef] id: mged:has_clinical_finding comment: property indicating that the class has a clinical finding property_value: rdfs:comment "property indicating that the class has a clinical finding" xsd:string property_value: mged:unique_identifier "MO_316" xsd:string [Typedef] id: mged:has_clinical_record comment: property indicating that the class has a clinical record property_value: mged:unique_identifier "MO_247" xsd:string property_value: rdfs:comment "property indicating that the class has a clinical record" xsd:string [Typedef] id: mged:has_clinical_treatment comment: property indicating that the class has a clinical treatment property_value: mged:unique_identifier "MO_282" xsd:string property_value: rdfs:comment "property indicating that the class has a clinical treatment" xsd:string [Typedef] id: mged:has_compound comment: property indicating that the class has a compound property_value: mged:unique_identifier "MO_302" xsd:string property_value: rdfs:comment "property indicating that the class has a compound" xsd:string [Typedef] id: mged:has_cubic_volume comment: property indicating that the class contains a cubic volume measurement property_value: rdfs:comment "property indicating that the class contains a cubic volume measurement" xsd:string property_value: mged:unique_identifier "MO_245" xsd:string [Typedef] id: mged:has_database comment: property indicating that the class has a database property_value: mged:unique_identifier "MO_233" xsd:string property_value: rdfs:comment "property indicating that the class has a database" xsd:string [Typedef] id: mged:has_database_entry_type comment: property indicating that the class has a database entry type property_value: mged:unique_identifier "MO_240" xsd:string property_value: rdfs:comment "property indicating that the class has a database entry type" xsd:string [Typedef] id: mged:has_description comment: property indicating that the class has a description property_value: rdfs:comment "property indicating that the class has a description" xsd:string property_value: mged:unique_identifier "MO_334" xsd:string [Typedef] id: mged:has_diameter comment: property indicating that the class has a diameter property_value: rdfs:comment "property indicating that the class has a diameter" xsd:string property_value: mged:unique_identifier "MO_301" xsd:string [Typedef] id: mged:has_disease_location comment: property indicating the location of the disease. property_value: rdfs:comment "property indicating the location of the disease." xsd:string property_value: mged:unique_identifier "MO_290" xsd:string [Typedef] id: mged:has_disease_staging comment: property indicating that the class has disease staging property_value: mged:unique_identifier "MO_275" xsd:string property_value: rdfs:comment "property indicating that the class has disease staging" xsd:string [Typedef] id: mged:has_disease_state comment: property indicating that the class has a disease state property_value: rdfs:comment "property indicating that the class has a disease state" xsd:string property_value: mged:unique_identifier "MO_305" xsd:string [Typedef] id: mged:has_donor comment: property indicating that the class has a donor property_value: rdfs:comment "property indicating that the class has a donor" xsd:string property_value: mged:unique_identifier "MO_342" xsd:string [Typedef] id: mged:has_editor comment: property indicating that the class has an editor property_value: rdfs:comment "property indicating that the class has an editor" xsd:string property_value: mged:unique_identifier "MO_256" xsd:string [Typedef] id: mged:has_email comment: property indicating that the class has an email address property_value: mged:unique_identifier "MO_293" xsd:string property_value: rdfs:comment "property indicating that the class has an email address" xsd:string [Typedef] id: mged:has_experiment_design comment: property indicating that the class has an experiment design property_value: rdfs:comment "property indicating that the class has an experiment design" xsd:string property_value: mged:unique_identifier "MO_291" xsd:string [Typedef] id: mged:has_experiment_design_type comment: property indicating that the class has an experiment design type property_value: rdfs:comment "property indicating that the class has an experiment design type" xsd:string property_value: mged:unique_identifier "MO_288" xsd:string [Typedef] id: mged:has_experiment_factors comment: property indicating that the class has experiment factors property_value: mged:unique_identifier "MO_328" xsd:string property_value: rdfs:comment "property indicating that the class has experiment factors" xsd:string [Typedef] id: mged:has_factor_value comment: property indicating that the class has a factor value property_value: rdfs:comment "property indicating that the class has a factor value" xsd:string property_value: mged:unique_identifier "MO_236" xsd:string [Typedef] id: mged:has_factor_value_ontology_entry comment: property indicating that the class has an ontology entry property_value: rdfs:comment "property indicating that the class has an ontology entry" xsd:string property_value: mged:unique_identifier "MO_263" xsd:string [Typedef] id: mged:has_family_member comment: property indicating that the class has a family member property_value: mged:unique_identifier "MO_243" xsd:string property_value: rdfs:comment "property indicating that the class has a family member" xsd:string [Typedef] id: mged:has_family_relationship comment: property indicating that the class has a family relationship property_value: mged:unique_identifier "MO_250" xsd:string property_value: rdfs:comment "property indicating that the class has a family relationship" xsd:string [Typedef] id: mged:has_fax comment: property indicating that the class has a fax property_value: rdfs:comment "property indicating that the class has a fax" xsd:string property_value: mged:unique_identifier "MO_289" xsd:string [Typedef] id: mged:has_feature_shape comment: property indicating that the class has a feature shape property_value: mged:unique_identifier "MO_268" xsd:string property_value: rdfs:comment "property indicating that the class has a feature shape" xsd:string [Typedef] id: mged:has_fiducials comment: property indicating that the class has fiducials property_value: rdfs:comment "property indicating that the class has fiducials" xsd:string property_value: mged:unique_identifier "MO_267" xsd:string [Typedef] id: mged:has_first_name comment: property indicating that the class has a first name property_value: mged:unique_identifier "MO_258" xsd:string property_value: rdfs:comment "property indicating that the class has a first name" xsd:string [Typedef] id: mged:has_hardware comment: property indicating that the class has hardware property_value: mged:unique_identifier "MO_286" xsd:string property_value: rdfs:comment "property indicating that the class has hardware" xsd:string [Typedef] id: mged:has_height comment: property indicating that the class has a height property_value: mged:unique_identifier "MO_317" xsd:string property_value: rdfs:comment "property indicating that the class has a height" xsd:string [Typedef] id: mged:has_host comment: property indicating that the class has a host domain: mged:Host property_value: rdfs:comment "property indicating that the class has a host" xsd:string property_value: mged:unique_identifier "MO_313" xsd:string [Typedef] id: mged:has_host_part comment: property indicating that the class has a host part domain: mged:Host property_value: mged:unique_identifier "MO_283" xsd:string property_value: rdfs:comment "property indicating that the class has a host part" xsd:string [Typedef] id: mged:has_human_readable_URI comment: property indicating that the contents found at this uri are human readable property_value: mged:unique_identifier "MO_330" xsd:string property_value: rdfs:comment "property indicating that the contents found at this uri are human readable" xsd:string [Typedef] id: mged:has_image_format comment: property indicating that the class has an image format domain: mged:PhysicalBioAssay property_value: rdfs:comment "property indicating that the class has an image format" xsd:string property_value: mged:unique_identifier "MO_234" xsd:string [Typedef] id: mged:has_individual comment: property indicating that the class has an individual property_value: mged:unique_identifier "MO_327" xsd:string property_value: rdfs:comment "property indicating that the class has an individual" xsd:string [Typedef] id: mged:has_individual_genetic_characteristics comment: property indicating that the class has individual genetic characteristics property_value: mged:unique_identifier "MO_254" xsd:string property_value: rdfs:comment "property indicating that the class has individual genetic characteristics" xsd:string [Typedef] id: mged:has_initial_time_point comment: property indicating that the class has an individual time point domain: mged:Age property_value: rdfs:comment "property indicating that the class has an individual time point" xsd:string property_value: mged:unique_identifier "MO_292" xsd:string [Typedef] id: mged:has_issue comment: property indicating that the class has an issue domain: mged:BibliographicReference property_value: mged:unique_identifier "MO_294" xsd:string property_value: rdfs:comment "property indicating that the class has an issue" xsd:string [Typedef] id: mged:has_laboratory_test comment: property indicating that the class has a laboratory test property_value: mged:unique_identifier "MO_281" xsd:string property_value: rdfs:comment "property indicating that the class has a laboratory test" xsd:string [Typedef] id: mged:has_last_name comment: property indicating that the class has a last name property_value: rdfs:comment "property indicating that the class has a last name" xsd:string property_value: mged:unique_identifier "MO_255" xsd:string [Typedef] id: mged:has_length [Typedef] id: mged:has_machine_readable_URI comment: property indicating that the contents found at this uri are machine readable (i.e. in a standard format) property_value: rdfs:comment "property indicating that the contents found at this uri are machine readable (i.e. in a standard format)" xsd:string property_value: mged:unique_identifier "MO_336" xsd:string [Typedef] id: mged:has_make comment: property indicating that the class has a make domain: mged:Hardware property_value: mged:unique_identifier "MO_271" xsd:string property_value: rdfs:comment "property indicating that the class has a make" xsd:string [Typedef] id: mged:has_manufacturer comment: property indicating that the class has a manufacturer property_value: mged:unique_identifier "MO_232" xsd:string property_value: rdfs:comment "property indicating that the class has a manufacturer" xsd:string [Typedef] id: mged:has_mass comment: property indicating that the class has a mass property_value: rdfs:comment "property indicating that the class has a mass" xsd:string property_value: mged:unique_identifier "MO_280" xsd:string [Typedef] id: mged:has_maximum_measurement comment: property indicating that the class has a maximum measurement domain: mged:Age property_value: rdfs:comment "property indicating that the class has a maximum measurement" xsd:string property_value: mged:unique_identifier "MO_297" xsd:string [Typedef] id: mged:has_measurement comment: property indicating that the class has a measurement property_value: mged:unique_identifier "MO_325" xsd:string property_value: rdfs:comment "property indicating that the class has a measurement" xsd:string [Typedef] id: mged:has_measurement_type comment: property indicating that the class has a measurement type domain: mged:Measurement property_value: rdfs:comment "property indicating that the class has a measurement type" xsd:string property_value: mged:unique_identifier "MO_242" xsd:string [Typedef] id: mged:has_mid_initials comment: property indicating that the class has a middle initials property_value: mged:unique_identifier "MO_237" xsd:string property_value: rdfs:comment "property indicating that the class has a middle initials" xsd:string [Typedef] id: mged:has_model comment: property indicating that the class has a model domain: mged:Hardware property_value: rdfs:comment "property indicating that the class has a model" xsd:string property_value: mged:unique_identifier "MO_270" xsd:string [Typedef] id: mged:has_name comment: property indicating that the class has a name property_value: mged:unique_identifier "MO_296" xsd:string property_value: rdfs:comment "property indicating that the class has a name" xsd:string [Typedef] id: mged:has_node_value comment: property indicating that the class has a node value property_value: mged:unique_identifier "MO_310" xsd:string property_value: rdfs:comment "property indicating that the class has a node value" xsd:string [Typedef] id: mged:has_node_value_type comment: property indicating that the class has a node value type property_value: mged:unique_identifier "MO_264" xsd:string property_value: rdfs:comment "property indicating that the class has a node value type" xsd:string [Typedef] id: mged:has_nodes comment: property indicating that the class has a node property_value: mged:unique_identifier "MO_307" xsd:string property_value: rdfs:comment "property indicating that the class has a node" xsd:string [Typedef] id: mged:has_nutrient_component comment: property indicating that the class has a nutrient component property_value: rdfs:comment "property indicating that the class has a nutrient component" xsd:string property_value: mged:unique_identifier "MO_321" xsd:string [Typedef] id: mged:has_order comment: property indicating that the class has an order property_value: rdfs:comment "property indicating that the class has an order" xsd:string property_value: mged:unique_identifier "MO_335" xsd:string [Typedef] id: mged:has_organism_part comment: property indicating that the class has an organism part property_value: rdfs:comment "property indicating that the class has an organism part" xsd:string property_value: mged:unique_identifier "MO_285" xsd:string [Typedef] id: mged:has_owner comment: property indicating that the class has an owner property_value: rdfs:comment "property indicating that the class has an owner" xsd:string property_value: mged:unique_identifier "MO_278" xsd:string [Typedef] id: mged:has_pages comment: property indicating that the class has pages domain: mged:BibliographicReference property_value: rdfs:comment "property indicating that the class has pages" xsd:string property_value: mged:unique_identifier "MO_246" xsd:string [Typedef] id: mged:has_parent_organization comment: property indicating that the class has a parent organization property_value: rdfs:comment "property indicating that the class has a parent organization" xsd:string property_value: mged:unique_identifier "MO_257" xsd:string [Typedef] id: mged:has_part_modified comment: property indicating that the class has a modified part property_value: rdfs:comment "property indicating that the class has a modified part" xsd:string property_value: mged:unique_identifier "MO_241" xsd:string [Typedef] id: mged:has_performer comment: property indicating that the protocol has a performer or contact person property_value: rdfs:comment "property indicating that the protocol has a performer or contact person" xsd:string property_value: mged:unique_identifier "MO_273" xsd:string [Typedef] id: mged:has_phone comment: property indicating that the class has a phone property_value: rdfs:comment "property indicating that the class has a phone" xsd:string property_value: mged:unique_identifier "MO_235" xsd:string [Typedef] id: mged:has_prior_disease_state comment: property indicating that the class has a prior disease state property_value: mged:unique_identifier "MO_276" xsd:string property_value: rdfs:comment "property indicating that the class has a prior disease state" xsd:string [Typedef] id: mged:has_property_set comment: property indicating that the class has a property set property_value: rdfs:comment "property indicating that the class has a property set" xsd:string property_value: mged:unique_identifier "MO_266" xsd:string [Typedef] id: mged:has_protocol comment: property indicating that the class has a protocol property_value: rdfs:comment "property indicating that the class has a protocol" xsd:string property_value: mged:unique_identifier "MO_300" xsd:string [Typedef] id: mged:has_providers comment: property indicating that the class has providers property_value: mged:unique_identifier "MO_303" xsd:string property_value: rdfs:comment "property indicating that the class has providers" xsd:string [Typedef] id: mged:has_publication comment: property indicating that the class has a publication property_value: mged:unique_identifier "MO_251" xsd:string property_value: rdfs:comment "property indicating that the class has a publication" xsd:string [Typedef] id: mged:has_publisher comment: property indicating that the class has a publisher property_value: rdfs:comment "property indicating that the class has a publisher" xsd:string property_value: mged:unique_identifier "MO_295" xsd:string [Typedef] id: mged:has_reason_for_deprecation comment: property to indicate the reason for deprecating a term property_value: rdfs:comment "property to indicate the reason for deprecating a term" xsd:string property_value: mged:unique_identifier "MO_306" xsd:string [Typedef] id: mged:has_result comment: property indicating the class has a result property_value: mged:unique_identifier "MO_324" xsd:string property_value: rdfs:comment "property indicating the class has a result" xsd:string [Typedef] id: mged:has_scale comment: property indicating that the class has a scale property_value: mged:unique_identifier "MO_287" xsd:string property_value: rdfs:comment "property indicating that the class has a scale" xsd:string [Typedef] id: mged:has_software comment: property indicating that the class has software property_value: mged:unique_identifier "MO_284" xsd:string property_value: rdfs:comment "property indicating that the class has software" xsd:string [Typedef] id: mged:has_species comment: property indicating that the class has species property_value: rdfs:comment "property indicating that the class has species" xsd:string property_value: mged:unique_identifier "MO_320" xsd:string [Typedef] id: mged:has_test_protocol comment: property indicating that the test has a test protocol property_value: rdfs:comment "property indicating that the test has a test protocol" xsd:string property_value: mged:unique_identifier "MO_244" xsd:string [Typedef] id: mged:has_test_result comment: property indicating that the test has a test result property_value: rdfs:comment "property indicating that the test has a test result" xsd:string property_value: mged:unique_identifier "MO_261" xsd:string [Typedef] id: mged:has_test_type comment: property indicating that the class has a clinical test property_value: rdfs:comment "property indicating that the class has a clinical test" xsd:string property_value: mged:unique_identifier "MO_311" xsd:string [Typedef] id: mged:has_text comment: property indicating that the class has text property_value: mged:unique_identifier "MO_298" xsd:string property_value: rdfs:comment "property indicating that the class has text" xsd:string [Typedef] id: mged:has_title comment: property indicating that the class has a title property_value: mged:unique_identifier "MO_337" xsd:string property_value: rdfs:comment "property indicating that the class has a title" xsd:string [Typedef] id: mged:has_toll_free_phone comment: property indicating that the class has a toll free phone property_value: mged:unique_identifier "MO_329" xsd:string property_value: rdfs:comment "property indicating that the class has a toll free phone" xsd:string [Typedef] id: mged:has_treatment comment: property indicating that the class has a treatment property_value: mged:unique_identifier "MO_262" xsd:string property_value: rdfs:comment "property indicating that the class has a treatment" xsd:string [Typedef] id: mged:has_type comment: property indicating that the class has a type property_value: mged:unique_identifier "MO_319" xsd:string property_value: rdfs:comment "property indicating that the class has a type" xsd:string [Typedef] id: mged:has_units comment: property indicating that the class has units property_value: mged:unique_identifier "MO_269" xsd:string property_value: rdfs:comment "property indicating that the class has units" xsd:string [Typedef] id: mged:has_value comment: property indicating that the class has a value property_value: rdfs:comment "property indicating that the class has a value" xsd:string property_value: mged:unique_identifier "MO_326" xsd:string [Typedef] id: mged:has_version comment: property indicating that the class has a version property_value: rdfs:comment "property indicating that the class has a version" xsd:string property_value: mged:unique_identifier "MO_239" xsd:string [Typedef] id: mged:has_volume comment: property indicating that the class has a volume domain: mged:BibliographicReference property_value: rdfs:comment "property indicating that the class has a volume" xsd:string property_value: mged:unique_identifier "MO_308" xsd:string [Typedef] id: mged:has_year comment: property indicating that the class has a year property_value: rdfs:comment "property indicating that the class has a year" xsd:string property_value: mged:unique_identifier "MO_322" xsd:string [Typedef] id: mged:is_solvent comment: property indicating that the class is a solvent property_value: rdfs:comment "property indicating that the class is a solvent" xsd:string property_value: mged:unique_identifier "MO_332" xsd:string [Typedef] id: mged:is_user_defined comment: property indicating that the class is user defined property_value: mged:unique_identifier "MO_279" xsd:string property_value: rdfs:comment "property indicating that the class is user defined" xsd:string [Typedef] id: mged:replaced_with_term comment: The value of the property indicates the replacement term. property_value: mged:unique_identifier "MO_1018" xsd:string property_value: rdfs:comment "The value of the property indicates the replacement term." xsd:string [Typedef] id: mged:replaced_with_term comment: The value of the property indicates the replacement term. property_value: mged:unique_identifier "MO_1018" xsd:string property_value: rdfs:comment "The value of the property indicates the replacement term." xsd:string [Typedef] id: mged:split_to_term comment: The value of the property indicates a replacement term since the term was split. property_value: mged:unique_identifier "MO_1017" xsd:string property_value: rdfs:comment "The value of the property indicates a replacement term since the term was split." xsd:string [Typedef] id: mged:split_to_term comment: The value of the property indicates a replacement term since the term was split. property_value: mged:unique_identifier "MO_1017" xsd:string property_value: rdfs:comment "The value of the property indicates a replacement term since the term was split." xsd:string [Typedef] id: mged:synonym comment: This property is used to indicate additional terms that have the same meaning as the term that the property is applied to. The terms that have the same meaning as the term that this property is applied to will be the value of the property. range: xsd:string property_value: mged:unique_identifier "MO_333" xsd:string property_value: rdfs:comment "This property is used to indicate additional terms that have the same meaning as the term that the property is applied to. The terms that have the same meaning as the term that this property is applied to will be the value of the property." xsd:string [Typedef] id: mged:synonym comment: This property is used to indicate additional terms that have the same meaning as the term that the property is applied to. The terms that have the same meaning as the term that this property is applied to will be the value of the property. range: xsd:string property_value: mged:unique_identifier "MO_333" xsd:string property_value: rdfs:comment "This property is used to indicate additional terms that have the same meaning as the term that the property is applied to. The terms that have the same meaning as the term that this property is applied to will be the value of the property." xsd:string [Typedef] id: mged:unique_identifier comment: A unique alphanumeric identifier for the term. This will exist in the form of MO_someNumber, e.g. MO_123. property_value: mged:unique_identifier "MO_331" xsd:string property_value: rdfs:comment "A unique alphanumeric identifier for the term. This will exist in the form of MO_someNumber, e.g. MO_123." xsd:string [Typedef] id: mged:unique_identifier comment: A unique alphanumeric identifier for the term. This will exist in the form of MO_someNumber, e.g. MO_123. property_value: mged:unique_identifier "MO_331" xsd:string property_value: rdfs:comment "A unique alphanumeric identifier for the term. This will exist in the form of MO_someNumber, e.g. MO_123." xsd:string [Typedef] id: mged:was_replaced_by comment: instance property to indicate what the term was replaced by property_value: rdfs:comment "instance property to indicate what the term was replaced by" xsd:string property_value: mged:unique_identifier "MO_304" xsd:string [Typedef] id: mged:was_tested_for comment: property indicating that the class was tested for property_value: mged:unique_identifier "MO_265" xsd:string property_value: rdfs:comment "property indicating that the class was tested for" xsd:string [Instance] id: mged:A instance_of: mged:DistanceUnit property_value: rdfs:comment "Angstrom, unit of distance, 1 angstrom is one tenth of a nanometer" xsd:string property_value: mged:unique_identifier "MO_515" xsd:string [Instance] id: mged:ATCC_Cultures instance_of: mged:CellLineDatabase property_value: rdfs:comment "database resource for bacteria, bacteriophages, cell lines, fungi and yeast, plant tissue cultures, plant seeds, protozoa and algae and plant and animal viruses" xsd:string property_value: mged:has_human_readable_URI "http://www.atcc.org/Cultures/Products.cfm" xsd:string property_value: mged:unique_identifier "MO_979" xsd:string [Instance] id: mged:ATCC_Cultures instance_of: mged:CellLineDatabase property_value: rdfs:comment "database resource for bacteria, bacteriophages, cell lines, fungi and yeast, plant tissue cultures, plant seeds, protozoa and algae and plant and animal viruses" xsd:string property_value: mged:has_human_readable_URI "http://www.atcc.org/Cultures/Products.cfm" xsd:string property_value: mged:unique_identifier "MO_979" xsd:string [Instance] id: mged:Adult_Mouse_Anatomy instance_of: mged:OrganismPartDatabase property_value: mged:unique_identifier "MO_992" xsd:string property_value: rdfs:comment "This ontology describes the anatomy of the adult mouse. It contains anatomical structures for the postnatal mouse (Theiler stage 28)." xsd:string property_value: mged:has_machine_readable_URI "http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/MA.ontology?rev=1.1&view=markup" xsd:string [Instance] id: mged:Affymetrix_DAT instance_of: mged:ImageFormat property_value: mged:unique_identifier "MO_786" xsd:string property_value: rdfs:comment "A proprietary image data format that is lossless and containing one channel of data." xsd:string [Instance] id: mged:Affymetrix_average_difference instance_of: mged:DerivedBioAssayType property_value: mged:unique_identifier "MO_649" xsd:string property_value: rdfs:comment "the method used by Affymetrix to obtain mean signal intensity from a group of related Features. This involves calculation of the overall sum of perfect match minus mismatch pairs divided by the number of pairs." xsd:string [Instance] id: mged:BAC instance_of: mged:DeprecatedTerms property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_replacement_term mged:PhysicalBioSequenceType property_value: mged:deprecation_old_parent mged:PhysicalBioSequenceType property_value: rdfs:comment "sequence from a bacterial artificial chromosome\nexact synonym: bacterial artificial chromosome" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:synonym "bacterial artificial chromosome" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_985" xsd:string [Instance] id: mged:CABRI_Bacteria_and_Archaea_Strains instance_of: mged:StrainOrLineDatabase property_value: mged:has_human_readable_URI "http://www.cabri.org/HyperCat/bact/all_A.htm" xsd:string property_value: rdfs:comment "List of CABRI bacteria and archaea strains sorted by genus and species. It includes more than 40,000 resources that are available from seven European collections participating in the CABRI (Common Access to Biological Resources and Information) initiative (see http://www.cabri.org/ ). Detailed descriptions can be reached from the list and strains of interest can be requested." xsd:string property_value: mged:unique_identifier "MO_1008" xsd:string [Instance] id: mged:CABRI_Filamentous_Fungi_Strains instance_of: mged:StrainOrLineDatabase property_value: rdfs:comment "List of CABRI filamentous fungi strains sorted by genus and species. It includes more than 30,000 resources that are available from five European collections participating in the CABRI (Common Access to Biological Resources and Information) initiative (see http://www.cabri.org/ ). Detailed descriptions can be reached from the list and strains of interest can be requested." xsd:string property_value: mged:unique_identifier "MO_1009" xsd:string property_value: mged:has_human_readable_URI "http://www.cabri.org/HyperCat/fun/all_A.htm" xsd:string [Instance] id: mged:CABRI_HLA_typed_B_Cell_lines instance_of: mged:CellLineDatabase property_value: mged:has_human_readable_URI "http://www.cabri.org/HyperCat/cells/hla.htm" xsd:string property_value: rdfs:comment "List of CABRI HLA typed B cell lines sorted by name. It includes 238 resources that are available from a European collection participating in the CABRI (Common Access to Biological Resources\n and Information) initiative (see http://www.cabri.org/ ). Detailed \ndescriptions can be reached from the list and cell lines of interest can be requested." xsd:string property_value: mged:unique_identifier "MO_1005" xsd:string [Instance] id: mged:CABRI_Human_and_Animal_Cell_lines instance_of: mged:CellLineDatabase property_value: mged:unique_identifier "MO_536" xsd:string property_value: mged:has_human_readable_URI "http://www.cabri.org/HyperCat/cells/all.htm" xsd:string property_value: rdfs:comment "Database entry from CABRI, a database listing sources such as cell lines, bacteria, plasmids etc." xsd:string [Instance] id: mged:CABRI_Hybridomas instance_of: mged:CellLineDatabase property_value: mged:unique_identifier "MO_1006" xsd:string property_value: rdfs:comment "List of CABRI hybridomas sorted by name. It includes 397 resources that are available from European collections participating in the CABRI (Common Access to Biological Resources and Information) initiative (see http://www.cabri.org/ ). 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Detailed descriptions can be reached from the list and strains of interest can be requested." xsd:string property_value: mged:unique_identifier "MO_1010" xsd:string property_value: mged:has_human_readable_URI "http://www.cabri.org/HyperCat/yeast/all_A.htm" xsd:string [Instance] id: mged:CBIL_CV instance_of: mged:CellTypeDatabase property_value: mged:has_human_readable_URI "http://www.cbil.upenn.edu/anatomy.php3" xsd:string property_value: rdfs:comment "a controlled vocabulary provided by CBIL" xsd:string property_value: mged:unique_identifier "MO_886" xsd:string [Instance] id: mged:CBIL_CV instance_of: mged:CellTypeDatabase property_value: mged:has_human_readable_URI "http://www.cbil.upenn.edu/anatomy.php3" xsd:string property_value: rdfs:comment "a controlled vocabulary provided by CBIL" xsd:string property_value: mged:unique_identifier "MO_886" xsd:string [Instance] id: mged:CBIL_CV instance_of: mged:CellTypeDatabase property_value: mged:has_human_readable_URI "http://www.cbil.upenn.edu/anatomy.php3" xsd:string property_value: rdfs:comment "a controlled vocabulary provided by CBIL" xsd:string property_value: mged:unique_identifier "MO_886" xsd:string [Instance] id: mged:CLDB_Human_and_Animal_Cell_Line instance_of: mged:CellLineDatabase property_value: mged:has_human_readable_URI __file:///Users/cjm/obo-utils/obo-all/mged/mged.owl#__Description201 property_value: mged:unique_identifier "MO_1007" xsd:string property_value: rdfs:comment "List of cell lines available in the Cell Line Database (CLDB), that includes more than 4,000 resources from many European collections and Italian laboratories. Indexes are given by species/strain, pathology, tumour, tissue/organ, and transforming agent." xsd:string [Instance] id: mged:CellML instance_of: mged:OrganismPartDatabase property_value: mged:has_human_readable_URI "http://portal.bioengineering.elyt.ods.org/ontology/" xsd:string property_value: mged:unique_identifier "MO_967" xsd:string property_value: rdfs:comment "Ontology describing anatomical and physiological relationships. " xsd:string [Instance] id: mged:ChEBI instance_of: mged:CompoundDatabase property_value: mged:unique_identifier "MO_857" xsd:string property_value: rdfs:comment "A freely available dictionary of small molecular entities. The term molecular entity encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms." xsd:string property_value: mged:has_human_readable_URI "http://www.ebi.ac.uk/chebi" xsd:string [Instance] id: mged:ChemID instance_of: mged:CompoundDatabase property_value: rdfs:comment "Database entry from the ChemIDplus database which stores information on the structure, identifiers etc for compounds." xsd:string property_value: mged:unique_identifier "MO_426" xsd:string property_value: mged:has_human_readable_URI "http://chem.sis.nlm.nih.gov/chemidplus" xsd:string [Instance] id: mged:Ci instance_of: mged:RadiationUnit property_value: rdfs:comment "Curie. Unit of the rate of radioactive decay, i.e., the activity of that quantity of radioactive material in which the number of disintegrations per second is 3.7E10. 1 Ci = 3.75 x1010 atom disintegrations per second (dps). 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The precise definition of one IU differs from substance to substance and is established by international agreement and is based on a reference provided by the Committee on Biological Standardization of the World Health Organization." xsd:string property_value: mged:unique_identifier "1011" xsd:string [Instance] id: mged:IUPAC_Clinical_Chemistry_Guidelines instance_of: mged:TestTypeDatabase property_value: mged:has_human_readable_URI "http://www.iupac.org/publications/pac/2000/205/205olesen.html" xsd:string property_value: mged:unique_identifier "MO_593" xsd:string property_value: rdfs:comment " A resource of vocabularies for describing clinical tests, e.g. blood chemistry." xsd:string [Instance] id: mged:JAX_mouse_strains instance_of: mged:StrainOrLineDatabase property_value: rdfs:comment "Database entry from the resource at The Jackson Laboratory which has details of approved mouse strain nomenclature." xsd:string property_value: mged:has_human_readable_URI "http://www.informatics.jax.org/external/festing/mouse/STRAINS.shtml" xsd:string property_value: mged:unique_identifier "MO_369" xsd:string [Instance] id: mged:JPEG instance_of: mged:ImageFormat property_value: mged:unique_identifier "MO_746" xsd:string property_value: rdfs:comment "Joint Photographic Experts Group format, a common image data format containing grayscale or RGB data compressed with little to high data loss." xsd:string [Instance] id: mged:K instance_of: mged:TemperatureUnit property_value: rdfs:comment "Kelvin, unit of temperature" xsd:string property_value: mged:unique_identifier "MO_614" xsd:string [Instance] id: mged:L instance_of: mged:VolumeUnit property_value: mged:unique_identifier "MO_444" xsd:string property_value: rdfs:comment "liter, unit of volume" xsd:string [Instance] id: mged:LOINC instance_of: mged:TestTypeDatabase property_value: mged:unique_identifier "MO_731" xsd:string property_value: mged:has_machine_readable_URI "http://www.loinc.org/download" xsd:string property_value: rdfs:comment "Database resource for universal identifiers for laboratory and other clinical observations" xsd:string [Instance] id: mged:M instance_of: mged:ConcentrationUnit property_value: rdfs:comment "Mole per liter or molarity, concentration unit" xsd:string property_value: mged:unique_identifier "MO_936" xsd:string [Instance] id: mged:MAD_stage instance_of: mged:DevelopmentalStageDatabase property_value: rdfs:comment "database entry from mouse anatomical dictionary for developmental stage term" xsd:string property_value: mged:unique_identifier "MO_693" xsd:string property_value: mged:has_human_readable_URI "http://www.informatics.jax.org/mgihome/GXD/AD/" xsd:string [Instance] id: mged:MAD_stage instance_of: mged:DevelopmentalStageDatabase property_value: rdfs:comment "database entry from mouse anatomical dictionary for developmental stage term" xsd:string property_value: mged:unique_identifier "MO_693" xsd:string property_value: mged:has_human_readable_URI "http://www.informatics.jax.org/mgihome/GXD/AD/" xsd:string [Instance] id: mged:MAD_stage instance_of: mged:DevelopmentalStageDatabase property_value: rdfs:comment "database entry from mouse anatomical dictionary for developmental stage term" xsd:string property_value: mged:unique_identifier "MO_693" xsd:string property_value: mged:has_human_readable_URI "http://www.informatics.jax.org/mgihome/GXD/AD/" xsd:string [Instance] id: mged:MAS4_average_difference instance_of: mged:DerivedBioAssayType property_value: mged:unique_identifier "MO_782" xsd:string property_value: rdfs:comment "A quantitative measure of the relative abundance of a transcript. 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mged:has_human_readable_URI "http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C7057" xsd:string property_value: rdfs:comment "a controlled vocabulary for disease states" xsd:string [Instance] id: mged:NCI_geographic_location_database instance_of: mged:GeographicLocationDatabase property_value: mged:unique_identifier "MO_630" xsd:string property_value: rdfs:comment "a controlled vocabulary for geographic locations" xsd:string property_value: mged:has_human_readable_URI "http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C16632" xsd:string [Instance] id: mged:NCI_histology_database instance_of: mged:HistologyDatabase property_value: rdfs:comment "a controlled vocabulary for histology" xsd:string property_value: mged:unique_identifier "MO_537" xsd:string property_value: mged:has_human_readable_URI "http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C4741" xsd:string [Instance] id: mged:NCI_organism_part_database instance_of: mged:OrganismPartDatabase property_value: rdfs:comment "a controlled vocabulary of organism parts" xsd:string property_value: mged:unique_identifier "MO_690" xsd:string property_value: mged:has_human_readable_URI "http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C13007" xsd:string [Instance] id: mged:NCI_strain_or_line_database instance_of: mged:StrainOrLineDatabase property_value: mged:unique_identifier "MO_397" xsd:string property_value: rdfs:comment "a controlled vocabulary for strains or lines" xsd:string property_value: mged:has_human_readable_URI "http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C16403" xsd:string [Instance] id: mged:NCI_targeted_cell_type_database instance_of: mged:TargetedCellTypeDatabase property_value: rdfs:comment "a controlled vocabulary of targeted cell types" xsd:string property_value: mged:unique_identifier "MO_351" xsd:string property_value: mged:has_human_readable_URI "http://nciterms.nci.nih.gov:80/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12596" xsd:string [Instance] id: mged:NCI_tumor_grading_database instance_of: mged:TumorGradingDatabase property_value: mged:has_human_readable_URI "http://nciterms.nci.nih.gov/NCIBrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C28076" xsd:string property_value: rdfs:comment "a controlled vocabulary of tumor grading terms" xsd:string property_value: mged:unique_identifier "MO_819" xsd:string [Instance] id: mged:ORF instance_of: mged:DeprecatedTerms property_value: mged:deprecation_old_parent mged:TheoreticalBioSequenceType property_value: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: rdfs:comment "sequence which represents an open reading frame, a series of codon triplets deduced from a DNA sequence, that contain a start and a stop codon." xsd:string property_value: mged:unique_identifier "MO_413" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:PAC instance_of: mged:DeprecatedTerms property_value: mged:deprecation_old_parent mged:PhysicalBioSequenceType property_value: mged:deprecation_replacement_term mged:PhysicalBioSequenceType property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_909" xsd:string property_value: rdfs:comment "sequence from a P1 artificial chromosome" xsd:string [Instance] id: mged:PCR instance_of: mged:DesignElement property_value: rdfs:comment "Polymerase chain reaction. An element generated using this procedure." xsd:string property_value: mged:unique_identifier "MO_915" xsd:string [Instance] id: mged:PCR_amplicon instance_of: mged:PhysicalBioSequenceType property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:unique_identifier "MO_450" xsd:string property_value: rdfs:comment "BioSequence generated by means of polymerase chain reaction" xsd:string [Instance] id: mged:PCR_amplification instance_of: mged:ExperimentalProtocolType property_value: mged:unique_identifier "MO_358" xsd:string property_value: rdfs:comment "Amplification of nucleic acid sequence by use of the polymerase chain reaction whereby the number of templates grows geometrically with each cycle. " xsd:string [Instance] id: mged:PCR_amplification instance_of: mged:ExperimentalProtocolType property_value: mged:unique_identifier "MO_358" xsd:string property_value: rdfs:comment "Amplification of nucleic acid sequence by use of the polymerase chain reaction whereby the number of templates grows geometrically with each cycle. " xsd:string [Instance] id: mged:PCR_fail instance_of: mged:FailType property_value: rdfs:comment "PCR where no products of any kind appear in gel-separated reaction products." xsd:string property_value: mged:unique_identifier "MO_667" xsd:string [Instance] id: mged:PCR_primer instance_of: mged:DeprecatedTerms property_value: mged:deprecation_replacement_term mged:PhysicalBioSequenceType property_value: mged:deprecation_old_parent mged:PhysicalBioSequenceType property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:unique_identifier "MO_651" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: rdfs:comment "single oligo used for polymerase chain reaction direction unspecified" xsd:string [Instance] id: mged:PCR_primer_forward instance_of: mged:DeprecatedTerms property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_replacement_term mged:PhysicalBioSequenceType property_value: mged:deprecation_old_parent mged:PhysicalBioSequenceType property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:unique_identifier "MO_381" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: rdfs:comment "single stranded oligo used for polymerase chain reaction" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:PCR_primer_reverse instance_of: mged:DeprecatedTerms property_value: mged:deprecation_old_parent mged:PhysicalBioSequenceType property_value: mged:deprecation_replacement_term mged:PhysicalBioSequenceType property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: rdfs:comment "single stranded oligo used for polymerase chain reaction" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:unique_identifier "MO_640" xsd:string [Instance] id: mged:PCR_questionable instance_of: mged:FailType property_value: mged:unique_identifier "MO_620" xsd:string property_value: rdfs:comment "PCR with multiple bands, or smear, in gel-separated reaction products" xsd:string [Instance] id: mged:PNG instance_of: mged:ImageFormat property_value: rdfs:comment "Portable Network Graphic, a lossless image data format." xsd:string property_value: mged:unique_identifier "MO_1001" xsd:string [Instance] id: mged:Pathbase instance_of: mged:HistologyDatabase property_value: mged:unique_identifier "MO_972" xsd:string property_value: mged:has_human_readable_URI "http://eulep.anat.cam.ac.uk/Search_Pathbase/index.php" xsd:string property_value: rdfs:comment "database of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice" xsd:string [Instance] id: mged:Pearson_correlation instance_of: mged:NodeValueType property_value: rdfs:comment "The Pearson correlation is defined as the covariance of two data series divided by the product of their standard deviations." xsd:string property_value: mged:unique_identifier "MO_632" xsd:string [Instance] id: mged:R instance_of: mged:RadiationUnit property_value: mged:unique_identifier "MO_725" xsd:string property_value: rdfs:comment "Roentgen. Unit of exposure to gamma or x-rays in the air. 1 R= 2.58E-4 coulombs per kg." xsd:string [Instance] id: mged:RMA instance_of: mged:DerivedBioAssayType property_value: rdfs:comment "Robust Multiarray Average. A quantitative measure of the relative abundance of a transcript. RMA is a summary measure of related Ôperfect matchÕ Features on an Affymetrix array. The values are background-adjusted, normalized and log-transformed values." xsd:string property_value: mged:unique_identifier "MO_987" xsd:string [Instance] id: mged:RNA instance_of: mged:PolymerType property_value: mged:unique_identifier "MO_594" xsd:string property_value: rdfs:comment "Ribonucleic acid." xsd:string [Instance] id: mged:RNA_stability_design instance_of: mged:BioMolecularAnnotation property_value: mged:unique_identifier "MO_553" xsd:string property_value: rdfs:comment "A RNA stability experiment design type examines the stability and/or decay of RNA transcripts." xsd:string [Instance] id: mged:Rad instance_of: mged:RadiationUnit property_value: mged:unique_identifier "MO_585" xsd:string property_value: rdfs:comment "Radiation absorbed dose. Unit of energy absorbed per unit mass as a result of exposure to radiation. 1 rad = Absorption of 100 ergs per gram of material = 0.01Gy." xsd:string [Instance] id: mged:Rem instance_of: mged:RadiationUnit property_value: rdfs:comment "Roentgen Equivalent Man. Unit of dose equivalent, i.e., the measure of potential biological damage caused by exposure and absorption of radiation. Rem = absorbed dose (rad) x quality factor (Q). Q is unique to the type of incident radiation." xsd:string property_value: mged:unique_identifier "MO_908" xsd:string [Instance] id: mged:SequenceOntology instance_of: mged:SequenceOntologyDatabase property_value: mged:unique_identifier "MO_724" xsd:string property_value: rdfs:comment "The Sequence Ontology is a set of terms used to describe features on a nucleotide or protein sequence." xsd:string property_value: mged:has_machine_readable_URI "http://song.sourceforge.net/" xsd:string [Instance] id: mged:Spearmans_rank_correlation instance_of: mged:NodeValueType property_value: mged:unique_identifier "MO_552" xsd:string property_value: rdfs:comment "Computed as the ordinary Pearson correlation coefficient between two groups of rankings." xsd:string [Instance] id: mged:TAIR instance_of: mged:StrainOrLineDatabase property_value: rdfs:comment "The Arabidopsis Information Resource." xsd:string property_value: mged:unique_identifier "MO_660" xsd:string property_value: mged:has_human_readable_URI "http://www.arabidopsis.org/servlets/Search?action=new_search&type=ecotype" xsd:string [Instance] id: mged:TAIR instance_of: mged:StrainOrLineDatabase property_value: rdfs:comment "The Arabidopsis Information Resource." xsd:string property_value: mged:unique_identifier "MO_660" xsd:string property_value: mged:has_human_readable_URI "http://www.arabidopsis.org/servlets/Search?action=new_search&type=ecotype" xsd:string [Instance] id: mged:TAIR_arabidopsis_anatomy_ontology instance_of: mged:OrganismPartDatabase property_value: rdfs:comment "A structured controlled vocabulary for the anatomy of Arabidopsis." xsd:string property_value: mged:unique_identifier "MO_809" xsd:string property_value: mged:has_machine_readable_URI "http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/anatomy/gross_anatomy/plant_gross_anatomy/Arabidopsis/Attic/arabidopsis_anatomy.ontology" xsd:string [Instance] id: mged:TAIR_arabidopsis_development_ontology instance_of: mged:DevelopmentalStageDatabase property_value: mged:has_machine_readable_URI "http://cvs.sourceforge.net/viewcvs.py/obo/obo/ontology/developmental/plant_development/Arabidopsis/temporal.tair?rev=1.21&view=markup" xsd:string property_value: rdfs:comment "An ontology of stages of growth and development of the model plant Arabidopsis thaliana." xsd:string property_value: mged:unique_identifier "MO_919" xsd:string [Instance] id: mged:TDMS instance_of: mged:OrganismPartDatabase property_value: rdfs:comment "Toxicology Data Management System, a database resource for systems, organs, pathology, etc." xsd:string property_value: mged:unique_identifier "MO_718" xsd:string property_value: mged:has_human_readable_URI "http://hazel.niehs.nih.gov/user_spt/pct_terms.htm" xsd:string [Instance] id: mged:TDMS instance_of: mged:OrganismPartDatabase property_value: rdfs:comment "Toxicology Data Management System, a database resource for systems, organs, pathology, etc." xsd:string property_value: mged:unique_identifier "MO_718" xsd:string property_value: mged:has_human_readable_URI "http://hazel.niehs.nih.gov/user_spt/pct_terms.htm" xsd:string [Instance] id: mged:TDMS instance_of: mged:OrganismPartDatabase property_value: rdfs:comment "Toxicology Data Management System, a database resource for systems, organs, pathology, etc." xsd:string property_value: mged:unique_identifier "MO_718" xsd:string property_value: mged:has_human_readable_URI "http://hazel.niehs.nih.gov/user_spt/pct_terms.htm" xsd:string [Instance] id: mged:TDMS instance_of: mged:OrganismPartDatabase property_value: rdfs:comment "Toxicology Data Management System, a database resource for systems, organs, pathology, etc." xsd:string property_value: mged:unique_identifier "MO_718" xsd:string property_value: mged:has_human_readable_URI "http://hazel.niehs.nih.gov/user_spt/pct_terms.htm" xsd:string [Instance] id: mged:TIFF instance_of: mged:ImageFormat property_value: rdfs:comment "Tag Image File Format (TIFF) is a common format to describe and store raster image data from scanners and other imaging devices. TIFFs may contain one or more channels and the data may be compressed using a lossless compression algorithm." xsd:string property_value: mged:unique_identifier "MO_638" xsd:string [Instance] id: mged:UMLS instance_of: mged:DiseaseStateDatabase property_value: mged:unique_identifier "MO_947" xsd:string property_value: mged:has_human_readable_URI "http://www.nlm.nih.gov/research/umls/" xsd:string property_value: rdfs:comment "Database resource, unified medical language system, an ontology constructed by merging several disparate ontologies, available from NIH." xsd:string [Instance] id: mged:U_per_L instance_of: mged:ConcentrationUnit property_value: rdfs:comment "units per liter" xsd:string property_value: mged:unique_identifier "MO_875" xsd:string [Instance] id: mged:U_per_week instance_of: mged:OtherUnit property_value: rdfs:comment "units per week, e.g. the number of units of alcohol consumed over a period of 7 days" xsd:string property_value: mged:unique_identifier "MO_388" xsd:string [Instance] id: mged:WebRENI instance_of: mged:DiseaseStateDatabase property_value: mged:unique_identifier "MO_737" xsd:string property_value: mged:has_human_readable_URI "http://www.item.fraunhofer.de/reni/index/htm" xsd:string property_value: rdfs:comment "database entry from WebReni A resource for rat and mouse unified nomenclature describing lesions" xsd:string [Instance] id: mged:YAC instance_of: mged:DeprecatedTerms property_value: mged:deprecation_old_parent mged:PhysicalBioSequenceType property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_replacement_term mged:PhysicalBioSequenceType property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_794" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: rdfs:comment "sequence from yeast artificial chromosome" xsd:string [Instance] id: mged:_32P instance_of: mged:LabelCompound property_value: rdfs:comment "32 P, radioactive isotope of phosphorus used for labeling/detection purposes" xsd:string property_value: mged:unique_identifier "MO_839" xsd:string [Instance] id: mged:_33P instance_of: mged:LabelCompound property_value: rdfs:comment "33 P, radioactive isotope of phosphorus, used for labeling/detection purposes." xsd:string property_value: mged:unique_identifier "MO_427" xsd:string [Instance] id: mged:absolute instance_of: mged:MeasurementType property_value: mged:unique_identifier "MO_741" xsd:string property_value: rdfs:comment "a measurement where the value is independent of other measurements" xsd:string [Instance] id: mged:acclimatization instance_of: mged:ComplexAction property_value: mged:unique_identifier "MO_776" xsd:string property_value: rdfs:comment "The action of stabilizing an organism prior to treatment" xsd:string [Instance] id: mged:acclimatization instance_of: mged:ComplexAction property_value: mged:unique_identifier "MO_776" xsd:string property_value: rdfs:comment "The action of stabilizing an organism prior to treatment" xsd:string [Instance] id: mged:acrossBioAssay_mean_and_coefficient_of_variation instance_of: mged:DerivedBioAssayType property_value: mged:unique_identifier "MO_840" xsd:string property_value: rdfs:comment "The mean and coefficient of variation values resulting from computationally combining 2 or more sets of bioassay data." xsd:string [Instance] id: mged:acrossBioAssay_mean_and_p_values instance_of: mged:DerivedBioAssayType property_value: rdfs:comment "The mean and associated p-values resulting from computationally combining 2 or more sets of bioassay data." xsd:string property_value: mged:unique_identifier "MO_671" xsd:string [Instance] id: mged:acrossBioAssay_mean_and_standard_deviation instance_of: mged:DerivedBioAssayType property_value: mged:unique_identifier "MO_946" xsd:string property_value: rdfs:comment "The mean and standard deviation values resulting from computationally combining 2 or more sets of bioassay data." xsd:string [Instance] id: mged:acrossBioAssay_mean_and_variance instance_of: mged:DerivedBioAssayType property_value: rdfs:comment "The mean and variance values resulting from computationally combining 2 or more sets of bioassay data." xsd:string property_value: mged:unique_identifier "MO_400" xsd:string [Instance] id: mged:across_bioassay_data_set_function instance_of: mged:DataTransformationProtocolType property_value: mged:unique_identifier "MO_606" xsd:string property_value: rdfs:comment "A function applied to corresponding values coming from a set of compatible Measured/Derived bioassay data sets. Two Measured/Derived bioassay data sets are compatible if there is a natural one-to-one correspondence between them." xsd:string [Instance] id: mged:activity_units_per_ml instance_of: mged:OtherUnit property_value: mged:deprecated_from_version mged:version_1.3.1 property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:unique_identifier "MO_870" xsd:string property_value: rdfs:comment "Units of defined biological activity, e.g. cytokine stimulation, per ml." xsd:string [Instance] id: mged:ad_libitum instance_of: mged:DeliveryMethod property_value: mged:unique_identifier "MO_592" xsd:string property_value: rdfs:comment "A delivery method for compounds/drugs where the compound or drug is freely available." xsd:string [Instance] id: mged:add instance_of: mged:AtomicAction property_value: mged:unique_identifier "MO_815" xsd:string property_value: rdfs:comment "The procedure of placing one physical object in the same container/physical space as another." xsd:string [Instance] id: mged:agar instance_of: mged:Media property_value: rdfs:comment "A type of solid media commonly used for growing organisms" xsd:string property_value: mged:unique_identifier "MO_935" xsd:string [Instance] id: mged:agar_stab instance_of: mged:BioSourceType property_value: mged:unique_identifier "MO_971" xsd:string property_value: rdfs:comment "agar stab, a cell culture inoculated into agar for long term storage" xsd:string [Instance] id: mged:age instance_of: mged:BioMaterialCharacteristicCategory property_value: mged:unique_identifier "MO_467" xsd:string property_value: rdfs:comment "A descriptor for FactorValue where age is compared." xsd:string [Instance] id: mged:alexa_350 instance_of: mged:LabelCompound property_value: rdfs:comment "Absorbs at 346 nm, emission maxima at 442 nm (blue). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble. \n" xsd:string property_value: mged:unique_identifier "MO_512" xsd:string [Instance] id: mged:alexa_430 instance_of: mged:LabelCompound property_value: rdfs:comment "Absorbs at 433 nm, emission maxima at 539 nm (yellow-green), Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble. \n" xsd:string property_value: mged:unique_identifier "MO_401" xsd:string [Instance] id: mged:alexa_488 instance_of: mged:LabelCompound property_value: mged:unique_identifier "MO_446" xsd:string property_value: rdfs:comment "Absorbs at 495 nm, emission maxima at 519 nm (green). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble. " xsd:string [Instance] id: mged:alexa_532 instance_of: mged:LabelCompound property_value: mged:unique_identifier "MO_375" xsd:string property_value: rdfs:comment "Absorbs at 532 nm, emission maxima at 554 nm (yellow). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble. \n" xsd:string [Instance] id: mged:alexa_546 instance_of: mged:LabelCompound property_value: mged:unique_identifier "MO_493" xsd:string property_value: rdfs:comment "Absorbs at 556 nm, emission maxima at 573 nm (orange). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble. \n" xsd:string [Instance] id: mged:alexa_568 instance_of: mged:LabelCompound property_value: mged:unique_identifier "MO_736" xsd:string property_value: rdfs:comment "Absorbs at 556 nm, emission maxima at 573 nm (orange). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble. \n" xsd:string [Instance] id: mged:alexa_594 instance_of: mged:LabelCompound property_value: rdfs:comment "Absorbs at 590 nm, emission maxima at 617 nm (red). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble. \n" xsd:string property_value: mged:unique_identifier "MO_461" xsd:string [Instance] id: mged:alexa_633 instance_of: mged:LabelCompound property_value: mged:unique_identifier "MO_345" xsd:string property_value: rdfs:comment "Absorbs at 632 nm, emission maxima at 647 nm (red). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble. \n" xsd:string [Instance] id: mged:alexa_660 instance_of: mged:LabelCompound property_value: rdfs:comment "Absorbs at 663 nm, emission maxima at 690 nm (far-red). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble. \n" xsd:string property_value: mged:unique_identifier "MO_547" xsd:string [Instance] id: mged:alexa_680 instance_of: mged:LabelCompound property_value: mged:unique_identifier "MO_799" xsd:string property_value: rdfs:comment "Absorbs at 679 nm, emission maxima at 702 nm (far-red). Alexa dyes are have intense fluorescence, are photostable, stable over a wide range of pH, and are water soluble. \n" xsd:string [Instance] id: mged:all_pairs instance_of: mged:MethodologicalDesign property_value: mged:unique_identifier "MO_565" xsd:string property_value: rdfs:comment "An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. " xsd:string [Instance] id: mged:amino_acid_primary_sequence_record instance_of: mged:DatabaseEntryType property_value: mged:unique_identifier "MO_829" xsd:string property_value: rdfs:comment "A record which describes and identifies an amino acid sequence which is encoded by a CDS from a primary_nucleic_acid_sequence_record" xsd:string [Instance] id: mged:aminosilane instance_of: mged:SurfaceType property_value: mged:unique_identifier "MO_747" xsd:string property_value: rdfs:comment "a surface coating type for immobilization with the compound aminosilane" xsd:string [Instance] id: mged:amol instance_of: mged:QuantityUnit property_value: rdfs:comment "attomole, quantity unit" xsd:string property_value: mged:unique_identifier "MO_977" xsd:string [Instance] id: mged:aneuploid instance_of: mged:Ploidy property_value: mged:unique_identifier "MO_918" xsd:string property_value: rdfs:comment "Describes a cell, nucleus or an organism whose chromosome number is not an exact multiple of the haploid number (n)." xsd:string [Instance] id: mged:antibody instance_of: mged:PhysicalBioSequenceType property_value: rdfs:comment "glycoprotein of the immunoglobulin family that can combine specifically non-covalently, reversibly with a corresponding antigen " xsd:string property_value: mged:unique_identifier "MO_833" xsd:string [Instance] id: mged:array_manufacture_software instance_of: mged:SoftwareType property_value: mged:unique_identifier "MO_502" xsd:string property_value: rdfs:comment "Software to control an arrayer." xsd:string [Instance] id: mged:array_manufacturer instance_of: mged:Roles property_value: mged:unique_identifier "MO_890" xsd:string property_value: rdfs:comment "Person or organization that manufactured the array." xsd:string [Instance] id: mged:array_manufacturing instance_of: mged:ExperimentalProtocolType property_value: rdfs:comment "The process of physically creating the array." xsd:string property_value: mged:unique_identifier "MO_818" xsd:string [Instance] id: mged:array_platform_variation_design instance_of: mged:MethodologicalDesign property_value: rdfs:comment "An experiment in which the array platform is compared, e.g. Agilent versus \n Affy." xsd:string property_value: mged:unique_identifier "MO_899" xsd:string [Instance] id: mged:array_scanner instance_of: mged:HardwareType property_value: mged:unique_identifier "MO_824" xsd:string property_value: rdfs:comment "An instrument capable of acquiring images of arrays." xsd:string [Instance] id: mged:arrayer instance_of: mged:HardwareType property_value: mged:unique_identifier "MO_697" xsd:string property_value: rdfs:comment "An instrument capable of manufacturing arrays by spotting material." xsd:string [Instance] id: mged:atmosphere instance_of: mged:EnvironmentalFactorCategory property_value: mged:unique_identifier "MO_498" xsd:string property_value: rdfs:comment "The atmospheric conditions used to culture or grow an organism." xsd:string [Instance] id: mged:aunt instance_of: mged:FamilyRelationship property_value: rdfs:comment "The sister of one's father or mother." xsd:string property_value: mged:unique_identifier "MO_354" xsd:string [Instance] id: mged:averaged_intensity instance_of: mged:DerivedBioAssayType property_value: rdfs:comment "Results of data reduction involving computation of the average of multiple \n intensities of identical type. These could include identical Features, \n Reporters or CompositeSequences in different microarray hybridizations, \n matched replicate spots on 2D gels run from the same sample, or repeat \n measurements of the same metabolite in replicate cell cultures." xsd:string property_value: mged:unique_identifier "MO_362" xsd:string [Instance] id: mged:barrier_facility instance_of: mged:EnvironmentalFactorCategory property_value: mged:unique_identifier "MO_511" xsd:string property_value: rdfs:comment "The rating of containment system used to protect organisms from infectious agents." xsd:string [Instance] id: mged:bedding instance_of: mged:DeprecatedTerms property_value: mged:deprecation_replacement_term mged:BioMaterialCharacteristicCategory property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecated_from_version mged:version_1.1.7 property_value: mged:deprecation_old_parent mged:BioMaterialCharacteristicCategory property_value: mged:deprecation_in_version "1.1.7" xsd:string property_value: mged:unique_identifier "MO_615" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: rdfs:comment "The material (e.g. straw) that an animal sleeps on" xsd:string [Instance] id: mged:beginning_of_stage instance_of: mged:InitialTimePoint property_value: rdfs:comment "time point that indicates the start of some developmental stage" xsd:string property_value: mged:unique_identifier "MO_608" xsd:string [Instance] id: mged:behavior_design instance_of: mged:DeprecatedTerms property_value: mged:deprecation_old_parent mged:BiologicalProperty property_value: mged:split_to_term mged:innate_behavior_design property_value: mged:has_reason_for_deprecation mged:split_term property_value: mged:split_to_term mged:stimulated_design_type property_value: mged:deprecated_from_version mged:version_1.1.9 property_value: mged:deprecation_reason "split_term" xsd:string property_value: mged:deprecation_in_version "1.1.9" xsd:string property_value: rdfs:comment "The specific actions or reactions of an organism in response to external or internal stimuli. Patterned activity of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions." xsd:string property_value: mged:unique_identifier "MO_532" xsd:string [Instance] id: mged:behavioral_design_type instance_of: mged:DeprecatedTerms property_value: mged:was_replaced_by mged:innate_behavior_design property_value: mged:deprecated_from_version mged:version_1.1.9 property_value: mged:replaced_with_term mged:innate_behavior_design property_value: mged:deprecation_old_parent mged:PerturbationalDesign property_value: mged:has_reason_for_deprecation mged:replaced_term property_value: mged:deprecation_reason "replaced_term" xsd:string property_value: mged:deprecation_in_version "1.1.9" xsd:string property_value: rdfs:comment "A design type in which some behavior(s) of an organism is studied. The behavior can be innate, such as path finding in bees, or in response to an\nexperimental behavioral stimulus such as sleep deprivation." xsd:string property_value: mged:unique_identifier "MO_766" xsd:string [Instance] id: mged:behavioral_stimulus instance_of: mged:ComplexAction property_value: rdfs:comment "The organism is forced to respond to a stimulus with some behavior (e.g., avoidance, obtaining a reward, etc.) " xsd:string property_value: mged:unique_identifier "MO_674" xsd:string [Instance] id: mged:behavioral_stimulus instance_of: mged:ComplexAction property_value: rdfs:comment "The organism is forced to respond to a stimulus with some behavior (e.g., avoidance, obtaining a reward, etc.) " xsd:string property_value: mged:unique_identifier "MO_674" xsd:string [Instance] id: mged:bibliographic_record instance_of: mged:DatabaseEntryType property_value: rdfs:comment "A record which describes and identifies a paper publication e.g. a medline record" xsd:string property_value: mged:unique_identifier "MO_923" xsd:string [Instance] id: mged:binding_site_identification_design instance_of: mged:BioMolecularAnnotation property_value: mged:synonym "ChIP-chip" xsd:string property_value: mged:synonym "chromatin_immunoprecipitation" xsd:string property_value: rdfs:comment "A binding site identification design type investigates protein binding sites on nucleic acids\nnon-exact synonym: ChIP, chromatin immunoprecipitation, chromatin IP" xsd:string property_value: mged:synonym "chromatin IP" xsd:string property_value: mged:unique_identifier "MO_933" xsd:string property_value: mged:synonym "chromatin immunoprecipitation" xsd:string [Instance] id: mged:binding_site_identification_design instance_of: mged:BioMolecularAnnotation property_value: mged:synonym "ChIP-chip" xsd:string property_value: mged:synonym "chromatin_immunoprecipitation" xsd:string property_value: rdfs:comment "A binding site identification design type investigates protein binding sites on nucleic acids\nnon-exact synonym: ChIP, chromatin immunoprecipitation, chromatin IP" xsd:string property_value: mged:synonym "chromatin IP" xsd:string property_value: mged:unique_identifier "MO_933" xsd:string property_value: mged:synonym "chromatin immunoprecipitation" xsd:string [Instance] id: mged:bioassay_data_transformation_software instance_of: mged:SoftwareType property_value: rdfs:comment "Software used to transform the Measured or DerivedBioAssay data e.g. normalization.\nNon-exact synonym: normalization software" xsd:string property_value: mged:unique_identifier "MO_672" xsd:string property_value: mged:synonym "normalization software" xsd:string [Instance] id: mged:bioassay_replicate_reduction instance_of: mged:DerivedBioAssayType property_value: rdfs:comment "Results of data reduction involving computation of a representative value, e.g. averaging across a group of identical Features, Reporters or CompositeSequences from 2 or more hybridizations, matched replicate spots on 2D gels run from the same or an equivalent sample, or repeat measurements of the same metabolite in replicate cell cultures." xsd:string property_value: mged:unique_identifier "MO_976" xsd:string [Instance] id: mged:biological_fluid_collection instance_of: mged:ComplexAction property_value: rdfs:comment "The action of collecting biological fluids including bodily secretions, exudates, transudates etc. and sampling of cytoplasm. The purpose of sampling may range from collecting other organisms (i.e. pathogens) to studying fluid composition." xsd:string property_value: mged:unique_identifier "MO_685" xsd:string [Instance] id: mged:biological_fluid_collection instance_of: mged:ComplexAction property_value: rdfs:comment "The action of collecting biological fluids including bodily secretions, exudates, transudates etc. and sampling of cytoplasm. The purpose of sampling may range from collecting other organisms (i.e. pathogens) to studying fluid composition." xsd:string property_value: mged:unique_identifier "MO_685" xsd:string [Instance] id: mged:biological_replicate instance_of: mged:ReplicateDescriptionType property_value: mged:unique_identifier "MO_952" xsd:string property_value: rdfs:comment "A replicate that consists of independent biological replicates made from different individual BioSources." xsd:string [Instance] id: mged:biological_replicate instance_of: mged:ReplicateDescriptionType property_value: mged:unique_identifier "MO_952" xsd:string property_value: rdfs:comment "A replicate that consists of independent biological replicates made from different individual BioSources." xsd:string [Instance] id: mged:biological_resource_record instance_of: mged:DatabaseEntryType property_value: mged:unique_identifier "MO_989" xsd:string property_value: rdfs:comment "A record which describes and identifies a biological resource such as a cone or strain e.g. an ATCC record Jax strain list" xsd:string [Instance] id: mged:biomaterial_provider instance_of: mged:BioMaterialCharacteristicCategory property_value: rdfs:comment "Term used to describe a role or factor value for the person or organization that provides a BioMaterial. " xsd:string property_value: mged:unique_identifier "MO_591" xsd:string [Instance] id: mged:biomaterial_provider instance_of: mged:BioMaterialCharacteristicCategory property_value: rdfs:comment "Term used to describe a role or factor value for the person or organization that provides a BioMaterial. " xsd:string property_value: mged:unique_identifier "MO_591" xsd:string [Instance] id: mged:biopsy instance_of: mged:ComplexAction property_value: mged:unique_identifier "MO_711" xsd:string property_value: rdfs:comment "The process of removing tissue from a living organism." xsd:string [Instance] id: mged:biosequence_provider instance_of: mged:Roles property_value: rdfs:comment "Provider of biosequences (clones, oligos etc) for deposition on the array." xsd:string property_value: mged:unique_identifier "MO_881" xsd:string [Instance] id: mged:biotin instance_of: mged:LabelCompound property_value: mged:unique_identifier "MO_793" xsd:string property_value: rdfs:comment "a compound used for labeling/detection purposes" xsd:string [Instance] id: mged:birth instance_of: mged:InitialTimePoint property_value: rdfs:comment "the action of emergence and separation of offspring from the mother." xsd:string property_value: mged:unique_identifier "MO_710" xsd:string [Instance] id: mged:blood instance_of: mged:DeprecatedTerms property_value: mged:deprecation_replacement_term mged:BioSourceType property_value: mged:deprecated_from_version mged:version_1.1.9 property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_old_parent mged:BioSourceType property_value: rdfs:comment "A biomaterial obtained as fluid consisting of plasma, blood cells and platelets." xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_409" xsd:string property_value: mged:deprecation_in_version "1.1.9" xsd:string [Instance] id: mged:book instance_of: mged:PublicationType property_value: rdfs:comment "A publication type which has an ISBN." xsd:string property_value: mged:unique_identifier "MO_627" xsd:string [Instance] id: mged:boolean instance_of: mged:DataType property_value: mged:unique_identifier "MO_826" xsd:string property_value: rdfs:comment "The values are either TRUE or FALSE, which can be expressed as 1 and 0." xsd:string [Instance] id: mged:brother instance_of: mged:FamilyRelationship property_value: mged:unique_identifier "MO_655" xsd:string property_value: rdfs:comment " A male having the same genetic parents as another, or one genetic parent in common with another." xsd:string [Instance] id: mged:cDNA_clone instance_of: mged:DeprecatedTerms property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_replacement_term mged:PhysicalBioSequenceType property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:deprecation_old_parent mged:PhysicalBioSequenceType property_value: mged:unique_identifier "MO_966" xsd:string property_value: mged:synonym "cDNA" xsd:string property_value: rdfs:comment "sequence of complementary cDNA copy of an RNA molecule contained on a plasmid including the plasmid sequence, used when the entire clone is spotted\nnon-exact synonym: cDNA, complementary DNA" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:synonym "complementary DNA" xsd:string [Instance] id: mged:candela instance_of: mged:LightUnit property_value: rdfs:comment "One lumen per steradian. A steradian is a fraction of the surface area of a sphere that is equal to the square of the radius divided by the total surface area. This is approximately 8% of the total surface area.\nExact synonym: candle power" xsd:string property_value: mged:synonym "candle power" xsd:string property_value: mged:unique_identifier "MO_572" xsd:string [Instance] id: mged:candelas_per_square_meter instance_of: mged:LightUnit property_value: rdfs:comment "Unit of brightness or luminance." xsd:string property_value: mged:unique_identifier "MO_813" xsd:string [Instance] id: mged:cc instance_of: mged:VolumeUnit property_value: rdfs:comment "a cubic centimeter, volume unit" xsd:string property_value: mged:unique_identifier "MO_834" xsd:string [Instance] id: mged:cell instance_of: mged:MaterialType property_value: mged:unique_identifier "MO_612" xsd:string property_value: rdfs:comment "One or more dissociated cell(s) possibly heterogeneous, excluding single cell organisms." xsd:string [Instance] id: mged:cell_cycle_design instance_of: mged:BiologicalProperty property_value: mged:unique_identifier "MO_822" xsd:string property_value: rdfs:comment "A cell cycle design experiment design type is one that assays events that occurs in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells." xsd:string [Instance] id: mged:cell_line instance_of: mged:BioMaterialCharacteristicCategory property_value: mged:unique_identifier "MO_562" xsd:string property_value: rdfs:comment "A descriptor for FactorValue where CellLine is compared. " xsd:string [Instance] id: mged:cell_lysate instance_of: mged:MaterialType property_value: mged:unique_identifier "MO_903" xsd:string property_value: rdfs:comment "cell lysate, a collection of cells whose membranes have been disrupted" xsd:string [Instance] id: mged:cell_ontology instance_of: mged:TargetedCellTypeDatabase property_value: mged:has_machine_readable_URI "http://cvs.sourceforge.net/views.py/obo/obo/ontology/anatomy/cell_type/cell.ontology?rev=HEAD&content-type=text/vnd.viewcvs-markup" xsd:string property_value: rdfs:comment "database of cell ontology terms" xsd:string property_value: mged:unique_identifier "MO_404" xsd:string [Instance] id: mged:cell_ontology instance_of: mged:TargetedCellTypeDatabase property_value: mged:has_machine_readable_URI "http://cvs.sourceforge.net/views.py/obo/obo/ontology/anatomy/cell_type/cell.ontology?rev=HEAD&content-type=text/vnd.viewcvs-markup" xsd:string property_value: rdfs:comment "database of cell ontology terms" xsd:string property_value: mged:unique_identifier "MO_404" xsd:string [Instance] id: mged:cell_type instance_of: mged:BioMaterialCharacteristicCategory property_value: rdfs:comment "A descriptor for FactorValue where CellType is compared. " xsd:string property_value: mged:unique_identifier "MO_548" xsd:string [Instance] id: mged:cell_type_comparison_design instance_of: mged:BiologicalProperty property_value: mged:unique_identifier "MO_764" xsd:string property_value: rdfs:comment "A cell type comparison design experiment design type compares cells of different type for example different cell lines." xsd:string [Instance] id: mged:cells_per_ml instance_of: mged:ConcentrationUnitOther property_value: mged:unique_identifier "MO_727" xsd:string property_value: rdfs:comment "the number of cells per ml" xsd:string [Instance] id: mged:cellular_modification_design instance_of: mged:TechnologicalDesign property_value: mged:unique_identifier "MO_392" xsd:string property_value: mged:synonym "RNAi" xsd:string property_value: rdfs:comment "A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. " xsd:string [Instance] id: mged:cellular_modification_design instance_of: mged:TechnologicalDesign property_value: mged:unique_identifier "MO_392" xsd:string property_value: mged:synonym "RNAi" xsd:string property_value: rdfs:comment "A cellular modification design type is where a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. " xsd:string [Instance] id: mged:cellular_process_design instance_of: mged:BiologicalProperty property_value: rdfs:comment "Processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." xsd:string property_value: mged:unique_identifier "MO_810" xsd:string [Instance] id: mged:centrifuge instance_of: mged:HardwareType property_value: mged:unique_identifier "MO_476" xsd:string property_value: rdfs:comment "An instrument capable of applying centrifugal force to tubes or microtiter plates." xsd:string [Instance] id: mged:cfu_per_ml instance_of: mged:ConcentrationUnitOther property_value: rdfs:comment "the number of colony forming units per ml" xsd:string property_value: mged:unique_identifier "MO_788" xsd:string [Instance] id: mged:change_biomaterial_characteristics instance_of: mged:ExperimentalProtocolType property_value: mged:synonym "change growth condition" xsd:string property_value: rdfs:comment "Indicates that one or more BioMaterialCharacteristics have changed during the treatment of a BioMaterial. \nNon exact synonym: change growth condition, change environment" xsd:string property_value: mged:synonym "change environment" xsd:string property_value: mged:unique_identifier "MO_383" xsd:string [Instance] id: mged:change_biomaterial_characteristics instance_of: mged:ExperimentalProtocolType property_value: mged:synonym "change growth condition" xsd:string property_value: rdfs:comment "Indicates that one or more BioMaterialCharacteristics have changed during the treatment of a BioMaterial. \nNon exact synonym: change growth condition, change environment" xsd:string property_value: mged:synonym "change environment" xsd:string property_value: mged:unique_identifier "MO_383" xsd:string [Instance] id: mged:change_humidity instance_of: mged:AtomicAction property_value: rdfs:comment "The action of changing the relative humidity, e.g. from 1% to 10%." xsd:string property_value: mged:unique_identifier "MO_917" xsd:string [Instance] id: mged:change_light instance_of: mged:AtomicAction property_value: mged:unique_identifier "MO_549" xsd:string property_value: rdfs:comment "Change in light intensity or wavelength. " xsd:string [Instance] id: mged:change_temperature instance_of: mged:AtomicAction property_value: rdfs:comment "Change in temperature. " xsd:string property_value: mged:unique_identifier "MO_677" xsd:string [Instance] id: mged:chrome_border instance_of: mged:FiducialType property_value: mged:unique_identifier "MO_491" xsd:string property_value: rdfs:comment "the chrome border on an Affymetrix type array which is used as a point of\nreference for orientation (fiducial)" xsd:string [Instance] id: mged:chromosomal_deletion instance_of: mged:ChromosomalAberrationClassification property_value: mged:unique_identifier "MO_922" xsd:string property_value: rdfs:comment "The loss of a segment of the genetic material from a chromosome." xsd:string [Instance] id: mged:chromosomal_duplication instance_of: mged:ChromosomalAberrationClassification property_value: rdfs:comment "An irregularity in the number of chromosomes, usually in the form of a gain of genetic material." xsd:string property_value: mged:unique_identifier "MO_1002" xsd:string [Instance] id: mged:chromosomal_insertion instance_of: mged:ChromosomalAberrationClassification property_value: mged:unique_identifier "MO_518" xsd:string property_value: rdfs:comment "The gain of a segment of the genetic material in a chromosome by fragmentation of a chromosome and transfer of the broken-off portion of another chromosome or other sources." xsd:string [Instance] id: mged:chromosomal_inversion instance_of: mged:ChromosomalAberrationClassification property_value: mged:unique_identifier "MO_622" xsd:string property_value: rdfs:comment "Chromosome segments that have been turned through 180 degrees with the result that the gene sequence for the segment is reversed with respect to the rest of the chromosome." xsd:string [Instance] id: mged:chromosomal_substitution instance_of: mged:GeneticModification property_value: rdfs:comment "A state/condition describing a cell, or organism, in which all, or part, of a chromosome from a donor replaces that of the recipient. Examples include strains created by repeated backcrossing as well as those created by recombinant methods. For single gene insertion, use the term gene_knock_in." xsd:string property_value: mged:unique_identifier "MO_995" xsd:string [Instance] id: mged:chromosomal_translocation instance_of: mged:ChromosomalAberrationClassification property_value: rdfs:comment "A type of aberration characterized by fragmentation of a chromosome and transfer of the broken-off portion to another chromosome, often of a different pair." xsd:string property_value: mged:unique_identifier "MO_368" xsd:string [Instance] id: mged:chromosome instance_of: mged:DeprecatedTerms property_value: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType property_value: mged:deprecation_replacement_term mged:PhysicalBioSequenceType property_value: mged:deprecation_old_parent mged:PhysicalBioSequenceType property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_old_parent mged:TheoreticalBioSequenceType property_value: mged:unique_identifier "MO_578" xsd:string property_value: rdfs:comment "Physical or theoretical sequence of, or representing a chromosome, one of the DNA molecules that comprises the genome. " xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string [Instance] id: mged:circadian_rhythm_design instance_of: mged:DeprecatedTerms property_value: mged:has_reason_for_deprecation mged:replaced_term property_value: mged:deprecation_old_parent mged:BiologicalProperty property_value: mged:replaced_with_term mged:physiological_process_design property_value: mged:deprecated_from_version mged:version_1.1.7 property_value: mged:was_replaced_by mged:physiological_process_design property_value: rdfs:comment "A circadian rhythm experiment design type assays the events associated with the circadian rhythm which is a biological activity that exhibits an endogenous periodicity independently of any daily variation in the environment." xsd:string property_value: mged:deprecation_reason "replaced_term" xsd:string property_value: mged:deprecation_in_version "1.1.7" xsd:string property_value: mged:unique_identifier "MO_539" xsd:string [Instance] id: mged:clinical_history_design instance_of: mged:EpidemiologicalDesign property_value: mged:unique_identifier "MO_832" xsd:string property_value: rdfs:comment "A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied." xsd:string [Instance] id: mged:clinical_information instance_of: mged:BioMaterialCharacteristicCategory property_value: mged:unique_identifier "MO_816" xsd:string property_value: rdfs:comment "A descriptor for FactorValue where ClinicalInformation is compared. " xsd:string [Instance] id: mged:clinical_record instance_of: mged:DatabaseEntryType property_value: rdfs:comment "record which describes and identifies clinical information about an organism" xsd:string property_value: mged:unique_identifier "MO_852" xsd:string [Instance] id: mged:clinical_treatment instance_of: mged:BioMaterialCharacteristicCategory property_value: rdfs:comment "A descriptor for a clinical treatment for a patient." xsd:string property_value: mged:unique_identifier "MO_384" xsd:string [Instance] id: mged:clone_of_unknown_source instance_of: mged:PhysicalBioSequenceType property_value: mged:unique_identifier "MO_371" xsd:string property_value: rdfs:comment "Sequence from some nucleic acid copy and the associated vector for which the source clone supplier is unknown." xsd:string [Instance] id: mged:clustered_data instance_of: mged:DerivedBioAssayType property_value: mged:unique_identifier "MO_418" xsd:string property_value: rdfs:comment "Results of an analysis method that groups data based on a measure of similarity, e.g. Pearson correlation coefficient, Euclidean distance. " xsd:string [Instance] id: mged:clustering_software instance_of: mged:SoftwareType property_value: mged:unique_identifier "MO_464" xsd:string property_value: rdfs:comment "Software used to cluster the data." xsd:string [Instance] id: mged:cm instance_of: mged:DistanceUnit property_value: mged:unique_identifier "MO_837" xsd:string property_value: rdfs:comment "centimeter, a unit of distance" xsd:string [Instance] id: mged:co-expression_design instance_of: mged:BioMolecularAnnotation property_value: mged:synonym "guilt by association" xsd:string property_value: mged:unique_identifier "MO_904" xsd:string property_value: rdfs:comment "A co-expression experiment design type identifies genes which are coordinately expressed and are potentially used to infer a role in a biological process(es)\nnon-exact synonym: guilt by association" xsd:string [Instance] id: mged:coitus instance_of: mged:InitialTimePoint property_value: rdfs:comment "the physical act of copulation that occurs during the process of sexual reproduction\nsynonyms: copulation, insemination" xsd:string property_value: mged:synonym "copulation" xsd:string property_value: mged:unique_identifier "MO_783" xsd:string property_value: mged:synonym "insemination" xsd:string [Instance] id: mged:collapsed_spot_replicate instance_of: mged:DerivedBioAssayType property_value: mged:unique_identifier "MO_789" xsd:string property_value: rdfs:comment "Results of data reduction involving computation of a representative value, e.g. by averaging, for a group of replicated Features, Reporters or CompositeSequences from a single hybridization." xsd:string [Instance] id: mged:comparative_genome_hybridization_design instance_of: mged:TechnologicalDesign property_value: mged:synonym "CGH" xsd:string property_value: mged:unique_identifier "MO_856" xsd:string property_value: mged:synonym "array CGH" xsd:string property_value: rdfs:comment "Experiment design type in which genomic content is studied using an array based assay." xsd:string property_value: mged:synonym "array_CGH" xsd:string [Instance] id: mged:comparative_genome_hybridization_design instance_of: mged:TechnologicalDesign property_value: mged:synonym "CGH" xsd:string property_value: mged:unique_identifier "MO_856" xsd:string property_value: mged:synonym "array CGH" xsd:string property_value: rdfs:comment "Experiment design type in which genomic content is studied using an array based assay." xsd:string property_value: mged:synonym "array_CGH" xsd:string [Instance] id: mged:compound_based_treatment instance_of: mged:ExperimentalProtocolType property_value: rdfs:comment "The treatment is effected by a defined chemical or biological compound. The compound may be a drug, solvent, chemical, etc., with a property that can be measured such as concentration." xsd:string property_value: mged:unique_identifier "MO_798" xsd:string [Instance] id: mged:compound_based_treatment instance_of: mged:ExperimentalProtocolType property_value: rdfs:comment "The treatment is effected by a defined chemical or biological compound. The compound may be a drug, solvent, chemical, etc., with a property that can be measured such as concentration." xsd:string property_value: mged:unique_identifier "MO_798" xsd:string [Instance] id: mged:compound_record instance_of: mged:DatabaseEntryType property_value: rdfs:comment "a record which describes and identifies a compound e.g. drug record part of NCI thesaurus" xsd:string property_value: mged:unique_identifier "MO_546" xsd:string [Instance] id: mged:compound_treatment_design instance_of: mged:PerturbationalDesign property_value: mged:unique_identifier "MO_555" xsd:string property_value: rdfs:comment "A compound treatment design type is where the response to administration of a compound or chemical (including biological compounds such as hormones) is assayed." xsd:string [Instance] id: mged:computational_feature instance_of: mged:SeqFeatureBasis property_value: rdfs:comment "Computationally derived sequence feature." xsd:string property_value: mged:unique_identifier "MO_411" xsd:string [Instance] id: mged:computed_amino_acid_sequence_feature_record instance_of: mged:DatabaseEntryType property_value: mged:unique_identifier "MO_797" xsd:string property_value: rdfs:comment "a record which describes and identifies an amino acid feature which is computationally derived e.g. PFAM" xsd:string [Instance] id: mged:computed_nucleic_acid_sequence_feature_record instance_of: mged:DatabaseEntryType property_value: mged:unique_identifier "MO_774" xsd:string property_value: rdfs:comment "A record which identifies and describes a nucleic sequence feature which has been computationally determined or predicted E.g. and Ensembl record" xsd:string [Instance] id: mged:computed_protein_structure_record instance_of: mged:DatabaseEntryType property_value: rdfs:comment "a record which describes and identifies a protein structure e.g. PDB" xsd:string property_value: mged:unique_identifier "MO_765" xsd:string [Instance] id: mged:computer instance_of: mged:HardwareType property_value: rdfs:comment " A device capable of applying software." xsd:string property_value: mged:unique_identifier "MO_510" xsd:string [Instance] id: mged:concentrate instance_of: mged:AtomicAction property_value: rdfs:comment "Increasing the concentration of solutes in a solution or suspension. " xsd:string property_value: mged:unique_identifier "MO_883" xsd:string [Instance] id: mged:condition_specificity instance_of: mged:HigherLevelAnalysisProtocolType property_value: mged:unique_identifier "MO_417" xsd:string property_value: rdfs:comment "An analysis aimed at ranking genes or transcripts according to the uniformity of expression across a set of conditions. For example, the analysis can be used to rank genes according to the degree of tissue or developmental stage specificity." xsd:string [Instance] id: mged:consensus_DNA instance_of: mged:TheoreticalBioSequenceType property_value: rdfs:comment "DNA sequence produced from some base calling or alignment algorithm which uses multiple sequence as input" xsd:string property_value: mged:unique_identifier "MO_361" xsd:string [Instance] id: mged:consensus_mRNA instance_of: mged:TheoreticalBioSequenceType property_value: rdfs:comment "mRNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple sequences as input." xsd:string property_value: mged:unique_identifier "MO_423" xsd:string [Instance] id: mged:consortium_member instance_of: mged:Roles property_value: rdfs:comment "A member of a consortium of institutions." xsd:string property_value: mged:unique_identifier "MO_778" xsd:string [Instance] id: mged:consultant instance_of: mged:Roles property_value: rdfs:comment "A contact who provides some service related to some aspect of the experiment which is not data coding or analysis. E.g. help with an experimental design." xsd:string property_value: mged:unique_identifier "MO_984" xsd:string [Instance] id: mged:control_biosequence instance_of: mged:ControlType property_value: rdfs:comment "A Reporter associated with a BioSequence that has a context dependent predicted signal. e.g. a yeast reporter on a human array is a control_biosequence expected to be of low signal if no spikes are used. If spikes are used, the signal is expected to be high." xsd:string property_value: mged:unique_identifier "MO_940" xsd:string [Instance] id: mged:control_buffer instance_of: mged:ControlType property_value: mged:unique_identifier "MO_505" xsd:string property_value: rdfs:comment "A Reporter where only buffer was deposited on the array" xsd:string [Instance] id: mged:control_design_element_group_type instance_of: mged:DesignElementGroupType property_value: mged:unique_identifier "MO_414" xsd:string property_value: rdfs:comment "A grouping of DesignElements features/Reporters/Composites which are not designed to detect a signal in the biomaterial and which are on the array for control purposes e.g. a grouping of controls used for spiking." xsd:string [Instance] id: mged:control_empty instance_of: mged:ControlType property_value: rdfs:comment "A Reporter where no material or buffer was deposited on the array" xsd:string property_value: mged:unique_identifier "MO_830" xsd:string [Instance] id: mged:control_genomic_DNA instance_of: mged:ControlType property_value: rdfs:comment "A Reporter where genomic DNA has been deposited, the genomic DNA may be fragmented, e.g. salmon sperm DNA, Cot1DNA. " xsd:string property_value: mged:unique_identifier "MO_449" xsd:string [Instance] id: mged:control_hybridization_quality instance_of: mged:ControlType property_value: mged:unique_identifier "MO_385" xsd:string property_value: rdfs:comment "A Reporter that could be used to determine the quality and general performance of the labeled extract. An example is a pool of BioSequences representing widely-expressed genes (i.e., housekeeping genes)." xsd:string [Instance] id: mged:control_label instance_of: mged:ControlType property_value: mged:unique_identifier "MO_708" xsd:string property_value: rdfs:comment "Reporter used as a control where some label has been deposited. This includes fluor and radioactively labeled oligos and fluors alone.\n " xsd:string [Instance] id: mged:control_reporter_size instance_of: mged:ControlType property_value: rdfs:comment "A Reporter of whose BioSequence is of known length used as a methodological control for hybridization efficiency." xsd:string property_value: mged:unique_identifier "MO_431" xsd:string [Instance] id: mged:control_spike_calibration instance_of: mged:ControlType property_value: rdfs:comment "A Reporter that could be hybridized to an exogenously added nucleic acid or protein (spike) before or during hybridization and is used as a control for data processing. It may be deposited at one or more known concentrations (calibration). A reporter may be a spike, a calibration control or both." xsd:string property_value: mged:unique_identifier "MO_364" xsd:string [Instance] id: mged:control_unknown_type instance_of: mged:ControlType property_value: mged:unique_identifier "MO_925" xsd:string property_value: rdfs:comment "A Reporter indicated as being a control of unknown type. " xsd:string [Instance] id: mged:cosine_distance instance_of: mged:NodeValueType property_value: mged:unique_identifier "MO_550" xsd:string property_value: rdfs:comment "The cosine distance of two vectors is the cosine of the angle between them. This measures the difference in direction between two vectors, irrespective of their lengths." xsd:string [Instance] id: mged:cosmid instance_of: mged:DeprecatedTerms property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_old_parent mged:PhysicalBioSequenceType property_value: mged:deprecation_replacement_term mged:PhysicalBioSequenceType property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_888" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: rdfs:comment "sequence from cosmid, a hybrid cloning vector containing cos sites, usually of ~40kB size" xsd:string [Instance] id: mged:count instance_of: mged:QuantityUnitOther property_value: rdfs:comment "Unit for a simple count of things" xsd:string property_value: mged:unique_identifier "MO_500" xsd:string [Instance] id: mged:cpm instance_of: mged:RadiationUnit property_value: mged:unique_identifier "MO_348" xsd:string property_value: rdfs:comment "counts per minute, unit of light emissions produced by ionizing radiation." xsd:string [Instance] id: mged:ctDNA instance_of: mged:PhysicalBioSequenceType property_value: mged:unique_identifier "MO_586" xsd:string property_value: mged:synonym "chloroplast DNA" xsd:string property_value: rdfs:comment "ctDNA: sequence from the chloroplast \nsynonym: chloroplast DNA" xsd:string [Instance] id: mged:curated_amino_acid_sequence_record instance_of: mged:DatabaseEntryType property_value: mged:unique_identifier "MO_451" xsd:string property_value: rdfs:comment "A record which describes and identifies an amino acid sequence which has been curated" xsd:string [Instance] id: mged:curated_gene_record instance_of: mged:DatabaseEntryType property_value: mged:unique_identifier "MO_913" xsd:string property_value: rdfs:comment "A record which describes and identifies nucleic acid sequence which has been identified as a gene by a curator. e.g. Flybase gene record" xsd:string [Instance] id: mged:curated_nucleic_acid_sequence_feature_record instance_of: mged:DatabaseEntryType property_value: mged:unique_identifier "MO_644" xsd:string property_value: rdfs:comment "A record which identifies a nucleic acid sequence feature(s) and which has been curated." xsd:string [Instance] id: mged:curator instance_of: mged:Roles property_value: rdfs:comment "person who checks the consistency of the data and MAGE-ML file" xsd:string property_value: mged:unique_identifier "MO_893" xsd:string [Instance] id: mged:cytoplasmic_RNA instance_of: mged:MaterialType property_value: mged:unique_identifier "MO_978" xsd:string property_value: rdfs:comment "RNA obtained from the cytoplasm." xsd:string [Instance] id: mged:data_analyst instance_of: mged:Roles property_value: mged:unique_identifier "MO_753" xsd:string property_value: rdfs:comment "A contact who performs data analysis, e.g. statistician." xsd:string [Instance] id: mged:data_coder instance_of: mged:Roles property_value: rdfs:comment "person who prepares the MAGE-ML file" xsd:string property_value: mged:unique_identifier "MO_695" xsd:string [Instance] id: mged:date instance_of: mged:DataType property_value: rdfs:comment "Time stated in terms of the day, month, and year." xsd:string property_value: mged:unique_identifier "MO_587" xsd:string [Instance] id: mged:daughter instance_of: mged:FamilyRelationship property_value: mged:unique_identifier "MO_665" xsd:string property_value: rdfs:comment "The female offspring of the patient or individual under study." xsd:string [Instance] id: mged:days instance_of: mged:TimeUnit property_value: mged:synonym "d" xsd:string property_value: rdfs:comment "24 hours, time unit" xsd:string property_value: mged:unique_identifier "MO_513" xsd:string [Instance] id: mged:decontaminate instance_of: mged:ExperimentalProtocolType property_value: mged:unique_identifier "MO_389" xsd:string property_value: rdfs:comment "Treatment to remove organisms present that were not planned as part of the study (e.g., mycoplasma). " xsd:string [Instance] id: mged:decontaminate instance_of: mged:ExperimentalProtocolType property_value: mged:unique_identifier "MO_389" xsd:string property_value: rdfs:comment "Treatment to remove organisms present that were not planned as part of the study (e.g., mycoplasma). " xsd:string [Instance] id: mged:degrees_C instance_of: mged:TemperatureUnit property_value: rdfs:comment "degrees celsius, unit of temperature" xsd:string property_value: mged:unique_identifier "MO_980" xsd:string [Instance] id: mged:degrees_F instance_of: mged:TemperatureUnit property_value: rdfs:comment "degrees Fahrenheit, unit of temperature" xsd:string property_value: mged:unique_identifier "MO_812" xsd:string [Instance] id: mged:deleted_term instance_of: mged:DeprecationReason property_value: rdfs:comment "The term was deleted from the MGED CoreOntology." xsd:string [Instance] id: mged:development_or_differentiation_design instance_of: mged:BiologicalProperty property_value: rdfs:comment "A development or differentiation experiment design type assays events associated with development or differentiation or moving through a life cycle. Development applies to organism(s) acquiring a mature state, and differentiation applies to cells acquiring specialized functions." xsd:string property_value: mged:unique_identifier "MO_892" xsd:string [Instance] id: mged:developmental_stage instance_of: mged:BioMaterialCharacteristicCategory property_value: rdfs:comment "A descriptor for FactorValue where DevelopmentalStage is compared. " xsd:string property_value: mged:unique_identifier "MO_878" xsd:string [Instance] id: mged:diameter_aberration instance_of: mged:DefectType property_value: rdfs:comment "The diameter of the Feature is much smaller or much larger than expected based on the spotting pin diameter." xsd:string property_value: mged:unique_identifier "MO_781" xsd:string [Instance] id: mged:differential_expression instance_of: mged:HigherLevelAnalysisProtocolType property_value: rdfs:comment "An analysis aimed at identifying differentially expressed genes in two or more conditions." xsd:string property_value: mged:unique_identifier "MO_874" xsd:string [Instance] id: mged:differential_expression_software instance_of: mged:SoftwareType property_value: rdfs:comment "A software implementing a Higher Level Analysis protocol of type differential_expresssion." xsd:string property_value: mged:unique_identifier "MO_350" xsd:string [Instance] id: mged:dilute instance_of: mged:AtomicAction property_value: rdfs:comment "Decreasing the concentration of solutes in a solution or suspension. " xsd:string property_value: mged:unique_identifier "MO_962" xsd:string [Instance] id: mged:diploid instance_of: mged:Ploidy property_value: mged:unique_identifier "MO_836" xsd:string property_value: rdfs:comment "Describes a cell, nucleus or an organism with two copies of each chromosome." xsd:string [Instance] id: mged:disease_staging instance_of: mged:BioMaterialCharacteristicCategory property_value: rdfs:comment "The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression. " xsd:string property_value: mged:unique_identifier "MO_792" xsd:string [Instance] id: mged:disease_state instance_of: mged:BioMaterialCharacteristicCategory property_value: mged:unique_identifier "MO_787" xsd:string property_value: rdfs:comment "A descriptor for FactorValue where DiseaseState is compared. " xsd:string [Instance] id: mged:disease_state_design instance_of: mged:EpidemiologicalDesign property_value: rdfs:comment "An experiment design type in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress." xsd:string property_value: mged:unique_identifier "MO_902" xsd:string [Instance] id: mged:disease_state_design instance_of: mged:EpidemiologicalDesign property_value: rdfs:comment "An experiment design type in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress." xsd:string property_value: mged:unique_identifier "MO_902" xsd:string [Instance] id: mged:displaced_feature_or_zone instance_of: mged:DefectType property_value: rdfs:comment " The Feature or Zone is displaced from its expected position, due to e.g. a bent spotting pin(s)." xsd:string property_value: mged:unique_identifier "MO_959" xsd:string [Instance] id: mged:dissect instance_of: mged:ExperimentalProtocolType property_value: mged:unique_identifier "MO_374" xsd:string property_value: rdfs:comment "The action of removing one or more organism parts." xsd:string [Instance] id: mged:dissect instance_of: mged:ExperimentalProtocolType property_value: mged:unique_identifier "MO_374" xsd:string property_value: rdfs:comment "The action of removing one or more organism parts." xsd:string [Instance] id: mged:dl instance_of: mged:VolumeUnit property_value: rdfs:comment "deciliter, unit of volume" xsd:string property_value: mged:unique_identifier "MO_624" xsd:string [Instance] id: mged:dose_response_design instance_of: mged:PerturbationalDesign property_value: rdfs:comment "A dose response design type examines the relationship between the size of the administered dose and the extent of the response of the organism(s). " xsd:string property_value: mged:unique_identifier "MO_485" xsd:string [Instance] id: mged:double_stranded instance_of: mged:StrandType property_value: rdfs:comment "a nucleic acid consisting of two polynucleotide chains having antiparallel orientation and being bound together by hydrogen bonding between the chains. This would apply to DNA and some RNA genomes, but not to rRNA or tRNA, etc." xsd:string property_value: mged:unique_identifier "MO_828" xsd:string [Instance] id: mged:dpm instance_of: mged:RadiationUnit property_value: rdfs:comment "disintegrations per minute, unit of atom disintegrations per minute. dpm = (cpm - measured background)/efficiency. Efficiency is dependent on the radioisotope used and the instrument." xsd:string property_value: mged:unique_identifier "MO_583" xsd:string [Instance] id: mged:ds_oligo instance_of: mged:DeprecatedTerms property_value: mged:deprecation_replacement_term mged:PhysicalBioSequenceType property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_old_parent mged:PhysicalBioSequenceType property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: rdfs:comment " a double stranded oligonucleotide" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_344" xsd:string [Instance] id: mged:dye_swap_design instance_of: mged:MethodologicalDesign property_value: mged:synonym "flip dye" xsd:string property_value: mged:unique_identifier "MO_858" xsd:string property_value: mged:synonym "dye flip" xsd:string property_value: rdfs:comment "An experiment design type where the label orientations are reversed.\nexact synonym: flip dye, dye flip" xsd:string [Instance] id: mged:dye_swap_merge instance_of: mged:DataTransformationProtocolType property_value: mged:unique_identifier "MO_448" xsd:string property_value: rdfs:comment "A method of merging expression results from 2 dye-swap hybridizations on a Feature by Feature basis, with possible flagging if the results do not pass consistency checking criteria." xsd:string [Instance] id: mged:dye_swap_quality_control instance_of: mged:QualityControlDescriptionType property_value: rdfs:comment "Indicates that a dye swap was performed for some or all hybridizations within an experiment " xsd:string property_value: mged:unique_identifier "MO_524" xsd:string [Instance] id: mged:dye_swap_replicate instance_of: mged:ReplicateDescriptionType property_value: rdfs:comment "One of a pair of replicate assays in which LabeledExtracts derived from the same BioMaterial used for both assays (e.g., a hybridization or a 2-D gel run) differ only in that the dyes used for labeling have been reversed, e.g., assay 1: A-Cy3 vs. B-Cy5, and assay 2: A-Cy5 vs. B-Cy3. The purpose of using dye-swap replicate pairs is to assess or remove dye-specific biases from the combined experimental results." xsd:string property_value: mged:unique_identifier "MO_901" xsd:string [Instance] id: mged:dye_swap_replicate_reduction instance_of: mged:DerivedBioAssayType property_value: mged:unique_identifier "MO_750" xsd:string property_value: rdfs:comment "Results of data reduction involving computation of a representative value from identical reporters or features obtained from two, or more, hybridizations in which each LabelExtract is labeled with each of the labels or dyes. Computation of a representative value for reporter X using data from Hybridizations 1 and 2, where LabeledExtract A is labeled with Cy3 (and LabeledExtract B is labeled with Cy5) in Hybridization 1 and LabeledExtract A is labeled with Cy5 (and LabeledExtract B is labeled with Cy3) in Hybridization 2. " xsd:string [Instance] id: mged:eVOC instance_of: mged:OrganismPartDatabase property_value: mged:unique_identifier "MO_684" xsd:string property_value: rdfs:comment "Ontology of human terms that describe the sample source of human cDNA and SAGE libraries." xsd:string property_value: mged:has_human_readable_URI "http://www.sanbi.ac.za/evoc/ontologies.html" xsd:string [Instance] id: mged:eVOC instance_of: mged:OrganismPartDatabase property_value: mged:unique_identifier "MO_684" xsd:string property_value: rdfs:comment "Ontology of human terms that describe the sample source of human cDNA and SAGE libraries." xsd:string property_value: mged:has_human_readable_URI "http://www.sanbi.ac.za/evoc/ontologies.html" xsd:string [Instance] id: mged:eVOC instance_of: mged:OrganismPartDatabase property_value: mged:unique_identifier "MO_684" xsd:string property_value: rdfs:comment "Ontology of human terms that describe the sample source of human cDNA and SAGE libraries." xsd:string property_value: mged:has_human_readable_URI "http://www.sanbi.ac.za/evoc/ontologies.html" xsd:string [Instance] id: mged:eVOC instance_of: mged:OrganismPartDatabase property_value: mged:unique_identifier "MO_684" xsd:string property_value: rdfs:comment "Ontology of human terms that describe the sample source of human cDNA and SAGE libraries." xsd:string property_value: mged:has_human_readable_URI "http://www.sanbi.ac.za/evoc/ontologies.html" xsd:string [Instance] id: mged:eclosion instance_of: mged:InitialTimePoint property_value: mged:unique_identifier "MO_876" xsd:string property_value: rdfs:comment "Emergence of an adult insect from its pupa or cocoon." xsd:string [Instance] id: mged:egg_laying instance_of: mged:InitialTimePoint property_value: rdfs:comment "The point at which the egg(s) is laid by an organism." xsd:string property_value: mged:unique_identifier "MO_767" xsd:string [Instance] id: mged:element_design instance_of: mged:ExperimentalProtocolType property_value: mged:unique_identifier "MO_523" xsd:string property_value: rdfs:comment "protocol that describes how the features, reporters and composites were designed and or selected for inclusion in an array design " xsd:string [Instance] id: mged:ellipsoid_feature instance_of: mged:FeatureShape property_value: rdfs:comment "The shape of the feature on the array is circular or oval." xsd:string property_value: mged:unique_identifier "MO_459" xsd:string [Instance] id: mged:environmental_history_design instance_of: mged:EnvironmentalHistory property_value: rdfs:comment "An environmental history design type is where some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc." xsd:string property_value: mged:unique_identifier "MO_698" xsd:string [Instance] id: mged:ex_vivo_design instance_of: mged:MethodologicalDesign property_value: rdfs:comment "An experiment design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A\ncell culture with an established cell line is an in vitro experiment." xsd:string property_value: mged:unique_identifier "MO_808" xsd:string [Instance] id: mged:exemplar_mRNA instance_of: mged:TheoreticalBioSequenceType property_value: mged:unique_identifier "MO_621" xsd:string property_value: rdfs:comment "An exemplar is a representative cDNA sequence for each gene. The exemplar\napproach is a method that usually involves some initial clustering into gene\ngroups and the subsequent selection of a representative from each gene\ngroup." xsd:string [Instance] id: mged:exon instance_of: mged:DeprecatedTerms property_value: mged:deprecation_old_parent mged:TheoreticalBioSequenceType property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_619" xsd:string property_value: rdfs:comment "sequence which represents regions of a transcript that are joined to another exon during splicing" xsd:string [Instance] id: mged:experimental_and_computational_feature instance_of: mged:SeqFeatureBasis property_value: rdfs:comment "Sequence features derived by both computational and experimental methods." xsd:string property_value: mged:unique_identifier "MO_516" xsd:string [Instance] id: mged:experimental_design_element_group_type instance_of: mged:DesignElementGroupType property_value: rdfs:comment "A grouping of DesignElements, Features/Reporters/Composite Sequences which are expected to detect a signal in the biomaterial." xsd:string property_value: mged:unique_identifier "MO_755" xsd:string [Instance] id: mged:experimental_feature instance_of: mged:SeqFeatureBasis property_value: mged:unique_identifier "MO_452" xsd:string property_value: rdfs:comment "An experimentally defined sequence feature." xsd:string [Instance] id: mged:extract instance_of: mged:BioSampleType property_value: mged:unique_identifier "MO_895" xsd:string property_value: rdfs:comment "The BioSample immediately before labeling." xsd:string [Instance] id: mged:fM instance_of: mged:ConcentrationUnit property_value: rdfs:comment "femtomolar, concentration unit" xsd:string property_value: mged:unique_identifier "MO_898" xsd:string [Instance] id: mged:family_history_design instance_of: mged:EpidemiologicalDesign property_value: rdfs:comment "A family history design type is where the family history such as traits, characteristics, susceptibility to disease is studied" xsd:string property_value: mged:unique_identifier "MO_544" xsd:string [Instance] id: mged:father instance_of: mged:FamilyRelationship property_value: rdfs:comment "A male parent." xsd:string property_value: mged:unique_identifier "MO_762" xsd:string [Instance] id: mged:feature_extraction instance_of: mged:ExperimentalProtocolType property_value: mged:synonym "image quantification" xsd:string property_value: rdfs:comment "The process of obtaining quantifiable values from the scanned image of the \n array. Exact synonyms: image analysis, image quantification" xsd:string property_value: mged:synonym "image analysis" xsd:string property_value: mged:unique_identifier "MO_928" xsd:string [Instance] id: mged:feature_extraction_software instance_of: mged:SoftwareType property_value: rdfs:comment "Software to create MeasuredBioAssayData from images.\nExact Synonym: image analysis software, image quantification software." xsd:string property_value: mged:unique_identifier "MO_633" xsd:string property_value: mged:synonym "image analysis software" xsd:string property_value: mged:synonym "image quantification software" xsd:string [Instance] id: mged:feces instance_of: mged:DeprecatedTerms property_value: mged:deprecated_from_version mged:version_1.1.9 property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_old_parent mged:BioSourceType property_value: mged:deprecation_replacement_term mged:BioSourceType property_value: mged:deprecation_in_version "1.1.9" xsd:string property_value: rdfs:comment "A biosource obtained as fecal matter." xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_636" xsd:string [Instance] id: mged:feeding instance_of: mged:DeliveryMethod property_value: rdfs:comment "Delivery method where a compound/drug is administered in food or water." xsd:string property_value: mged:unique_identifier "MO_993" xsd:string [Instance] id: mged:female instance_of: mged:Sex property_value: rdfs:comment "of, pertaining to, or designating the sex that only produces gametes that can be fertilized by male gametes." xsd:string property_value: mged:unique_identifier "MO_506" xsd:string [Instance] id: mged:fertilization instance_of: mged:InitialTimePoint property_value: rdfs:comment "The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. (from the GO)" xsd:string property_value: mged:unique_identifier "MO_701" xsd:string [Instance] id: mged:fg instance_of: mged:MassUnit property_value: rdfs:comment "femtogram, unit of mass" xsd:string property_value: mged:unique_identifier "MO_732" xsd:string [Instance] id: mged:filtered_data instance_of: mged:DerivedBioAssayType property_value: mged:unique_identifier "MO_625" xsd:string property_value: rdfs:comment "Data from which a subset has been removed based on some criteria, e.g. data below an intensity threshhold." xsd:string [Instance] id: mged:fl instance_of: mged:VolumeUnit property_value: mged:unique_identifier "MO_721" xsd:string property_value: rdfs:comment "femtoliter, unit of volume" xsd:string [Instance] id: mged:flag_filter instance_of: mged:DataTransformationProtocolType property_value: rdfs:comment "transformation method that involves removal of values in a data set based \n on visual or computed flags (e.g. the GenePix feature_extraction software \n standard flags). This includes low-intensity filtering methods, where the \n flag indicates low intensity values in the data set (for microarrays and \n gels the threshold for exclusion is usually based on some estimation of \n local or global background intensity; for mass spectrometry and NMR, it is \n usually based on the signal-to-noise ratio in the spectrum)." xsd:string [Instance] id: mged:flip-dye_consistency instance_of: mged:NormalizationDescriptionType property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:was_replaced_by mged:dye_swap_merge property_value: mged:has_reason_for_deprecation mged:replaced_term property_value: rdfs:comment "A method of checking the consistency of expression levels between a pair of features from flip-dye hybridizations by studying the distribution of the logarithm of ratios of intensity ratios from the two spots." xsd:string property_value: mged:unique_identifier "MO_907" xsd:string [Instance] id: mged:float instance_of: mged:DataType property_value: rdfs:comment "A value which is a floating point number (i.e. real number) with arbitrary precision (e.g. 2.34)." xsd:string property_value: mged:unique_identifier "MO_860" xsd:string [Instance] id: mged:fmol instance_of: mged:QuantityUnit property_value: mged:unique_identifier "MO_689" xsd:string property_value: rdfs:comment "femtomole, unit of quantity" xsd:string [Instance] id: mged:forward instance_of: mged:StrandType property_value: rdfs:comment "the forward strand\nexact synonym: +" xsd:string property_value: mged:synonym "+" xsd:string property_value: mged:unique_identifier "MO_820" xsd:string [Instance] id: mged:fractionate instance_of: mged:ExperimentalProtocolType property_value: rdfs:comment "The action of separating a BioMaterial into one or more fractions e.g. differential centrifugation or FACS when used for cell sorting (see purify)." xsd:string property_value: mged:unique_identifier "MO_872" xsd:string [Instance] id: mged:fractionate instance_of: mged:ExperimentalProtocolType property_value: rdfs:comment "The action of separating a BioMaterial into one or more fractions e.g. differential centrifugation or FACS when used for cell sorting (see purify)." xsd:string property_value: mged:unique_identifier "MO_872" xsd:string [Instance] id: mged:freeze_dried_sample instance_of: mged:BioSourceType property_value: rdfs:comment "A biomaterial that has been lyophilized or dried by freezing under a vacuum." xsd:string property_value: mged:unique_identifier "MO_589" xsd:string [Instance] id: mged:french_railway_distance instance_of: mged:NodeValueType property_value: rdfs:comment "The \"French railway distance\" is based on the fact that (at least in the past) most of the railways in France headed straight to Paris. Thus, the French railway distance between two points is the usual distance if the straight line through them passes to a designated ÒParisÓ point, or is the sum of their distances to the ÒParisÓ point otherwise." xsd:string property_value: mged:unique_identifier "MO_964" xsd:string [Instance] id: mged:fresh_sample instance_of: mged:BioSourceType property_value: mged:unique_identifier "MO_730" xsd:string property_value: rdfs:comment "A sample freshly obtained from the organism(s). E.g. a liver freshly removed from a rat." xsd:string [Instance] id: mged:frozen_sample instance_of: mged:BioSourceType property_value: rdfs:comment "A biomaterial obtained frozen" xsd:string property_value: mged:unique_identifier "MO_610" xsd:string [Instance] id: mged:frozen_storage instance_of: mged:PreservationType property_value: rdfs:comment "Storage where the thing stored is stored below 0 degrees celsius." xsd:string property_value: mged:unique_identifier "MO_481" xsd:string [Instance] id: mged:function_record instance_of: mged:DatabaseEntryType property_value: mged:unique_identifier "MO_538" xsd:string property_value: rdfs:comment "a record which identifies and describes the function of a gene product, e.g. E.C. record" xsd:string [Instance] id: mged:funder instance_of: mged:Roles property_value: mged:unique_identifier "MO_520" xsd:string property_value: rdfs:comment "Contact which provides funding for experiments." xsd:string [Instance] id: mged:g instance_of: mged:MassUnit property_value: rdfs:comment "gram, unit of mass" xsd:string property_value: mged:unique_identifier "MO_825" xsd:string [Instance] id: mged:g_per_L instance_of: mged:ConcentrationUnit property_value: mged:unique_identifier "MO_805" xsd:string property_value: rdfs:comment "grams per liter, concentration unit" xsd:string [Instance] id: mged:gene instance_of: mged:DeprecatedTerms property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:deprecation_old_parent mged:TheoreticalBioSequenceType property_value: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType property_value: rdfs:comment "genomic sequence which corresponds to the primary transcript and uses the furthest 5' and 3' UTR's, doesn't include non transcribed regulatory regions. Can be experimentally or computationally determined" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_503" xsd:string [Instance] id: mged:gene_fragment instance_of: mged:TheoreticalBioSequenceType property_value: mged:unique_identifier "MO_853" xsd:string property_value: rdfs:comment "sequence of part of a gene, which is missing one or both ends" xsd:string [Instance] id: mged:gene_knock_in instance_of: mged:GeneticModification property_value: mged:unique_identifier "MO_437" xsd:string property_value: rdfs:comment "A modification whereby a functional gene, or a functional part of a gene, is inserted into an organism', e.g. by recombination, P-element insertion." xsd:string [Instance] id: mged:gene_knock_out instance_of: mged:GeneticModification property_value: rdfs:comment "The modification of an organism that renders a gene non-functional e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods." xsd:string property_value: mged:unique_identifier "MO_771" xsd:string [Instance] id: mged:genetic_modification instance_of: mged:ComplexAction property_value: mged:unique_identifier "MO_927" xsd:string property_value: rdfs:comment "An action whereby an organism(s) has had genetic material removed, added, or rearranged." xsd:string [Instance] id: mged:genetic_modification instance_of: mged:ComplexAction property_value: mged:unique_identifier "MO_927" xsd:string property_value: rdfs:comment "An action whereby an organism(s) has had genetic material removed, added, or rearranged." xsd:string [Instance] id: mged:genetic_modification_design instance_of: mged:PerturbationalDesign property_value: rdfs:comment "A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out" xsd:string property_value: mged:unique_identifier "MO_447" xsd:string [Instance] id: mged:genetic_variation instance_of: mged:DeprecatedTerms property_value: mged:deprecated_from_version mged:version_1.1.8 property_value: mged:deprecation_old_parent mged:BioMaterialCharacteristicCategory property_value: mged:deprecation_replacement_term mged:BioMaterialCharacteristicCategory property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: rdfs:comment "A descriptor for FactorValue where GeneticVariation is compared. " xsd:string property_value: mged:deprecation_in_version "1.1.8" xsd:string property_value: mged:unique_identifier "MO_557" xsd:string [Instance] id: mged:genomic_DNA instance_of: mged:MaterialType property_value: mged:unique_identifier "MO_599" xsd:string property_value: rdfs:comment "high molecular weight DNA" xsd:string [Instance] id: mged:genomic_region_amplification instance_of: mged:ChromosomalAberrationClassification property_value: rdfs:comment "increment in copy number of a genomic region, includes gene amplification, genomic amplification, and DNA amplification" xsd:string property_value: mged:unique_identifier "MO_609" xsd:string [Instance] id: mged:genotyping_design instance_of: mged:BioMolecularAnnotation property_value: mged:unique_identifier "MO_560" xsd:string property_value: rdfs:comment "A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. " xsd:string [Instance] id: mged:germination instance_of: mged:InitialTimePoint property_value: mged:unique_identifier "MO_590" xsd:string property_value: rdfs:comment "The physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth (from the GO)." xsd:string [Instance] id: mged:glass instance_of: mged:SubstrateType property_value: rdfs:comment "The array is made on a glass slide." xsd:string property_value: mged:unique_identifier "MO_742" xsd:string [Instance] id: mged:gram_percent instance_of: mged:ConcentrationUnit property_value: mged:unique_identifier "MO_582" xsd:string property_value: rdfs:comment "grams per deciliter, concentration unit" xsd:string [Instance] id: mged:granddaughter instance_of: mged:FamilyRelationship property_value: mged:unique_identifier "MO_703" xsd:string property_value: rdfs:comment "A daughter of one's son or daughter." xsd:string [Instance] id: mged:grandfather instance_of: mged:FamilyRelationship property_value: mged:unique_identifier "MO_478" xsd:string property_value: rdfs:comment "The father of one's father or mother." xsd:string [Instance] id: mged:grandmother instance_of: mged:FamilyRelationship property_value: rdfs:comment "The mother of one's father or mother." xsd:string property_value: mged:unique_identifier "MO_924" xsd:string [Instance] id: mged:grandson instance_of: mged:FamilyRelationship property_value: mged:unique_identifier "MO_831" xsd:string property_value: rdfs:comment "A son of one's son or daughter." xsd:string [Instance] id: mged:grow instance_of: mged:ExperimentalProtocolType property_value: rdfs:comment "A ComplexAction or ProtocolType describing growth of an organism or cell culture." xsd:string property_value: mged:unique_identifier "MO_758" xsd:string [Instance] id: mged:grow instance_of: mged:ExperimentalProtocolType property_value: rdfs:comment "A ComplexAction or ProtocolType describing growth of an organism or cell culture." xsd:string property_value: mged:unique_identifier "MO_758" xsd:string [Instance] id: mged:growth_condition_design instance_of: mged:PerturbationalDesign property_value: rdfs:comment "A growth condition experiment design type is where some part of the growth condition is changed for the purposes of the experiment, examples of growth conditions changed are media, temperature, humidity, light, nutrients. " xsd:string property_value: mged:unique_identifier "MO_588" xsd:string [Instance] id: mged:half-life instance_of: mged:TimeUnitOther property_value: mged:unique_identifier "MO_595" xsd:string property_value: rdfs:comment "t1/2. The period over which the activity or concentration of a specified chemical or element falls to half its original activity or concentration. Typically applied to the half-life of radioactive atoms but also applicable to any other situation where the population is of molecules of diminishing concentration or activity." xsd:string [Instance] id: mged:haploid instance_of: mged:Ploidy property_value: rdfs:comment "Describes a cell, nucleus or an organism with one copy of each chromosome.\n" xsd:string property_value: mged:unique_identifier "MO_719" xsd:string [Instance] id: mged:hardware_manufacturer instance_of: mged:Roles property_value: rdfs:comment "Person or organization that manufactured the hardware." xsd:string property_value: mged:unique_identifier "MO_763" xsd:string [Instance] id: mged:hardware_variation_design instance_of: mged:MethodologicalDesign property_value: rdfs:comment "A hardware variation experiment design type compares different types of hardware for performance, reproducibility, accuracy and precision." xsd:string property_value: mged:unique_identifier "MO_734" xsd:string [Instance] id: mged:harvest instance_of: mged:ComplexAction property_value: rdfs:comment "The process of harvesting cells from culture." xsd:string property_value: mged:unique_identifier "MO_982" xsd:string [Instance] id: mged:harvest instance_of: mged:ComplexAction property_value: rdfs:comment "The process of harvesting cells from culture." xsd:string property_value: mged:unique_identifier "MO_982" xsd:string [Instance] id: mged:hatching instance_of: mged:InitialTimePoint property_value: rdfs:comment "The point at which an organism emerges from an egg." xsd:string property_value: mged:unique_identifier "MO_745" xsd:string [Instance] id: mged:heating_block instance_of: mged:HardwareType property_value: rdfs:comment "A device for controlling temperature." xsd:string property_value: mged:unique_identifier "MO_663" xsd:string [Instance] id: mged:heavy_background instance_of: mged:DefectType property_value: mged:unique_identifier "MO_571" xsd:string property_value: rdfs:comment "The Zone is excluded due to smearing, streaking, or dense background in the Zone." xsd:string [Instance] id: mged:hermaphrodite instance_of: mged:Sex property_value: rdfs:comment "an organism with both male and female sexual organs in one individual\nsynonym: intersex" xsd:string property_value: mged:synonym "intersex" xsd:string property_value: mged:unique_identifier "MO_356" xsd:string [Instance] id: mged:histological_slide_preparation instance_of: mged:ComplexAction property_value: mged:unique_identifier "MO_611" xsd:string property_value: rdfs:comment "The action of preparing a slide for the microscopical examination of organism parts or cell types." xsd:string [Instance] id: mged:histological_slide_preparation instance_of: mged:ComplexAction property_value: mged:unique_identifier "MO_611" xsd:string property_value: rdfs:comment "The action of preparing a slide for the microscopical examination of organism parts or cell types." xsd:string [Instance] id: mged:homogenizer instance_of: mged:HardwareType property_value: mged:unique_identifier "MO_714" xsd:string property_value: rdfs:comment "An instrument which fragments tissues or other biomaterials." xsd:string [Instance] id: mged:hours instance_of: mged:TimeUnit property_value: mged:unique_identifier "MO_486" xsd:string property_value: mged:synonym "h" xsd:string property_value: rdfs:comment "60 minutes, time unit" xsd:string [Instance] id: mged:hybridization instance_of: mged:ComplexAction property_value: mged:unique_identifier "MO_884" xsd:string property_value: rdfs:comment "The process of incubating one or more labeled extracts with an array." xsd:string [Instance] id: mged:hybridization instance_of: mged:ComplexAction property_value: mged:unique_identifier "MO_884" xsd:string property_value: rdfs:comment "The process of incubating one or more labeled extracts with an array." xsd:string [Instance] id: mged:hybridization_chamber instance_of: mged:HardwareType property_value: rdfs:comment "A chamber in which the hybridization is performed which maintains constant conditions." xsd:string property_value: mged:unique_identifier "MO_563" xsd:string [Instance] id: mged:hybridization_station instance_of: mged:HardwareType property_value: rdfs:comment "An instrument which controls hybridization conditions, into which a hybridization chamber may fit." xsd:string property_value: mged:unique_identifier "MO_497" xsd:string [Instance] id: mged:image_acquisition instance_of: mged:ExperimentalProtocolType property_value: rdfs:comment "The process of generating an image from the array." xsd:string property_value: mged:unique_identifier "MO_929" xsd:string [Instance] id: mged:image_acquisition_software instance_of: mged:SoftwareType property_value: mged:unique_identifier "MO_1003" xsd:string property_value: mged:synonym "scanning software" xsd:string property_value: rdfs:comment "Software to control a scanner and manipulate and save images.\nExact synonym: scanning software" xsd:string [Instance] id: mged:image_record instance_of: mged:DatabaseEntryType property_value: mged:unique_identifier "MO_691" xsd:string property_value: rdfs:comment "A record which describes and identifies an image, e.g. an image from the mouse atlas" xsd:string [Instance] id: mged:imprinting_design instance_of: mged:BiologicalProperty property_value: rdfs:comment "An experiment design type where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared." xsd:string property_value: mged:unique_identifier "MO_914" xsd:string [Instance] id: mged:in_medium instance_of: mged:DeliveryMethod property_value: mged:unique_identifier "MO_733" xsd:string property_value: rdfs:comment "Delivery method where a compound/drug is administered in the culture medium (e.g., for in vitro treatment)." xsd:string [Instance] id: mged:in_situ_oligo_features instance_of: mged:TechnologyType property_value: rdfs:comment "The TechnologyType of the FeatureGroup is manufactured using in situ methods such as photolithography (e.g. Affymetrix) or chemical synthesis (e.g. Agilent)" xsd:string property_value: mged:unique_identifier "MO_514" xsd:string [Instance] id: mged:in_vitro_design instance_of: mged:MethodologicalDesign property_value: rdfs:comment "An experiment done in a test tube or a culture dish, e.g. \nA bacterial invasion assay in an established cell culture." xsd:string property_value: mged:unique_identifier "MO_347" xsd:string [Instance] id: mged:in_vivo_design instance_of: mged:MethodologicalDesign property_value: rdfs:comment "An experiment design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model." xsd:string property_value: mged:unique_identifier "MO_454" xsd:string [Instance] id: mged:inconclusive instance_of: mged:Result property_value: mged:unique_identifier "MO_744" xsd:string property_value: rdfs:comment "a result which can not be interpreted as positive or negative" xsd:string [Instance] id: mged:incubate instance_of: mged:ComplexAction property_value: mged:unique_identifier "MO_965" xsd:string property_value: rdfs:comment "The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity for the purposes of obtaining a different product." xsd:string [Instance] id: mged:incubate instance_of: mged:ComplexAction property_value: mged:unique_identifier "MO_965" xsd:string property_value: rdfs:comment "The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity for the purposes of obtaining a different product." xsd:string [Instance] id: mged:individual instance_of: mged:BioMaterialCharacteristicCategory property_value: mged:unique_identifier "MO_639" xsd:string property_value: rdfs:comment "A descriptor for FactorValue where BioSources are compared. " xsd:string [Instance] id: mged:individual_genetic_characteristic instance_of: mged:BioMaterialCharacteristicCategory property_value: rdfs:comment "A descriptor for FactorValue where IndividualGeneticCharacteristic is compared. " xsd:string property_value: mged:unique_identifier "MO_722" xsd:string [Instance] id: mged:individual_genetic_characteristics_design instance_of: mged:BiologicalProperty property_value: rdfs:comment "An experiment design type where genotype, haplotype, or other individual genetic characteristics are compared." xsd:string property_value: mged:unique_identifier "MO_527" xsd:string [Instance] id: mged:induced_mutation instance_of: mged:GeneticModification property_value: mged:unique_identifier "MO_564" xsd:string property_value: rdfs:comment "The modification of the genetic material (either coding or non-coding) of an organism by mutagenic compounds or irradiation." xsd:string [Instance] id: mged:infect instance_of: mged:DeprecatedTerms property_value: mged:replaced_with_term mged:inoculate property_value: mged:was_replaced_by mged:inoculate property_value: mged:deprecated_from_version mged:version_1.3.0 property_value: mged:deprecation_old_parent mged:ComplexAction property_value: mged:deprecation_old_parent mged:ExperimentalProtocolType property_value: mged:has_reason_for_deprecation mged:replaced_term property_value: mged:unique_identifier "MO_616" xsd:string property_value: mged:deprecation_reason "replaced_term" xsd:string property_value: mged:deprecation_in_version "1.3.0" xsd:string property_value: rdfs:comment "The organism (or organism part) has been exposed to a virus or pathogen. " xsd:string [Instance] id: mged:injury_design instance_of: mged:PerturbationalDesign property_value: mged:unique_identifier "MO_726" xsd:string property_value: rdfs:comment "An injury experiment design type is where the response of an organism(s) to injury or damage is studied." xsd:string [Instance] id: mged:innate_behavior_design instance_of: mged:BiologicalProperty property_value: mged:unique_identifier "MO_355" xsd:string property_value: rdfs:comment "A design in which the innate behavior of the organism is examined, e.g. \n path finding in bees." xsd:string [Instance] id: mged:inoculate instance_of: mged:ExperimentalProtocolType property_value: mged:unique_identifier "MO_559" xsd:string property_value: rdfs:comment "The process of introducing a foreign agent such as serum, vaccine, antigenic substance or organism." xsd:string property_value: mged:synonym "infect" xsd:string [Instance] id: mged:inoculate instance_of: mged:ExperimentalProtocolType property_value: mged:unique_identifier "MO_559" xsd:string property_value: rdfs:comment "The process of introducing a foreign agent such as serum, vaccine, antigenic substance or organism." xsd:string property_value: mged:synonym "infect" xsd:string [Instance] id: mged:institution instance_of: mged:Roles property_value: rdfs:comment "A contact's affiliation, e.g. university, research institute or business." xsd:string property_value: mged:unique_identifier "MO_601" xsd:string [Instance] id: mged:integer instance_of: mged:DataType property_value: mged:unique_identifier "MO_435" xsd:string property_value: rdfs:comment "A value which is a whole number (e.g. 10)." xsd:string [Instance] id: mged:intergenic instance_of: mged:DeprecatedTerms property_value: mged:deprecation_old_parent mged:TheoreticalBioSequenceType property_value: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:unique_identifier "MO_463" xsd:string property_value: rdfs:comment "sequence from the region between genes" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:intramuscular_injection instance_of: mged:DeliveryMethod property_value: mged:unique_identifier "MO_617" xsd:string property_value: rdfs:comment "Delivery method for a compound or drug where the substance is administered via an injection into the muscle." xsd:string [Instance] id: mged:intraperitoneal_injection instance_of: mged:DeliveryMethod property_value: rdfs:comment "A delivery method for compound or drug whereby the substance is administered via the peritoneum." xsd:string property_value: mged:unique_identifier "MO_473" xsd:string [Instance] id: mged:intravenous instance_of: mged:DeliveryMethod property_value: rdfs:comment "delivery method whereby a compound or drug is administered via a vein" xsd:string property_value: mged:unique_identifier "MO_432" xsd:string [Instance] id: mged:intron instance_of: mged:DeprecatedTerms property_value: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:deprecation_old_parent mged:TheoreticalBioSequenceType property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:unique_identifier "MO_709" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: rdfs:comment "sequence spliced out from a transcript" xsd:string [Instance] id: mged:investigator instance_of: mged:Roles property_value: mged:unique_identifier "MO_769" xsd:string property_value: rdfs:comment "Person who contributed to the study." xsd:string [Instance] id: mged:irradiate instance_of: mged:ExperimentalProtocolType property_value: mged:unique_identifier "MO_770" xsd:string property_value: rdfs:comment "treatment of a biomaterial with radiation e.g. electromagnetic radiation" xsd:string [Instance] id: mged:irradiate instance_of: mged:ExperimentalProtocolType property_value: mged:unique_identifier "MO_770" xsd:string property_value: rdfs:comment "treatment of a biomaterial with radiation e.g. electromagnetic radiation" xsd:string [Instance] id: mged:irregular_shape instance_of: mged:DefectType property_value: mged:unique_identifier "MO_669" xsd:string property_value: rdfs:comment "The perimeter of the spotted DNA on the slide is irregular." xsd:string [Instance] id: mged:is_contaminated instance_of: mged:WarningType property_value: rdfs:comment "The clone used to originate the BioSequence which corresponds to the reporter was found to be contaminated (e.g. well-well contamination) on examination." xsd:string property_value: mged:unique_identifier "MO_489" xsd:string [Instance] id: mged:is_expressed_design instance_of: mged:BiologicalProperty property_value: rdfs:comment "A design aimed at identifying genes expressed in biomaterials of interest. " xsd:string property_value: mged:unique_identifier "MO_487" xsd:string [Instance] id: mged:iterative_mean_log_centering instance_of: mged:NormalizationDescriptionType property_value: rdfs:comment "A method of re-scaling ratio data by iteratively subtracting the mean log base 2 ratio from each log2(ratio). This adjusts the mean log2(ratio) to zero. In each subsequent iteration, outliers are removed based on user-specified criteria, the mean log(2) ratio is recalculated based on the remaining data, and the entire data set is rescaled again. This continues until the mean log(2) ratio converges." xsd:string property_value: mged:unique_identifier "MO_957" xsd:string [Instance] id: mged:jackknife_Pearson_correlation instance_of: mged:NodeValueType property_value: rdfs:comment "The jackknife Pearson correlation is the lowest Pearson correlation between two data series where one pair of values in the data series are omitted." xsd:string property_value: mged:unique_identifier "MO_784" xsd:string [Instance] id: mged:journal_article instance_of: mged:PublicationType property_value: mged:unique_identifier "MO_430" xsd:string property_value: rdfs:comment "A article published in a print or online journal having an ISSN." xsd:string [Instance] id: mged:kat_per_L instance_of: mged:ConcentrationUnitOther property_value: mged:unique_identifier "MO_869" xsd:string property_value: rdfs:comment "katal per liter, catalytic-activity concentration unit" xsd:string [Instance] id: mged:kg instance_of: mged:MassUnit property_value: mged:unique_identifier "MO_846" xsd:string property_value: rdfs:comment "kilogram, 1000 grams, unit of mass" xsd:string [Instance] id: mged:kg_per_m2 instance_of: mged:OtherUnit property_value: rdfs:comment "The mass of an object in kilograms divided by the surface area in meters squared. Also known as the Body Mass Index (when applied to a person) which is a measure of leaness/obesity. Exact synonym:kg/m2" xsd:string property_value: mged:synonym "kg/m2" xsd:string property_value: mged:unique_identifier "MO_658" xsd:string [Instance] id: mged:labeling instance_of: mged:ExperimentalProtocolType property_value: rdfs:comment "The procedure of labeling a biosample." xsd:string property_value: mged:unique_identifier "MO_471" xsd:string [Instance] id: mged:labeling instance_of: mged:ExperimentalProtocolType property_value: rdfs:comment "The procedure of labeling a biosample." xsd:string property_value: mged:unique_identifier "MO_471" xsd:string [Instance] id: mged:laser_ablation_mark instance_of: mged:FiducialType property_value: mged:unique_identifier "MO_910" xsd:string property_value: rdfs:comment "mark made on slide using a laser which is used as a point of reference for orientation (fiducial)" xsd:string [Instance] id: mged:light_duration instance_of: mged:EnvironmentalFactorCategory property_value: mged:synonym "photoperiod" xsd:string property_value: mged:unique_identifier "MO_604" xsd:string property_value: rdfs:comment "The length of the light period that a sample is subjected to.\nExact synonym:photoperiod" xsd:string [Instance] id: mged:light_intensity instance_of: mged:EnvironmentalFactorCategory property_value: mged:unique_identifier "MO_517" xsd:string property_value: rdfs:comment "The amount of light actually striking the surface of samples which are being assayed. It has a unit association as well, usually uEinstein /m2 /min or uEinstein /m2/s." xsd:string [Instance] id: mged:linear_amplification instance_of: mged:ExperimentalProtocolType property_value: mged:synonym "Eberwine procedure" xsd:string property_value: mged:unique_identifier "MO_997" xsd:string property_value: rdfs:comment "Amplification of nucleic acid sequence by making many copies off the same template. An example is the use of the T7 promoter for amplification by transcribing many RNA copies.\nnon exact synonym: Eberwine procedure" xsd:string [Instance] id: mged:linear_amplification instance_of: mged:ExperimentalProtocolType property_value: mged:synonym "Eberwine procedure" xsd:string property_value: mged:unique_identifier "MO_997" xsd:string property_value: rdfs:comment "Amplification of nucleic acid sequence by making many copies off the same template. An example is the use of the T7 promoter for amplification by transcribing many RNA copies.\nnon exact synonym: Eberwine procedure" xsd:string [Instance] id: mged:linear_regression_normalization instance_of: mged:NormalizationDescriptionType property_value: rdfs:comment "A method to re-scale paired-assay data from one data set relative to the other, based on regression of the values in the one set to those in the other, where the latter utilizes either all values in the data set, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins). The slope of the regression line is used to re-scale all the values in the data set being normalized. This single parameter method assumes that there is a linear relationship between the data sets. A similar approach could be employed to re-scale data from a standalone assay to another standalone (baseline) assay." xsd:string property_value: mged:unique_identifier "MO_823" xsd:string [Instance] id: mged:linear_scale instance_of: mged:Scale property_value: mged:unique_identifier "MO_751" xsd:string property_value: rdfs:comment "The scale is a standard base 10, non logarithmic scale." xsd:string [Instance] id: mged:linlog_normalization instance_of: mged:NormalizationDescriptionType property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:has_reason_for_deprecation mged:replaced_term property_value: rdfs:comment "A transformation method in which low intensities are linearly scaled while high intensities are logarithmically scaled. The transition point is determined by minimizing the absolute deviation of the variance of log ratios." xsd:string property_value: mged:unique_identifier "MO_956" xsd:string [Instance] id: mged:linlog_transformation instance_of: mged:DataTransformationProtocolType property_value: mged:unique_identifier "MO_845" xsd:string property_value: rdfs:comment "A transformation method in which low intensities are linearly scaled while high intensities are logarithmically scaled. The transition point is determined by minimizing the absolute deviation of the variance of log ratios." xsd:string [Instance] id: mged:liquid instance_of: mged:Media property_value: rdfs:comment "media type, usually some sort of broth" xsd:string property_value: mged:unique_identifier "MO_715" xsd:string [Instance] id: mged:liquid_handler instance_of: mged:HardwareType property_value: rdfs:comment "Hardware for automated liquid transfer and handling." xsd:string property_value: mged:unique_identifier "MO_868" xsd:string [Instance] id: mged:liquid_handler_software instance_of: mged:SoftwareType property_value: mged:unique_identifier "MO_761" xsd:string property_value: rdfs:comment "Software used to control automated liquid handler." xsd:string [Instance] id: mged:list_of_booleans instance_of: mged:DataType property_value: mged:unique_identifier "MO_712" xsd:string property_value: rdfs:comment "An ordered, finite set of booleans." xsd:string [Instance] id: mged:list_of_floats instance_of: mged:DataType property_value: mged:unique_identifier "MO_760" xsd:string property_value: rdfs:comment "An ordered, finite set of floats." xsd:string [Instance] id: mged:list_of_integers instance_of: mged:DataType property_value: mged:unique_identifier "MO_891" xsd:string property_value: rdfs:comment "An ordered, finite set of integers." xsd:string [Instance] id: mged:list_of_negative_floats instance_of: mged:DataType property_value: rdfs:comment "An ordered, finite set of negative floats." xsd:string property_value: mged:unique_identifier "MO_851" xsd:string [Instance] id: mged:list_of_negative_integers instance_of: mged:DataType property_value: mged:unique_identifier "MO_900" xsd:string property_value: rdfs:comment "An ordered, finite set of negative integers." xsd:string [Instance] id: mged:list_of_nonnegative_floats instance_of: mged:DataType property_value: mged:unique_identifier "MO_360" xsd:string property_value: rdfs:comment "An ordered, finite set of nonnegative floats." xsd:string [Instance] id: mged:list_of_nonnegative_integers instance_of: mged:DataType property_value: rdfs:comment "An ordered, finite set of nonnegative integers." xsd:string property_value: mged:unique_identifier "MO_973" xsd:string [Instance] id: mged:list_of_nonpositive_floats instance_of: mged:DataType property_value: rdfs:comment "An ordered, finite set of nonpositive floats." xsd:string property_value: mged:unique_identifier "MO_1000" xsd:string [Instance] id: mged:list_of_nonpositive_integers instance_of: mged:DataType property_value: rdfs:comment "An ordered, finite set of nonpositive integers." xsd:string property_value: mged:unique_identifier "MO_804" xsd:string [Instance] id: mged:list_of_positive_floats instance_of: mged:DataType property_value: mged:unique_identifier "MO_777" xsd:string property_value: rdfs:comment "An ordered, finite set of positive floats." xsd:string [Instance] id: mged:list_of_positive_integers instance_of: mged:DataType property_value: rdfs:comment "An ordered, finite set of positive integers." xsd:string property_value: mged:unique_identifier "MO_873" xsd:string [Instance] id: mged:list_of_strings instance_of: mged:DataType property_value: rdfs:comment "An ordered, finite set of strings." xsd:string property_value: mged:unique_identifier "MO_800" xsd:string [Instance] id: mged:loess_global_normalization instance_of: mged:DataTransformationProtocolType property_value: rdfs:comment "Application of a normalization of type loess_normalization where the same normalization curve is used for all points in the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample." xsd:string property_value: mged:unique_identifier "MO_443" xsd:string [Instance] id: mged:loess_group_normalization instance_of: mged:DataTransformationProtocolType property_value: mged:unique_identifier "MO_377" xsd:string property_value: rdfs:comment "Application of a normalization of type loess_normalization where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed." xsd:string [Instance] id: mged:loess_normalization instance_of: mged:NormalizationDescriptionType property_value: rdfs:comment "A method of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can \nbe applied globally, or limited by one or more specified criteria." xsd:string property_value: mged:unique_identifier "MO_428" xsd:string [Instance] id: mged:loess_scaled_group_normalization instance_of: mged:DataTransformationProtocolType property_value: rdfs:comment "Application of a scale adjustment following loess_group_normalization, to render the group variances similar." xsd:string property_value: mged:unique_identifier "MO_521" xsd:string [Instance] id: mged:log_base_10 instance_of: mged:Scale property_value: mged:unique_identifier "MO_735" xsd:string property_value: rdfs:comment "The values presented are logarithm, base 10." xsd:string [Instance] id: mged:log_base_2 instance_of: mged:Scale property_value: rdfs:comment "The values presented are logarithm, base 2." xsd:string property_value: mged:unique_identifier "MO_647" xsd:string [Instance] id: mged:log_base_e instance_of: mged:Scale property_value: mged:unique_identifier "MO_554" xsd:string property_value: rdfs:comment "The values presented are logarithm, base e." xsd:string [Instance] id: mged:log_ratio instance_of: mged:DerivedBioAssayType property_value: mged:unique_identifier "MO_896" xsd:string property_value: rdfs:comment "Logarithmic transformation of ratio data." xsd:string [Instance] id: mged:long_oligo instance_of: mged:DesignElement property_value: rdfs:comment "An element that is an oligonucleotide of at least 50 nucleotides in length." xsd:string property_value: mged:unique_identifier "MO_598" xsd:string [Instance] id: mged:loop_design instance_of: mged:MethodologicalDesign property_value: mged:synonym "circular design" xsd:string property_value: rdfs:comment "A loop experiment design is where labeled extracts are compared in consecutive pairs.\nsynonym: circular design" xsd:string property_value: mged:unique_identifier "MO_912" xsd:string [Instance] id: mged:low_intensity_filter instance_of: mged:DeprecatedTerms property_value: mged:deprecation_old_parent mged:DataTransformationProtocolType property_value: mged:has_reason_for_deprecation mged:replaced_term property_value: mged:deprecated_from_version mged:version_1.3.0 property_value: mged:replaced_with_term mged:flag_filter property_value: mged:was_replaced_by mged:flag_filter property_value: mged:deprecation_in_version "1.3.0" xsd:string property_value: mged:deprecation_reason "replaced_term" xsd:string property_value: rdfs:comment "A transformation method that involves removal of low intensity values in a data set. For microarrays and gels the threshold for exclusion is usually based on some estimation of local or global background intensity; for mass spectrometry and NMR, it is usually based on the signal-to-noise ratio in the spectrum." xsd:string property_value: mged:unique_identifier "MO_706" xsd:string [Instance] id: mged:lowess_global_normalization instance_of: mged:DataTransformationProtocolType property_value: mged:unique_identifier "MO_692" xsd:string property_value: rdfs:comment "Application of a normalization of type lowess_normalization where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample." xsd:string [Instance] id: mged:lowess_group_normalization instance_of: mged:DataTransformationProtocolType property_value: mged:unique_identifier "MO_861" xsd:string property_value: rdfs:comment "Application of a normalization of type lowess_normalization where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed." xsd:string [Instance] id: mged:lowess_normalization instance_of: mged:NormalizationDescriptionType property_value: rdfs:comment "A method of normalizing ratio data by using a locally weighted polynomial \n regression (typically after a log transformation). The regression can be \n performed on log ratios resulting from the relation of two data sets \n versus the average log intensity data from the same two data sets or it \n can be performed on raw or log transformed values from one data set versus \n values from another. The goal could be to remove intensity-dependent \n dye-specific effects from the set of pair wise ratios. This method can be \n applied globally, or limited by one or more specified criteria." xsd:string property_value: mged:unique_identifier "MO_720" xsd:string [Instance] id: mged:lowess_scaled_group_normalization instance_of: mged:DataTransformationProtocolType property_value: rdfs:comment "Application of a scale adjustment following lowess_group_normalization, to render the group variances similar." xsd:string property_value: mged:unique_identifier "MO_410" xsd:string [Instance] id: mged:lumen instance_of: mged:LightUnit property_value: mged:unique_identifier "MO_603" xsd:string property_value: rdfs:comment "The unit of total light output from a light source." xsd:string [Instance] id: mged:lux instance_of: mged:LightUnit property_value: mged:unique_identifier "MO_573" xsd:string property_value: rdfs:comment "A metric unit equal to one lumen per square meter. This unit is the modern equivalent of foot-candles where one footcandle is 10.76 lux." xsd:string [Instance] id: mged:m instance_of: mged:DistanceUnit property_value: mged:unique_identifier "MO_367" xsd:string property_value: rdfs:comment "meter, distance unit" xsd:string [Instance] id: mged:mL_per_L instance_of: mged:ConcentrationUnit property_value: mged:unique_identifier "MO_801" xsd:string property_value: rdfs:comment "milliliters per liter, concentration unit" xsd:string [Instance] id: mged:mM instance_of: mged:ConcentrationUnit property_value: rdfs:comment "milimolar, concentration unit" xsd:string property_value: mged:unique_identifier "MO_509" xsd:string [Instance] id: mged:mOsm_per_kg_H2O instance_of: mged:ConcentrationUnitOther property_value: mged:unique_identifier "MO_661" xsd:string property_value: rdfs:comment "osmolality per kilogram of water, concentration of the solute per unit of solvent" xsd:string [Instance] id: mged:mRNA instance_of: mged:DeprecatedTerms property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_old_parent mged:TheoreticalBioSequenceType property_value: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: rdfs:comment "sequence of a processed transcript capable of directing protein synthesis" xsd:string property_value: mged:unique_identifier "MO_803" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string [Instance] id: mged:male instance_of: mged:Sex property_value: mged:unique_identifier "MO_652" xsd:string property_value: rdfs:comment "individual whose sex organs contain only male gametes" xsd:string [Instance] id: mged:manhattan_distance instance_of: mged:NodeValueType property_value: mged:unique_identifier "MO_567" xsd:string property_value: rdfs:comment "The \"Manhattan distance\" is the shortest path between two points in a block format, e.g. the length of the path along Manthattan city streets." xsd:string [Instance] id: mged:mating_type_a instance_of: mged:Sex property_value: rdfs:comment "Mating type of S. cerevisiae." xsd:string property_value: mged:unique_identifier "MO_659" xsd:string [Instance] id: mged:mating_type_alpha instance_of: mged:Sex property_value: rdfs:comment "Mating type of S. cerevisiae." xsd:string property_value: mged:unique_identifier "MO_637" xsd:string [Instance] id: mged:mating_type_h_minus instance_of: mged:Sex property_value: rdfs:comment "Mating type of S.pombe." xsd:string property_value: mged:unique_identifier "MO_407" xsd:string [Instance] id: mged:mating_type_h_plus instance_of: mged:Sex property_value: mged:unique_identifier "MO_855" xsd:string property_value: rdfs:comment "Mating type of S.pombe." xsd:string [Instance] id: mged:mean_and_coefficient_of_variation instance_of: mged:DerivedBioAssayType property_value: rdfs:comment "the mean and coefficient of variation values resulting from computationally combining 2 or more sets of BioAssayData" xsd:string property_value: mged:unique_identifier "MO_425" xsd:string [Instance] id: mged:mean_and_confidence_indicators instance_of: mged:DeprecatedTerms property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:deprecation_replacement_term mged:DerivedBioAssayType property_value: mged:deprecation_old_parent mged:DerivedBioAssayType property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:unique_identifier "MO_702" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: rdfs:comment "the mean and associated confidence values resulting from combining the data from 2 or more sets of BioAssayData. Confidence indicators include, but are not limited to: confidence interval, standard deviation, coefficient of variation, and p-value." xsd:string [Instance] id: mged:mean_and_p_values instance_of: mged:DerivedBioAssayType property_value: mged:unique_identifier "MO_943" xsd:string property_value: rdfs:comment "the mean and associated p-values resulting from computationally combining 2 or more sets of BioAssayData" xsd:string [Instance] id: mged:mean_and_standard_deviation instance_of: mged:DerivedBioAssayType property_value: mged:unique_identifier "MO_445" xsd:string property_value: rdfs:comment "the mean and standard deviation values resulting from computationally combining 2 or more sets of BioAssayData" xsd:string [Instance] id: mged:mean_and_variance instance_of: mged:DerivedBioAssayType property_value: rdfs:comment "the mean and variance values resulting from computationally combining 2 or more sets of BioAssayData" xsd:string property_value: mged:unique_identifier "MO_458" xsd:string [Instance] id: mged:mean_log_centering instance_of: mged:NormalizationDescriptionType property_value: rdfs:comment "A method of normalizing log ratio data by subtraction of the mean log ratios computed across all data points, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins)." xsd:string property_value: mged:unique_identifier "MO_398" xsd:string [Instance] id: mged:mean_log_normalization instance_of: mged:DataTransformationProtocolType property_value: rdfs:comment "Application of a normalization of type mean_log_centering." xsd:string property_value: mged:unique_identifier "MO_657" xsd:string [Instance] id: mged:media instance_of: mged:EnvironmentalFactorCategory property_value: rdfs:comment "The physical state or matrix used to provide nutrients to the organism (e.g., liquid, agar, soil) " xsd:string property_value: mged:unique_identifier "MO_545" xsd:string [Instance] id: mged:median_log_centering instance_of: mged:NormalizationDescriptionType property_value: rdfs:comment "A method of normalizing log ratio data by subtraction of the median log ratios computed across all data points, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins)." xsd:string property_value: mged:unique_identifier "MO_811" xsd:string [Instance] id: mged:median_log_normalization instance_of: mged:DataTransformationProtocolType property_value: rdfs:comment "Application of a normalization of type median_log_centering." xsd:string property_value: mged:unique_identifier "MO_931" xsd:string [Instance] id: mged:merged_term instance_of: mged:DeprecationReason property_value: rdfs:comment "the term has been subsumed into a more general term" xsd:string [Instance] id: mged:metastatic_site instance_of: mged:CancerSite property_value: rdfs:comment "the organism part in which additional tumors are identified remote from the primary site" xsd:string property_value: mged:unique_identifier "MO_806" xsd:string [Instance] id: mged:mg instance_of: mged:MassUnit property_value: mged:unique_identifier "MO_949" xsd:string property_value: rdfs:comment "milligram, mass unit" xsd:string [Instance] id: mged:mg_per_kg_per_day instance_of: mged:ConcentrationUnitOther property_value: mged:unique_identifier "MO_353" xsd:string property_value: rdfs:comment "milligram per kilogram per day" xsd:string [Instance] id: mged:mg_per_ml instance_of: mged:ConcentrationUnit property_value: rdfs:comment "milligrams per milliliter, concentration unit" xsd:string property_value: mged:unique_identifier "MO_522" xsd:string [Instance] id: mged:microarray_experiment_record instance_of: mged:DatabaseEntryType property_value: rdfs:comment "A record which describes and identifies a microarray experiment e.g. GEO" xsd:string property_value: mged:unique_identifier "MO_346" xsd:string [Instance] id: mged:microeinstein_per_minute_and_square_meter instance_of: mged:LightUnit property_value: mged:unique_identifier "MO_526" xsd:string property_value: rdfs:comment "Microeinstein per minute and square meter (µE m-2 min-1 or uEinstein m-2 min-1). One einstein is one mole or 6.02x10e23 (avogadro constant) photons. It is commonly used as a unit for photosynthetically active radiation (PAR), however the einstein is not an SI unit. Therefore, microEinsteins per m2 per second is identical to micromoles per m2 per second (SI unit for light irradiance). i.e. (1000 µE m-2 s-1 = 1000 µmol m-2 s-1)." xsd:string [Instance] id: mged:microeinstein_per_second_and_square_meter instance_of: mged:LightUnit property_value: rdfs:comment "Microeinstein per second and square meter (µE m-2 s-1 or uEinstein m-2 s-1). One einstein is one mole or 6.02x10e23 (Avogadro constant) photons. It is commonly used as a unit for photosynthetically active radiation (PAR), however the einstein is not an SI unit. Therefore, microEinsteins per m2 per second is identical to micromoles per m2 per second (SI unit for light irradiance). i.e. (1000 µE m-2 s-1 = 1000 µmol m-2 s-1)." xsd:string property_value: mged:unique_identifier "MO_584" xsd:string [Instance] id: mged:micromole_per_second_and_square_meter instance_of: mged:OtherUnit property_value: rdfs:comment "Number of photons in a certain waveband incident per unit time (s) on a unit area (m2) divided by the Avogadro constant (6.022 x 10e23 mol-1). It is used commonly to describe photosynthetically active radiation (PAR) in the 400-700 nm waveband." xsd:string property_value: mged:unique_identifier "MO_848" xsd:string [Instance] id: mged:minutes instance_of: mged:TimeUnit property_value: mged:synonym "m" xsd:string property_value: rdfs:comment "60 seconds, unit of time" xsd:string property_value: mged:unique_identifier "MO_877" xsd:string [Instance] id: mged:missing_feature_or_zone instance_of: mged:DefectType property_value: mged:unique_identifier "MO_405" xsd:string property_value: rdfs:comment "The source DNA was not printed for a Feature or Zone on the slide, possibly due to lack of sample, broken or clogged spotting pin." xsd:string [Instance] id: mged:mix_by_inversion instance_of: mged:AtomicAction property_value: mged:unique_identifier "MO_700" xsd:string property_value: rdfs:comment "Mix through the process of inverting." xsd:string [Instance] id: mged:mix_by_pipette instance_of: mged:AtomicAction property_value: mged:unique_identifier "MO_479" xsd:string property_value: rdfs:comment "Mix by drawing up and down with a pipette." xsd:string [Instance] id: mged:mix_by_vortex instance_of: mged:AtomicAction property_value: rdfs:comment "Mix through the use of a vortexer." xsd:string property_value: mged:unique_identifier "MO_880" xsd:string [Instance] id: mged:mix_general instance_of: mged:AtomicAction property_value: mged:unique_identifier "MO_944" xsd:string property_value: rdfs:comment "The procedure of agitating 2 or more materials in order to combine them. The materials may be of any state solid/liquid/gas." xsd:string [Instance] id: mged:mixed_design_element_group_type instance_of: mged:DesignElementGroupType property_value: mged:unique_identifier "MO_528" xsd:string property_value: rdfs:comment "a design element group consisting of multiple types " xsd:string [Instance] id: mged:mixed_sex instance_of: mged:Sex property_value: mged:unique_identifier "MO_436" xsd:string property_value: rdfs:comment "A population of multiple sexes, e.g. a mixture of females and males, or males and hermaphrodites." xsd:string [Instance] id: mged:ml instance_of: mged:VolumeUnit property_value: rdfs:comment "milliliter, volume unit" xsd:string property_value: mged:unique_identifier "MO_488" xsd:string [Instance] id: mged:ml_per_kg instance_of: mged:ConcentrationUnitOther property_value: rdfs:comment "milliliter per kilogram" xsd:string property_value: mged:unique_identifier "MO_403" xsd:string [Instance] id: mged:mm instance_of: mged:DistanceUnit property_value: rdfs:comment "millimeter, unit of distance" xsd:string property_value: mged:unique_identifier "MO_648" xsd:string [Instance] id: mged:mol instance_of: mged:QuantityUnit property_value: rdfs:comment "mole, unit of quantity" xsd:string property_value: mged:unique_identifier "MO_998" xsd:string [Instance] id: mged:molecular_mixture instance_of: mged:MaterialType property_value: rdfs:comment "an unspecified collection of heterogeneous molecules, e.g. lipids, carbohydrate , nucleic acids and proteins" xsd:string property_value: mged:unique_identifier "MO_889" xsd:string [Instance] id: mged:molecules instance_of: mged:QuantityUnit property_value: mged:unique_identifier "MO_707" xsd:string property_value: rdfs:comment "number of molecules, quantity unit" xsd:string [Instance] id: mged:monosomy instance_of: mged:DeprecatedTerms property_value: mged:deprecation_old_parent mged:ChromosomalAberrationClassification property_value: mged:deprecated_from_version mged:version_1.1.9 property_value: mged:has_reason_for_deprecation mged:replaced_term property_value: mged:replaced_with_term mged:oligosomy property_value: mged:was_replaced_by mged:oligosomy property_value: mged:deprecation_in_version "1.1.9" xsd:string property_value: mged:deprecation_reason "replaced_term" xsd:string property_value: mged:unique_identifier "MO_424" xsd:string property_value: rdfs:comment "Absence of one chromosome of a pair of homologous chromosomes. In a normally diploid cell it is represented symbolically as 2N-1." xsd:string [Instance] id: mged:months instance_of: mged:TimeUnit property_value: mged:unique_identifier "MO_631" xsd:string property_value: rdfs:comment "Unit of time corresponding to approx. one cycle of the moon's phases." xsd:string [Instance] id: mged:mother instance_of: mged:FamilyRelationship property_value: mged:unique_identifier "MO_387" xsd:string property_value: rdfs:comment "A female parent." xsd:string [Instance] id: mged:moving_average instance_of: mged:DataTransformationProtocolType property_value: rdfs:comment "A type of data transformation in which an average, usually the mean, is calculated across values within a sliding window. e.g. The moving average of signal intensity, or array CGH, data may be used in normalization." xsd:string property_value: mged:unique_identifier "MO_681" xsd:string [Instance] id: mged:ms instance_of: mged:TimeUnit property_value: rdfs:comment "millisecond, time unit" xsd:string property_value: mged:unique_identifier "MO_920" xsd:string [Instance] id: mged:mtDNA instance_of: mged:PhysicalBioSequenceType property_value: mged:unique_identifier "MO_581" xsd:string property_value: rdfs:comment "sequence from the mitochondrial genome" xsd:string [Instance] id: mged:multiple_testing_correction instance_of: mged:HigherLevelAnalysisProtocolType property_value: mged:unique_identifier "MO_561" xsd:string property_value: rdfs:comment "Multiple testing correction uses individual p-values derived from multiple statistical tests to control either the family-wise error rate or the false discovery rate." xsd:string [Instance] id: mged:negative instance_of: mged:Result property_value: mged:unique_identifier "MO_802" xsd:string property_value: rdfs:comment "false or no " xsd:string [Instance] id: mged:negative_float instance_of: mged:DataType property_value: mged:unique_identifier "MO_728" xsd:string property_value: rdfs:comment "A float that is < 0." xsd:string [Instance] id: mged:negative_integer instance_of: mged:DataType property_value: rdfs:comment "An integer < 0." xsd:string property_value: mged:unique_identifier "MO_864" xsd:string [Instance] id: mged:ng instance_of: mged:MassUnit property_value: rdfs:comment "nanogram, a mass unit" xsd:string property_value: mged:unique_identifier "MO_796" xsd:string [Instance] id: mged:nitrocellulose instance_of: mged:SubstrateType property_value: rdfs:comment "The array is made on a nitrocellulose filter." xsd:string property_value: mged:unique_identifier "MO_455" xsd:string [Instance] id: mged:nl instance_of: mged:VolumeUnit property_value: mged:unique_identifier "MO_754" xsd:string property_value: rdfs:comment "nanoliter unit of volume" xsd:string [Instance] id: mged:nm instance_of: mged:DistanceUnit property_value: rdfs:comment "nanometer distance unit" xsd:string property_value: mged:unique_identifier "MO_862" xsd:string [Instance] id: mged:nmol instance_of: mged:QuantityUnit property_value: rdfs:comment "nanomoles, quantity unit" xsd:string property_value: mged:unique_identifier "MO_743" xsd:string [Instance] id: mged:no instance_of: mged:DeprecatedTerms property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecated_from_version mged:version_1.1.7 property_value: mged:unique_identifier "MO_556" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: rdfs:comment "false" xsd:string property_value: mged:deprecation_in_version "1.1.7" xsd:string [Instance] id: mged:non-targeted_transgenic_variation_design instance_of: mged:PerturbationalDesign property_value: mged:unique_identifier "MO_775" xsd:string property_value: rdfs:comment "The modification of an organism due to the presence of DNA from another individual, e.g. of a different strain, species or breed. These do not include targeted transgenics such as knock-ins and knock-outs." xsd:string [Instance] id: mged:nonnegative_float instance_of: mged:DataType property_value: rdfs:comment "A float greater than or equal to 0." xsd:string property_value: mged:unique_identifier "MO_386" xsd:string [Instance] id: mged:nonnegative_integer instance_of: mged:DataType property_value: mged:unique_identifier "MO_390" xsd:string property_value: rdfs:comment "An integer >= 0." xsd:string [Instance] id: mged:nonpositive_float instance_of: mged:DataType property_value: mged:unique_identifier "MO_656" xsd:string property_value: rdfs:comment "A float less than or equal to zero." xsd:string [Instance] id: mged:nonpositive_integer instance_of: mged:DataType property_value: mged:unique_identifier "MO_623" xsd:string property_value: rdfs:comment "An integer less than or equal to zero." xsd:string [Instance] id: mged:normalization_testing_design instance_of: mged:MethodologicalDesign property_value: rdfs:comment "A normalization testing experiment design tests different normalization procedures." xsd:string property_value: mged:unique_identifier "MO_729" xsd:string [Instance] id: mged:normalized_intensities instance_of: mged:DerivedBioAssayType property_value: rdfs:comment "Results of normalization, by some method, of a bioassay data set such as; intensities from one or both channels of a microarray-based assay; orthologous spot sets on 2D gels; or repeat measurements of the same metabolite in replicate cell cultures." xsd:string property_value: mged:unique_identifier "MO_994" xsd:string [Instance] id: mged:normalized_ratios instance_of: mged:DerivedBioAssayType property_value: rdfs:comment "Results obtained by either taking the pair wise ratios of two bioassay data sets and then normalizing, or normalizing each bioassay data set and then taking ratios." xsd:string property_value: mged:unique_identifier "MO_664" xsd:string [Instance] id: mged:not_extract instance_of: mged:BioSampleType property_value: mged:unique_identifier "MO_894" xsd:string property_value: rdfs:comment "The BioSample at any stage other than immediately before labeling." xsd:string [Instance] id: mged:not_sequence_verified instance_of: mged:WarningType property_value: rdfs:comment "The sequence of the BioSequence that relates to this reporter has not been sequence verified by the experimenter." xsd:string property_value: mged:unique_identifier "MO_970" xsd:string [Instance] id: mged:not_uniform instance_of: mged:DefectType property_value: mged:unique_identifier "MO_906" xsd:string property_value: rdfs:comment "The source DNA for a Feature was not uniformly deposited." xsd:string [Instance] id: mged:nuclear_RNA instance_of: mged:MaterialType property_value: rdfs:comment "RNA obtained from the nucleus." xsd:string property_value: mged:unique_identifier "MO_679" xsd:string [Instance] id: mged:nucleic_acid_extraction instance_of: mged:ComplexAction property_value: rdfs:comment "The procedure of extracting nucleic acid from the biomaterial." xsd:string property_value: mged:unique_identifier "MO_607" xsd:string [Instance] id: mged:nucleic_acid_extraction instance_of: mged:ComplexAction property_value: rdfs:comment "The procedure of extracting nucleic acid from the biomaterial." xsd:string property_value: mged:unique_identifier "MO_607" xsd:string [Instance] id: mged:nucleic_acid_primary_sequence_record instance_of: mged:DatabaseEntryType property_value: rdfs:comment "A record which describes and identifies a primary sequence record e.g. DDBJ/EMBL/Genbank" xsd:string property_value: mged:unique_identifier "MO_757" xsd:string [Instance] id: mged:number_per_day instance_of: mged:OtherUnit property_value: rdfs:comment "number of items or events per day" xsd:string property_value: mged:unique_identifier "MO_670" xsd:string [Instance] id: mged:nutrients instance_of: mged:EnvironmentalFactorCategory property_value: rdfs:comment "The food provided to the organism (e.g., chow, fertilizer, DEMM 10%FBS, etc.)." xsd:string property_value: mged:unique_identifier "MO_867" xsd:string [Instance] id: mged:nylon instance_of: mged:SubstrateType property_value: rdfs:comment "The array is made on a nylon membrane." xsd:string property_value: mged:unique_identifier "MO_492" xsd:string [Instance] id: mged:oligo_synthesizer instance_of: mged:HardwareType property_value: rdfs:comment "Hardware for synthesizing oligos." xsd:string property_value: mged:unique_identifier "MO_930" xsd:string [Instance] id: mged:oligosomy instance_of: mged:ChromosomalAberrationClassification property_value: rdfs:comment "A state or condition describing a cell or organism that has fewer copies of a single chromosome than the usual complement." xsd:string [Instance] id: mged:online_resource instance_of: mged:PublicationType property_value: rdfs:comment "A publication type which is available online and which is not an online journal article, e.g. a web site or service." xsd:string property_value: mged:unique_identifier "MO_991" xsd:string [Instance] id: mged:ontology_record instance_of: mged:DatabaseEntryType property_value: mged:unique_identifier "MO_529" xsd:string property_value: rdfs:comment "A record which describes and identifies a term, class or instance in an ontology or controlled vocabulary e.g. ICD" xsd:string [Instance] id: mged:openGALEN instance_of: mged:OrganismPartDatabase property_value: mged:unique_identifier "MO_613" xsd:string property_value: mged:has_human_readable_URI "http://www.opengalen.org/open/crm/crm-anatomy.html" xsd:string property_value: rdfs:comment "OpenGALEN Human Anatomy - open source database of approx. ten thousand\nhuman anatomy concepts together with extensive semantic relationships between them including part-of, connects, branch-of, serves, laterality. Also includes some human physiological processes together with functional relationships between these and the anatomy concepts." xsd:string [Instance] id: mged:operating_system instance_of: mged:SoftwareType property_value: mged:unique_identifier "MO_847" xsd:string property_value: rdfs:comment "Software upon which other software runs." xsd:string [Instance] id: mged:operator_variation_design instance_of: mged:MethodologicalDesign property_value: rdfs:comment "An operator variation experiment design type assesses the operator performance and relation to data consistency and quality." xsd:string property_value: mged:unique_identifier "MO_519" xsd:string [Instance] id: mged:operon instance_of: mged:DeprecatedTerms property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:deprecation_old_parent mged:TheoreticalBioSequenceType property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType property_value: mged:unique_identifier "MO_759" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: rdfs:comment "sequence which represents an operon, a unit of genetically linked genes displaying coordinated and regulated gene activity, originally described in prokaryotes" xsd:string [Instance] id: mged:operon_identification_design instance_of: mged:BioMolecularAnnotation property_value: rdfs:comment "An operon identification experiment type is designed to identify locations and members of operons in a genome." xsd:string property_value: mged:unique_identifier "MO_772" xsd:string [Instance] id: mged:optimization_design instance_of: mged:MethodologicalDesign property_value: mged:unique_identifier "MO_934" xsd:string property_value: rdfs:comment "An optimization experiment design type is where different protocols or protocol parameters are compared." xsd:string [Instance] id: mged:oral_gavage instance_of: mged:DeliveryMethod property_value: rdfs:comment "delivery method for drug or compound whereby the drug is administered via the mouth" xsd:string property_value: mged:unique_identifier "MO_975" xsd:string [Instance] id: mged:organellar_DNA instance_of: mged:MaterialType property_value: rdfs:comment "DNA from organelles such as the mitochondria or chloroplast." xsd:string property_value: mged:unique_identifier "MO_645" xsd:string [Instance] id: mged:organellar_RNA instance_of: mged:MaterialType property_value: mged:unique_identifier "MO_574" xsd:string property_value: rdfs:comment "RNA obtained from an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus." xsd:string [Instance] id: mged:organism instance_of: mged:BioMaterialCharacteristicCategory property_value: mged:unique_identifier "MO_508" xsd:string property_value: rdfs:comment "one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria" xsd:string [Instance] id: mged:organism_part instance_of: mged:BioMaterialCharacteristicCategory property_value: rdfs:comment "The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm)." xsd:string property_value: mged:unique_identifier "MO_954" xsd:string [Instance] id: mged:organism_part instance_of: mged:BioMaterialCharacteristicCategory property_value: rdfs:comment "The part of organism's anatomy or substance arising from an organism from which the biomaterial was derived, excludes cells. E.g. tissue, organ, system, sperm, blood or body location (arm)." xsd:string property_value: mged:unique_identifier "MO_954" xsd:string [Instance] id: mged:organism_part_comparison_design instance_of: mged:BiologicalProperty property_value: rdfs:comment "An organism part comparison experiment design type compares tissues, regions, organs within or between organisms " xsd:string property_value: mged:unique_identifier "MO_953" xsd:string [Instance] id: mged:organism_status instance_of: mged:BioMaterialCharacteristicCategory property_value: mged:unique_identifier "MO_871" xsd:string property_value: rdfs:comment "The stage premortem or postmortem at which the sample was processed for extraction of biomaterials. " xsd:string [Instance] id: mged:organism_status_design instance_of: mged:BiologicalProperty property_value: rdfs:comment "A design that compares samples from live and dead organisms." xsd:string property_value: mged:unique_identifier "MO_841" xsd:string [Instance] id: mged:pH instance_of: mged:ConcentrationUnitOther property_value: mged:unique_identifier "MO_814" xsd:string property_value: rdfs:comment "potential of hydrogen" xsd:string [Instance] id: mged:pM instance_of: mged:ConcentrationUnit property_value: rdfs:comment "picomolar, concentration unit" xsd:string property_value: mged:unique_identifier "MO_628" xsd:string [Instance] id: mged:paraffin_sample instance_of: mged:BioSourceType property_value: mged:unique_identifier "MO_990" xsd:string property_value: rdfs:comment "A biomaterial obtained embedded in paraffin (wax)." xsd:string [Instance] id: mged:pathogenicity_design instance_of: mged:PerturbationalDesign property_value: mged:unique_identifier "MO_807" xsd:string property_value: rdfs:comment "A pathogenicity experiment design type is where an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed." xsd:string [Instance] id: mged:pathway_record instance_of: mged:DatabaseEntryType property_value: mged:unique_identifier "MO_780" xsd:string property_value: rdfs:comment "a record which identifies and describes biological pathways, e.g. a KEGG record" xsd:string [Instance] id: mged:pearson_correlation_coefficient instance_of: mged:NodeValueType property_value: mged:unique_identifier "MO_558" xsd:string property_value: rdfs:comment "The Pearson's correlation coefficient between two variables. Its values can range between -1.00 to +1.00. The closer the absolute value of the Pearson correlation coefficient is to 0, the smaller the linear relationship between the two variables. A Pearson correlation coefficient with absolute value 1 indicates perfect linear relationship." xsd:string [Instance] id: mged:pedigree_record instance_of: mged:DatabaseEntryType property_value: rdfs:comment "A record which describes and identifies a pedigree or lineage for a strain, line, individual or cell whose lineage traceable e.g. a wormbase cell lineage record, or a pedigree record for a mouse" xsd:string property_value: mged:unique_identifier "MO_969" xsd:string [Instance] id: mged:peer_review_quality_control instance_of: mged:QualityControlDescriptionType property_value: mged:unique_identifier "MO_365" xsd:string property_value: rdfs:comment "An experiment which has a peer reviewed publication attached." xsd:string [Instance] id: mged:percent_confluence instance_of: mged:ConcentrationUnitOther property_value: rdfs:comment "A measure of the density of an attached or monolayer culture (e.g., cell culture), e.g., 80 percent_confluence.\n " xsd:string property_value: mged:unique_identifier "MO_378" xsd:string [Instance] id: mged:percent_purity instance_of: mged:ConcentrationUnitOther property_value: rdfs:comment "A relative measurement of homogeneity of a biomaterial e.g. tumor biopsy." xsd:string property_value: mged:unique_identifier "MO_482" xsd:string [Instance] id: mged:percent_vol_per_vol instance_of: mged:ConcentrationUnit property_value: mged:unique_identifier "MO_916" xsd:string property_value: rdfs:comment "percentage volume per volume, concentration unit" xsd:string [Instance] id: mged:percent_weight_per_vol instance_of: mged:ConcentrationUnit property_value: rdfs:comment "percent weight per volume, concentration unit " xsd:string property_value: mged:unique_identifier "MO_420" xsd:string [Instance] id: mged:percent_weight_per_weight instance_of: mged:ConcentrationUnit property_value: mged:unique_identifier "MO_474" xsd:string property_value: rdfs:comment "percent weight per weight, concentration unit" xsd:string [Instance] id: mged:pfu_per_ml instance_of: mged:ConcentrationUnitOther property_value: mged:unique_identifier "MO_768" xsd:string property_value: rdfs:comment "the number of plaque forming units per ml" xsd:string [Instance] id: mged:pg instance_of: mged:MassUnit property_value: mged:unique_identifier "MO_363" xsd:string property_value: rdfs:comment "picogram, mass unit" xsd:string [Instance] id: mged:phylogeny_record instance_of: mged:DatabaseEntryType property_value: mged:unique_identifier "MO_662" xsd:string property_value: rdfs:comment "A record which describes and identifies the relationship between species and is\ncomputationally determined and based on sequences e.g. Treebase record" xsd:string [Instance] id: mged:physical_characteristics instance_of: mged:BioMaterialCharacteristicCategory property_value: mged:unique_identifier "MO_863" xsd:string property_value: rdfs:comment "A descriptor for FactorValue where PhysicalCharacteristics are compared. " xsd:string [Instance] id: mged:physiological_process_design instance_of: mged:BiologicalProperty property_value: rdfs:comment "Those processes specifically pertinent to the functioning of integrated \n living units: cells, tissues, organs, and organisms. This includes those \n processes that exhibit an endogenous periodicity independently of any \n daily variation in the environment such as circadian rhythm or aging." xsd:string [Instance] id: mged:pl instance_of: mged:VolumeUnit property_value: rdfs:comment "picoliter, volume unit" xsd:string property_value: mged:unique_identifier "MO_905" xsd:string [Instance] id: mged:place instance_of: mged:AtomicAction property_value: rdfs:comment "The procedure of putting a physical object in a container/physical space." xsd:string property_value: mged:unique_identifier "MO_470" xsd:string [Instance] id: mged:planting instance_of: mged:InitialTimePoint property_value: rdfs:comment "The act of placing a plant in media (e.g. soil) to allow it to grow. This excludes sowing." xsd:string property_value: mged:unique_identifier "MO_495" xsd:string [Instance] id: mged:plasmid instance_of: mged:DeprecatedTerms property_value: mged:deprecation_replacement_term mged:PhysicalBioSequenceType property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:deprecation_old_parent mged:PhysicalBioSequenceType property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: rdfs:comment "sequence from a plasmid, an extrachromosomal autonomously replicating piece of DNA excluding mitochondria and chloroplasts " xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:unique_identifier "MO_439" xsd:string [Instance] id: mged:pmol instance_of: mged:QuantityUnit property_value: rdfs:comment "picomoles, quantity unit" xsd:string property_value: mged:unique_identifier "MO_688" xsd:string [Instance] id: mged:polyA_RNA instance_of: mged:MaterialType property_value: rdfs:comment "RNA which has been obtained by selection for polyA tracts. \nExact synonym: polyA+_RNA\nNon-exact synonym: mRNA" xsd:string property_value: mged:synonym "polyA+_RNA" xsd:string property_value: mged:unique_identifier "MO_600" xsd:string property_value: mged:synonym "mRNA" xsd:string [Instance] id: mged:polylysine instance_of: mged:SurfaceType property_value: mged:unique_identifier "MO_569" xsd:string property_value: rdfs:comment "a surface coating for immobilization with the polypeptide, polylysine" xsd:string [Instance] id: mged:polypeptide instance_of: mged:DeprecatedTerms property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType property_value: mged:deprecation_old_parent mged:PhysicalBioSequenceType property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_replacement_term mged:PhysicalBioSequenceType property_value: mged:deprecation_old_parent mged:TheoreticalBioSequenceType property_value: rdfs:comment "sequence of a protein, a linear amino acid polymer" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_530" xsd:string [Instance] id: mged:polyploid instance_of: mged:Ploidy property_value: rdfs:comment "Describes a cell, nucleus or organism with three or more copies of each chromosome." xsd:string property_value: mged:unique_identifier "MO_394" xsd:string [Instance] id: mged:polysomy instance_of: mged:ChromosomalAberrationClassification property_value: rdfs:comment "A state or condition describing a cell or organism that has more copies of a single chromosome than the usual complement." xsd:string [Instance] id: mged:pool instance_of: mged:ComplexAction property_value: mged:unique_identifier "MO_779" xsd:string property_value: mged:synonym "combine" xsd:string property_value: rdfs:comment "The process of combining two or more BioMaterials. \nExact synonym: combine" xsd:string [Instance] id: mged:pool instance_of: mged:ComplexAction property_value: mged:unique_identifier "MO_779" xsd:string property_value: mged:synonym "combine" xsd:string property_value: rdfs:comment "The process of combining two or more BioMaterials. \nExact synonym: combine" xsd:string [Instance] id: mged:population_density instance_of: mged:EnvironmentalFactorCategory property_value: rdfs:comment "The concentration range of the organism." xsd:string property_value: mged:unique_identifier "MO_650" xsd:string [Instance] id: mged:positive instance_of: mged:Result property_value: rdfs:comment "true or yes" xsd:string property_value: mged:unique_identifier "MO_429" xsd:string [Instance] id: mged:positive_float instance_of: mged:DataType property_value: rdfs:comment "A float > 0." xsd:string property_value: mged:unique_identifier "MO_501" xsd:string [Instance] id: mged:positive_integer instance_of: mged:DataType property_value: mged:unique_identifier "MO_629" xsd:string property_value: rdfs:comment "An integer > 0." xsd:string [Instance] id: mged:postmortem instance_of: mged:OrganismStatus property_value: mged:unique_identifier "MO_416" xsd:string property_value: rdfs:comment "biomaterial removed after the death of the organism" xsd:string [Instance] id: mged:predicted_gene instance_of: mged:TheoreticalBioSequenceType property_value: rdfs:comment "gene sequence which has been computationally predicted" xsd:string property_value: mged:unique_identifier "MO_838" xsd:string [Instance] id: mged:premortem instance_of: mged:OrganismStatus property_value: rdfs:comment "sample which has been removed prior to the death of an organism" xsd:string property_value: mged:unique_identifier "MO_705" xsd:string [Instance] id: mged:preservation instance_of: mged:ComplexAction property_value: mged:unique_identifier "MO_415" xsd:string property_value: rdfs:comment "The type of protocol used to preserve (including storage or keep in stasis) the biomaterial." xsd:string [Instance] id: mged:preservation instance_of: mged:ComplexAction property_value: mged:unique_identifier "MO_415" xsd:string property_value: rdfs:comment "The type of protocol used to preserve (including storage or keep in stasis) the biomaterial." xsd:string [Instance] id: mged:primary_protein_structure_record instance_of: mged:DatabaseEntryType property_value: mged:unique_identifier "MO_785" xsd:string property_value: rdfs:comment "A record which describes and identifies an experimentally derived protein structure e.g. MSD" xsd:string [Instance] id: mged:primary_site instance_of: mged:CancerSite property_value: mged:unique_identifier "MO_408" xsd:string property_value: rdfs:comment "the organism part in which the tumor originated" xsd:string [Instance] id: mged:promoter instance_of: mged:DeprecatedTerms property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:deprecation_old_parent mged:TheoreticalBioSequenceType property_value: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType property_value: mged:unique_identifier "MO_911" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: rdfs:comment "genomic sequence 5' to a gene where the transcription initiation complex forms." xsd:string [Instance] id: mged:protein instance_of: mged:MaterialType property_value: mged:unique_identifier "MO_683" xsd:string property_value: rdfs:comment "Polymer of amino acids." xsd:string [Instance] id: mged:protein instance_of: mged:MaterialType property_value: mged:unique_identifier "MO_683" xsd:string property_value: rdfs:comment "Polymer of amino acids." xsd:string [Instance] id: mged:purify instance_of: mged:ExperimentalProtocolType property_value: rdfs:comment "The action of enriching a BioMaterial (organism, cell, nucleic acid etc) or Compound e.g. for FACS for positive selection or RNA cleanup the Action or ProtocolType is purify (see fractionate). " xsd:string property_value: mged:unique_identifier "MO_406" xsd:string [Instance] id: mged:purify instance_of: mged:ExperimentalProtocolType property_value: rdfs:comment "The action of enriching a BioMaterial (organism, cell, nucleic acid etc) or Compound e.g. for FACS for positive selection or RNA cleanup the Action or ProtocolType is purify (see fractionate). " xsd:string property_value: mged:unique_identifier "MO_406" xsd:string [Instance] id: mged:quality_control_testing_design instance_of: mged:MethodologicalDesign property_value: mged:unique_identifier "MO_981" xsd:string property_value: rdfs:comment "A quality control testing experiment design type is where some aspect of the experiment is quality controlled for the purposes of quality assurance " xsd:string [Instance] id: mged:quantile_normalization instance_of: mged:NormalizationDescriptionType property_value: rdfs:comment "A method of normalizing a set of MeasuredBioAssayData aimed at rendering the distribution of intensities for each assay in the set the same, by forcing the values of quantiles to be equal across assays." xsd:string property_value: mged:unique_identifier "MO_951" xsd:string [Instance] id: mged:quantile_normalization_protocol_type instance_of: mged:DataTransformationProtocolType property_value: rdfs:comment "Application of a normalization of type quantile_normalization." xsd:string property_value: mged:unique_identifier "MO_457" xsd:string [Instance] id: mged:rRNA_gene instance_of: mged:DeprecatedTerms property_value: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_old_parent mged:TheoreticalBioSequenceType property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:unique_identifier "MO_955" xsd:string property_value: mged:synonym "ribosomal RNA gene" xsd:string property_value: rdfs:comment "sequence from gene coding for ribosomal RNA\nexact synonym: ribosomal RNA gene" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:ratio instance_of: mged:DerivedBioAssayType property_value: mged:unique_identifier "MO_597" xsd:string property_value: rdfs:comment "Result of data reduction involving computation of the quotient of a pair of numerical values, such as signal intensities obtained from the hybridization of two or more labeled extracts to one or more microarrays; volumes of matched spots from comparative 2D gel electrophoresis of two or more labeled extracts; or comparative profiling of a particular metabolite in health and disease by NMR." xsd:string [Instance] id: mged:ratio_statistics_normalization instance_of: mged:NormalizationDescriptionType property_value: rdfs:comment "A method to re-scale paired-assay data from one data set relative to the other, based on an iterative regression method of calculating single parameter linear normalization factors. This method allows calculation of the mean, standard deviation and confidence interval limits for the distribution of measured ratio values." xsd:string property_value: mged:unique_identifier "MO_349" xsd:string [Instance] id: mged:real_time_PCR_quality_control instance_of: mged:QualityControlDescriptionType property_value: mged:unique_identifier "MO_434" xsd:string property_value: rdfs:comment "A PCR based quantitative validation of a subset of the array based data used for experimental QC purposes." xsd:string [Instance] id: mged:rectangular_feature instance_of: mged:FeatureShape property_value: mged:unique_identifier "MO_897" xsd:string property_value: rdfs:comment "The shape of the feature on the array is rectangular." xsd:string [Instance] id: mged:reference_design instance_of: mged:MethodologicalDesign property_value: rdfs:comment "A reference experiment design type is where all samples are compared to a common reference. " xsd:string property_value: mged:unique_identifier "MO_699" xsd:string [Instance] id: mged:relative instance_of: mged:MeasurementType property_value: rdfs:comment "a measurement where the value is dependent on another measurement" xsd:string property_value: mged:unique_identifier "MO_396" xsd:string [Instance] id: mged:relative_humidity instance_of: mged:EnvironmentalFactorCategory property_value: rdfs:comment "The amount of moisture in the air expressed as a percentage of the maximum amount the air is capable of holding." xsd:string property_value: mged:unique_identifier "MO_453" xsd:string [Instance] id: mged:remove instance_of: mged:AtomicAction property_value: mged:unique_identifier "MO_713" xsd:string property_value: rdfs:comment "The procedure of extracting/taking out a part of a reaction/contents of a container." xsd:string [Instance] id: mged:replaced_term instance_of: mged:DeprecationReason property_value: rdfs:comment "The term name was changed to one more appropriate to the intent of the definition." xsd:string [Instance] id: mged:replicate_analysis instance_of: mged:DataTransformationProtocolType property_value: rdfs:comment "A transformation method in which replicate intensity or ratio data sets are combined. Analysis of the mean and standard deviation values for replicate data points can be used to identify and potentially exclude low quality data." xsd:string property_value: mged:unique_identifier "MO_433" xsd:string [Instance] id: mged:replicate_design instance_of: mged:MethodologicalDesign property_value: mged:unique_identifier "MO_885" xsd:string property_value: rdfs:comment "A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments." xsd:string [Instance] id: mged:resuspend instance_of: mged:AtomicAction property_value: rdfs:comment "The procedure in which solid material is dispensed or dissolved in a liquid." xsd:string property_value: mged:unique_identifier "MO_466" xsd:string [Instance] id: mged:reverse instance_of: mged:StrandType property_value: mged:unique_identifier "MO_402" xsd:string property_value: mged:synonym "-" xsd:string property_value: rdfs:comment "the reverse strand\nexact synonym: -" xsd:string [Instance] id: mged:reverse_transcription instance_of: mged:ComplexAction property_value: rdfs:comment "Generation of a DNA strand from an RNA strand using reverse transcriptase." xsd:string property_value: mged:unique_identifier "MO_480" xsd:string [Instance] id: mged:reverse_transcription instance_of: mged:ComplexAction property_value: rdfs:comment "Generation of a DNA strand from an RNA strand using reverse transcriptase." xsd:string property_value: mged:unique_identifier "MO_480" xsd:string [Instance] id: mged:reverse_transcription_PCR_quality_control instance_of: mged:QualityControlDescriptionType property_value: rdfs:comment "A PCR based semi quantitative validation of a subset of the array based data used for experimental QC purposes." xsd:string property_value: mged:unique_identifier "MO_986" xsd:string [Instance] id: mged:sacrifice instance_of: mged:ComplexAction property_value: rdfs:comment "The procedure of euthanizing an organism." xsd:string property_value: mged:unique_identifier "MO_602" xsd:string [Instance] id: mged:sacrifice instance_of: mged:ComplexAction property_value: rdfs:comment "The procedure of euthanizing an organism." xsd:string property_value: mged:unique_identifier "MO_602" xsd:string [Instance] id: mged:sampling_time_point instance_of: mged:BioMaterialCharacteristicCategory property_value: rdfs:comment "<pre>The time point that a sample was taken. Not to be used where the sample is part of a time\ncourse. SamplingTimePoint is not related to age. An instance could be summer, a date, a time, or a range value</pre>" xsd:string property_value: mged:unique_identifier "MO_866" xsd:string [Instance] id: mged:seconds instance_of: mged:TimeUnit property_value: mged:unique_identifier "MO_391" xsd:string property_value: rdfs:comment "time unit" xsd:string [Instance] id: mged:secreted_protein_identification_design instance_of: mged:BioMolecularAnnotation property_value: mged:unique_identifier "MO_694" xsd:string property_value: rdfs:comment "A secreted protein identification design type identifies transcripts associated with a secretory pathway during translation and is used to infer which proteins are secreted or membrane bound. " xsd:string [Instance] id: mged:seed_dormancy instance_of: mged:PreservationType property_value: rdfs:comment "preservation type whereby the seed is maintained in a dormant state" xsd:string property_value: mged:unique_identifier "MO_666" xsd:string [Instance] id: mged:self_vs_self_design instance_of: mged:MethodologicalDesign property_value: mged:unique_identifier "MO_490" xsd:string property_value: rdfs:comment "A self vs. self experiment design investigates variance and error estimates in the experimental system, and is where the same extract is compared. " xsd:string [Instance] id: mged:semisolid instance_of: mged:Media property_value: mged:unique_identifier "MO_635" xsd:string property_value: rdfs:comment "semisolid media type" xsd:string [Instance] id: mged:set_temperature instance_of: mged:AtomicAction property_value: mged:unique_identifier "MO_393" xsd:string property_value: rdfs:comment "An action where the temperature is specified. " xsd:string [Instance] id: mged:sex instance_of: mged:BioMaterialCharacteristicCategory property_value: rdfs:comment "A descriptor for FactorValue where Sex is compared. " xsd:string property_value: mged:unique_identifier "MO_680" xsd:string [Instance] id: mged:sex_design instance_of: mged:BiologicalProperty property_value: rdfs:comment "A sex experiment design type assays differences associated with an organism's sex, gender or mating type." xsd:string property_value: mged:unique_identifier "MO_575" xsd:string [Instance] id: mged:short_oligo instance_of: mged:DesignElement property_value: rdfs:comment "An element that is an oligonucleotide of less than 50 nucleotides in length (usually 20 to 25 nt as in Affymetrix probes)." xsd:string property_value: mged:unique_identifier "MO_749" xsd:string [Instance] id: mged:signal instance_of: mged:DerivedBioAssayType property_value: rdfs:comment "A quantitative measure of the relative abundance of a transcript (MAS 4.0 version of the Affymetrix analysis software)." xsd:string property_value: mged:unique_identifier "MO_534" xsd:string [Instance] id: mged:signal_log_ratio instance_of: mged:DeprecatedTerms property_value: mged:deprecation_old_parent mged:DerivedBioAssayType property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_replacement_term mged:DerivedBioAssayType property_value: mged:deprecated_from_version mged:version_1.1.7 property_value: rdfs:comment "The change in expression level for a transcript between a baseline and an experiment array. This change is expressed as the log2 ratio. A signal log \nratio of 1 is the same as a Fold Change of 2." xsd:string property_value: mged:unique_identifier "MO_941" xsd:string property_value: mged:deprecation_in_version "1.1.7" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:silicon instance_of: mged:SubstrateType property_value: mged:unique_identifier "MO_382" xsd:string property_value: rdfs:comment "the array is made on silicon " xsd:string [Instance] id: mged:single_stranded instance_of: mged:StrandType property_value: mged:unique_identifier "MO_576" xsd:string property_value: rdfs:comment "a nucleic acid consisting of a single polynucleotide chain." xsd:string [Instance] id: mged:sister instance_of: mged:FamilyRelationship property_value: mged:unique_identifier "MO_723" xsd:string property_value: rdfs:comment "A female having the same genetic parents as another, or one genetic parent in common with another." xsd:string [Instance] id: mged:slice_analysis instance_of: mged:DeprecatedTerms property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_replacement_term mged:NormalizationDescriptionType property_value: mged:deprecation_old_parent mged:NormalizationDescriptionType property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: rdfs:comment "A method of analyzing the significant expression level of a Feature by calculating the intensity-dependent Z distribution value for the logarithm of the intensity ratios from the two channels." xsd:string property_value: mged:unique_identifier "MO_531" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:snRNA_gene instance_of: mged:DeprecatedTerms property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:deprecation_old_parent "deleted_term" xsd:string property_value: rdfs:comment "sequence from gene coding for small nuclear RNA\nexact synonym: small nuclear RNA gene" xsd:string property_value: mged:unique_identifier "MO_961" xsd:string property_value: mged:synonym "small nuclear RNA gene" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:software_manufacturer instance_of: mged:Roles property_value: rdfs:comment "Person or organization that manufactured the software." xsd:string property_value: mged:unique_identifier "MO_475" xsd:string [Instance] id: mged:software_variation_design instance_of: mged:MethodologicalDesign property_value: rdfs:comment "A software variation design type compares different types of software for performance, accuracy, precision and reproducibility." xsd:string property_value: mged:unique_identifier "MO_643" xsd:string [Instance] id: mged:soil instance_of: mged:Media property_value: mged:unique_identifier "MO_821" xsd:string property_value: rdfs:comment "soil, growth media for plants and other soil living organisms" xsd:string [Instance] id: mged:son instance_of: mged:FamilyRelationship property_value: mged:unique_identifier "MO_465" xsd:string property_value: rdfs:comment "The male offspring of the patient or individual under study." xsd:string [Instance] id: mged:sonicator instance_of: mged:HardwareType property_value: rdfs:comment "An instrument for sonicating biomaterials." xsd:string property_value: mged:unique_identifier "MO_477" xsd:string [Instance] id: mged:sowing instance_of: mged:InitialTimePoint property_value: rdfs:comment "the process of placing a seed or spore in some media with the intention to invoke germination." xsd:string property_value: mged:unique_identifier "MO_748" xsd:string [Instance] id: mged:species_design instance_of: mged:BiologicalProperty property_value: mged:unique_identifier "MO_675" xsd:string property_value: rdfs:comment "A species experiment design type assays differences between distinct species." xsd:string [Instance] id: mged:species_specific_design_element_group_type instance_of: mged:DesignElementGroupType property_value: mged:unique_identifier "MO_395" xsd:string property_value: rdfs:comment "A grouping of DesignElements, Features, Reporters, Composite Sequences on the basis of a common species." xsd:string [Instance] id: mged:specified_biomaterial_action instance_of: mged:AtomicAction property_value: rdfs:comment "Conceptual action for specified protocol applied in treatment." xsd:string property_value: mged:unique_identifier "MO_968" xsd:string [Instance] id: mged:specified_biomaterial_action instance_of: mged:AtomicAction property_value: rdfs:comment "Conceptual action for specified protocol applied in treatment." xsd:string property_value: mged:unique_identifier "MO_968" xsd:string [Instance] id: mged:specified_biomaterial_action instance_of: mged:AtomicAction property_value: rdfs:comment "Conceptual action for specified protocol applied in treatment." xsd:string property_value: mged:unique_identifier "MO_968" xsd:string [Instance] id: mged:spectrophotometer instance_of: mged:HardwareType property_value: rdfs:comment "Hardware for measuring light at different wavelengths." xsd:string property_value: mged:synonym "thermocycler" xsd:string property_value: mged:unique_identifier "MO_716" xsd:string [Instance] id: mged:spike_quality_control instance_of: mged:QualityControlDescriptionType property_value: rdfs:comment "An experiment in which spikes were introduced into some or all of the hybridizations for quality control or data transformation purposes." xsd:string property_value: mged:unique_identifier "MO_937" xsd:string [Instance] id: mged:spin instance_of: mged:AtomicAction property_value: mged:synonym "centrifuge" xsd:string property_value: mged:unique_identifier "MO_879" xsd:string property_value: rdfs:comment "The procedure of applying a centrifugal force to a physical object.\nExact synonym: centrifuge" xsd:string [Instance] id: mged:split instance_of: mged:ComplexAction property_value: mged:synonym "sample" xsd:string property_value: rdfs:comment "The procedure of separating a BioMaterial into two or more BioMaterials of similar composition e.g. aliquoting a sample. The BioMaterial may be a BioSource (e.g., a tissue) or a BioSample (e.g. RNA extracted from a BioSource).\nNon exact Synonym: sample" xsd:string property_value: mged:unique_identifier "MO_835" xsd:string [Instance] id: mged:split instance_of: mged:ComplexAction property_value: mged:synonym "sample" xsd:string property_value: rdfs:comment "The procedure of separating a BioMaterial into two or more BioMaterials of similar composition e.g. aliquoting a sample. The BioMaterial may be a BioSource (e.g., a tissue) or a BioSample (e.g. RNA extracted from a BioSource).\nNon exact Synonym: sample" xsd:string property_value: mged:unique_identifier "MO_835" xsd:string [Instance] id: mged:split_term instance_of: mged:DeprecationReason property_value: rdfs:comment "the term has been decomposed into more specific terms" xsd:string [Instance] id: mged:spotted_antibody_features instance_of: mged:TechnologyType property_value: mged:unique_identifier "MO_483" xsd:string property_value: rdfs:comment "TechnologyType of FeatureGroup where antibodies are spotted directly." xsd:string [Instance] id: mged:spotted_colony_features instance_of: mged:TechnologyType property_value: rdfs:comment "TechnologyType of FeatureGroup where bacterial or other colonies are spotted directly." xsd:string property_value: mged:unique_identifier "MO_618" xsd:string [Instance] id: mged:spotted_ds_DNA_features instance_of: mged:TechnologyType property_value: mged:unique_identifier "MO_499" xsd:string property_value: rdfs:comment "A descriptor for the TechnologyType for a group of features where double stranded DNA is spotted on the array e.g. a PCR of a cDNA clone." xsd:string [Instance] id: mged:spotted_protein_features instance_of: mged:TechnologyType property_value: mged:unique_identifier "MO_996" xsd:string property_value: rdfs:comment "TechnologyType of FeatureGroup where protein (other than antibody) is spotted directly." xsd:string [Instance] id: mged:spotted_ss_PCR_amplicon_features instance_of: mged:TechnologyType property_value: rdfs:comment "A descriptor for the TechnologyType for a group of features where single stranded DNA PCR product is spotted on the array." xsd:string property_value: mged:unique_identifier "MO_921" xsd:string [Instance] id: mged:spotted_ss_oligo_features instance_of: mged:TechnologyType property_value: rdfs:comment "The TechnologyType of the FeatureGroup is spotted single stranded oligonucleotides (of any length) on the substrate." xsd:string property_value: mged:unique_identifier "MO_579" xsd:string [Instance] id: mged:square_feature instance_of: mged:FeatureShape property_value: rdfs:comment "The shape of the feature on the array is square." xsd:string property_value: mged:unique_identifier "MO_817" xsd:string [Instance] id: mged:ss_oligo instance_of: mged:DeprecatedTerms property_value: mged:deprecation_old_parent mged:PhysicalBioSequenceType property_value: mged:deprecation_replacement_term mged:PhysicalBioSequenceType property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: rdfs:comment "sequence of a single stranded synthesized oligonucleotide" xsd:string property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_570" xsd:string [Instance] id: mged:starvation instance_of: mged:ExperimentalProtocolType property_value: rdfs:comment "Depriving an organism of food or nutrients" xsd:string property_value: mged:unique_identifier "MO_370" xsd:string [Instance] id: mged:starvation instance_of: mged:ExperimentalProtocolType property_value: rdfs:comment "Depriving an organism of food or nutrients" xsd:string property_value: mged:unique_identifier "MO_370" xsd:string [Instance] id: mged:stimulated_design_type instance_of: mged:PerturbationalDesign property_value: mged:unique_identifier "MO_958" xsd:string property_value: rdfs:comment "A design in which a behavior is invoked by a variable controlled by the experimenter - e.g. administration of a drug that effects aggressivity." xsd:string [Instance] id: mged:stimulus_or_stress_design instance_of: mged:PerturbationalDesign property_value: rdfs:comment "A stimulus or stress experiment design type is where the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc." xsd:string property_value: mged:unique_identifier "MO_568" xsd:string [Instance] id: mged:store instance_of: mged:ExperimentalProtocolType property_value: rdfs:comment "The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity, for the purposes of keeping it in the same state." xsd:string property_value: mged:unique_identifier "MO_442" xsd:string [Instance] id: mged:store instance_of: mged:ExperimentalProtocolType property_value: rdfs:comment "The procedure of placing a physical object under specified conditions e.g. time, temperature, humidity, for the purposes of keeping it in the same state." xsd:string property_value: mged:unique_identifier "MO_442" xsd:string [Instance] id: mged:strain_or_line instance_of: mged:BioMaterialCharacteristicCategory property_value: mged:unique_identifier "MO_859" xsd:string property_value: rdfs:comment "A descriptor of FactorValue where comparisons of strains or lines are made. " xsd:string [Instance] id: mged:strain_or_line_design instance_of: mged:BiologicalProperty property_value: rdfs:comment "A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species." xsd:string property_value: mged:unique_identifier "MO_462" xsd:string [Instance] id: mged:string_datatype instance_of: mged:DataType property_value: rdfs:comment "The values are a sequence of one or more characters." xsd:string property_value: mged:unique_identifier "MO_352" xsd:string [Instance] id: mged:subcutaneous instance_of: mged:DeliveryMethod property_value: rdfs:comment "Delivery method whereby a drug or compound is administered under the skin of the organism." xsd:string property_value: mged:unique_identifier "MO_960" xsd:string [Instance] id: mged:submitter instance_of: mged:Roles property_value: mged:unique_identifier "MO_882" xsd:string property_value: rdfs:comment "Person who is the primary contact for data submitted to a database." xsd:string [Instance] id: mged:synthetic_DNA instance_of: mged:MaterialType property_value: rdfs:comment "DNA which is generated by chemical or enzymatic (non cellular) means.\nnon-exact synonym: cDNA" xsd:string property_value: mged:unique_identifier "MO_577" xsd:string property_value: mged:synonym "cDNA" xsd:string [Instance] id: mged:synthetic_RNA instance_of: mged:MaterialType property_value: mged:unique_identifier "MO_543" xsd:string property_value: rdfs:comment "RNA which is generated by chemical or enzymatic (non cellular) means. E.g. T7 promotor generated RNA.\nNon-exact synonym:\ncRNA, complementary RNA\naRNA, amplified RNA" xsd:string property_value: mged:synonym "amplified RNA" xsd:string property_value: mged:synonym "cRNA" xsd:string property_value: mged:synonym "aRNA" xsd:string property_value: mged:synonym "complementary RNA" xsd:string [Instance] id: mged:tRNA_gene instance_of: mged:DeprecatedTerms property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_old_parent mged:TheoreticalBioSequenceType property_value: mged:deprecation_replacement_term mged:TheoreticalBioSequenceType property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: rdfs:comment "sequence from a gene coding for transfer RNA\nexact synonym: transfer RNA gene" xsd:string property_value: mged:unique_identifier "MO_850" xsd:string property_value: mged:synonym "transfer RNA gene" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:tau_rank_correlation instance_of: mged:DeprecatedTerms property_value: mged:deprecated_from_version mged:version_1.1.7 property_value: mged:deprecation_replacement_term mged:NodeValueType property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_old_parent mged:NodeValueType property_value: mged:deprecation_in_version "1.1.7" xsd:string property_value: mged:unique_identifier "MO_673" xsd:string property_value: rdfs:comment "a nonparametric measure of the agreement between two rankings" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string [Instance] id: mged:technical_replicate instance_of: mged:ReplicateDescriptionType property_value: mged:unique_identifier "MO_641" xsd:string property_value: rdfs:comment "A replicate where the same BioSample is use e.g. the same pool of RNA used to assess technical (as opposed to biological) variation within an experiment." xsd:string [Instance] id: mged:technical_replicate instance_of: mged:ReplicateDescriptionType property_value: mged:unique_identifier "MO_641" xsd:string property_value: rdfs:comment "A replicate where the same BioSample is use e.g. the same pool of RNA used to assess technical (as opposed to biological) variation within an experiment." xsd:string [Instance] id: mged:temperature instance_of: mged:EnvironmentalFactorCategory property_value: mged:unique_identifier "MO_791" xsd:string property_value: rdfs:comment "Temperature associated with a particular environment." xsd:string [Instance] id: mged:thermal_cycler instance_of: mged:HardwareType property_value: rdfs:comment "An instrument designed to automatically raise and lower the temperature of wells or tubes. Usually used to perform PCR.\nExact Synonym: thermocycler" xsd:string property_value: mged:unique_identifier "MO_854" xsd:string [Instance] id: mged:tiling_path_design instance_of: mged:BioMolecularAnnotation property_value: mged:unique_identifier "MO_507" xsd:string property_value: rdfs:comment "An experiment in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using arrays containing oligonucleotides that are either overlapping or spaced at regular intervals." xsd:string [Instance] id: mged:time_series_design instance_of: mged:MethodologicalDesign property_value: mged:unique_identifier "MO_887" xsd:string property_value: rdfs:comment "Groups of assays that are related as part of a time series." xsd:string [Instance] id: mged:timepoint instance_of: mged:ComplexAction property_value: mged:unique_identifier "MO_738" xsd:string property_value: rdfs:comment "Time point at which a sample or observation is made or taken from a biomaterial as measured from some reference point." xsd:string [Instance] id: mged:total_RNA instance_of: mged:MaterialType property_value: mged:unique_identifier "MO_373" xsd:string property_value: rdfs:comment "Total cellular and nuclear RNA." xsd:string [Instance] id: mged:total_intensity_normalization instance_of: mged:DeprecatedTerms property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:deprecation_old_parent mged:NormalizationDescriptionType property_value: mged:deprecation_replacement_term mged:NormalizationDescriptionType property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: rdfs:comment "A method of re-scaling intensity data from one channel relative to another based on the ratio of the sums of the fluorescent intensities from each channel for all Features: N = sum(Ri) / sum(Gi) . The ratio is used to re-scale the intensities in one channel for each Feature. This is a single parameter linear normalization method." xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_441" xsd:string [Instance] id: mged:total_intensity_normalization_paired instance_of: mged:DataTransformationProtocolType property_value: rdfs:comment "A method to normalize paired-assay data that uses as a normalization coefficient the sum of intensity values from one assay divided by the sum of intensities from the other, where those sums are taken over all data points, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins). This normalization coefficient is used to rescale the intensity data in one data set relative to the other. Note that a normalization method that employs the average intensity rather than the sum (of all data points, or an appropriate subset) falls into this category as well." xsd:string property_value: mged:unique_identifier "MO_686" xsd:string [Instance] id: mged:total_intensity_normalization_single instance_of: mged:DataTransformationProtocolType property_value: mged:unique_identifier "MO_472" xsd:string property_value: rdfs:comment "A normalization method that uses as a coefficient the sum of all intensities in the data set, or an appropriate subset of these (e.g. special control Features on a microarray, or 2DE spots containing constitutively expressed proteins). The intensities are normalized through division by such a coefficient (and possible subsequent multiplication by a target constant). Note that a normalization method that\nemploys the average intensity rather than the sum (of all data points, or an appropriate subset) falls into this category as well." xsd:string [Instance] id: mged:transcript instance_of: mged:TheoreticalBioSequenceType property_value: rdfs:comment "sequence that represents the product of an RNA polymerase engaged in transcription " xsd:string property_value: mged:unique_identifier "MO_827" xsd:string [Instance] id: mged:transcript_identification_design instance_of: mged:BioMolecularAnnotation property_value: mged:unique_identifier "MO_533" xsd:string property_value: mged:synonym "gene expression" xsd:string property_value: mged:synonym "gene_expression" xsd:string property_value: rdfs:comment "A transcript identification design type characterizes the length and \n position of transcripts and allows identification of all forms of \n transcripts in the genome." xsd:string property_value: mged:synonym "expression_profiling" xsd:string property_value: mged:synonym "transcription_profiling" xsd:string property_value: mged:synonym "expression profiling" xsd:string property_value: mged:synonym "transcription profiling" xsd:string [Instance] id: mged:transcript_identification_design instance_of: mged:BioMolecularAnnotation property_value: mged:unique_identifier "MO_533" xsd:string property_value: mged:synonym "gene expression" xsd:string property_value: mged:synonym "gene_expression" xsd:string property_value: rdfs:comment "A transcript identification design type characterizes the length and \n position of transcripts and allows identification of all forms of \n transcripts in the genome." xsd:string property_value: mged:synonym "expression_profiling" xsd:string property_value: mged:synonym "transcription_profiling" xsd:string property_value: mged:synonym "expression profiling" xsd:string property_value: mged:synonym "transcription profiling" xsd:string [Instance] id: mged:transfect instance_of: mged:ExperimentalProtocolType property_value: mged:unique_identifier "MO_849" xsd:string property_value: rdfs:comment "The process of bringing about genetic alteration of any cell or organism by a variety of means including recombinant DNA technology, viruses, chemical mutagens, and X-rays." xsd:string [Instance] id: mged:transfect instance_of: mged:ExperimentalProtocolType property_value: mged:unique_identifier "MO_849" xsd:string property_value: rdfs:comment "The process of bringing about genetic alteration of any cell or organism by a variety of means including recombinant DNA technology, viruses, chemical mutagens, and X-rays." xsd:string [Instance] id: mged:transfection instance_of: mged:GeneticModification property_value: rdfs:comment "Introduction of genetic material into an organism often in the form of a plasmid." xsd:string property_value: mged:unique_identifier "MO_366" xsd:string [Instance] id: mged:translational_bias_design instance_of: mged:BioMolecularAnnotation property_value: mged:unique_identifier "MO_939" xsd:string property_value: rdfs:comment "A translational bias is an experiment design which characterizes the association of transcripts and translation machinery." xsd:string [Instance] id: mged:trisomy instance_of: mged:DeprecatedTerms property_value: mged:deprecation_old_parent mged:ChromosomalAberrationClassification property_value: mged:replaced_with_term mged:polysomy property_value: mged:deprecated_from_version mged:version_1.1.9 property_value: mged:has_reason_for_deprecation mged:replaced_term property_value: mged:was_replaced_by mged:polysomy property_value: mged:deprecation_reason "replaced_term" xsd:string property_value: rdfs:comment "The possession of a third chromosome of any one type in an otherwise diploid cell." xsd:string property_value: mged:unique_identifier "MO_494" xsd:string property_value: mged:deprecation_in_version "1.1.9" xsd:string [Instance] id: mged:tumor_grading instance_of: mged:BioMaterialCharacteristicCategory property_value: rdfs:comment "A descriptor used in cancer biology to describe abnormalities of tumor cells." xsd:string property_value: mged:unique_identifier "MO_843" xsd:string [Instance] id: mged:uM instance_of: mged:ConcentrationUnit property_value: mged:unique_identifier "MO_740" xsd:string property_value: rdfs:comment "Micromole per liter or micromolar, concentration unit" xsd:string [Instance] id: mged:ug instance_of: mged:MassUnit property_value: rdfs:comment "microgram, unit of mass" xsd:string property_value: mged:unique_identifier "MO_438" xsd:string [Instance] id: mged:ul instance_of: mged:VolumeUnit property_value: mged:unique_identifier "MO_926" xsd:string property_value: rdfs:comment "microliter, unit of volume" xsd:string [Instance] id: mged:um instance_of: mged:DistanceUnit property_value: rdfs:comment "micrometer, unit of distance" xsd:string property_value: mged:unique_identifier "MO_421" xsd:string [Instance] id: mged:umol instance_of: mged:QuantityUnit property_value: mged:unique_identifier "MO_752" xsd:string property_value: rdfs:comment "micromoles, quantity unit" xsd:string [Instance] id: mged:uncentered_Pearson_correlation instance_of: mged:NodeValueType property_value: mged:unique_identifier "MO_974" xsd:string property_value: rdfs:comment "The uncentered Pearson correlation is defined as the Pearson correlation for two data series where the mean of each data series is assumed to be zero." xsd:string [Instance] id: mged:uncle instance_of: mged:FamilyRelationship property_value: mged:unique_identifier "MO_950" xsd:string property_value: rdfs:comment "The brother of one's father or mother." xsd:string [Instance] id: mged:unknown_basis_feature instance_of: mged:SeqFeatureBasis property_value: rdfs:comment "Sequence feature whose derivation is unknown." xsd:string property_value: mged:unique_identifier "MO_525" xsd:string [Instance] id: mged:unknown_experiment_design_type instance_of: mged:BiologicalProperty property_value: mged:unique_identifier "MO_634" xsd:string property_value: rdfs:comment "ExperimentDesignType of unknown type." xsd:string [Instance] id: mged:unknown_experiment_design_type instance_of: mged:BiologicalProperty property_value: mged:unique_identifier "MO_634" xsd:string property_value: rdfs:comment "ExperimentDesignType of unknown type." xsd:string [Instance] id: mged:unknown_experiment_design_type instance_of: mged:BiologicalProperty property_value: mged:unique_identifier "MO_634" xsd:string property_value: rdfs:comment "ExperimentDesignType of unknown type." xsd:string [Instance] id: mged:unknown_experiment_design_type instance_of: mged:BiologicalProperty property_value: mged:unique_identifier "MO_634" xsd:string property_value: rdfs:comment "ExperimentDesignType of unknown type." xsd:string [Instance] id: mged:unknown_experiment_design_type instance_of: mged:BiologicalProperty property_value: mged:unique_identifier "MO_634" xsd:string property_value: rdfs:comment "ExperimentDesignType of unknown type." xsd:string [Instance] id: mged:unknown_protocol_type instance_of: mged:ExperimentalProtocolType property_value: rdfs:comment "ProtocolType of unknown type." xsd:string property_value: mged:unique_identifier "MO_460" xsd:string [Instance] id: mged:unknown_sequence instance_of: mged:PhysicalBioSequenceType property_value: mged:unique_identifier "MO_535" xsd:string property_value: rdfs:comment "BioSequence of unknown type" xsd:string [Instance] id: mged:unknown_sequence instance_of: mged:PhysicalBioSequenceType property_value: mged:unique_identifier "MO_535" xsd:string property_value: rdfs:comment "BioSequence of unknown type" xsd:string [Instance] id: mged:unknown_sex instance_of: mged:Sex property_value: rdfs:comment "organism(s) whose sex is unknown" xsd:string property_value: mged:unique_identifier "MO_999" xsd:string [Instance] id: mged:unknown_substrate_type instance_of: mged:SubstrateType property_value: rdfs:comment "SubstrateType of unknown type." xsd:string property_value: mged:unique_identifier "MO_484" xsd:string [Instance] id: mged:unknown_surface_type instance_of: mged:SurfaceType property_value: rdfs:comment "A SurfaceType of unknown type." xsd:string property_value: mged:unique_identifier "MO_359" xsd:string [Instance] id: mged:unscaled instance_of: mged:Scale property_value: rdfs:comment "The values are unordered and have no scale." xsd:string property_value: mged:unique_identifier "MO_542" xsd:string [Instance] id: mged:urine instance_of: mged:BioSourceType property_value: mged:unique_identifier "MO_399" xsd:string property_value: rdfs:comment "The fluid and dissolved substances excreted by the kidney." xsd:string [Instance] id: mged:us instance_of: mged:TimeUnit property_value: rdfs:comment "microsecond, unit of time" xsd:string property_value: mged:unique_identifier "MO_795" xsd:string [Instance] id: mged:vacuum_dryer instance_of: mged:HardwareType property_value: rdfs:comment "An instrument designed to remove excess liquid by vacuum and heating." xsd:string property_value: mged:unique_identifier "MO_696" xsd:string [Instance] id: mged:vector instance_of: mged:DeprecatedTerms property_value: mged:deprecation_replacement_term mged:PhysicalBioSequenceType property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecated_from_version mged:version_1.2.0 property_value: mged:deprecation_old_parent mged:PhysicalBioSequenceType property_value: mged:deprecation_in_version "1.2.0" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string property_value: mged:unique_identifier "MO_551" xsd:string property_value: rdfs:comment "Sequence from a vector, DNA of any transmissible agent e.g. plasmid or virus into which a segment of foreign DNA can be spliced, does not include insert sequence. These terms should be used when other terms such as plasmid, YAC, BAC are used. " xsd:string [Instance] id: mged:version_1.1.7 instance_of: mged:MGEDOntologyVersion property_value: rdfs:comment "Version of the MGED Ontology." xsd:string [Instance] id: mged:version_1.1.8 instance_of: mged:MGEDOntologyVersion property_value: rdfs:comment "Version of the MGED Ontology." xsd:string property_value: mged:unique_identifier "MO_469" xsd:string [Instance] id: mged:version_1.1.9 instance_of: mged:MGEDOntologyVersion property_value: rdfs:comment "Version of the MGEDOntology." xsd:string [Instance] id: mged:version_1.2.0 instance_of: mged:MGEDOntologyVersion property_value: rdfs:comment "Version of the MGEDOntology." xsd:string [Instance] id: mged:version_1.3.0 instance_of: mged:MGEDOntologyVersion property_value: mged:unique_identifier "MO_440" xsd:string property_value: rdfs:comment "Version of the MGEDOntology." xsd:string [Instance] id: mged:version_1.3.1 instance_of: mged:MGEDOntologyVersion [Instance] id: mged:virus instance_of: mged:MaterialType property_value: mged:unique_identifier "MO_372" xsd:string property_value: rdfs:comment "one or more DNA or RNA based non cellular infective agent, including bacteriophage" xsd:string [Instance] id: mged:vortexer instance_of: mged:HardwareType property_value: rdfs:comment "An instrument that mixes by rapid oscillation." xsd:string property_value: mged:unique_identifier "MO_983" xsd:string [Instance] id: mged:wait instance_of: mged:AtomicAction property_value: mged:unique_identifier "MO_988" xsd:string property_value: rdfs:comment "Allow time to pass. It's measurement should be a unit of time. " xsd:string [Instance] id: mged:wash instance_of: mged:ComplexAction property_value: mged:unique_identifier "MO_596" xsd:string property_value: rdfs:comment "The process of applying a solvent (e.g. water) or a solution (e.g. SSC/SDS) to a BioMaterial or an array to remove impurities or unwanted compounds." xsd:string [Instance] id: mged:wash instance_of: mged:ComplexAction property_value: mged:unique_identifier "MO_596" xsd:string property_value: rdfs:comment "The process of applying a solvent (e.g. water) or a solution (e.g. SSC/SDS) to a BioMaterial or an array to remove impurities or unwanted compounds." xsd:string [Instance] id: mged:wash_station instance_of: mged:HardwareType property_value: rdfs:comment "An instrument designed to mechanically wash or stain arrays." xsd:string property_value: mged:unique_identifier "MO_626" xsd:string [Instance] id: mged:water instance_of: mged:EnvironmentalFactorCategory property_value: mged:unique_identifier "MO_380" xsd:string property_value: rdfs:comment "Water consumed by or enveloping the organism that the biosource is derived from. " xsd:string [Instance] id: mged:waterbath instance_of: mged:HardwareType property_value: rdfs:comment "A device for controlling temperature by immersion in water." xsd:string property_value: mged:unique_identifier "MO_541" xsd:string [Instance] id: mged:weeks instance_of: mged:TimeUnit property_value: rdfs:comment "7 days, unit of time" xsd:string property_value: mged:unique_identifier "MO_842" xsd:string [Instance] id: mged:whole_organism instance_of: mged:MaterialType property_value: mged:unique_identifier "MO_566" xsd:string property_value: rdfs:comment "one or more of any unicellular or multicellular pro or eukaryote, including archaebacteria" xsd:string [Instance] id: mged:wild_type instance_of: mged:Allele property_value: mged:unique_identifier "MO_605" xsd:string property_value: rdfs:comment "The genotype or phenotype that is found in nature or in standard laboratory stocks for a given organism. For a single locus, the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism." xsd:string [Instance] id: mged:wild_type instance_of: mged:Allele property_value: mged:unique_identifier "MO_605" xsd:string property_value: rdfs:comment "The genotype or phenotype that is found in nature or in standard laboratory stocks for a given organism. For a single locus, the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism." xsd:string [Instance] id: mged:within_bioassay_data_set_function instance_of: mged:DataTransformationProtocolType property_value: rdfs:comment "A function applied to subsets of values from the same Measured/Derived bioassay data set." xsd:string property_value: mged:unique_identifier "MO_668" xsd:string [Instance] id: mged:x_times instance_of: mged:ConcentrationUnitOther property_value: mged:unique_identifier "MO_496" xsd:string property_value: rdfs:comment "multiple of stock solution concentration, concentration unit" xsd:string [Instance] id: mged:years instance_of: mged:TimeUnit property_value: rdfs:comment "365 days, time unit" xsd:string property_value: mged:unique_identifier "MO_948" xsd:string [Instance] id: mged:yes instance_of: mged:DeprecatedTerms property_value: mged:deprecated_from_version mged:version_1.1.7 property_value: mged:has_reason_for_deprecation mged:deleted_term property_value: mged:deprecation_in_version "1.1.7" xsd:string property_value: rdfs:comment "true" xsd:string property_value: mged:unique_identifier "MO_540" xsd:string property_value: mged:deprecation_reason "deleted_term" xsd:string go-perl-0.15/t/data/process.ontology000644 000765 000024 00022541533 11615622157 017373 0ustar00cjmstaff000000 000000 !autogenerated-by: DAG-Edit version 1.406 !saved-by: jlomax !date: Fri Dec 05 15:55:34 GMT 2003 !version: $Revision: 1.1 $ !type: % is_a is a !type: < part_of Part of $Gene_Ontology ; GO:0003673 This ontology contains logical relations to be shared across the different OBO ontologies. Each OBO ontology is free to extend this set with relations specific to the biology within that ontology. This ontology should remain largely invisible to the casual user

This ontology is designed to be used by the following groups of people:

OBO curators
each OBO ontology should use relations that are consistent with the relations defined here
Database administrators and developers, and other software developers
This ontology file is a partial computable specification of the core relationships in OBO. (The full semantics can not be specified using the OBO format, please refer to the paper for a full specification). This obo format file can be loaded into a database such as GO-DB or Chado in order to make relations between classes and instance data interoperable
Advanced users
The formal relations specified here allow for formal reasoning over the ontologies in OBO

Notes:

In the above, variables c, d, ..., p, q, ... range over instances of continuants and processes respectively. C, D, ..., P, Q, ... range over the corresponding classes

[Typedef] id: OBO_REL:relationship name: relationship def: "A relationship between two classes (terms). Relationships between classes are expressed in terms of relations on underlying instances. For more details see Smith B et al 'Relations in Bio Ontologies' [in press]." [obo:smith_et_al] [Typedef] id: OBO_REL:is_a name: is_a builtin: true def: "For continuants: C is_a C' if and only if: given any c that instantiates C at a time t, c instantiates C' at t. For processes: P is_a P' if and only if: that given any p that instantiates P, then p instantiates P'." [obo:smith_et_al] comment: The is_a relationship is considered axiomatic by the obo file format specification; ie it is taken for granted. The is_a relation is still included in this ontology for uniqueness exact_synonym: is_subtype_of xref_analog: owl:subClassOf inverse_of: has_subclass is_reflexive: true is_anti_symmetric: true is_transitive: true [Typedef] id: OBO_REL:part_of name: part_of is_a: OBO_REL:relationship def: "For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)" [obo:smith_et_al] inverse_of: has_part is_reflexive: true is_anti_symmetric: true is_transitive: true [Typedef] id: OBO_REL:integral_part_of name: integral_part_of is_a: OBO_REL:part_of def: "C integral_part_of C' if and only if: C part_of C' AND C' has_part C" [obo:smith_et_al] inverse_of: has_integral_part is_reflexive: true is_anti_symmetric: true is_transitive: true [Typedef] id: OBO_REL:proper_part_of name: proper_part_of is_a: OBO_REL:part_of def: "As for part_of, with the additional constraint that subject and object are distinct" [obo:smith_et_al] inverse_of: has_proper_part is_transitive: true [Typedef] id: OBO_REL:improper_part_of name: improper_part_of is_a: OBO_REL:part_of def: "As for part_of, with the additional constraint that subject and object are identical" [obo:smith_et_al] inverse_of: has_improper_part is_reflexive: true is_transitive: true [Typedef] id: OBO_REL:located_in name: located_in is_a: OBO_REL:relationship def: "C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)" [obo:smith_et_al] inverse_of: location_of is_transitive: true is_reflexive: true [Typedef] id: OBO_REL:contained_in name: contained_in is_a: OBO_REL:relationship inverse_of: contains def: "C contained_in C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c located_in c' at t, and it is not the case that c *part_of* c' at t. (c' is a conduit or cavity.)" [obo:smith_et_al] is_transitive: true [Typedef] id: OBO_REL:adjacent_to name: adjacent_to is_a: OBO_REL:relationship def: "C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' occupy neighboring spatial regions." [obo:smith_et_al] inverse_of: adjacent_to is_symmetric: true is_reflexive: true [Typedef] id: OBO_REL:transformation_of name: transformation_of is_a: OBO_REL:relationship def: "Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Examples: larval oenocyte transformation_of embryonic oenocyte, mature_mRNA transformation of pre_mRNA. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t." [obo:smith_et_al] inverse_of: transformed_into is_transitive: true [Typedef] id: OBO_REL:derives_from name: derives_from is_a: OBO_REL:relationship def: "Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'." [obo:smith_et_al] inverse_of: derived_into is_transitive: true [Typedef] id: OBO_REL:preceded_by name: preceded_by is_a: OBO_REL:relationship def: "P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t. " [obo:smith_et_al] inverse_of: precedes is_transitive: true [Typedef] id: OBO_REL:has_participant name: has_participant is_a: OBO_REL:relationship def: "P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates p at t and c participates in p at t" [obo:smith_et_al] inverse_of: participates_in [Typedef] id: OBO_REL:has_agent name: has_agent is_a: OBO_REL:relationship def: "As for has_participant, but with the additional condition that the component instance is causally active in the relevant process" [obo:smith_et_al] inverse_of: agent_in [Typedef] id: OBO_REL:instance_of name: instance_of is_a: OBO_REL:relationship def: "A relation between an instance and a class. For components: a primitive relation between a component instance and a class which it instantiates at a specific time. For processes: a primitive relation, between a process instance and a class which it instantiates, holding independently of time" [obo:smith_et_al] comment: The is_a relationship is considered axiomatic by the obo file format specification; ie it is taken for granted. The is_a relation is still included in this ontology for uniqueness inverse_of: has_instance go-perl-0.15/t/data/sample.ncbi_taxonomy000644 000765 000024 00000115203 11615622157 020160 0ustar00cjmstaff000000 000000 ID : 1 PARENT ID : 0 RANK : no rank GC ID : 1 SCIENTIFIC NAME : root SYNONYM : all // ID : 2 PARENT ID : 131567 RANK : superkingdom GC ID : 11 SCIENTIFIC NAME : Bacteria GENBANK COMMON NAME : eubacteria SYNONYM : not Bacteria Haeckel 1894 IN-PART : Prokaryota IN-PART : Monera IN-PART : Procaryotae IN-PART : Prokaryotae BLAST NAME : eubacteria // ID : 6 PARENT ID : 335928 RANK : genus GC ID : 11 SCIENTIFIC NAME : Azorhizobium SYNONYM : Azorhizobium Dreyfus et al. 1988 EQUIVALENT NAME : Azotirhizobium // ID : 7 PARENT ID : 6 RANK : species GC ID : 11 SCIENTIFIC NAME : Azorhizobium caulinodans SYNONYM : Azorhizobium caulinodans Dreyfus et al. 1988 INCLUDES : Rhizobium sp. ORS571 INCLUDES : Rhizobium sp. ORS 571 INCLUDES : Rhizobium sp. (strain ORS571) INCLUDES : Rhizobium ORS571 EQUIVALENT NAME : Azotirhizobium caulinodans // ID : 9 PARENT ID : 32199 RANK : species GC ID : 11 SCIENTIFIC NAME : Buchnera aphidicola SYNONYM : Buchnera aphidicola Munson et al. 1991 INCLUDES : Acyrthosiphon pisum symbiont P // ID : 10 PARENT ID : 135621 RANK : genus GC ID : 11 SCIENTIFIC NAME : Cellvibrio SYNONYM : "Cellvibrio" Winogradsky 1929 SYNONYM : Cellvibrio (ex Winogradsky 1929) Blackall et al. 1986 emend. Humphry et al. 2003 // ID : 11 PARENT ID : 10 RANK : species GC ID : 11 SCIENTIFIC NAME : Cellvibrio gilvus SYNONYM : 'Cellvibrio gilvus' // ID : 13 PARENT ID : 203488 RANK : genus GC ID : 11 SCIENTIFIC NAME : Dictyoglomus SYNONYM : Dictyoglomus Saiki et al. 1985 // ID : 14 PARENT ID : 13 RANK : species GC ID : 11 SCIENTIFIC NAME : Dictyoglomus thermophilum SYNONYM : Dictyoglomus thermophilum Saiki et al. 1985 // ID : 16 PARENT ID : 32011 RANK : genus GC ID : 11 SCIENTIFIC NAME : Methylophilus SYNONYM : Methylophilus Jenkins et al. 1987 MISSPELLING : Methylotrophus EQUIVALENT NAME : Methyliphilus // ID : 17 PARENT ID : 16 RANK : species GC ID : 11 SCIENTIFIC NAME : Methylophilus methylotrophus SYNONYM : Methylotrophus methylophilus SYNONYM : Methylophilus methylotrophus Jenkins et al. 1987 EQUIVALENT NAME : Methyliphilus methylitrophus EQUIVALENT NAME : Methyliphilus methylotrophus EQUIVALENT NAME : Methylophilus methylitrophus // ID : 18 PARENT ID : 213423 RANK : genus GC ID : 11 SCIENTIFIC NAME : Pelobacter SYNONYM : Pelobacter Schink and Pfennig 1983 // ID : 19 PARENT ID : 18 RANK : species GC ID : 11 SCIENTIFIC NAME : Pelobacter carbinolicus SYNONYM : Pelobacter carbinolicus Schink 1984 // ID : 20 PARENT ID : 76892 RANK : genus GC ID : 11 SCIENTIFIC NAME : Phenylobacterium SYNONYM : Phenylobacterium Lingens et al. 1985 emend. Kanso and Patel 2004 // ID : 21 PARENT ID : 20 RANK : species GC ID : 11 SCIENTIFIC NAME : Phenylobacterium immobile {test} SYNONYM : Phenylobacterium immobile Lingens et al. 1985 // ID : 22 PARENT ID : 267890 RANK : genus GC ID : 11 SCIENTIFIC NAME : Shewanella SYNONYM : Shewanella MacDonell and Colwell 1986 // ID : 23 PARENT ID : 22 RANK : species GC ID : 11 SCIENTIFIC NAME : Shewanella colwelliana SYNONYM : Alteromonas colwelliana SYNONYM : Shewanella colwelliana (Weiner et al. 1988) Coyne et al. 1990 // ID : 24 PARENT ID : 22 RANK : species GC ID : 11 SCIENTIFIC NAME : Shewanella putrefaciens SYNONYM : Alteromonas putrefaciens SYNONYM : Pseudomonas putrefaciens SYNONYM : Shewanella putrefaciens (Lee et al. 1981) MacDonell and Colwell 1986 SYNONYM : Alteromonas putrefaciens (ex Derby and Hammer) Lee et al. 1981 SYNONYM : "Pseudomonas putrefaciens" (Derby and Hammer) Long and Hammer 1941 MISSPELLING : Alteromonas putrifaciens MISSPELLING : Shewanella putrifaciens // ID : 25 PARENT ID : 22 RANK : species GC ID : 11 SCIENTIFIC NAME : Shewanella hanedai SYNONYM : Alteromonas hanedai Jensen et al. 1981 SYNONYM : Shewanella hanedai (Jensen et al. 1981) MacDonell and Colwell 1986 SYNONYM : Alteromonas hanedai // ID : 27 PARENT ID : 49928 RANK : species GC ID : 11 SCIENTIFIC NAME : halophilic eubacterium NRCC 41227 SYNONYM : halophilic eubacterium NRCC41227 SYNONYM : halophilic eubacterium (NRCC 41227) // ID : 28 PARENT ID : 49928 RANK : species GC ID : 11 SCIENTIFIC NAME : halophilic eubacterium // ID : 29 PARENT ID : 28221 RANK : order GC ID : 11 SCIENTIFIC NAME : Myxococcales GENBANK COMMON NAME : fruiting gliding bacteria SYNONYM : Myxobacteria SYNONYM : Myxococcales Tchan et al. 1948 SYNONYM : The Myxobacteria // ID : 31 PARENT ID : 80811 RANK : family GC ID : 11 SCIENTIFIC NAME : Myxococcaceae SYNONYM : Myxococcaceae Jahn 1924 // ID : 32 PARENT ID : 31 RANK : genus GC ID : 11 SCIENTIFIC NAME : Myxococcus SYNONYM : Myxococcus Thaxter 1892 // ID : 33 PARENT ID : 32 RANK : species GC ID : 11 SCIENTIFIC NAME : Myxococcus fulvus SYNONYM : Micrococcus fulvus SYNONYM : Myxococcus fulvus (Cohn 1875) Jahn 1911 SYNONYM : "Micrococcus fulvus" Cohn 1875 // ID : 34 PARENT ID : 32 RANK : species GC ID : 11 SCIENTIFIC NAME : Myxococcus xanthus SYNONYM : Myxococcus xanthus Beebe 1941 INCLUDES : Myxococcus xanthus retron Mx65 INCLUDES : Myxococcus xanthus retron Mx162 // ID : 35 PARENT ID : 32 RANK : species GC ID : 11 SCIENTIFIC NAME : Myxococcus macrosporus SYNONYM : Myxococcus macrosporus (Krzemieniewska and Krzemieniewski 1926) Zahler and McCurdy 1974 SYNONYM : "Chondrococcus macrosporus" Krzemieniewska and Krzemieniewski 1926 SYNONYM : not "Myxococcus macrosporus" Zukal 1897 SYNONYM : Chondrococcus macrosporus // ID : 36 PARENT ID : 32 RANK : species GC ID : 11 SCIENTIFIC NAME : Myxococcus coralloides SYNONYM : Chondrococcus coralloides SYNONYM : "Chondrococcus coralloides" (Thaxter 1892) Jahn 1924 SYNONYM : "Chondrococcus polycystus" (Kofler 1913) Krzemieniewska and Krzemieniewski 1926 SYNONYM : "Myxococcus clavatus" Quehl 1906 SYNONYM : "Myxococcus digitatus" Quehl 1906 SYNONYM : "Myxococcus exiguus" Kofler 1913 SYNONYM : "Myxococcus polycystus" Kofler 1913 SYNONYM : Myxococcus coralloides Thaxter 1892 SYNONYM : Myxococcus polycystus SYNONYM : Chondrococcus polycystus SYNONYM : Myxococcus exiguus SYNONYM : Myxococcus digitatus SYNONYM : Myxococcus clavatus // ID : 38 PARENT ID : 42 RANK : species GC ID : 11 SCIENTIFIC NAME : Angiococcus disciformis SYNONYM : "Angiococcus disciformis" (Thaxter 1904) Jahn 1924 SYNONYM : Angiococcus disciformis (Thaxter 1904) Hook et al. 1980 SYNONYM : Myxococcus disciformis Thaxter 1904 (Approved Lists 1980) SYNONYM : Cystobacter disciformis SYNONYM : Myxococcus disciformis SYNONYM : 'Cystobacter disciformis' // ID : 39 PARENT ID : 80811 RANK : family GC ID : 11 SCIENTIFIC NAME : Cystobacteraceae SYNONYM : Cystobacteraceae McCurdy 1970 INCLUDES : Archangiaceae Jahn 1924 INCLUDES : Archangiaceae // ID : 40 PARENT ID : 39 RANK : genus GC ID : 11 SCIENTIFIC NAME : Stigmatella SYNONYM : Stigmatella Berkeley and Curtis 1875 // ID : 41 PARENT ID : 40 RANK : species GC ID : 11 SCIENTIFIC NAME : Stigmatella aurantiaca SYNONYM : Chondromyces aurantiacus SYNONYM : "Chondromyces aurantiacus" (Berkeley and Curtis) Thaxter 1892 SYNONYM : Stigmatella aurantiaca Berkeley and Curtis 1875 // ID : 42 PARENT ID : 39 RANK : genus GC ID : 11 SCIENTIFIC NAME : Cystobacter SYNONYM : Cystobacter Schroeter 1886 INCLUDES : Angiococcus INCLUDES : Angiococcus (ex Jahn 1924) Hook et al. 1980 INCLUDES : "Angiococcus" Jahn 1924 // ID : 43 PARENT ID : 42 RANK : species GC ID : 11 SCIENTIFIC NAME : Cystobacter fuscus SYNONYM : Polyangium fuscum SYNONYM : Cystobacter fuscus Schroeter 1886 SYNONYM : "Polyangium fuscum" (Schroeter 1886) Thaxter 1904 // ID : 44 PARENT ID : 39 RANK : genus GC ID : 11 SCIENTIFIC NAME : Melittangium SYNONYM : Melittangium Jahn 1924 // ID : 45 PARENT ID : 44 RANK : species GC ID : 11 SCIENTIFIC NAME : Melittangium lichenicola SYNONYM : Podangium gracilipes SYNONYM : Podangium lichenicolum SYNONYM : Chondromyces minor SYNONYM : Chondromyces lichenicolus SYNONYM : Chondromyces gracilipes SYNONYM : "Chondromyces minor" Krzemieniewska and Krzemieniewski 1930 SYNONYM : "Chondromyces lichenicolus" Thaxter 1892 SYNONYM : "Chondromyces gracilipes" Thaxter 1897 SYNONYM : "Podangium gracilipes" (Thaxter 1897) Jahn 1924 SYNONYM : "Podangium lichenicolum" (Thaxter 1892) Jahn 1924 SYNONYM : Melittangium lichenicola (Thaxter 1892) McCurdy 1971 // ID : 47 PARENT ID : 39 RANK : genus GC ID : 11 SCIENTIFIC NAME : Archangium SYNONYM : Archangium Jahn 1924 // ID : 48 PARENT ID : 47 RANK : species GC ID : 11 SCIENTIFIC NAME : Archangium gephyra SYNONYM : "Chondrococcus cerebriformis" (Kofler) Jahn 1924 SYNONYM : "Chondromyces serpens" Quehl 1906 SYNONYM : "Myxococcus cerebriformis" Kofler 1913 SYNONYM : Archangium gephyra Jahn 1924 SYNONYM : Chondrococcus cerebriformis SYNONYM : Chondromyces serpens SYNONYM : Myxococcus cerebriformis // ID : 49 PARENT ID : 80812 RANK : family GC ID : 11 SCIENTIFIC NAME : Polyangiaceae SYNONYM : Polyangiaceae Jahn 1924 INCLUDES : "Sorangiaceae" Jahn 1924 INCLUDES : Sorangiaceae // ID : 50 PARENT ID : 49 RANK : genus GC ID : 11 SCIENTIFIC NAME : Chondromyces SYNONYM : "Myxobotrys" Zukal 1896 SYNONYM : "Polycephalum" Kalchbrenner and Cooke 1880 SYNONYM : Chondromyces Berkeley and Curtis 1874 SYNONYM : Polycephalum SYNONYM : Myxobotrys MISSPELLING : Chrondromyces // ID : 51 PARENT ID : 50 RANK : species GC ID : 11 SCIENTIFIC NAME : Chondromyces apiculatus SYNONYM : Chondromyces apiculatus Thaxter 1897 MISSPELLING : Chrondromyces apiculatus // ID : 52 PARENT ID : 50 RANK : species GC ID : 11 SCIENTIFIC NAME : Chondromyces crocatus SYNONYM : Chondromyces crocatus Berkeley and Curtis 1874 SYNONYM : "Myxobotrys variabilis" Zukal 1896 (putative synonym) SYNONYM : Myxobotrys variabilis MISSPELLING : Chrondromyces crocatus // ID : 53 PARENT ID : 224463 RANK : genus GC ID : 11 SCIENTIFIC NAME : Nannocystis SYNONYM : Nannocystis Reichenbach 1970 // ID : 54 PARENT ID : 53 RANK : species GC ID : 11 SCIENTIFIC NAME : Nannocystis exedens SYNONYM : Nannocystis exedens Reichenbach 1970 // ID : 55 PARENT ID : 49 RANK : genus GC ID : 11 SCIENTIFIC NAME : Polyangium SYNONYM : Polyangium Link 1809 // ID : 56 PARENT ID : 55 RANK : species GC ID : 11 SCIENTIFIC NAME : Polyangium cellulosum SYNONYM : Sorangium cellulosum SYNONYM : "Polyangium cellulosum" Imshenetski and Solntseva 1936 SYNONYM : "Sorangium cellulosum" (Imshenetski and Solntseva 1936) Imshenetski and Solntseva 1937 SYNONYM : "Sorangium nigrescens" Krzemieniewska and Krzemieniewski 1938 SYNONYM : "Sorangium nigrum" Krzemieniewska and Krzemieniewski 1938 SYNONYM : Polyangium cellulosum (ex Imshenetski and Solntseva 1936) Brockman 1989 SYNONYM : Sorangium nigrescens SYNONYM : Sorangium nigrum // ID : 57 PARENT ID : 55 RANK : species GC ID : 11 SCIENTIFIC NAME : Polyangium sp. // ID : 59 PARENT ID : 90153 RANK : genus GC ID : 11 SCIENTIFIC NAME : Vitreoscilla SYNONYM : Vitreoscilla Pringsheim 1949 // ID : 60 PARENT ID : 59 RANK : species GC ID : 11 SCIENTIFIC NAME : Vitreoscilla sp. // ID : 61 PARENT ID : 59 RANK : species GC ID : 11 SCIENTIFIC NAME : Vitreoscilla stercoraria SYNONYM : Vitreoscilla stercoraria Pringsheim 1951 (Approved Lists 1980) emend. Strohl et al. 1986 // ID : 62 PARENT ID : 59 RANK : species GC ID : 11 SCIENTIFIC NAME : Vitreoscilla beggiatoides SYNONYM : Vitreoscilla beggiatoides Pringsheim 1949 (Approved Lists 1980) emend. Strohl et al. 1986 // ID : 63 PARENT ID : 59 RANK : species GC ID : 11 SCIENTIFIC NAME : Vitreoscilla filiformis SYNONYM : "Vitreoscilla filiformis" Pringsheim 1951 SYNONYM : Vitreoscilla filiformis (ex Pringsheim 1951) Strohl et al. 1986 // ID : 64 PARENT ID : 189773 RANK : genus GC ID : 11 SCIENTIFIC NAME : Herpetosiphon SYNONYM : Herpetosiphon Holt and Lewin 1968 // ID : 65 PARENT ID : 64 RANK : species GC ID : 11 SCIENTIFIC NAME : Herpetosiphon aurantiacus SYNONYM : Herpetosiphon giganteus SYNONYM : Herpetosiphon aurantiacus Holt and Lewin 1968 // ID : 68 PARENT ID : 32033 RANK : genus GC ID : 11 SCIENTIFIC NAME : Lysobacter SYNONYM : Lysobacter Christensen and Cook 1978 // ID : 69 PARENT ID : 68 RANK : species GC ID : 11 SCIENTIFIC NAME : Lysobacter enzymogenes SYNONYM : Lysobacter enzymogenes Christensen and Cook 1978 // ID : 71 PARENT ID : 481 RANK : genus GC ID : 11 SCIENTIFIC NAME : Simonsiella SYNONYM : Simonsiella Schmid 1922 // ID : 72 PARENT ID : 71 RANK : species GC ID : 11 SCIENTIFIC NAME : Simonsiella muelleri SYNONYM : Simonsiella muelleri Schmid 1922 SYNONYM : Caryophanon muelleri SYNONYM : "Caryophanon muelleri" (Schmid 1922) Peshkoff 1948 COMMON NAME : Scheibenbakterien COMMON NAME : Scheibenbakterien Muller 1911 // ID : 75 PARENT ID : 76892 RANK : genus GC ID : 11 SCIENTIFIC NAME : Caulobacter SYNONYM : Caulobacter Henrici and Johnson 1935 (Approved Lists 1980) emend. Abraham et al. 1999 // ID : 78 PARENT ID : 75 RANK : species GC ID : 11 SCIENTIFIC NAME : Caulobacter sp. // ID : 80 PARENT ID : 75 RANK : species GC ID : 11 SCIENTIFIC NAME : Caulobacter spinosum SYNONYM : 'Caulobacter spinosum' // ID : 81 PARENT ID : 45401 RANK : genus GC ID : 11 SCIENTIFIC NAME : Hyphomicrobium SYNONYM : Hyphomicrobium Stutzer and Hartleb 1898 SYNONYM : Hyphomicrobium Stutzer and Hartleb 1899 (sic) // ID : 82 PARENT ID : 81 RANK : species GC ID : 11 SCIENTIFIC NAME : Hyphomicrobium sp. // ID : 83 PARENT ID : 81 RANK : species GC ID : 11 SCIENTIFIC NAME : Hyphomicrobium vulgare SYNONYM : Hyphomicrobium vulgare Stutzer and Hartleb 1898 SYNONYM : Hyphomicrobium vulgare Stutzer and Hartleb 1899 (sic) // ID : 84 PARENT ID : 81 RANK : species GC ID : 11 SCIENTIFIC NAME : Hyphomicrobium methylovorum SYNONYM : Hyphomicrobium methylovorum Izumi et al. 1983 // ID : 85 PARENT ID : 69657 RANK : genus GC ID : 11 SCIENTIFIC NAME : Hyphomonas SYNONYM : Hyphomonas (ex Pongratz 1957) Moore et al. 1984 emend. Weiner et al. 2000 // ID : 86 PARENT ID : 85 RANK : species GC ID : 11 SCIENTIFIC NAME : Hyphomonas jannaschiana SYNONYM : Hyphomonas jannaschiana Weiner et al. 1985 // ID : 87 PARENT ID : 85 RANK : species GC ID : 11 SCIENTIFIC NAME : Hyphomonas sp. // ID : 88 PARENT ID : 224471 RANK : genus GC ID : 11 SCIENTIFIC NAME : Leptothrix SYNONYM : Detoniella SYNONYM : "Chlamydothrix" Migula 1900 SYNONYM : "Detoniella" Trevisan in de Toni and Trevisan 1889 SYNONYM : Leptothrix Kutzing 1843 SYNONYM : Chlamydothrix // ID : 89 PARENT ID : 88 RANK : species GC ID : 11 SCIENTIFIC NAME : Leptothrix discophora SYNONYM : "Leptothrix discophora" (Schwers 1912) Dorff 1934 SYNONYM : "Leptothrix crassa" Cholodny 1924 SYNONYM : "Megalothrix discophora" Schwers 1912 SYNONYM : Leptothrix discophora (ex Schwers 1912) Spring et al. 1997 SYNONYM : Leptothrix crassa SYNONYM : Megalothrix discophora // ID : 93 PARENT ID : 433 RANK : genus GC ID : 11 SCIENTIFIC NAME : Stella SYNONYM : Stella Vasilyeva 1985 // ID : 94 PARENT ID : 93 RANK : species GC ID : 11 SCIENTIFIC NAME : Stella humosa SYNONYM : Stella humosa Vasilyeva 1985 // ID : 96 PARENT ID : 90627 RANK : genus GC ID : 11 SCIENTIFIC NAME : Gallionella SYNONYM : Gallionella Ehrenberg 1838 // ID : 97 PARENT ID : 96 RANK : species GC ID : 11 SCIENTIFIC NAME : Gallionella ferruginea SYNONYM : Spirophyllum ferrugineum SYNONYM : Spirillum ferrugineum SYNONYM : "Spirophyllum ferrugineum" (Ehrenberg 1838) Ellis 1907 SYNONYM : Chlamydothrix ferruginea SYNONYM : Gallionella ferruginea Ehrenberg 1838 SYNONYM : "Spirillum ferrugineum" (Ehrenberg 1838) de Toni and Trevisan 1889 SYNONYM : "Chlamydothrix ferruginea" (Ehrenberg 1838) Migula 1900 // ID : 99 PARENT ID : 335928 RANK : genus GC ID : 11 SCIENTIFIC NAME : Ancylobacter SYNONYM : Ancylobacter Raj 1983 SYNONYM : Microcyclus SYNONYM : Microcyclus Orskov 1928 (Approved Lists 1980) // ID : 100 PARENT ID : 99 RANK : species GC ID : 11 SCIENTIFIC NAME : Ancylobacter aquaticus SYNONYM : Microcyclus aquaticus SYNONYM : Ancylobacter aquaticus (Orskov 1928) Raj 1983 SYNONYM : Microcyclus aquaticus Orskov 1928 (Approved Lists 1980) // ID : 101 PARENT ID : 89373 RANK : genus GC ID : 11 SCIENTIFIC NAME : Flectobacillus SYNONYM : Flectobacillus Larkin et al. 1977 (Approved Lists 1980) emend. Raj and Maloy 1990 // ID : 102 PARENT ID : 52959 RANK : species GC ID : 11 SCIENTIFIC NAME : Polaribacter glomeratus SYNONYM : Flectobacillus glomeratus McGuire et al. 1988 SYNONYM : Polaribacter glomeratus (McGuire et al. 1988) Gosink et al. 1998 SYNONYM : Flectobacillus glomeratus // ID : 103 PARENT ID : 101 RANK : species GC ID : 11 SCIENTIFIC NAME : Flectobacillus major SYNONYM : "Microcyclus major" Gromov 1963 SYNONYM : Flectobacillus major (Gromov 1963) Larkin et al. 1977 SYNONYM : Microcyclus major // ID : 104 PARENT ID : 68288 RANK : species GC ID : 11 SCIENTIFIC NAME : Cyclobacterium marinum SYNONYM : Microcyclus marinus SYNONYM : Cyclobacterium marinus SYNONYM : "Microcyclus marinus" Raj 1976 SYNONYM : Cyclobacterium marinum corrig. (Raj 1976) Raj and Maloy 1990 SYNONYM : Flectobacillus marinus SYNONYM : Flectobacillus marinus (Raj 1976) Borrall and Larkin 1978 (Approved Lists 1980) EQUIVALENT NAME : Cyclibacterium marinum // ID : 105 PARENT ID : 89373 RANK : genus GC ID : 11 SCIENTIFIC NAME : Runella SYNONYM : Runella Larkin and Williams 1978 // ID : 106 PARENT ID : 105 RANK : species GC ID : 11 SCIENTIFIC NAME : Runella slithyformis SYNONYM : Runella slithyformis Larkin and Williams 1978 // ID : 107 PARENT ID : 89373 RANK : genus GC ID : 11 SCIENTIFIC NAME : Spirosoma SYNONYM : Spirosoma Migula 1894 // ID : 108 PARENT ID : 107 RANK : species GC ID : 11 SCIENTIFIC NAME : Spirosoma linguale SYNONYM : Spirosoma linguale Migula 1894 // ID : 109 PARENT ID : 41294 RANK : genus GC ID : 11 SCIENTIFIC NAME : Blastobacter SYNONYM : Blastobacter Zavarzin 1961 (Approved Lists 1980) emend. Sly 1985 // ID : 110 PARENT ID : 279 RANK : species GC ID : 11 SCIENTIFIC NAME : Xanthobacter viscosus SYNONYM : "Blastobacter viscosus" Loginova and Trotsenok 1979 SYNONYM : Xanthobacter viscosus Doronina and Trotsenko 2003 SYNONYM : Blastobacter viscosus SYNONYM : "Blastobacter viscosus" Loginova and Trotensko 1979 INCLUDES : Blastobacter viscosus 7d // ID : 111 PARENT ID : 109 RANK : species GC ID : 11 SCIENTIFIC NAME : Blastobacter denitrificans SYNONYM : Blastobacter denitrificans Hirsch and Muller 1986 // ID : 112 PARENT ID : 203683 RANK : order GC ID : 11 SCIENTIFIC NAME : Planctomycetales SYNONYM : Planctomycetales Schlesner and Stackebrandt 1987 BLAST NAME : planctomycetes // ID : 113 PARENT ID : 126 RANK : genus GC ID : 11 SCIENTIFIC NAME : Gemmata SYNONYM : Gemmata Franzmann and Skerman 1985 // ID : 114 PARENT ID : 113 RANK : species GC ID : 11 SCIENTIFIC NAME : Gemmata obscuriglobus SYNONYM : Gemmata obscuriglobus Franzmann and Skerman 1985 // ID : 117 PARENT ID : 123 RANK : species GC ID : 11 SCIENTIFIC NAME : Pirellula sp. MISSPELLING : Pirella sp. // ID : 118 PARENT ID : 126 RANK : genus GC ID : 11 SCIENTIFIC NAME : Planctomyces SYNONYM : "Acinothrix" Novacek 1938 SYNONYM : Blastocaulis SYNONYM : Acinothrix SYNONYM : "Blastocaulis" Henrici and Johnson 1935 SYNONYM : Planctomyces Gimesi 1924 // ID : 119 PARENT ID : 118 RANK : species GC ID : 11 SCIENTIFIC NAME : Planctomyces brasiliensis SYNONYM : Planctomyces brasiliensis Schlesner 1990 // ID : 120 PARENT ID : 118 RANK : species GC ID : 11 SCIENTIFIC NAME : Planctomyces limnophilus SYNONYM : Planctomyces limnophilus Hirsch and Muller 1986 // ID : 122 PARENT ID : 118 RANK : species GC ID : 11 SCIENTIFIC NAME : Planctomyces maris SYNONYM : Planctomyces maris (ex Bauld and Staley 1976) Bauld and Staley 1980 SYNONYM : "Planctomyces maris" Bauld and Staley 1976 // ID : 123 PARENT ID : 126 RANK : genus GC ID : 11 SCIENTIFIC NAME : Pirellula SYNONYM : Pirellula Schlesner and Hirsch 1987 emend. Schlesner et al. 2004 MISNOMER : Pirella Schlesner and Hirsch 1984 MISNOMER : Pirella MISSPELLING : Pivellula // ID : 124 PARENT ID : 265487 RANK : species GC ID : 11 SCIENTIFIC NAME : Blastopirellula marina SYNONYM : Blastopirellula marina (Schlesner 1987) Schlesner et al. 2004 SYNONYM : Pirellula marina SYNONYM : Pirellula marina (Schlesner 1987) Schlesner and Hirsch 1987 MISNOMER : Pirella marina Schlesner 1987 MISNOMER : Pirella marina MISSPELLING : Pivellula marina // ID : 125 PARENT ID : 123 RANK : species GC ID : 11 SCIENTIFIC NAME : Pirellula staleyi SYNONYM : Pirellula staleyi (Schlesner and Hirsch 1984) Schlesner and Hirsch 1987 INCLUDES : Pasteuria ramosa ATCC 27377 MISNOMER : Planctomyces staleyi MISNOMER : Pirella staleyi Schlesner and Hirsch 1984 MISNOMER : Pirella staleyi // ID : 126 PARENT ID : 112 RANK : family GC ID : 11 SCIENTIFIC NAME : Planctomycetaceae SYNONYM : Planctomycetaceae Schlesner and Stackebrandt 1987 // ID : 127 PARENT ID : 126 RANK : genus GC ID : 11 SCIENTIFIC NAME : Isosphaera SYNONYM : Isosphaera Giovannoni et al. 1995 // ID : 128 PARENT ID : 127 RANK : species GC ID : 11 SCIENTIFIC NAME : Isosphaera pallida SYNONYM : "Isocystis pallida" Woronichin 1927 (as cyanobacterium) SYNONYM : "Torulopsidosira pallida" (Woronichin 1927) Geitler 1963 (as a yeast) SYNONYM : Isocystis pallida SYNONYM : Isosphaera pallida (ex Woronichin 1927) Giovannoni et al. 1995 SYNONYM : Torulopsidosira pallida // ID : 129 PARENT ID : 82117 RANK : genus GC ID : 11 SCIENTIFIC NAME : Renobacter SYNONYM : 'Renobacter' SYNONYM : "Renobacter" Nikitin 1971 // ID : 130 PARENT ID : 129 RANK : species GC ID : 11 SCIENTIFIC NAME : Renobacter vaculatum SYNONYM : "Renobacter vaculatum" Nikitin 1971 SYNONYM : 'Renobacter vaculatum' EQUIVALENT NAME : Renobacter vacuolatum // ID : 131 PARENT ID : 82117 RANK : genus GC ID : 11 SCIENTIFIC NAME : Tuberoidobacter // ID : 132 PARENT ID : 131 RANK : species GC ID : 11 SCIENTIFIC NAME : Tuberoidobacter mutans SYNONYM : 'Tuberoidobacter mutans' // ID : 133 PARENT ID : 31993 RANK : genus GC ID : 11 SCIENTIFIC NAME : Methylocystis SYNONYM : Methylocystis Bowman et al. 1993 // ID : 134 PARENT ID : 133 RANK : species GC ID : 11 SCIENTIFIC NAME : Methylocystis parvus SYNONYM : Methylocystis parvus Bowman et al. 1993 // ID : 136 PARENT ID : 203692 RANK : order GC ID : 11 SCIENTIFIC NAME : Spirochaetales SYNONYM : Spirochaetales Buchanan 1917 BLAST NAME : spirochetes // ID : 137 PARENT ID : 136 RANK : family GC ID : 11 SCIENTIFIC NAME : Spirochaetaceae SYNONYM : Spirochaetaceae Swellengrebel 1907 IN-PART : Treponemataceae IN-PART : Treponemataceae Robinson 1948 (Approved Lists 1980) // ID : 138 PARENT ID : 137 RANK : genus GC ID : 11 SCIENTIFIC NAME : Borrelia SYNONYM : Borrelia Swellengrebel 1907 // ID : 139 PARENT ID : 64895 RANK : species GC ID : 11 SCIENTIFIC NAME : Borrelia burgdorferi GENBANK COMMON NAME : Lyme disease spirochete SYNONYM : Borrelia burgdorferi Johnson et al. 1984 emend. Baranton et al. 1992 MISSPELLING : Borrelia burdorferi MISSPELLING : Borrelia burgdorffragment EQUIVALENT NAME : Borrelia burgdorferi sensu stricto // ID : 140 PARENT ID : 138 RANK : species GC ID : 11 SCIENTIFIC NAME : Borrelia hermsii SYNONYM : Spirochaeta hermsi SYNONYM : "Spirochaeta hermsi" (sic) Davis 1942 SYNONYM : Borrelia hermsii (Davis 1942) Steinhaus 1946 // ID : 141 PARENT ID : 138 RANK : species GC ID : 11 SCIENTIFIC NAME : Borrelia parkeri SYNONYM : "Spirochaeta parkeri" Davis 1942 SYNONYM : Borrelia parkeri (Davis 1942) Steinhaus 1946 SYNONYM : Spirochaeta parkeri // ID : 142 PARENT ID : 138 RANK : species GC ID : 11 SCIENTIFIC NAME : Borrelia turicatae SYNONYM : Borrelia turicatae (Brumpt 1933) Steinhaus 1946 SYNONYM : "Spirochaeta turicatae" Brumpt 1933 SYNONYM : Spirochaeta turicatae // ID : 143 PARENT ID : 138 RANK : species GC ID : 11 SCIENTIFIC NAME : Borrelia anserina SYNONYM : Spirochaeta anserina SYNONYM : Spirochaete gallinarum SYNONYM : Spiroschaudinnia anserina SYNONYM : Borrelia anserina (Sakharoff 1891) Bergey et al. 1925 SYNONYM : "Spiroschaudinnia anserina" (Sakharoff 1891) Sambon 1907 SYNONYM : "Spirochaete gallinarum" (sic) Stephens and Christopher 1904 SYNONYM : "Spirochaeta anserina" Sakharoff 1891 // ID : 144 PARENT ID : 138 RANK : species GC ID : 11 SCIENTIFIC NAME : Borrelia coriaceae SYNONYM : Borrelia coriaceae Johnson et al. 1987 // ID : 145 PARENT ID : 138 RANK : species GC ID : 11 SCIENTIFIC NAME : Borrelia sp. // go-perl-0.15/t/data/spkw2go000644 000765 000024 00000132544 11615622157 015432 0ustar00cjmstaff000000 000000 !date: 2005/10/18 14:10:12 !Mapping of SWISS-PROT KEYWORDS to GO terms. !Evelyn Camon, SWISS-PROT. ! SP_KW:2Fe-2S > GO:2 iron, 2 sulfur cluster binding ; GO:0051537 SP_KW:3Fe-4S > GO:3 iron, 4 sulfur cluster binding ; GO:0051538 SP_KW:4Fe-4S > GO:4 iron, 4 sulfur cluster binding ; GO:0051539 SP_KW:ATP synthesis > GO:metal ion binding ; GO:0046872 SP_KW:ATP synthesis > GO:ATP biosynthesis ; GO:0006754 SP_KW:ATP-binding > GO:ATP binding ; GO:0005524 SP_KW:Acetoin biosynthesis > GO:acetoin biosynthesis ; GO:0045151 SP_KW:Acetoin catabolism > GO:acetoin catabolism ; GO:0045150 SP_KW:Acetylcholine receptor inhibitor > GO:acetylcholine receptor inhibitor activity ; GO:0030550 SP_KW:Actin capping > GO:barbed-end actin filament capping ; GO:0051016 SP_KW:Actin-binding > GO:actin binding ; GO:0003779 SP_KW:Acute phase > GO:acute-phase response ; GO:0006953 SP_KW:Acyltransferase > GO:acyltransferase activity ; GO:0008415 SP_KW:Alginate biosynthesis > GO:alginic acid biosynthesis ; GO:0042121 SP_KW:Alkaloid metabolism > GO:alkaloid metabolism ; GO:0009820 SP_KW:Alkylphosphonate uptake > GO:phosphonate transport ; GO:0015716 SP_KW:Allergen > GO:type I hypersensitivity ; GO:0016068 SP_KW:Allosteric enzyme > GO:catalytic activity ; GO:0003824 SP_KW:Alpha-amylase inhibitor > GO:alpha-amylase inhibitor activity ; GO:0015066 SP_KW:Amino-acid biosynthesis > GO:amino acid biosynthesis ; GO:0008652 SP_KW:Amino-acid transport > GO:amino acid transporter activity ; GO:0015171 SP_KW:Amino-acid transport > GO:amino acid transport ; GO:0006865 SP_KW:Aminoacyl-tRNA synthetase > GO:tRNA ligase activity ; GO:0004812 SP_KW:Aminopeptidase > GO:aminopeptidase activity ; GO:0004177 SP_KW:Aminotransferase > GO:transaminase activity ; GO:0008483 SP_KW:Ammonia transport > GO:ammonium transport ; GO:0015696 SP_KW:Amphibian defense peptide > GO:defense response ; GO:0006952 SP_KW:Amyloplast > GO:amyloplast ; GO:0009501 SP_KW:Angiogenesis > GO:angiogenesis ; GO:0001525 SP_KW:Anion exchange > GO:anion exchanger activity ; GO:0015380 SP_KW:Antenna complex > GO:light-harvesting complex ; GO:0030076 SP_KW:Anti-oncogene > GO:negative regulation of progression through cell cycle ; GO:0045786 SP_KW:Antibiotic > GO:defense response to bacteria ; GO:0042742 SP_KW:Antibiotic biosynthesis > GO:antibiotic biosynthesis ; GO:0017000 SP_KW:Antibiotic resistance > GO:response to antibiotic ; GO:0046677 SP_KW:Antifreeze protein > GO:ice binding ; GO:0050825 SP_KW:Antifreeze protein > GO:homoiothermy ; GO:0042309 SP_KW:Antifreeze protein > GO:response to freezing ; GO:0050826 SP_KW:Antioxidant > GO:antioxidant activity ; GO:0016209 SP_KW:Antiport > GO:antiporter activity ; GO:0015297 SP_KW:Antiviral defense > GO:response to virus ; GO:0009615 SP_KW:Apoplast > GO:apoplast ; GO:0048046 SP_KW:Apoptosis > GO:apoptosis ; GO:0006915 SP_KW:Arabinose catabolism > GO:arabinose catabolism ; GO:0019568 SP_KW:Arginine biosynthesis > GO:arginine biosynthesis ; GO:0006526 SP_KW:Arginine metabolism > GO:arginine metabolism ; GO:0006525 SP_KW:Aromatic amino acid biosynthesis > GO:aromatic amino acid family biosynthesis ; GO:0009073 SP_KW:Aromatic hydrocarbons catabolism > GO:aromatic compound catabolism ; GO:0019439 SP_KW:Arsenical resistance > GO:response to arsenic ; GO:0046685 SP_KW:Ascorbate biosynthesis > GO:L-ascorbic acid biosynthesis ; GO:0019853 SP_KW:Asparagine biosynthesis > GO:asparagine biosynthesis ; GO:0006529 SP_KW:Aspartic protease inhibitor > GO:aspartic-type endopeptidase inhibitor activity ; GO:0019828 SP_KW:Aspartyl esterase > GO:aspartyl esterase activity ; GO:0045330 SP_KW:Aspartyl protease > GO:aspartic-type endopeptidase activity ; GO:0004190 SP_KW:Autophagy > GO:autophagy ; GO:0006914 SP_KW:Auxin biosynthesis > GO:auxin biosynthesis ; GO:0009851 SP_KW:Auxin signaling pathway > GO:auxin mediated signaling pathway ; GO:0009734 SP_KW:B-cell activation > GO:B cell activation ; GO:0042113 SP_KW:Bacterial capsule > GO:capsule (sensu Bacteria) ; GO:0030113 SP_KW:Bacteriochlorophyll > GO:bacteriochlorophyll binding ; GO:0042314 SP_KW:Bacteriochlorophyll biosynthesis > GO:bacteriochlorophyll biosynthesis ; GO:0030494 SP_KW:Bacteriocin > GO:receptor binding ; GO:0005102 SP_KW:Bacteriocin > GO:cytolysis ; GO:0019835 SP_KW:Bacteriocin biosynthesis > GO:bacteriocin biosynthesis ; GO:0030152 SP_KW:Bacteriocin immunity > GO:bacteriocin immunity ; GO:0030153 SP_KW:Bacteriocin transport > GO:bacteriocin transport ; GO:0043213 SP_KW:Bacteriolytic enzyme > GO:catalytic activity ; GO:0003824 SP_KW:Bacteriolytic enzyme > GO:cytolysis ; GO:0019835 SP_KW:Bacteriolytic enzyme > GO:defense response to bacteria ; GO:0042742 SP_KW:Bait region > GO:wide-spectrum protease inhibitor activity ; GO:0017114 SP_KW:Basement membrane > GO:basement membrane ; GO:0005604 SP_KW:Behavior > GO:behavior ; GO:0007610 SP_KW:Bile acid catabolism > GO:bile acid catabolism ; GO:0030573 SP_KW:Biological rhythms > GO:rhythmic process ; GO:0048511 SP_KW:Biomineralization > GO:ossification ; GO:0001503 SP_KW:Biotin biosynthesis > GO:biotin biosynthesis ; GO:0009102 SP_KW:Blood coagulation > GO:blood coagulation ; GO:0007596 SP_KW:Branched-chain amino acid biosynthesis > GO:branched chain family amino acid biosynthesis ; GO:0009082 SP_KW:Branched-chain amino acid catabolism > GO:branched chain family amino acid catabolism ; GO:0009083 SP_KW:CF(0) > GO:proton-transporting ATP synthase complex, coupling factor F(o) ; GO:0045263 SP_KW:CF(1) > GO:proton-transporting ATP synthase complex, catalytic core F(1) ; GO:0045261 SP_KW:Cadmium > GO:cadmium ion binding ; GO:0046870 SP_KW:Cadmium resistance > GO:response to cadmium ion ; GO:0046686 SP_KW:Calcium > GO:calcium ion binding ; GO:0005509 SP_KW:Calcium channel > GO:calcium channel activity ; GO:0005262 SP_KW:Calcium channel inhibitor > GO:calcium channel inhibitor activity ; GO:0019855 SP_KW:Calcium transport > GO:calcium ion transport ; GO:0006816 SP_KW:Calcium/phospholipid-binding > GO:calcium-dependent phospholipid binding ; GO:0005544 SP_KW:Calmodulin-binding > GO:calmodulin binding ; GO:0005516 SP_KW:Calvin cycle > GO:reductive pentose-phosphate cycle ; GO:0019253 SP_KW:Capsid assembly > GO:viral capsid assembly ; GO:0019069 SP_KW:Capsid maturation > GO:viral procapsid maturation ; GO:0046797 SP_KW:Capsid protein > GO:structural molecule activity ; GO:0005198 SP_KW:Capsid protein > GO:viral capsid ; GO:0019028 SP_KW:Carbohydrate metabolism > GO:carbohydrate metabolism ; GO:0005975 SP_KW:Carbon dioxide fixation > GO:carbon utilization by fixation of carbon dioxide ; GO:0015977 SP_KW:Carboxypeptidase > GO:carboxypeptidase activity ; GO:0004180 SP_KW:Cardiotoxin > GO:pathogenesis ; GO:0009405 SP_KW:Carnitine biosynthesis > GO:carnitine biosynthesis ; GO:0045329 SP_KW:Carotenoid biosynthesis > GO:carotenoid biosynthesis ; GO:0016117 SP_KW:Catecholamine biosynthesis > GO:catecholamine biosynthesis ; GO:0042423 SP_KW:Catecholamine metabolism > GO:catecholamine metabolism ; GO:0006584 SP_KW:Cell adhesion > GO:protein binding ; GO:0005515 SP_KW:Cell adhesion > GO:cell adhesion ; GO:0007155 SP_KW:Cell cycle > GO:cell cycle ; GO:0007049 SP_KW:Cell division > GO:cell division ; GO:0051301 SP_KW:Cell shape > GO:regulation of cell shape ; GO:0008360 SP_KW:Cell wall > GO:cell wall ; GO:0005618 SP_KW:Cellulose biosynthesis > GO:cellulose biosynthesis ; GO:0030244 SP_KW:Cellulose degradation > GO:cellulose catabolism ; GO:0030245 SP_KW:Centromere > GO:chromosome, pericentric region ; GO:0000775 SP_KW:Chaperone > GO:unfolded protein binding ; GO:0051082 SP_KW:Chaperone > GO:protein folding ; GO:0006457 SP_KW:Chemotaxis > GO:chemotaxis ; GO:0006935 SP_KW:Chitin degradation > GO:chitin catabolism ; GO:0006032 SP_KW:Chitin-binding > GO:chitin binding ; GO:0008061 SP_KW:Chloride channel inhibitor > GO:chloride channel inhibitor activity ; GO:0019869 SP_KW:Chlorophyll biosynthesis > GO:chlorophyll biosynthesis ; GO:0015995 SP_KW:Chlorophyll catabolism > GO:chlorophyll catabolism ; GO:0015996 SP_KW:Chloroplast > GO:chloroplast ; GO:0009507 SP_KW:Chlorosome > GO:chlorosome ; GO:0046858 SP_KW:Cholesterol biosynthesis > GO:cholesterol biosynthesis ; GO:0006695 SP_KW:Cholesterol metabolism > GO:cholesterol metabolism ; GO:0008203 SP_KW:Chondrogenesis > GO:cartilage development ; GO:0051216 SP_KW:Chorion > GO:structural constituent of chorion (sensu Insecta) ; GO:0005213 SP_KW:Chromate resistance > GO:response to chromate ; GO:0046687 SP_KW:Chromatin regulator > GO:chromatin modification ; GO:0016568 SP_KW:Chromophore > GO:protein-chromophore linkage ; GO:0018298 SP_KW:Chromosomal protein > GO:chromosome ; GO:0005694 SP_KW:Chromosome partition > GO:chromosome segregation ; GO:0007059 SP_KW:Chylomicron > GO:chylomicron ; GO:0042627 SP_KW:Citrate utilization > GO:tricarboxylate carrier activity ; GO:0005371 SP_KW:Cnidocyst > GO:nematocyst ; GO:0042151 SP_KW:Coated pits > GO:coated pit ; GO:0005905 SP_KW:Cobalamin biosynthesis > GO:cobalamin biosynthesis ; GO:0009236 SP_KW:Cobalt > GO:cobalt ion binding ; GO:0050897 SP_KW:Cobalt transport > GO:cobalt ion transporter activity ; GO:0015087 SP_KW:Cobalt transport > GO:cobalt ion transport ; GO:0006824 SP_KW:Coenzyme A biosynthesis > GO:coenzyme A biosynthesis ; GO:0015937 SP_KW:Coenzyme M biosynthesis > GO:coenzyme M biosynthesis ; GO:0019295 SP_KW:Collagen degradation > GO:collagen catabolism ; GO:0030574 SP_KW:Competence > GO:establishment of competence for transformation ; GO:0030420 SP_KW:Complement alternate pathway > GO:complement activation, alternative pathway ; GO:0006957 SP_KW:Complement pathway > GO:complement activation, classical pathway ; GO:0006958 SP_KW:Cone-rod dystrophy > GO:visual perception ; GO:0007601 SP_KW:Conidiation > GO:conidium formation ; GO:0048315 SP_KW:Conjugation > GO:conjugation ; GO:0000746 SP_KW:Connective tissue > GO:extracellular matrix structural constituent ; GO:0005201 SP_KW:Copper > GO:copper ion binding ; GO:0005507 SP_KW:Copper transport > GO:copper ion transporter activity ; GO:0005375 SP_KW:Copper transport > GO:copper ion transport ; GO:0006825 SP_KW:Copulatory plug > GO:copulation ; GO:0007620 SP_KW:Core protein > GO:viral nucleocapsid ; GO:0019013 SP_KW:Covalent protein-DNA linkage > GO:DNA-protein covalent cross-linking ; GO:0018142 SP_KW:Covalent protein-RNA linkage > GO:RNA-protein covalent cross-linking ; GO:0018144 SP_KW:Cuticle > GO:structural constituent of cuticle ; GO:0042302 SP_KW:Cyanelle > GO:cyanelle ; GO:0009842 SP_KW:Cycloheximide resistance > GO:response to cycloheximide ; GO:0046898 SP_KW:Cyclosporin > GO:peptide binding ; GO:0042277 SP_KW:Cysteine biosynthesis > GO:cysteine biosynthesis ; GO:0019344 SP_KW:Cytadherence > GO:cytoadherence to microvasculature ; GO:0020035 SP_KW:Cytochrome c-type biogenesis > GO:cytochrome complex assembly ; GO:0017004 SP_KW:Cytokine > GO:cytokine activity ; GO:0005125 SP_KW:Cytokine > GO:extracellular space ; GO:0005615 SP_KW:Cytokinin biosynthesis > GO:cytokinin biosynthesis ; GO:0009691 SP_KW:Cytolysis > GO:cytolysis ; GO:0019835 SP_KW:Cytosine metabolism > GO:cytosine metabolism ; GO:0019858 SP_KW:Cytoskeleton > GO:cytoskeleton ; GO:0005856 SP_KW:DNA condensation > GO:mitotic chromosome condensation ; GO:0007076 SP_KW:DNA damage > GO:response to DNA damage stimulus ; GO:0006974 SP_KW:DNA excision > GO:base-excision repair ; GO:0006284 SP_KW:DNA integration > GO:DNA transposition ; GO:0006313 SP_KW:DNA invertase > GO:recombinase activity ; GO:0000150 SP_KW:DNA invertase > GO:DNA binding ; GO:0003677 SP_KW:DNA invertase > GO:DNA recombination ; GO:0006310 SP_KW:DNA packaging > GO:DNA packaging ; GO:0006323 SP_KW:DNA priming > GO:DNA replication, synthesis of RNA primer ; GO:0006269 SP_KW:DNA recombination > GO:DNA recombination ; GO:0006310 SP_KW:DNA repair > GO:DNA repair ; GO:0006281 SP_KW:DNA replication > GO:DNA replication ; GO:0006260 SP_KW:DNA replication inhibitor > GO:negative regulation of DNA replication ; GO:0008156 SP_KW:DNA synthesis > GO:DNA replication ; GO:0006260 SP_KW:DNA-binding > GO:DNA binding ; GO:0003677 SP_KW:DNA-directed DNA polymerase > GO:DNA-directed DNA polymerase activity ; GO:0003887 SP_KW:DNA-directed RNA polymerase > GO:DNA-directed RNA polymerase activity ; GO:0003899 SP_KW:Deafness > GO:sensory perception of sound ; GO:0007605 SP_KW:Decarboxylase > GO:carboxy-lyase activity ; GO:0016831 SP_KW:Defensin > GO:defense response ; GO:0006952 SP_KW:Dehydrin > GO:response to water deprivation ; GO:0009414 SP_KW:Dejerine-Sottas syndrome > GO:mechanosensory behavior ; GO:0007638 SP_KW:Deoxyribonucleotide synthesis > GO:deoxyribonucleotide biosynthesis ; GO:0009263 SP_KW:Detoxification > GO:xenobiotic metabolism ; GO:0006805 SP_KW:Detoxification > GO:response to toxin ; GO:0009636 SP_KW:Developmental protein > GO:development ; GO:0007275 SP_KW:Diaminopimelate biosynthesis > GO:diaminopimelate biosynthesis ; GO:0019877 SP_KW:Differentiation > GO:cell differentiation ; GO:0030154 SP_KW:Digestion > GO:digestion ; GO:0007586 SP_KW:Dioxygenase > GO:oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen ; GO:0016702 SP_KW:Dipeptidase > GO:dipeptidase activity ; GO:0016805 SP_KW:Dynein > GO:motor activity ; GO:0003774 SP_KW:Dynein > GO:dynein complex ; GO:0030286 SP_KW:ER-Golgi transport > GO:ER to Golgi transport ; GO:0006888 SP_KW:Egg white > GO:extracellular space ; GO:0005615 SP_KW:Electron transport > GO:electron transport ; GO:0006118 SP_KW:Elongation factor > GO:translation elongation factor activity ; GO:0003746 SP_KW:Endocytosis > GO:endocytosis ; GO:0006897 SP_KW:Endonuclease > GO:endonuclease activity ; GO:0004519 SP_KW:Endoplasmic reticulum > GO:endoplasmic reticulum ; GO:0005783 SP_KW:Endorphin > GO:neuropeptide signaling pathway ; GO:0007218 SP_KW:Enterobactin biosynthesis > GO:enterobactin biosynthesis ; GO:0009239 SP_KW:Enterotoxin > GO:pathogenesis ; GO:0009405 SP_KW:Envelope protein > GO:viral envelope ; GO:0019031 SP_KW:Erythrocyte maturation > GO:erythrocyte maturation ; GO:0043249 SP_KW:Ethylene biosynthesis > GO:ethylene biosynthesis ; GO:0009693 SP_KW:Excision nuclease > GO:nuclease activity ; GO:0004518 SP_KW:Excision nuclease > GO:nucleotide-excision repair ; GO:0006289 SP_KW:Exocytosis > GO:exocytosis ; GO:0006887 SP_KW:Exonuclease > GO:exonuclease activity ; GO:0004527 SP_KW:Exopolysaccharide synthesis > GO:polysaccharide biosynthesis ; GO:0000271 SP_KW:Exosome > GO:exosome (RNase complex) ; GO:0000178 SP_KW:Extracellular matrix > GO:extracellular matrix (sensu Metazoa) ; GO:0005578 SP_KW:Eye lens protein > GO:structural constituent of eye lens ; GO:0005212 SP_KW:Fatty acid biosynthesis > GO:fatty acid biosynthesis ; GO:0006633 SP_KW:Fatty acid metabolism > GO:fatty acid metabolism ; GO:0006631 SP_KW:Feather > GO:structural constituent of cutaneous appendage ; GO:0030281 SP_KW:Fertilization > GO:fertilization (sensu Metazoa) ; GO:0007338 SP_KW:Fibrinolysis > GO:fibrinolysis ; GO:0042730 SP_KW:Fimbria > GO:fimbrium ; GO:0009289 SP_KW:Flagellar rotation > GO:ciliary or flagellar motility ; GO:0001539 SP_KW:Flagellum > GO:flagellum ; GO:0019861 SP_KW:Flavonoid biosynthesis > GO:flavonoid biosynthesis ; GO:0009813 SP_KW:Flowering > GO:flower development ; GO:0009908 SP_KW:Folate biosynthesis > GO:folic acid biosynthesis ; GO:0046656 SP_KW:Folate-binding > GO:folic acid binding ; GO:0005542 SP_KW:Fruit ripening > GO:ripening ; GO:0009835 SP_KW:Fucose metabolism > GO:fucose metabolism ; GO:0006004 SP_KW:Fungicide > GO:xenobiotic metabolism ; GO:0006805 SP_KW:Fungicide > GO:defense response to fungi ; GO:0050832 SP_KW:G-protein coupled receptor > GO:G-protein coupled receptor activity ; GO:0004930 SP_KW:G-protein coupled receptor > GO:G-protein coupled receptor protein signaling pathway ; GO:0007186 SP_KW:GM2-gangliosidosis > GO:glycosphingolipid metabolism ; GO:0006687 SP_KW:GMP biosynthesis > GO:GMP biosynthesis ; GO:0006177 SP_KW:GTP-binding > GO:GTP binding ; GO:0005525 SP_KW:GTPase activation > GO:GTPase activator activity ; GO:0005096 SP_KW:Galactitol metabolism > GO:galactitol metabolism ; GO:0019402 SP_KW:Galactose metabolism > GO:galactose metabolism ; GO:0006012 SP_KW:Gap junction > GO:gap junction ; GO:0005921 SP_KW:Gap protein > GO:segmentation ; GO:0035282 SP_KW:Gaseous exchange > GO:respiratory gaseous exchange ; GO:0007585 SP_KW:Gastrulation > GO:gastrulation ; GO:0007369 SP_KW:Gaucher disease > GO:lysosome organization and biogenesis ; GO:0007040 SP_KW:Germination > GO:organismal physiological process ; GO:0050874 SP_KW:Gluconate utilization > GO:D-gluconate metabolism ; GO:0019521 SP_KW:Gluconeogenesis > GO:gluconeogenesis ; GO:0006094 SP_KW:Glucose metabolism > GO:glucose metabolism ; GO:0006006 SP_KW:Glutamate biosynthesis > GO:glutamate biosynthesis ; GO:0006537 SP_KW:Glutamine amidotransferase > GO:glutamine metabolism ; GO:0006541 SP_KW:Glutaricaciduria > GO:electron transport ; GO:0006118 SP_KW:Glutathione biosynthesis > GO:glutathione biosynthesis ; GO:0006750 SP_KW:Glycerol metabolism > GO:glycerol metabolism ; GO:0006071 SP_KW:Glycogen biosynthesis > GO:glycogen biosynthesis ; GO:0005978 SP_KW:Glycogen metabolism > GO:glycogen metabolism ; GO:0005977 SP_KW:Glycogen storage disease > GO:glycogen metabolism ; GO:0005977 SP_KW:Glycolate pathway > GO:oxidative photosynthetic carbon pathway ; GO:0009854 SP_KW:Glycolysis > GO:glycolysis ; GO:0006096 SP_KW:Glycosidase > GO:hydrolase activity, acting on glycosyl bonds ; GO:0016798 SP_KW:Glycosidase > GO:carbohydrate metabolism ; GO:0005975 SP_KW:Glycosome > GO:glycosome ; GO:0020015 SP_KW:Glycosyltransferase > GO:transferase activity, transferring glycosyl groups ; GO:0016757 SP_KW:Glyoxylate bypass > GO:glyoxylate cycle ; GO:0006097 SP_KW:Glyoxysome > GO:glyoxysome ; GO:0009514 SP_KW:Golgi stack > GO:Golgi stack ; GO:0005795 SP_KW:Gonadal differentiation > GO:gonadal mesoderm development ; GO:0007506 SP_KW:Growth arrest > GO:cell cycle arrest ; GO:0007050 SP_KW:Growth factor > GO:growth factor activity ; GO:0008083 SP_KW:Growth factor binding > GO:growth factor binding ; GO:0019838 SP_KW:Growth regulation > GO:regulation of cell growth ; GO:0001558 SP_KW:Guanine-nucleotide releasing factor > GO:guanyl-nucleotide exchange factor activity ; GO:0005085 SP_KW:HDL > GO:lipid transporter activity ; GO:0005319 SP_KW:Heat shock > GO:protein folding ; GO:0006457 SP_KW:Heat shock > GO:response to unfolded protein ; GO:0006986 SP_KW:Helicase > GO:helicase activity ; GO:0004386 SP_KW:Heme biosynthesis > GO:heme biosynthesis ; GO:0006783 SP_KW:Hemoglobin-binding > GO:hemoglobin binding ; GO:0030492 SP_KW:Hemolymph clotting > GO:hemolymph coagulation ; GO:0042381 SP_KW:Hemolysis > GO:hemolysis ; GO:0019836 SP_KW:Hemostasis > GO:hemostasis ; GO:0007599 SP_KW:Heparin-binding > GO:heparin binding ; GO:0008201 SP_KW:Herbicide resistance > GO:response to herbicide ; GO:0009635 SP_KW:Heterocyst > GO:heterocyst differentiation ; GO:0043158 SP_KW:Hexon protein > GO:structural molecule activity ; GO:0005198 SP_KW:Hexon protein > GO:virion ; GO:0019012 SP_KW:Hexon-associated protein > GO:hexon binding ; GO:0031423 SP_KW:Hibernation > GO:hibernation ; GO:0042750 SP_KW:Histidine biosynthesis > GO:histidine biosynthesis ; GO:0000105 SP_KW:Histidine metabolism > GO:histidine metabolism ; GO:0006547 SP_KW:Homeobox > GO:DNA binding ; GO:0003677 SP_KW:Hormone > GO:hormone activity ; GO:0005179 SP_KW:Hyaluronic acid > GO:hyaluronic acid binding ; GO:0005540 SP_KW:Hydrogen ion transport > GO:hydrogen ion transporter activity ; GO:0015078 SP_KW:Hydrogen ion transport > GO:proton transport ; GO:0015992 SP_KW:Hydrogen peroxide > GO:hydrogen peroxide catabolism ; GO:0042744 SP_KW:Hydrogenosome > GO:hydrogenosome ; GO:0042566 SP_KW:Hydrolase > GO:hydrolase activity ; GO:0016787 SP_KW:Hypersensitive response > GO:hypersensitive response ; GO:0009626 SP_KW:Hypotensive agent > GO:regulation of blood pressure ; GO:0008217 SP_KW:Hypusine biosynthesis > GO:hypusine biosynthesis from peptidyl-lysine ; GO:0008612 SP_KW:Ice nucleation > GO:ice binding ; GO:0050825 SP_KW:Ice nucleation > GO:pathogenesis ; GO:0009405 SP_KW:IgA-binding protein > GO:IgA binding ; GO:0019862 SP_KW:IgE-binding protein > GO:IgE binding ; GO:0019863 SP_KW:IgG-binding protein > GO:IgG binding ; GO:0019864 SP_KW:Immune response > GO:immune response ; GO:0006955 SP_KW:Immunoglobulin C region > GO:antigen binding ; GO:0003823 SP_KW:Immunoglobulin V region > GO:antigen binding ; GO:0003823 SP_KW:Inflammatory response > GO:inflammatory response ; GO:0006954 SP_KW:Initiation factor > GO:translation initiation factor activity ; GO:0003743 SP_KW:Inner membrane > GO:inner membrane ; GO:0019866 SP_KW:Inositol biosynthesis > GO:myo-inositol biosynthesis ; GO:0006021 SP_KW:Integrin > GO:integrin-mediated signaling pathway ; GO:0007229 SP_KW:Interferon antiviral system evasion > GO:viral evasion of host immune response ; GO:0030683 SP_KW:Interferon induction > GO:immune response ; GO:0006955 SP_KW:Intermediate filament > GO:intermediate filament ; GO:0005882 SP_KW:Intron homing > GO:intron homing ; GO:0006314 SP_KW:Ion transport > GO:ion transport ; GO:0006811 SP_KW:Ionic channel > GO:ion channel activity ; GO:0005216 SP_KW:Ionic channel inhibitor > GO:ion channel inhibitor activity ; GO:0008200 SP_KW:Iron > GO:iron ion binding ; GO:0005506 SP_KW:Iron storage > GO:iron ion homeostasis ; GO:0006879 SP_KW:Iron transport > GO:iron ion transport ; GO:0006826 SP_KW:Iron-sulfur > GO:iron ion binding ; GO:0005506 SP_KW:Iron-sulfur > GO:iron-sulfur cluster binding ; GO:0051536 SP_KW:Isoleucine biosynthesis > GO:isoleucine biosynthesis ; GO:0009097 SP_KW:Isomerase > GO:isomerase activity ; GO:0016853 SP_KW:Isoprene biosynthesis > GO:isoprenoid biosynthesis ; GO:0008299 SP_KW:Karyogamy > GO:karyogamy ; GO:0000741 SP_KW:Keratin > GO:intermediate filament ; GO:0005882 SP_KW:Keratinization > GO:keratinization ; GO:0031424 SP_KW:Kinase > GO:kinase activity ; GO:0016301 SP_KW:Kinetoplast > GO:kinetoplast ; GO:0020023 SP_KW:LDL > GO:lipid transporter activity ; GO:0005319 SP_KW:Lactation > GO:lactation ; GO:0007595 SP_KW:Lactose biosynthesis > GO:lactose biosynthesis ; GO:0005989 SP_KW:Lactose metabolism > GO:lactose metabolism ; GO:0005988 SP_KW:Lantibiotic > GO:receptor binding ; GO:0005102 SP_KW:Lantibiotic > GO:cytolysis ; GO:0019835 SP_KW:Lectin > GO:sugar binding ; GO:0005529 SP_KW:Leucine biosynthesis > GO:leucine biosynthesis ; GO:0009098 SP_KW:Leukotriene biosynthesis > GO:leukotriene biosynthesis ; GO:0019370 SP_KW:Ligase > GO:ligase activity ; GO:0016874 SP_KW:Light-harvesting polypeptide > GO:light-harvesting complex ; GO:0030076 SP_KW:Lignin biosynthesis > GO:lignin biosynthesis ; GO:0009809 SP_KW:Lignin degradation > GO:lignin catabolism ; GO:0046274 SP_KW:Lipid A biosynthesis > GO:lipid A biosynthesis ; GO:0009245 SP_KW:Lipid degradation > GO:lipid catabolism ; GO:0016042 SP_KW:Lipid metabolism > GO:lipid metabolism ; GO:0006629 SP_KW:Lipid synthesis > GO:lipid biosynthesis ; GO:0008610 SP_KW:Lipid transport > GO:lipid transport ; GO:0006869 SP_KW:Lipid-binding > GO:lipid binding ; GO:0008289 SP_KW:Lipocalin > GO:transport ; GO:0006810 SP_KW:Lipopolysaccharide biosynthesis > GO:lipopolysaccharide biosynthesis ; GO:0009103 SP_KW:Lipoyl > GO:lipoic acid binding ; GO:0031405 SP_KW:Luminescence > GO:bioluminescence ; GO:0008218 SP_KW:Lyase > GO:lyase activity ; GO:0016829 SP_KW:Lysine biosynthesis > GO:lysine biosynthesis ; GO:0009085 SP_KW:Lysosome > GO:lysosome ; GO:0005764 SP_KW:MHC I > GO:MHC class I receptor activity ; GO:0030106 SP_KW:MHC I > GO:antigen presentation, endogenous antigen ; GO:0019883 SP_KW:MHC I > GO:antigen processing, endogenous antigen via MHC class I ; GO:0019885 SP_KW:MHC II > GO:MHC class II receptor activity ; GO:0045012 SP_KW:MHC II > GO:antigen presentation, exogenous antigen ; GO:0019884 SP_KW:MHC II > GO:antigen processing, exogenous antigen via MHC class II ; GO:0019886 SP_KW:Magnesium > GO:magnesium ion binding ; GO:0000287 SP_KW:Maltose metabolism > GO:maltose metabolism ; GO:0000023 SP_KW:Manganese > GO:manganese ion binding ; GO:0030145 SP_KW:Mannose-binding > GO:mannose binding ; GO:0005537 SP_KW:Maple syrup urine disease > GO:alpha-ketoglutarate dehydrogenase complex (sensu Eukaryota) ; GO:0005947 SP_KW:Mast cell degranulation > GO:mast cell degranulation ; GO:0043303 SP_KW:Matrix protein > GO:structural molecule activity ; GO:0005198 SP_KW:Meiosis > GO:meiosis ; GO:0007126 SP_KW:Melanin biosynthesis > GO:melanin biosynthesis from tyrosine ; GO:0006583 SP_KW:Melatonin biosynthesis > GO:neuropeptide hormone activity ; GO:0005184 SP_KW:Melatonin biosynthesis > GO:melatonin biosynthesis ; GO:0030187 SP_KW:Melatonin biosynthesis > GO:rhythmic process ; GO:0048511 SP_KW:Membrane > GO:membrane ; GO:0016020 SP_KW:Membrane attack complex > GO:membrane attack complex ; GO:0005579 SP_KW:Menaquinone biosynthesis > GO:menaquinone biosynthesis ; GO:0009234 SP_KW:Mercuric resistance > GO:response to mercury ion ; GO:0046689 SP_KW:Metal-binding > GO:metal ion binding ; GO:0046872 SP_KW:Metal-thiolate cluster > GO:metal ion binding ; GO:0046872 SP_KW:Metalloenzyme inhibitor > GO:enzyme inhibitor activity ; GO:0004857 SP_KW:Metalloprotease > GO:metallopeptidase activity ; GO:0008237 SP_KW:Metalloprotease inhibitor > GO:metalloendopeptidase inhibitor activity ; GO:0008191 SP_KW:Methanogenesis > GO:methanogenesis ; GO:0015948 SP_KW:Methanol utilization > GO:methanol metabolism ; GO:0015945 SP_KW:Methionine biosynthesis > GO:methionine biosynthesis ; GO:0009086 SP_KW:Methotrexate resistance > GO:response to methotrexate ; GO:0031427 SP_KW:Methyltransferase > GO:methyltransferase activity ; GO:0008168 SP_KW:Microsome > GO:microsome ; GO:0005792 SP_KW:Microtubule > GO:microtubule ; GO:0005874 SP_KW:Mineral balance > GO:regulation of bone mineralization ; GO:0030500 SP_KW:Mitochondrion > GO:mitochondrion ; GO:0005739 SP_KW:Mitogen > GO:growth factor activity ; GO:0008083 SP_KW:Mitogen > GO:regulation of progression through cell cycle ; GO:0000074 SP_KW:Mitogen > GO:cell proliferation ; GO:0008283 SP_KW:Mitosis > GO:mitosis ; GO:0007067 SP_KW:Molybdenum > GO:molybdenum ion binding ; GO:0030151 SP_KW:Molybdenum cofactor biosynthesis > GO:Mo-molybdopterin cofactor biosynthesis ; GO:0006777 SP_KW:Monoclonal antibody > GO:antigen binding ; GO:0003823 SP_KW:Monooxygenase > GO:monooxygenase activity ; GO:0004497 SP_KW:Morphogen > GO:morphogen activity ; GO:0016015 SP_KW:Morphogen > GO:morphogenesis ; GO:0009653 SP_KW:Motor protein > GO:motor activity ; GO:0003774 SP_KW:Mucopolysaccharidosis > GO:glycosaminoglycan metabolism ; GO:0030203 SP_KW:Multifunctional enzyme > GO:catalytic activity ; GO:0003824 SP_KW:Muscle protein > GO:muscle development ; GO:0007517 SP_KW:Myogenesis > GO:striated muscle development ; GO:0007519 SP_KW:Myosin > GO:myosin ; GO:0016459 SP_KW:Neurodegeneration > GO:cell death ; GO:0008219 SP_KW:Neurogenesis > GO:nervous system development ; GO:0007399 SP_KW:Neuropeptide > GO:neuropeptide signaling pathway ; GO:0007218 SP_KW:Neurotoxin > GO:pathogenesis ; GO:0009405 SP_KW:Neurotransmitter > GO:synaptic transmission ; GO:0007268 SP_KW:Neurotransmitter biosynthesis > GO:synaptic transmission ; GO:0007268 SP_KW:Neurotransmitter biosynthesis > GO:neurotransmitter biosynthesis ; GO:0042136 SP_KW:Neurotransmitter degradation > GO:neurotransmitter catabolism ; GO:0042135 SP_KW:Neurotransmitter transport > GO:neurotransmitter transport ; GO:0006836 SP_KW:Nickel > GO:nickel ion binding ; GO:0016151 SP_KW:Nickel transport > GO:nickel ion transport ; GO:0015675 SP_KW:Nitrate assimilation > GO:nitrate assimilation ; GO:0042128 SP_KW:Nitrogen fixation > GO:nitrogen fixation ; GO:0009399 SP_KW:Nodulation > GO:nodulation ; GO:0009877 SP_KW:Noncapsid protein > GO:virion ; GO:0019012 SP_KW:Nonsense-mediated mRNA decay > GO:mRNA catabolism, nonsense-mediated decay ; GO:0000184 SP_KW:Notch signaling pathway > GO:Notch signaling pathway ; GO:0007219 SP_KW:Nuclear pore complex > GO:nuclear pore ; GO:0005643 SP_KW:Nuclear protein > GO:nucleus ; GO:0005634 SP_KW:Nuclease > GO:nuclease activity ; GO:0004518 SP_KW:Nucleocapsid > GO:viral nucleocapsid ; GO:0019013 SP_KW:Nucleosome core > GO:nucleosome ; GO:0000786 SP_KW:Nucleotide biosynthesis > GO:nucleotide biosynthesis ; GO:0009165 SP_KW:Nucleotide metabolism > GO:nucleotide metabolism ; GO:0009117 SP_KW:Nucleotide-binding > GO:nucleotide binding ; GO:0000166 SP_KW:Nucleotidyltransferase > GO:nucleotidyltransferase activity ; GO:0016779 SP_KW:Nylon degradation > GO:nylon catabolism ; GO:0019876 SP_KW:Oil body > GO:lipid storage body (sensu Viridiplantae) ; GO:0012511 SP_KW:Olfaction > GO:sensory perception of smell ; GO:0007608 SP_KW:One-carbon metabolism > GO:one-carbon compound metabolism ; GO:0006730 SP_KW:Oogenesis > GO:oogenesis ; GO:0048477 SP_KW:Opioid peptide > GO:opioid peptide activity ; GO:0001515 SP_KW:Osteogenesis > GO:ossification ; GO:0001503 SP_KW:Outer membrane > GO:outer membrane ; GO:0019867 SP_KW:Oxidoreductase > GO:oxidoreductase activity ; GO:0016491 SP_KW:Oxygen transport > GO:oxygen transporter activity ; GO:0005344 SP_KW:Oxygen transport > GO:oxygen transport ; GO:0015671 SP_KW:PHA biosynthesis > GO:poly(3-hydroxyalkanoate) biosynthesis ; GO:0042621 SP_KW:PHB biosynthesis > GO:poly-hydroxybutyrate biosynthesis ; GO:0042619 SP_KW:PQQ biosynthesis > GO:pyrroloquinoline quinone biosynthesis ; GO:0018189 SP_KW:Pair-rule protein > GO:development ; GO:0007275 SP_KW:Pair-rule protein > GO:periodic partitioning by pair rule gene ; GO:0007366 SP_KW:Pantothenate biosynthesis > GO:pantothenate biosynthesis ; GO:0015940 SP_KW:Pathogenesis-related protein > GO:response to biotic stimulus ; GO:0009607 SP_KW:Pentose shunt > GO:pentose-phosphate shunt ; GO:0006098 SP_KW:Peptide transport > GO:oligopeptide transporter activity ; GO:0015198 SP_KW:Peptide transport > GO:oligopeptide transport ; GO:0006857 SP_KW:Peptidoglycan synthesis > GO:peptidoglycan biosynthesis ; GO:0009252 SP_KW:Periplasmic > GO:periplasmic space ; GO:0042597 SP_KW:Peroxidase > GO:peroxidase activity ; GO:0004601 SP_KW:Peroxisome > GO:peroxisome ; GO:0005777 SP_KW:Phage lysis protein > GO:cell wall catabolism ; GO:0016998 SP_KW:Phage lysis protein > GO:cytolysis ; GO:0019835 SP_KW:Phage maturation > GO:viral assembly, maturation, egress, and release ; GO:0019067 SP_KW:Phage recognition > GO:detection of virus ; GO:0009597 SP_KW:Phage recognition > GO:viral entry into host cell ; GO:0046718 SP_KW:Phagocytosis > GO:phagocytosis ; GO:0006909 SP_KW:Phenylalanine biosynthesis > GO:L-phenylalanine biosynthesis ; GO:0009094 SP_KW:Phenylalanine catabolism > GO:L-phenylalanine catabolism ; GO:0006559 SP_KW:Phenylketonuria > GO:L-phenylalanine catabolism ; GO:0006559 SP_KW:Phenylpropanoid metabolism > GO:phenylpropanoid metabolism ; GO:0009698 SP_KW:Pheromone > GO:pheromone activity ; GO:0005186 SP_KW:Pheromone response > GO:response to pheromone ; GO:0019236 SP_KW:Pheromone-binding > GO:pheromone binding ; GO:0005550 SP_KW:Phorbol-ester binding > GO:diacylglycerol binding ; GO:0019992 SP_KW:Phosphate transport > GO:phosphate transport ; GO:0006817 SP_KW:Phospholipase A2 inhibitor > GO:phospholipase A2 inhibitor activity ; GO:0019834 SP_KW:Phospholipid biosynthesis > GO:phospholipid biosynthesis ; GO:0008654 SP_KW:Phospholipid degradation > GO:phospholipid catabolism ; GO:0009395 SP_KW:Phosphotransferase system > GO:phosphoenolpyruvate-dependent sugar phosphotransferase system ; GO:0009401 SP_KW:Photoprotein > GO:bioluminescence ; GO:0008218 SP_KW:Photorespiration > GO:photorespiration ; GO:0009853 SP_KW:Photosynthesis > GO:photosynthesis ; GO:0015979 SP_KW:Photosystem I > GO:photosystem I ; GO:0009522 SP_KW:Photosystem II > GO:photosystem II ; GO:0009523 SP_KW:Phycobilisome > GO:phycobilisome ; GO:0030089 SP_KW:Phytochrome > GO:G-protein coupled photoreceptor activity ; GO:0008020 SP_KW:Phytochrome > GO:red, far-red light phototransduction ; GO:0009585 SP_KW:Phytochrome signaling pathway > GO:red, far-red light phototransduction ; GO:0009585 SP_KW:Phytochrome signaling pathway > GO:red or far red light signaling pathway ; GO:0010017 SP_KW:Pigment > GO:pigment binding ; GO:0031409 SP_KW:Plant defense > GO:defense response ; GO:0006952 SP_KW:Plant toxin > GO:pathogenesis ; GO:0009405 SP_KW:Plant toxin > GO:extracellular region ; GO:0005576 SP_KW:Plasma > GO:extracellular space ; GO:0005615 SP_KW:Plasmid copy control > GO:plasmid maintenance ; GO:0006276 SP_KW:Plasmid partition > GO:plasmid partitioning ; GO:0030541 SP_KW:Plasminogen activation > GO:plasminogen activator activity ; GO:0008243 SP_KW:Plastoquinone > GO:oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor ; GO:0016655 SP_KW:Plastoquinone > GO:electron transport ; GO:0006118 SP_KW:Plastoquinone > GO:photosystem II ; GO:0009523 SP_KW:Polyamine biosynthesis > GO:polyamine biosynthesis ; GO:0006596 SP_KW:Polysaccharide degradation > GO:polysaccharide catabolism ; GO:0000272 SP_KW:Polysaccharide transport > GO:polysaccharide transport ; GO:0015774 SP_KW:Porin > GO:porin activity ; GO:0015288 SP_KW:Porin > GO:integral to membrane ; GO:0016021 SP_KW:Porin > GO:outer membrane ; GO:0019867 SP_KW:Porphyrin biosynthesis > GO:porphyrin biosynthesis ; GO:0006779 SP_KW:Postsynaptic membrane > GO:postsynaptic membrane ; GO:0045211 SP_KW:Postsynaptic neurotoxin > GO:acetylcholine receptor inhibitor activity ; GO:0030550 SP_KW:Postsynaptic neurotoxin > GO:synaptic transmission ; GO:0007268 SP_KW:Postsynaptic neurotoxin > GO:pathogenesis ; GO:0009405 SP_KW:Postsynaptic neurotoxin > GO:postsynaptic membrane ; GO:0045211 SP_KW:Potassium > GO:potassium ion binding ; GO:0030955 SP_KW:Potassium channel inhibitor > GO:potassium channel inhibitor activity ; GO:0019870 SP_KW:Potassium transport > GO:potassium ion transport ; GO:0006813 SP_KW:Pregnancy > GO:pregnancy ; GO:0007565 SP_KW:Prenyltransferase > GO:prenyltransferase activity ; GO:0004659 SP_KW:Presynaptic neurotoxin > GO:synaptic transmission ; GO:0007268 SP_KW:Presynaptic neurotoxin > GO:pathogenesis ; GO:0009405 SP_KW:Presynaptic neurotoxin > GO:presynaptic membrane ; GO:0042734 SP_KW:Primosome > GO:DNA replication, synthesis of RNA primer ; GO:0006269 SP_KW:Primosome > GO:alpha DNA polymerase:primase complex ; GO:0005658 SP_KW:Proline biosynthesis > GO:proline biosynthesis ; GO:0006561 SP_KW:Proline metabolism > GO:proline metabolism ; GO:0006560 SP_KW:Prostaglandin biosynthesis > GO:prostaglandin biosynthesis ; GO:0001516 SP_KW:Prostaglandin metabolism > GO:prostaglandin metabolism ; GO:0006693 SP_KW:Protease > GO:peptidase activity ; GO:0008233 SP_KW:Protease inhibitor > GO:endopeptidase inhibitor activity ; GO:0004866 SP_KW:Proteasome > GO:cytosol ; GO:0005829 SP_KW:Proteasome > GO:protein complex ; GO:0043234 SP_KW:Protein biosynthesis > GO:protein biosynthesis ; GO:0006412 SP_KW:Protein kinase inhibitor > GO:protein kinase inhibitor activity ; GO:0004860 SP_KW:Protein phosphatase > GO:phosphoprotein phosphatase activity ; GO:0004721 SP_KW:Protein phosphatase inhibitor > GO:protein phosphatase inhibitor activity ; GO:0004864 SP_KW:Protein splicing > GO:protein splicing ; GO:0030908 SP_KW:Protein synthesis inhibitor > GO:negative regulation of protein biosynthesis ; GO:0017148 SP_KW:Protein transport > GO:protein transport ; GO:0015031 SP_KW:Prothrombin activator > GO:prothrombin activator activity ; GO:0030567 SP_KW:Pseudohermaphroditism > GO:sex determination ; GO:0007530 SP_KW:Purine biosynthesis > GO:purine nucleotide biosynthesis ; GO:0006164 SP_KW:Purine metabolism > GO:purine base metabolism ; GO:0006144 SP_KW:Purine salvage > GO:purine ribonucleoside salvage ; GO:0006166 SP_KW:Putrescine biosynthesis > GO:putrescine biosynthesis ; GO:0009446 SP_KW:Pyridine nucleotide biosynthesis > GO:pyridine nucleotide biosynthesis ; GO:0019363 SP_KW:Pyridoxine biosynthesis > GO:pyridoxine biosynthesis ; GO:0008615 SP_KW:Pyrimidine biosynthesis > GO:pyrimidine nucleotide biosynthesis ; GO:0006221 SP_KW:Pyrogen > GO:fever ; GO:0001660 SP_KW:Pyrokinin > GO:neuropeptide hormone activity ; GO:0005184 SP_KW:Pyrokinin > GO:neuropeptide signaling pathway ; GO:0007218 SP_KW:Queuosine biosynthesis > GO:queuosine biosynthesis ; GO:0008616 SP_KW:Quinate metabolism > GO:quinate metabolism ; GO:0019630 SP_KW:Quinone > GO:quinone binding ; GO:0048038 SP_KW:Quorum sensing > GO:quorum sensing ; GO:0009372 SP_KW:RNA repair > GO:RNA repair ; GO:0042245 SP_KW:RNA replication > GO:transcription, RNA-dependent ; GO:0006410 SP_KW:RNA-binding > GO:RNA binding ; GO:0003723 SP_KW:RNA-directed DNA polymerase > GO:RNA-directed DNA polymerase activity ; GO:0003964 SP_KW:RNA-directed RNA polymerase > GO:RNA-directed RNA polymerase activity ; GO:0003968 SP_KW:Reaction center > GO:reaction center (sensu Proteobacteria) ; GO:0030090 SP_KW:Receptor > GO:receptor activity ; GO:0004872 SP_KW:Respiratory chain > GO:mitochondrial electron transport chain ; GO:0005746 SP_KW:Restriction system > GO:DNA restriction-modification system ; GO:0009307 SP_KW:Retinal protein > GO:phototransduction ; GO:0007602 SP_KW:Retinitis pigmentosa > GO:visual perception ; GO:0007601 SP_KW:Retinol-binding > GO:retinol binding ; GO:0019841 SP_KW:Rhamnose metabolism > GO:rhamnose metabolism ; GO:0019299 SP_KW:Riboflavin biosynthesis > GO:riboflavin biosynthesis ; GO:0009231 SP_KW:Ribonucleoprotein > GO:ribonucleoprotein complex ; GO:0030529 SP_KW:Ribosomal protein > GO:structural constituent of ribosome ; GO:0003735 SP_KW:Ribosome biogenesis > GO:ribosome biogenesis ; GO:0007046 SP_KW:Rotamase > GO:peptidyl-prolyl cis-trans isomerase activity ; GO:0003755 SP_KW:Rotamase > GO:protein folding ; GO:0006457 SP_KW:S-layer > GO:S-layer ; GO:0030115 SP_KW:SOS mutagenesis > GO:mutagenesis ; GO:0006280 SP_KW:SOS response > GO:DNA repair ; GO:0006281 SP_KW:SOS response > GO:SOS response ; GO:0009432 SP_KW:Sarcoplasmic reticulum > GO:sarcoplasmic reticulum ; GO:0016529 SP_KW:Seed storage protein > GO:nutrient reservoir activity ; GO:0045735 SP_KW:Segmentation polarity protein > GO:segment polarity determination ; GO:0007367 SP_KW:Selectin > GO:sugar binding ; GO:0005529 SP_KW:Selenium > GO:selenium binding ; GO:0008430 SP_KW:Sensory transduction > GO:sensory perception ; GO:0007600 SP_KW:Septation > GO:barrier septum formation ; GO:0000917 SP_KW:Serine biosynthesis > GO:L-serine biosynthesis ; GO:0006564 SP_KW:Serine esterase > GO:serine esterase activity ; GO:0004759 SP_KW:Serine protease > GO:serine-type endopeptidase activity ; GO:0004252 SP_KW:Serine protease inhibitor > GO:serine-type endopeptidase inhibitor activity ; GO:0004867 SP_KW:Serine/threonine-protein kinase > GO:protein serine/threonine kinase activity ; GO:0004674 SP_KW:Serotonin biosynthesis > GO:serotonin biosynthesis from tryptophan ; GO:0006587 SP_KW:Serpin > GO:serine-type endopeptidase inhibitor activity ; GO:0004867 SP_KW:Sexual differentiation > GO:sex differentiation ; GO:0007548 SP_KW:Sigma factor > GO:sigma factor activity ; GO:0016987 SP_KW:Sigma factor > GO:regulation of transcription, DNA-dependent ; GO:0006355 SP_KW:Signal recognition particle > GO:signal recognition particle (sensu Eukaryota) ; GO:0005786 SP_KW:Signal transduction inhibitor > GO:negative regulation of signal transduction ; GO:0009968 SP_KW:Signalosome > GO:signalosome complex ; GO:0008180 SP_KW:Sodium > GO:sodium ion binding ; GO:0031402 SP_KW:Sodium channel inhibitor > GO:sodium channel inhibitor activity ; GO:0019871 SP_KW:Sodium transport > GO:sodium ion transport ; GO:0006814 SP_KW:Sodium/potassium transport > GO:potassium ion transport ; GO:0006813 SP_KW:Sodium/potassium transport > GO:sodium ion transport ; GO:0006814 SP_KW:Spermatogenesis > GO:spermatogenesis ; GO:0007283 SP_KW:Spermidine biosynthesis > GO:spermidine biosynthesis ; GO:0008295 SP_KW:Sphingolipid metabolism > GO:sphingolipid metabolism ; GO:0006665 SP_KW:Spliceosome > GO:spliceosome complex ; GO:0005681 SP_KW:Sporulation > GO:sporulation ; GO:0030435 SP_KW:Starch biosynthesis > GO:starch biosynthesis ; GO:0019252 SP_KW:Steroid biosynthesis > GO:steroid biosynthesis ; GO:0006694 SP_KW:Steroid metabolism > GO:steroid metabolism ; GO:0008202 SP_KW:Steroid-binding > GO:steroid binding ; GO:0005496 SP_KW:Steroidogenesis > GO:C21-steroid hormone biosynthesis ; GO:0006700 SP_KW:Sterol biosynthesis > GO:sterol biosynthesis ; GO:0016126 SP_KW:Storage protein > GO:nutrient reservoir activity ; GO:0045735 SP_KW:Streptomycin biosynthesis > GO:streptomycin biosynthesis ; GO:0019872 SP_KW:Structural protein > GO:structural molecule activity ; GO:0005198 SP_KW:Sugar transport > GO:sugar porter activity ; GO:0005351 SP_KW:Sulfate respiration > GO:anaerobic respiration ; GO:0009061 SP_KW:Sulfate transport > GO:sulfate transport ; GO:0008272 SP_KW:Surface film > GO:regulation of liquid surface tension ; GO:0050828 SP_KW:Symport > GO:symporter activity ; GO:0015293 SP_KW:Synapse > GO:synapse ; GO:0045202 SP_KW:Synaptosome > GO:synaptosome ; GO:0019717 SP_KW:Tachykinin > GO:receptor binding ; GO:0005102 SP_KW:Taxol biosynthesis > GO:paclitaxel biosynthesis ; GO:0042617 SP_KW:Tegument protein > GO:viral tegument ; GO:0019033 SP_KW:Teichoic acid biosynthesis > GO:teichoic acid biosynthesis ; GO:0019350 SP_KW:Tellurium resistance > GO:response to tellurium ion ; GO:0046690 SP_KW:Telomere > GO:telomere maintenance ; GO:0000723 SP_KW:Telomere > GO:chromosome, telomeric region ; GO:0000781 SP_KW:Terminal addition > GO:DNA nucleotidylexotransferase activity ; GO:0003912 SP_KW:Terminal addition > GO:DNA modification ; GO:0006304 SP_KW:Tetrahydrobiopterin biosynthesis > GO:tetrahydrobiopterin biosynthesis ; GO:0006729 SP_KW:Thiamine biosynthesis > GO:thiamin biosynthesis ; GO:0009228 SP_KW:Thiamine catabolism > GO:thiamin catabolism ; GO:0009230 SP_KW:Thick filament > GO:striated muscle contraction ; GO:0006941 SP_KW:Thick filament > GO:striated muscle thick filament ; GO:0005863 SP_KW:Thiol protease > GO:cysteine-type peptidase activity ; GO:0008234 SP_KW:Thiol protease inhibitor > GO:cysteine protease inhibitor activity ; GO:0004869 SP_KW:Threonine biosynthesis > GO:threonine biosynthesis ; GO:0009088 SP_KW:Threonine protease > GO:threonine endopeptidase activity ; GO:0004298 SP_KW:Thylakoid > GO:thylakoid ; GO:0009579 SP_KW:Thyroid hormone > GO:thyroid hormone generation ; GO:0006590 SP_KW:Thyroid hormones biosynthesis > GO:hormone biosynthesis ; GO:0042446 SP_KW:Tight junction > GO:tight junction ; GO:0005923 SP_KW:Tissue remodeling > GO:tissue development ; GO:0009888 SP_KW:Topoisomerase > GO:DNA topoisomerase activity ; GO:0003916 SP_KW:Toxin > GO:pathogenesis ; GO:0009405 SP_KW:Trans-acting factor > GO:transcription factor activity ; GO:0003700 SP_KW:Transcription > GO:transcription ; GO:0006350 SP_KW:Transcription antitermination > GO:regulation of transcription ; GO:0045449 SP_KW:Transcription antitermination > GO:transcription antitermination ; GO:0031564 SP_KW:Transcription regulation > GO:regulation of transcription, DNA-dependent ; GO:0006355 SP_KW:Transcription termination > GO:transcription termination ; GO:0006353 SP_KW:Transducer > GO:signal transducer activity ; GO:0004871 SP_KW:Transducer > GO:signal transduction ; GO:0007165 SP_KW:Transferase > GO:transferase activity ; GO:0016740 SP_KW:Translation regulation > GO:regulation of protein biosynthesis ; GO:0006417 SP_KW:Translation regulation > GO:regulation of translation ; GO:0006445 SP_KW:Translocation > GO:protein targeting ; GO:0006605 SP_KW:Transmembrane > GO:integral to membrane ; GO:0016021 SP_KW:Transport > GO:transport ; GO:0006810 SP_KW:Transposable element > GO:DNA transposition ; GO:0006313 SP_KW:Transposition > GO:DNA transposition ; GO:0006313 SP_KW:Tricarboxylic acid cycle > GO:tricarboxylic acid cycle ; GO:0006099 SP_KW:Trimethoprim resistance > GO:response to antibiotic ; GO:0046677 SP_KW:Tryptophan biosynthesis > GO:tryptophan biosynthesis ; GO:0000162 SP_KW:Tryptophan catabolism > GO:tryptophan catabolism ; GO:0006569 SP_KW:Tyrosine biosynthesis > GO:tyrosine biosynthesis ; GO:0006571 SP_KW:Tyrosine catabolism > GO:tyrosine catabolism ; GO:0006572 SP_KW:Tyrosine-protein kinase > GO:protein-tyrosine kinase activity ; GO:0004713 SP_KW:Ubiquinone biosynthesis > GO:ubiquinone biosynthesis ; GO:0006744 SP_KW:Ubiquitin conjugation > GO:protein modification ; GO:0006464 SP_KW:Ubl conjugation pathway > GO:ubiquitin cycle ; GO:0006512 SP_KW:Unfolded protein response > GO:response to unfolded protein ; GO:0006986 SP_KW:Urea cycle > GO:urea cycle ; GO:0000050 SP_KW:VLDL > GO:lipid transporter activity ; GO:0005319 SP_KW:Vanadium > GO:vanadium ion binding ; GO:0051212 SP_KW:Vasoactive > GO:regulation of blood vessel size ; GO:0050880 SP_KW:Vasoconstrictor > GO:vasoconstriction ; GO:0042310 SP_KW:Vasodilator > GO:vasodilation ; GO:0042311 SP_KW:Viral immunoevasion > GO:viral evasion of host immune response ; GO:0030683 SP_KW:Viral movement protein > GO:viral spread within host, cell to cell ; GO:0046740 SP_KW:Viral occlusion body > GO:viral capsid ; GO:0019028 SP_KW:Virulence > GO:pathogenesis ; GO:0009405 SP_KW:Vision > GO:visual perception ; GO:0007601 SP_KW:Vitamin A > GO:retinal binding ; GO:0016918 SP_KW:Vitamin B12 > GO:cobalamin binding ; GO:0031419 SP_KW:Vitamin C > GO:L-ascorbic acid binding ; GO:0031418 SP_KW:Vitamin D > GO:vitamin D binding ; GO:0005499 SP_KW:Voltage-gated channel > GO:voltage-gated ion channel activity ; GO:0005244 SP_KW:Wnt signaling pathway > GO:Wnt receptor signaling pathway ; GO:0016055 SP_KW:Xylan degradation > GO:xylan catabolism ; GO:0045493 SP_KW:Xylose metabolism > GO:D-xylose metabolism ; GO:0042732 SP_KW:Zinc transport > GO:zinc ion transport ; GO:0006829 SP_KW:cAMP biosynthesis > GO:cAMP biosynthesis ; GO:0006171 SP_KW:cAMP-binding > GO:3',5'-cAMP binding ; GO:0030552 SP_KW:cGMP biosynthesis > GO:cGMP biosynthesis ; GO:0006182 SP_KW:cGMP-binding > GO:3',5'-cGMP binding ; GO:0030553 SP_KW:mRNA capping > GO:mRNA capping ; GO:0006370 SP_KW:mRNA processing > GO:mRNA processing ; GO:0006397 SP_KW:mRNA splicing > GO:nuclear mRNA splicing, via spliceosome ; GO:0000398 SP_KW:mRNA transport > GO:mRNA processing ; GO:0006397 SP_KW:mRNA transport > GO:mRNA export from nucleus ; GO:0006406 SP_KW:rRNA processing > GO:rRNA processing ; GO:0006364 SP_KW:rRNA-binding > GO:rRNA binding ; GO:0019843 SP_KW:tRNA processing > GO:tRNA processing ; GO:0008033 SP_KW:tRNA-binding > GO:tRNA binding ; GO:0000049 go-perl-0.15/t/data/systematic_synonym_test.obo000644 000765 000024 00000006454 11615622157 021634 0ustar00cjmstaff000000 000000 format-version: 1.2 date: 22:01:2008 11:41 saved-by: Tanya Berardini auto-generated-by: OBO-Edit 1.101 subsetdef: goslim_candida "Candida GO slim" subsetdef: goslim_generic "Generic GO slim" subsetdef: goslim_goa "GOA and proteome slim" subsetdef: goslim_pir "PIR GO slim" subsetdef: goslim_plant "Plant GO slim" subsetdef: goslim_yeast "Yeast GO slim" subsetdef: gosubset_prok "Prokaryotic GO subset" synonymtypedef: systematic_synonym "Systematic synonym" EXACT default-namespace: gene_ontology remark: cvs version: $Revision: 1.1 $ [Term] id: GO:0000001 name: mitochondrion inheritance namespace: biological_process def: "The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton." [GOC:mcc, PMID:10873824, PMID:11389764] synonym: "mitochondrial inheritance" EXACT [] is_a: GO:0048308 ! organelle inheritance is_a: GO:0048311 ! mitochondrion distribution [Term] id: GO:0000002 name: mitochondrial genome maintenance namespace: biological_process def: "The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome." [GOC:ai, GOC:vw] is_a: GO:0007005 ! mitochondrion organization and biogenesis [Term] id: GO:0000003 name: reproduction namespace: biological_process alt_id: GO:0019952 alt_id: GO:0050876 def: "The production by an organism of new individuals that contain some portion of their genetic material inherited from that organism." [GOC:go_curators, GOC:isa_complete, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"] subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "reproductive physiological process" EXACT [] is_a: GO:0008150 ! biological_process [Term] id: GO:0000005 name: ribosomal chaperone activity namespace: molecular_function def: "OBSOLETE. Assists in the correct assembly of ribosomes or ribosomal subunits in vivo, but is not a component of the assembled ribosome when performing its normal biological function." [GOC:jl, PMID:12150913] comment: This term was made obsolete because it refers to a class of gene products and a biological process rather than a molecular function. is_obsolete: true consider: GO:0042254 consider: GO:0051082 [Term] id: GO:0000006 name: high affinity zinc uptake transmembrane transporter activity namespace: molecular_function def: "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Zn2+(out) = Zn2+(in), probably powered by proton motive force. In high affinity transport the transporter is able to bind the solute even if it is only present at very low concentrations." [TC:2.A.5.1.1] is_a: GO:0005385 ! zinc ion transmembrane transporter activity [Term] id: GO:0000007 name: low-affinity zinc ion transmembrane transporter activity namespace: molecular_function def: "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Zn2+ = Zn2+, probably powered by proton motive force. In low affinity transport the transporter is able to bind the solute only if it is present at very high concentrations." [GOC:mtg_transport, ISBN:0815340729] is_a: GO:0005385 ! zinc ion transmembrane transporter activity go-perl-0.15/t/data/test-enrichment-genes.txt000644 000765 000024 00000004654 11615622157 021064 0ustar00cjmstaff000000 000000 SPAC1002.08c SPAC1002.09c SPAC11E3.02c SPAC11E3.07 SPAC12G12.08 SPAC13D6.05 SPAC13G6.05c SPAC144.15c SPAC1486.06 SPAC1486.07c SPAC15E1.08 SPAC16.02c SPAC167.03c SPAC1687.02 SPAC1687.20c SPAC16E8.02 SPAC16E8.04c SPAC16E8.10c SPAC1751.02c SPAC17A2.03c SPAC17A5.12 SPAC17C9.03 SPAC17G8.03c SPAC17H9.17c SPAC1834.02 SPAC1952.13 SPAC1952.14c SPAC19A8.15 SPAC19B12.02c SPAC19D5.04 SPAC1B3.14 SPAC1D4.14 SPAC1F3.01 SPAC1F5.06 SPAC21E11.07 SPAC22A12.08c SPAC22E12.08 SPAC22E12.09c SPAC22E12.10c SPAC22E12.17c SPAC22F3.05c SPAC22H10.10 SPAC23A1.19c SPAC23C11.12 SPAC23C11.15 SPAC23H3.07c SPAC23H3.10 SPAC23H4.03c SPAC23H4.04 SPAC23H4.11c SPAC24C9.06c SPAC24C9.09 SPAC24C9.13c SPAC24H6.05 SPAC24H6.12c SPAC25B8.02 SPAC25B8.14 SPAC26A3.03c SPAC26A3.05 SPAC26F1.03 SPAC26H5.12 SPAC27E2.06c SPAC29A4.03c SPAC2C4.04c SPAC2C4.13 SPAC2F3.03c SPAC2F3.04c SPAC2F3.10 SPAC2F3.17c SPAC2F7.15 SPAC31A2.03 SPAC31A2.08 SPAC31G5.05c SPAC323.06c SPAC328.08c SPAC343.02 SPAC343.05 SPAC343.08c SPAC343.13 SPAC3A12.15 SPAC3A12.19 SPAC3C7.11c SPAC3G6.10c SPAC3G9.13c SPAC3G9.14 SPAC4F10.03c SPAC4F10.10c SPAC4F8.02c SPAC4F8.05c SPAC4F8.06 SPAC4G8.09 SPAC4G9.17c SPAC4H3.08 SPAC56E4.05 SPAC56F8.03 SPAC56F8.10 SPAC607.04 SPAC637.05c SPAC644.17c SPAC688.11 SPAC6F12.05c SPAC6F6.08c SPAC6G10.07 SPAC6G10.09 SPAC732.01 SPAC7D4.09c SPAC7D4.10 SPAC7D4.15c SPAC823.07 SPAC9E9.06c SPAP19A11.05c SPAP27G11.07c SPAP27G11.09c SPAP7G5.02c SPAP8A3.09c SPAP8A3.10 SPAP8A3.11c SPAPB1A10.11c SPAPB2B4.05 SPBC1105.03c SPBC1105.07c SPBC119.17 SPBC119.18 SPBC1198.02 SPBC1198.10c SPBC11B10.03 SPBC11B10.04c SPBC11C11.04c SPBC1215.02c SPBC1271.13 SPBC1289.02c SPBC12D12.08c SPBC1306.01c SPBC1347.05c SPBC13A2.01c SPBC13G1.05 SPBC13G1.07 SPBC146.01 SPBC146.07 SPBC14C8.10 SPBC14C8.16c SPBC1539.01c SPBC1539.09c SPBC1604.13c SPBC1677.03c SPBC16A3.04 SPBC16A3.05c SPBC16A3.11 SPBC16E9.05 SPBC16G5.04 SPBC16G5.08 SPBC16G5.12c SPBC16G5.18 SPBC1709.17 SPBC1711.10c SPBC1718.06 SPBC1734.02c SPBC1778.08c SPBC17A3.07 SPBC1861.08c SPBC18H10.17c SPBC19C2.11c SPBC19C2.12 SPBC19F5.04 SPBC19G7.14c SPBC1A4.01 SPBC21C3.04c SPBC21D10.05c SPBC24C6.03 SPBC27B12.01c SPBC28E12.01c SPBC28F2.04c SPBC28F2.06c SPBC29A3.15c SPBC2A9.08c SPBC2F12.02c SPBC2F12.10 SPBC30D10.08 SPBC30D10.12c SPBC30D10.17c SPBC31E1.03 SPBC31E1.04 SPBC32F12.06 SPBC336.11 SPBC336.12c SPBC336.15 SPBC337.06c SPBC337.14 SPBC354.06 SPBC36.05c SPBC36B7.09 SPBC3B9.01 SPBC3B9.14c SPBC3B9.16c SPBC3B9.17 SPBC3B9.18c SPBC3D6.11c SPBC3E7.13c SPBC409.13 SPBC409.14c SPBC409.15 go-perl-0.15/t/data/test-function.dat000644 000765 000024 00000010516 11615622157 017401 0ustar00cjmstaff000000 000000 !THIS IS TEST DATA ! Even if the biology in this becomes superceded, please DO NOT edit ! this file, it is here as part of the test suite ! and lives in database go_mini $Gene_Ontology ; GO:0003673 $molecular_function ; GO:0003674 %nucleic acid binding ; GO:0003676 %DNA binding ; GO:0003677 %DNA helicase ; GO:0003678, GO:0003679 % helicase ; GO:0004386 %AT DNA binding ; GO:0003680 %bent DNA binding ; GO:0003681 %chromatin binding ; GO:0003682 %lamin/chromatin binding ; GO:0003683 %damaged DNA binding ; GO:0003684 %DNA bending ; GO:0008301 %DNA repair protein ; GO:0003685 %DNA repair enzyme ; GO:0003686 % enzyme ; GO:0003824 %DNA replication factor ; GO:0003687 %DNA replication origin binding ; GO:0003688 %DNA clamp loader ; GO:0003689 %double-stranded DNA binding ; GO:0003690 %double-stranded telomeric DNA binding ; GO:0003691 % telomerase ; GO:0003720 %recombinase ; GO:0000150 ; synonym:FLP recombinase ; synonym:YADDA %left-handed Z-DNA binding ; GO:0003692 %P-element binding ; GO:0003693 %plasmid-associated protein ; GO:0003694 %random coil DNA binding ; GO:0003695 %ribosomal DNA (rDNA) binding ; GO:0000182 %satellite DNA binding ; GO:0003696 %single-stranded DNA binding ; GO:0003697, GO:0003698, GO:0003699 %DNA secondary structure binding ; GO:0000217 %transcription factor ; GO:0003700, GO:0000130 %RNA polymerase I transcription factor ; GO:0003701 %RNA polymerase II transcription factor ; GO:0003702 %general RNA polymerase II transcription factor ; GO:0003703 %specific RNA polymerase II transcription factor ; GO:0003704 %enhancer binding ; GO:0003705 %ligand-regulated transcription factor ; GO:0003706 %steroid hormone receptor ; GO:0003707 % ligand-dependent nuclear receptor ; GO:0004879 %retinoic acid receptor ; GO:0003708 % ligand-dependent nuclear receptor ; GO:0004879 %RNA polymerase III transcription factor ; GO:0003709 %transcription activating factor ; GO:0003710 %transcription elongation factor ; GO:0003711 %negative transcription elongation factor ; GO:0008148 %positive transcription elongation factor ; GO:0008159 %transcription termination factor ; GO:0003715 %Pol I transcription termination factor ; GO:0003716 %Pol II transcription termination factor ; GO:0003717 %Pol III transcription termination factor ; GO:0003718 %telomerase ; GO:0003720 %telomeric RNA reverse transcriptase ; GO:0003721 ; EC:2.7.7.49 % RNA-directed DNA polymerase ; GO:0003964 %double-stranded telomeric DNA binding ; GO:0003691 % double-stranded DNA binding ; GO:3690 %enzyme ; GO:0003824 %alpha,alpha-trehalose-phosphate synthase (UDP-forming) ; GO:0003825 ; EC:2.4.1.15 %alpha-ketoacid dehydrogenase ; GO:0003826 %alpha-methylacyl-CoA racemase ; GO:0008111 ; EC:5.1.99.4 %alpha-N-acetylgalactosaminidase ; GO:0008456 ; EC:3.2.1.49 %beta-alanyl-dopamine hydrolase ; GO:0003832 %beta-alanyl-dopamine synthase ; GO:0003833 %beta-carotene 15,15'-dioxygenase ; GO:0003834 ; EC:1.13.11.21 %beta-ureidopropionase ; GO:0003837 ; EC:3.5.1.6 %delta,5-delta2,4-dienoyl-CoA isomerase ; GO:0008416 %delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase ; GO:0008461 ; EC:5.3.3.8 %gamma-butyrobetaine,2-oxoglutarate dioxygenase ; GO:0008336 ; EC:1.14.11.1 %gamma-glutamyl carboxylase ; GO:0008488 %gamma-glutamylcyclotransferase ; GO:0003839 ; EC:2.3.2.4 %gamma-glutamyl hydrolase ; GO:0008464 ; EC:3.4.19.9 %gamma-glutamyl transferase ; GO:0003840 ; EC:2.3.2.2 %DNA repair enzyme ; GO:0003686 % DNA repair protein ; GO:0003685 %deoxyribodipyrimidine photolyase ; GO:0003904 ; EC:4.1.99.3 % DNA photolyase ; GO:0003913 %DNA-3-methyladenine glycosidase II ; GO:0003905 ; EC:3.2.2.21 %DNA-(apurinic or apyrimidinic site) lyase ; GO:0003906 ; EC:4.2.99.18 %methylated-DNA--[protein]-cysteine S-methyltransferase ; GO:0003908 ; EC:2.1.1.63 % S-methyltransferase ; GO:0008172 %DNA glycolase ; GO:0008578 %8-oxoguanine DNA glycosylase ; GO:0008534 %G/T-mismatch-specific thymine-DNA glycosylase ; GO:0008263 % DNA repair enzyme ; GO:0003686 %formamidopyrimidine-DNA glycosylase ; GO:0003907 ; EC:3.2.2.23 % DNA repair enzyme ; GO:0003686 %uracil-DNA glycosylase ; GO:0004844 ; EC:3.2.2.- % DNA repair enzyme ; GO:0003686 go-perl-0.15/t/data/test-gene_association.fb000644 000765 000024 00000067406 11615622157 020717 0ustar00cjmstaff000000 000000 FB FBgn0004607 zfh2 GO:0009653 FB:FBrf0157154 IC P zfh2 zfh2|CG1449|ZFH-2|Zfh-2|zfh-2 gene taxon:7227 20040228 FB FB FBgn0004607 zfh2 GO:0030528 FB:FBrf0105495 ISS MGD:Atbf1; MGI:MGI:99948 F zfh2 zfh2|CG1449|ZFH-2|Zfh-2|zfh-2 gene taxon:7227 20040228 FB FB FBgn0004607 zfh2 GO:0005634 FB:FBrf0105495 ISS MGD:Atbf1; MGI:MGI:99948 C zfh2 zfh2|CG1449|ZFH-2|Zfh-2|zfh-2 gene taxon:7227 20040228 FB FB FBgn0004607 zfh2 GO:0006350 FB:FBrf0105495 ISS MGD:Atbf1; MGI:MGI:99948 P zfh2 zfh2|CG1449|ZFH-2|Zfh-2|zfh-2 gene taxon:7227 20040228 FB FB FBgn0004607 zfh2 GO:0003677 FB:FBrf0156721 NAS F zfh2 zfh2|CG1449|ZFH-2|Zfh-2|zfh-2 gene taxon:7227 20040228 FB FB FBgn0004607 zfh2 GO:0005634 FB:FBrf0156721 NAS C zfh2 zfh2|CG1449|ZFH-2|Zfh-2|zfh-2 gene taxon:7227 20040228 FB FB FBgn0004607 zfh2 GO:0009653 FB:FBrf0156721 NAS P zfh2 zfh2|CG1449|ZFH-2|Zfh-2|zfh-2 gene taxon:7227 20040228 FB FB FBgn0004607 zfh2 GO:0003677 FB:FBrf0054608|PMID:1680377 TAS F zfh2 zfh2|CG1449|ZFH-2|Zfh-2|zfh-2 gene taxon:7227 20040228 FB FB FBgn0021875 Zfrp8 GO:0003682 FB:FBrf0161459 IEA F Zfrp8 l(2)k13705|Zfrp8|zfrp8|CG3260|137/5 gene taxon:7227 20040228 FB FB FBgn0021875 Zfrp8 GO:0006350 FB:FBrf0161459 IEA P Zfrp8 l(2)k13705|Zfrp8|zfrp8|CG3260|137/5 gene taxon:7227 20040228 FB FB FBgn0021875 Zfrp8 GO:0008219 FB:FBrf0161459 IEA P Zfrp8 l(2)k13705|Zfrp8|zfrp8|CG3260|137/5 gene taxon:7227 20040228 FB FB FBgn0021875 Zfrp8 GO:0003677 FB:FBrf0111489|PMID:10471706 ISS F Zfrp8 l(2)k13705|Zfrp8|zfrp8|CG3260|137/5 gene taxon:7227 20040228 FB FB FBgn0021875 Zfrp8 GO:0005634 FB:FBrf0111489|PMID:10471706 ISS EMBL:AF077950 C Zfrp8 l(2)k13705|Zfrp8|zfrp8|CG3260|137/5 gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0005737 FB:FBrf0141473|PMID:11784030 IDA C zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0005198 FB:FBrf0161459 IEA F zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0007049 FB:FBrf0161459 IEA P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0008092 FB:FBrf0161459 IEA F zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0007582 FB:FBrf0141473|PMID:11784030 IMP P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0009653 FB:FBrf0090759|PMID:8946916 IMP P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0009790 FB:FBrf0090759|PMID:8946916 IMP P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0009653 FB:FBrf0151835|PMID:12176336 IMP P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0009790 FB:FBrf0151835|PMID:12176336 IMP P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0007582 FB:FBrf0151835|PMID:12176336 IMP P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0009653 FB:FBrf0141473|PMID:11784030 IMP P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0009653 FB:FBrf0141473|PMID:11784030 IMP P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0009653 FB:FBrf0151835|PMID:12176336 IMP P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0009790 FB:FBrf0151835|PMID:12176336 IMP P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0030154 FB:FBrf0151835|PMID:12176336 IMP P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0003774 FB:FBrf0132100 ISS SGD_LOCUS:MYO1; SGD:S0001065 F zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0005856 FB:FBrf0052857|PMID:2117279 ISS C zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0005856 FB:FBrf0132100 ISS C zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0016787 FB:FBrf0132100 ISS F zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0008283 FB:FBrf0156757 NAS P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0009653 FB:FBrf0156094|PMID:12414186 NAS P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0007010 FB:FBrf0156094|PMID:12414186 NAS P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0005856 FB:FBrf0110443|PMID:10449347 NAS C zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0005856 FB:FBrf0110443|PMID:10449347 NAS C zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0005856 FB:FBrf0156757 NAS C zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0009653 FB:FBrf0156757 NAS P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0009719 FB:FBrf0146208 NAS P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0007275 FB:FBrf0146208 NAS P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0008219 FB:FBrf0146208 NAS P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0000003 FB:FBrf0128450|PMID:10822261 TAS P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0007582 FB:FBrf0128450|PMID:10822261 TAS P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0009653 FB:FBrf0110443|PMID:10449347 TAS P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0009790 FB:FBrf0110443|PMID:10449347 TAS P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0009653 FB:FBrf0151280|PMID:12147138 TAS P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0009790 FB:FBrf0151280|PMID:12147138 TAS P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0009653 FB:FBrf0151280|PMID:12147138 TAS P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0005634 zip GO:0007010 FB:FBrf0151280|PMID:12147138 TAS P zip Enhancer of broad|nonmuscle myosin II|Mhc-c1|cytoplasmic myosin|cytoplasmic myosin heavy chain|MyoII|Mhc-c|E(br)|Dronm-MII|myosin II heavy chain|myosin II|Myosin II|CG15792|nonmuscle myosin-II heavy chain|Nonmuscle myosin-II|zip|nonmuscle myosin heavy chain|non muscle myosin|nmy-2|nmMHC|Myo|l(2)02957|cytoplasmic myosin II|zpr|DROMHC|Dm nmII|DmnmII|Myosin-II|myosin heavy chain|Myosin heavy chain|myosin|Myosin gene taxon:7227 20040228 FB FB FBgn0033096 ZIP1 GO:0006811 FB:FBrf0161459 IEA P ZIP1 CG9428|ZIP1 gene taxon:7227 20040228 FB FB FBgn0033096 ZIP1 GO:0005215 FB:FBrf0131674 NAS F ZIP1 CG9428|ZIP1 gene taxon:7227 20040228 FB FB FBgn0038412 Zip3 GO:0006811 FB:FBrf0161459 IEA P Zip3 CG6898|ZIP3|Zip3 gene taxon:7227 20040228 FB FB FBgn0038412 Zip3 GO:0005215 FB:FBrf0131675 NAS F Zip3 CG6898|ZIP3|Zip3 gene taxon:7227 20040228 FB FB FBgn0024595 ziplock GO:0000004 FB:FBrf0159398 ND P ziplock ziplock gene taxon:7227 20040228 FB FB FBgn0024595 ziplock GO:0005554 FB:FBrf0159398 ND F ziplock ziplock gene taxon:7227 20040228 FB FB FBgn0024595 ziplock GO:0008372 FB:FBrf0159398 ND C ziplock ziplock gene taxon:7227 20040228 FB FB FBgn0020243 ziti GO:0000003 FB:FBrf0091612 NAS P ziti ziti gene taxon:7227 20040228 FB FB FBgn0020243 ziti GO:0005554 FB:FBrf0159398 ND F ziti ziti gene taxon:7227 20040228 FB FB FBgn0020243 ziti GO:0008372 FB:FBrf0159398 ND C ziti ziti gene taxon:7227 20040228 FB FB FBgn0017453 Zn72D GO:0006350 FB:FBrf0161459 IEA P Zn72D Zn72D|CG5215 gene taxon:7227 20040228 FB FB FBgn0017453 Zn72D GO:0003723 FB:FBrf0105495 ISS EMBL:AF071059; protein_id:AAC25762.1 F Zn72D Zn72D|CG5215 gene taxon:7227 20040228 FB FB FBgn0052311 zormin GO:0007582 FB:FBrf0161459 IEA P zormin CG33484|CT36990|BcDNA:GH09541|CG32311|CG1282|CG5699|CG11850|D-Titin|CG32309|CG11952|CG11953|zormin gene taxon:7227 20040228 FB FB FBgn0052311 zormin GO:0005198 FB:FBrf0105495 ISS EMBL:D83390; protein_id:BAA11908 F zormin CG33484|CT36990|BcDNA:GH09541|CG32311|CG1282|CG5699|CG11850|D-Titin|CG32309|CG11952|CG11953|zormin gene taxon:7227 20040228 FB FB FBgn0052311 zormin GO:0005198 FB:FBrf0105495 ISS PIR:I38344 F zormin CG33484|CT36990|BcDNA:GH09541|CG32311|CG1282|CG5699|CG11850|D-Titin|CG32309|CG11952|CG11953|zormin gene taxon:7227 20040228 FB FB FBgn0024177 zpg GO:0007165 FB:FBrf0161459 IEA P zpg Dm-inx4|zpg|CG10125|inx4 gene taxon:7227 20040228 FB FB FBgn0024177 zpg GO:0000003 FB:FBrf0146994|PMID:11973283 IMP P zpg Dm-inx4|zpg|CG10125|inx4 gene taxon:7227 20040228 FB FB FBgn0024177 zpg GO:0005886 FB:FBrf0105495 ISS EMBL:AF115854; protein_id:AAD29306.1 C zpg Dm-inx4|zpg|CG10125|inx4 gene taxon:7227 20040228 FB FB FBgn0024177 zpg GO:0005886 FB:FBrf0132008 NAS C zpg Dm-inx4|zpg|CG10125|inx4 gene taxon:7227 20040228 FB FB FBgn0024177 zpg GO:0005886 FB:FBrf0133862 NAS C zpg Dm-inx4|zpg|CG10125|inx4 gene taxon:7227 20040228 FB FB FBgn0024177 zpg GO:0005886 FB:FBrf0134255 NAS C zpg Dm-inx4|zpg|CG10125|inx4 gene taxon:7227 20040228 FB FB FBgn0024177 zpg GO:0005215 FB:FBrf0132008 NAS F zpg Dm-inx4|zpg|CG10125|inx4 gene taxon:7227 20040228 FB FB FBgn0024177 zpg GO:0005215 FB:FBrf0133862 NAS F zpg Dm-inx4|zpg|CG10125|inx4 gene taxon:7227 20040228 FB FB FBgn0024177 zpg GO:0005215 FB:FBrf0134255 NAS F zpg Dm-inx4|zpg|CG10125|inx4 gene taxon:7227 20040228 FB FB FBgn0024177 zpg GO:0005215 FB:FBrf0155987|PMID:12459723 NAS F zpg Dm-inx4|zpg|CG10125|inx4 gene taxon:7227 20040228 FB FB FBgn0024177 zpg GO:0005623 FB:FBrf0132008 NAS C zpg Dm-inx4|zpg|CG10125|inx4 gene taxon:7227 20040228 FB FB FBgn0024177 zpg GO:0005886 FB:FBrf0155987|PMID:12459723 TAS C zpg Dm-inx4|zpg|CG10125|inx4 gene taxon:7227 20040228 FB FB FBgn0024177 zpg GO:0000003 FB:FBrf0155987|PMID:12459723 TAS P zpg Dm-inx4|zpg|CG10125|inx4 gene taxon:7227 20040228 FB FB FBgn0030096 Zpr1 GO:0005730 FB:FBrf0105495 ISS SGD_LOCUS:ZPR1; SGD:S0003443 C Zpr1 CG9060|Zpr1 gene taxon:7227 20040228 FB FB FBgn0030096 Zpr1 GO:0006350 FB:FBrf0105495 ISS SGD_LOCUS:ZPR1; SGD:S0003443 P Zpr1 CG9060|Zpr1 gene taxon:7227 20040228 FB FB FBgn0004056 zuc GO:0000003 FB:FBrf0054123|PMID:1783295 IMP P zuc zuc gene taxon:7227 20040228 FB FB FBgn0004056 zuc GO:0000003 FB:FBrf0054123|PMID:1783295 IMP P zuc zuc gene taxon:7227 20040228 FB FB FBgn0004056 zuc GO:0000003 FB:FBrf0110978|PMID:10449356 TAS P zuc zuc gene taxon:7227 20040228 FB FB FBgn0004057 Zw GO:0003824 FB:FBrf0105495 ISS EMBL:M34709 F Zw Glucose-6-phosphate dehydrogenase|glucose-6-phosphate dehydrogenase|G6PD|G6pd|g6pd|glucose-6-phosphate 1dehydrogenase|Zw|G-6-pdh|G6PDH|Glucose-6-phosphate DH|G-6-PD|CG12529|G-6PD|G-6pd|G6-pd gene taxon:7227 20040228 FB FB FBgn0004057 Zw GO:0005975 FB:FBrf0123556 NAS P Zw Glucose-6-phosphate dehydrogenase|glucose-6-phosphate dehydrogenase|G6PD|G6pd|g6pd|glucose-6-phosphate 1dehydrogenase|Zw|G-6-pdh|G6PDH|Glucose-6-phosphate DH|G-6-PD|CG12529|G-6PD|G-6pd|G6-pd gene taxon:7227 20040228 FB FB FBgn0004057 Zw GO:0006731 FB:FBrf0123556 NAS P Zw Glucose-6-phosphate dehydrogenase|glucose-6-phosphate dehydrogenase|G6PD|G6pd|g6pd|glucose-6-phosphate 1dehydrogenase|Zw|G-6-pdh|G6PDH|Glucose-6-phosphate DH|G-6-PD|CG12529|G-6PD|G-6pd|G6-pd gene taxon:7227 20040228 FB FB FBgn0004057 Zw GO:0009056 FB:FBrf0123556 NAS P Zw Glucose-6-phosphate dehydrogenase|glucose-6-phosphate dehydrogenase|G6PD|G6pd|g6pd|glucose-6-phosphate 1dehydrogenase|Zw|G-6-pdh|G6PDH|Glucose-6-phosphate DH|G-6-PD|CG12529|G-6PD|G-6pd|G6-pd gene taxon:7227 20040228 FB FB FBgn0004057 Zw GO:0006139 FB:FBrf0123556 NAS P Zw Glucose-6-phosphate dehydrogenase|glucose-6-phosphate dehydrogenase|G6PD|G6pd|g6pd|glucose-6-phosphate 1dehydrogenase|Zw|G-6-pdh|G6PDH|Glucose-6-phosphate DH|G-6-PD|CG12529|G-6PD|G-6pd|G6-pd gene taxon:7227 20040228 FB FB FBgn0004057 Zw GO:0006091 FB:FBrf0123556 NAS P Zw Glucose-6-phosphate dehydrogenase|glucose-6-phosphate dehydrogenase|G6PD|G6pd|g6pd|glucose-6-phosphate 1dehydrogenase|Zw|G-6-pdh|G6PDH|Glucose-6-phosphate DH|G-6-PD|CG12529|G-6PD|G-6pd|G6-pd gene taxon:7227 20040228 FB FB FBgn0004057 Zw GO:0003824 FB:FBrf0056264|PMID:1582561 TAS F Zw Glucose-6-phosphate dehydrogenase|glucose-6-phosphate dehydrogenase|G6PD|G6pd|g6pd|glucose-6-phosphate 1dehydrogenase|Zw|G-6-pdh|G6PDH|Glucose-6-phosphate DH|G-6-PD|CG12529|G-6PD|G-6pd|G6-pd gene taxon:7227 20040228 FB FB FBgn0061476 zwilch GO:0007049 FB:FBrf0146196 IMP P zwilch zwilch|CG18639|CG18729 gene taxon:7227 20040228 FB FB FBgn0062246 Zwim GO:0009653 FB:FBrf0145816 IMP P Zwim Zwim gene taxon:7227 20040228 FB FB FBgn0062246 Zwim GO:0004672 FB:FBrf0145816 TAS F Zwim Zwim gene taxon:7227 20040228 FB FB FBgn0011642 Zyx102EF GO:0005198 FB:FBrf0161459 IEA F Zyx102EF Lim102EF|DmLIM-1|lim|Zyxin|zyxin|DLim-1|CG32018|Zyx102EF|BcDNA:LD06023|zyx102|Zyx102|ZYX102 gene taxon:7227 20040228 FB FB FBgn0011642 Zyx102EF GO:0006350 FB:FBrf0161459 IEA P Zyx102EF Lim102EF|DmLIM-1|lim|Zyxin|zyxin|DLim-1|CG32018|Zyx102EF|BcDNA:LD06023|zyx102|Zyx102|ZYX102 gene taxon:7227 20040228 FB FB FBgn0011642 Zyx102EF GO:0007582 FB:FBrf0161459 IEA P Zyx102EF Lim102EF|DmLIM-1|lim|Zyxin|zyxin|DLim-1|CG32018|Zyx102EF|BcDNA:LD06023|zyx102|Zyx102|ZYX102 gene taxon:7227 20040228 FB FB FBgn0011642 Zyx102EF GO:0007010 FB:FBrf0161459 IEA P Zyx102EF Lim102EF|DmLIM-1|lim|Zyxin|zyxin|DLim-1|CG32018|Zyx102EF|BcDNA:LD06023|zyx102|Zyx102|ZYX102 gene taxon:7227 20040228 FB FB FBgn0011642 Zyx102EF GO:0007165 FB:FBrf0161459 IEA P Zyx102EF Lim102EF|DmLIM-1|lim|Zyxin|zyxin|DLim-1|CG32018|Zyx102EF|BcDNA:LD06023|zyx102|Zyx102|ZYX102 gene taxon:7227 20040228 FB FB FBgn0011642 Zyx102EF GO:0030528 FB:FBrf0161459 IEA F Zyx102EF Lim102EF|DmLIM-1|lim|Zyxin|zyxin|DLim-1|CG32018|Zyx102EF|BcDNA:LD06023|zyx102|Zyx102|ZYX102 gene taxon:7227 20040228 FB FB FBgn0011642 Zyx102EF GO:0005856 FB:FBrf0132100 ISS C Zyx102EF Lim102EF|DmLIM-1|lim|Zyxin|zyxin|DLim-1|CG32018|Zyx102EF|BcDNA:LD06023|zyx102|Zyx102|ZYX102 gene taxon:7227 20040228 FB FB bogus foo XYZ:0001 FB:FBrf0132100 ISS C Zyx102EF Lim102EF|DmLIM-1|lim|Zyxin|zyxin|DLim-1|CG32018|Zyx102EF|BcDNA:LD06023|zyx102|Zyx102|ZYX102 gene taxon:7227 20040228 FB go-perl-0.15/t/data/test-go.obo000644 000765 000024 00000024636 11615622157 016200 0ustar00cjmstaff000000 000000 format-version: 0.01_experimental date: Tue Apr 13 07:32:46 2004 default-namespace: unknown autogenerated-by: //home/cjm/cvs/go-dev/scripts/go2fmt.pl remark: THIS IS A TEST [Term] id: GO:0003674 name: molecular_function namespace: molecular_function [Term] id: GO:0003676 name: nucleic acid binding namespace: molecular_function is_a: GO:0003674 [Term] id: GO:0003677 name: DNA binding namespace: molecular_function is_a: GO:0003676 [Term] id: GO:0003678 name: DNA helicase namespace: molecular_function is_a: GO:0004386 is_a: GO:0003677 [Term] id: GO:0003680 name: AT DNA binding namespace: molecular_function is_a: GO:0003677 [Term] id: GO:0003681 name: bent DNA binding namespace: molecular_function is_a: GO:0003677 [Term] id: GO:0003682 name: chromatin binding namespace: molecular_function is_a: GO:0003677 [Term] id: GO:0003683 name: lamin/chromatin binding namespace: molecular_function is_a: GO:0003682 [Term] id: GO:0003684 name: damaged DNA binding namespace: molecular_function is_a: GO:0003677 [Term] id: GO:0008301 name: DNA bending namespace: molecular_function is_a: GO:0003677 [Term] id: GO:0003685 name: DNA repair protein namespace: molecular_function is_a: GO:0003677 [Term] id: GO:0003686 name: DNA repair enzyme namespace: molecular_function is_a: GO:0003824 is_a: GO:0003685 [Term] id: GO:0003687 name: DNA replication factor namespace: molecular_function is_a: GO:0003677 [Term] id: GO:0003688 name: DNA replication origin binding namespace: molecular_function is_a: GO:0003687 [Term] id: GO:0003689 name: DNA clamp loader namespace: molecular_function is_a: GO:0003687 [Term] id: GO:0003690 name: double-stranded DNA binding namespace: molecular_function is_a: GO:0003677 [Term] id: GO:0003691 name: double-stranded telomeric DNA binding namespace: molecular_function is_a: GO:0003720 is_a: GO:0003690 [Term] id: GO:0000150 name: recombinase namespace: molecular_function is_a: GO:0003690 [Term] id: GO:0003692 name: left-handed Z-DNA binding namespace: molecular_function is_a: GO:0003677 [Term] id: GO:0003693 name: P-element binding namespace: molecular_function is_a: GO:0003677 [Term] id: GO:0003694 name: plasmid-associated protein namespace: molecular_function is_a: GO:0003677 [Term] id: GO:0003695 name: random coil DNA binding namespace: molecular_function is_a: GO:0003677 [Term] id: GO:0000182 name: ribosomal DNA (rDNA) binding namespace: molecular_function is_a: GO:0003677 [Term] id: GO:0003696 name: satellite DNA binding namespace: molecular_function is_a: GO:0003677 [Term] id: GO:0003697 name: single-stranded DNA binding namespace: molecular_function is_a: GO:0003677 [Term] id: GO:0000217 name: DNA secondary structure binding namespace: molecular_function is_a: GO:0003677 [Term] id: GO:0003700 name: transcription factor namespace: molecular_function is_a: GO:0003677 [Term] id: GO:0003701 name: RNA polymerase I transcription factor namespace: molecular_function is_a: GO:0003700 [Term] id: GO:0003702 name: RNA polymerase II transcription factor namespace: molecular_function is_a: GO:0003700 [Term] id: GO:0003703 name: general RNA polymerase II transcription factor namespace: molecular_function is_a: GO:0003702 [Term] id: GO:0003704 name: specific RNA polymerase II transcription factor namespace: molecular_function is_a: GO:0003702 [Term] id: GO:0003705 name: enhancer binding namespace: molecular_function is_a: GO:0003702 [Term] id: GO:0003706 name: ligand-regulated transcription factor namespace: molecular_function is_a: GO:0003702 [Term] id: GO:0003707 name: steroid hormone receptor namespace: molecular_function is_a: GO:0004879 is_a: GO:0003706 [Term] id: GO:0003708 name: retinoic acid receptor namespace: molecular_function is_a: GO:0004879 is_a: GO:0003706 [Term] id: GO:0003709 name: RNA polymerase III transcription factor namespace: molecular_function is_a: GO:0003700 [Term] id: GO:0003710 name: transcription activating factor namespace: molecular_function is_a: GO:0003700 [Term] id: GO:0003711 name: transcription elongation factor namespace: molecular_function is_a: GO:0003700 [Term] id: GO:0008148 name: negative transcription elongation factor namespace: molecular_function is_a: GO:0003711 [Term] id: GO:0008159 name: positive transcription elongation factor namespace: molecular_function is_a: GO:0003711 [Term] id: GO:0003715 name: transcription termination factor namespace: molecular_function is_a: GO:0003700 [Term] id: GO:0003716 name: Pol I transcription termination factor namespace: molecular_function is_a: GO:0003715 [Term] id: GO:0003717 name: Pol II transcription termination factor namespace: molecular_function is_a: GO:0003715 [Term] id: GO:0003718 name: Pol III transcription termination factor namespace: molecular_function is_a: GO:0003715 [Term] id: GO:0003720 name: telomerase namespace: molecular_function is_a: GO:0003677 [Term] id: GO:0003721 name: telomeric RNA reverse transcriptase namespace: molecular_function is_a: GO:0003964 is_a: GO:0003720 [Term] id: GO:0003824 name: enzyme namespace: molecular_function is_a: GO:0003674 [Term] id: GO:0003825 name: alpha,alpha-trehalose-phosphate synthase (UDP-forming) namespace: molecular_function is_a: GO:0003824 [Term] id: GO:0003826 name: alpha-ketoacid dehydrogenase namespace: molecular_function is_a: GO:0003824 [Term] id: GO:0008111 name: alpha-methylacyl-CoA racemase namespace: molecular_function is_a: GO:0003824 [Term] id: GO:0008456 name: alpha-N-acetylgalactosaminidase namespace: molecular_function is_a: GO:0003824 [Term] id: GO:0003832 name: beta-alanyl-dopamine hydrolase namespace: molecular_function is_a: GO:0003824 [Term] id: GO:0003833 name: beta-alanyl-dopamine synthase namespace: molecular_function is_a: GO:0003824 [Term] id: GO:0003834 name: beta-carotene 15,15'-dioxygenase namespace: molecular_function is_a: GO:0003824 [Term] id: GO:0003837 name: beta-ureidopropionase namespace: molecular_function is_a: GO:0003824 [Term] id: GO:0008416 name: delta,5-delta2,4-dienoyl-CoA isomerase namespace: molecular_function is_a: GO:0003824 [Term] id: GO:0008461 name: delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase namespace: molecular_function is_a: GO:0003824 [Term] id: GO:0008336 name: gamma-butyrobetaine,2-oxoglutarate dioxygenase namespace: molecular_function is_a: GO:0003824 [Term] id: GO:0008488 name: gamma-glutamyl carboxylase namespace: molecular_function is_a: GO:0003824 [Term] id: GO:0003839 name: gamma-glutamylcyclotransferase namespace: molecular_function is_a: GO:0003824 [Term] id: GO:0008464 name: gamma-glutamyl hydrolase namespace: molecular_function is_a: GO:0003824 [Term] id: GO:0003840 name: gamma-glutamyl transferase namespace: molecular_function is_a: GO:0003824 [Term] id: GO:0003904 name: deoxyribodipyrimidine photolyase namespace: molecular_function is_a: GO:0003913 is_a: GO:0003824 [Term] id: GO:0003905 name: DNA-3-methyladenine glycosidase II namespace: molecular_function is_a: GO:0003824 [Term] id: GO:0003906 name: DNA-(apurinic or apyrimidinic site) lyase namespace: molecular_function is_a: GO:0003824 [Term] id: GO:0003908 name: methylated-DNA--[protein]-cysteine S-methyltransferase namespace: molecular_function is_a: GO:0008172 is_a: GO:0003824 [Term] id: GO:0008578 name: DNA glycolase namespace: molecular_function is_a: GO:0003824 [Term] id: GO:0008534 name: 8-oxoguanine DNA glycosylase namespace: molecular_function is_a: GO:0008578 [Term] id: GO:0008263 name: G/T-mismatch-specific thymine-DNA glycosylase namespace: molecular_function is_a: GO:0003686 is_a: GO:0008578 [Term] id: GO:0003907 name: formamidopyrimidine-DNA glycosylase namespace: molecular_function is_a: GO:0003686 is_a: GO:0008578 [Term] id: GO:0004844 name: uracil-DNA glycosylase namespace: molecular_function is_a: GO:0003686 is_a: GO:0008578 [Term] id: GO:0008150 name: biological_process namespace: biological_process [Term] id: GO:0007610 name: behavior namespace: biological_process is_a: GO:0008150 [Term] id: GO:0030534 name: adult behavior namespace: biological_process is_a: GO:0007610 [Term] id: GO:0008343 name: adult feeding behavior namespace: biological_process is_a: GO:0007631 is_a: GO:0030534 [Term] id: GO:0008344 name: adult locomotory behavior namespace: biological_process is_a: GO:0007626 is_a: GO:0030534 [Term] id: GO:0007628 name: adult walking behavior namespace: biological_process is_a: GO:0008344 [Term] id: GO:0007629 name: flight behavior namespace: biological_process is_a: GO:0008344 [Term] id: GO:0007630 name: jump response namespace: biological_process is_a: GO:0008344 [Term] id: GO:0007636 name: chemosensory jump behavior namespace: biological_process is_a: GO:0007635 is_a: GO:0007630 [Term] id: GO:0048148 name: behavioral response to cocaine namespace: biological_process is_a: GO:0042220 is_a: GO:0030534 [Term] id: GO:0048149 name: behavioral response to ethanol namespace: biological_process is_a: GO:0045471 is_a: GO:0030534 [Term] id: GO:0048150 name: behavioral response to ether namespace: biological_process is_a: GO:0045472 is_a: GO:0030534 [Term] id: GO:0001662 name: behavioral fear response namespace: biological_process is_a: GO:0042596 is_a: GO:0007610 [Term] id: GO:0005575 name: cellular_component namespace: cellular_component [Term] id: GO:0005623 name: cell namespace: cellular_component is_a: GO:0005575 [Term] id: GO:0005933 name: bud namespace: cellular_component relationship: part_of GO:0005623 [Term] id: GO:0005935 name: bud neck namespace: cellular_component relationship: part_of GO:0005933 is_a: GO:0000134 [Term] id: GO:0000142 name: contractile ring (sensu Saccharomyces) namespace: cellular_component relationship: part_of GO:0005935 is_a: GO:0030480 [Term] id: GO:0000144 name: septin ring (sensu Saccharomyces) namespace: cellular_component relationship: part_of GO:0000142 is_a: GO:0030481 [Term] id: GO:0000133 name: polarisome namespace: cellular_component relationship: part_of GO:0005934 relationship: part_of GO:0005938 relationship: part_of GO:0005935 [Term] id: GO:0005934 name: bud tip namespace: cellular_component relationship: part_of GO:0005933 is_a: GO:0000134 [Term] id: GO:0043025 name: cell body namespace: cellular_component relationship: part_of GO:0005623 [Term] id: GO:0000267 name: cell fraction namespace: cellular_component relationship: part_of GO:0005623 [Term] id: GO:0005626 name: insoluble fraction namespace: cellular_component is_a: GO:0000267 [Term] id: GO:0005624 name: membrane fraction namespace: cellular_component is_a: GO:0000267 [Term] id: GO:0000299 name: integral to membrane of membrane fraction namespace: cellular_component is_a: GO:0005624 go-perl-0.15/t/data/test-nucleolar.obo000644 000765 000024 00000021201 11615622157 017540 0ustar00cjmstaff000000 000000 format-version: 0.01_experimental date: Fri Oct 29 17:00:46 2004 default-namespace: unknown autogenerated-by: /Users/cjm/cvs/go-dev/scripts/go2fmt.pl remark: THIS IS A TEST id-mapping: part_of OBO_REL:part_of id-mapping: develops_from OBO_REL:derives_from synonymtypedef: UK_spelling "UK spelling" EXACT [Term] id: GO:0003673 name: Gene_Ontology namespace: Gene_Ontology [Term] id: GO:0008150 name: biological_process namespace: biological_process relationship: part_of GO:0003673 [Term] id: GO:0009987 name: cellular process namespace: biological_process is_a: GO:0008150 [Term] id: GO:0050875 name: cellular physiological process namespace: biological_process is_a: GO:0007582 is_a: GO:0009987 [Term] id: GO:0008219 name: cell death namespace: biological_process is_a: GO:0016265 is_a: GO:0050875 [Term] id: GO:0007569 name: cell aging namespace: biological_process relationship: part_of GO:0008219 is_a: GO:0007568 synonym: "cellular senescence" [Term] id: GO:0001303 name: nucleolar fragmentation during replicative aging namespace: biological_process relationship: part_of GO:0001302 is_a: GO:0007569 [Term] id: GO:0001302 name: replicative cell aging namespace: biological_process is_a: GO:0007569 [Term] id: GO:0008151 name: cell growth and/or maintenance namespace: biological_process is_a: GO:0050875 synonym: "cell physiology" [Term] id: GO:0016043 name: cell organization and biogenesis namespace: biological_process is_a: GO:0008151 [Term] id: GO:0006997 name: nuclear organization and biogenesis namespace: biological_process is_a: GO:0016043 synonym: "GO:0048287" synonym: EXACT UK_spelling "nuclear organisation and biogenesis" synonym: EXACT structured "nucleus organization and biogenesis" [Term] id: GO:0030575 name: nuclear body organization and biogenesis namespace: biological_process is_a: GO:0006997 [Term] id: GO:0007275 name: development namespace: biological_process is_a: GO:0008150 [Term] id: GO:0007568 name: aging namespace: biological_process relationship: part_of GO:0016265 is_a: GO:0007275 synonym: "GO:0016280" synonym: "senescence" [Term] id: GO:0007576 name: nucleolar fragmentation namespace: biological_process relationship: part_of GO:0007568 [Term] id: GO:0008371 name: obsolete biological process namespace: biological_process is_a: GO:0008150 [Term] id: GO:0046616 name: nucleolar fragmentation (sensu Saccharomyces) namespace: biological_process is_a: GO:0008371 [Term] id: GO:0007575 name: nucleolar size increase namespace: biological_process is_a: GO:0008371 [Term] id: GO:0046617 name: nucleolar size increase (sensu Saccharomyces) namespace: biological_process is_a: GO:0008371 [Term] id: GO:0007582 name: physiological process namespace: biological_process is_a: GO:0008150 [Term] id: GO:0016265 name: death namespace: biological_process is_a: GO:0007582 [Term] id: GO:0008152 name: metabolism namespace: biological_process is_a: GO:0007582 [Term] id: GO:0009056 name: catabolism namespace: biological_process is_a: GO:0008152 [Term] id: GO:0009057 name: macromolecule catabolism namespace: biological_process is_a: GO:0009056 [Term] id: GO:0006401 name: RNA catabolism namespace: biological_process is_a: GO:0016070 is_a: GO:0009057 [Term] id: GO:0016077 name: snoRNA catabolism namespace: biological_process is_a: GO:0016074 is_a: GO:0006401 [Term] id: GO:0006139 name: nucleobase, nucleoside, nucleotide and nucleic acid metabolism namespace: biological_process is_a: GO:0008152 [Term] id: GO:0016070 name: RNA metabolism namespace: biological_process is_a: GO:0006139 [Term] id: GO:0006396 name: RNA processing namespace: biological_process is_a: GO:0016070 synonym: "GO:0006394" [Term] id: GO:0043144 name: snoRNA processing namespace: biological_process is_a: GO:0016074 is_a: GO:0006396 [Term] id: GO:0016074 name: snoRNA metabolism namespace: biological_process is_a: GO:0016070 [Term] id: GO:0006350 name: transcription namespace: biological_process is_a: GO:0006139 [Term] id: GO:0006351 name: transcription, DNA-dependent namespace: biological_process is_a: GO:0006350 [Term] id: GO:0009302 name: snoRNA transcription namespace: biological_process def: "The synthesis of small nucleolar RNA (snoRNA) from a DNA template." [GO:curators] [testdb:001] comment: test comment is_a: GO:0006351 [Term] id: GO:0005575 name: cellular_component namespace: cellular_component relationship: part_of GO:0003673 [Term] id: GO:0005623 name: cell namespace: cellular_component is_a: GO:0005575 [Term] id: GO:0005622 name: intracellular namespace: cellular_component relationship: part_of GO:0005623 synonym: "protoplasm" [Term] id: GO:0005694 name: chromosome namespace: cellular_component relationship: part_of GO:0005622 [Term] id: GO:0000785 name: chromatin namespace: cellular_component relationship: part_of GO:0005694 [Term] id: GO:0000790 name: nuclear chromatin namespace: cellular_component relationship: part_of GO:0000228 is_a: GO:0000785 [Term] id: GO:0030874 name: nucleolar chromatin namespace: cellular_component relationship: part_of GO:0005730 relationship: part_of GO:0000790 [Term] id: GO:0000228 name: nuclear chromosome namespace: cellular_component relationship: part_of GO:0005634 is_a: GO:0005694 [Term] id: GO:0005737 name: cytoplasm namespace: cellular_component relationship: part_of GO:0005622 [Term] id: GO:0030684 name: preribosome namespace: cellular_component relationship: part_of GO:0005737 is_a: GO:0030529 [Term] id: GO:0030685 name: nucleolar preribosome namespace: cellular_component relationship: part_of GO:0005730 is_a: GO:0030684 [Term] id: GO:0030687 name: nucleolar preribosome, large subunit precursor namespace: cellular_component is_a: GO:0030685 synonym: "66S preribosome" [Term] id: GO:0030688 name: nucleolar preribosome, small subunit precursor namespace: cellular_component is_a: GO:0030685 synonym: "43S preribosome" [Term] id: GO:0005634 name: nucleus namespace: cellular_component relationship: part_of GO:0005622 [Term] id: GO:0005730 name: nucleolus namespace: cellular_component relationship: part_of GO:0005634 [Term] id: GO:0005655 name: nucleolar ribonuclease P complex namespace: cellular_component relationship: part_of GO:0005730 is_a: GO:0030677 synonym: "nucleolar RNase P complex" [Term] id: GO:0005732 name: small nucleolar ribonucleoprotein complex namespace: cellular_component relationship: part_of GO:0005730 is_a: GO:0030529 synonym: "snoRNP" [Term] id: GO:0005654 name: nucleoplasm namespace: cellular_component relationship: part_of GO:0005634 [Term] id: GO:0016585 name: chromatin remodeling complex namespace: cellular_component relationship: part_of GO:0005654 synonym: "chromatin remodelling complex" [Term] id: GO:0005677 name: chromatin silencing complex namespace: cellular_component is_a: GO:0016585 [Term] id: GO:0030869 name: RENT complex namespace: cellular_component is_a: GO:0005677 [Term] id: GO:0016604 name: nuclear body namespace: cellular_component relationship: part_of GO:0005654 [Term] id: GO:0016607 name: nuclear speck namespace: cellular_component is_a: GO:0016604 synonym: "nuclear speckle" synonym: "speckle domain" synonym: "speckle focus" synonym: "splicing speckle" [Term] id: GO:0030529 name: ribonucleoprotein complex namespace: cellular_component relationship: part_of GO:0005622 synonym: "RNP" [Term] id: GO:0030677 name: ribonuclease P complex namespace: cellular_component is_a: GO:0030529 synonym: "RNase P complex" [Term] id: GO:0008370 name: obsolete cellular component namespace: cellular_component is_a: GO:0005575 [Term] id: GO:0005733 name: small nucleolar RNA namespace: cellular_component is_a: GO:0008370 synonym: "snoRNA" [Term] id: GO:0003674 name: molecular_function namespace: molecular_function relationship: part_of GO:0003673 [Term] id: GO:0005488 name: binding namespace: molecular_function is_a: GO:0003674 synonym: "ligand" [Term] id: GO:0003676 name: nucleic acid binding namespace: molecular_function is_a: GO:0005488 [Term] id: GO:0003723 name: RNA binding namespace: molecular_function is_a: GO:0003676 [Term] id: GO:0030515 name: snoRNA binding namespace: molecular_function is_a: GO:0003723 [Term] id: GO:0043021 name: ribonucleoprotein binding namespace: molecular_function is_a: GO:0005488 synonym: "RNP binding" [Term] id: GO:0030519 name: snoRNP binding namespace: molecular_function is_a: GO:0043021 [Term] id: GO:0008369 name: obsolete molecular function namespace: molecular_function is_a: GO:0003674 [Term] id: GO:0030355 name: small nucleolar ribonucleoprotein namespace: molecular_function is_a: GO:0008369 synonym: "snoRNP" [Term] id: GO:0005569 name: small nucleolar RNA namespace: molecular_function is_a: GO:0008369 [Typedef] id: part_of name: part_of is_transitive: true [Typedef] id: develops_from name: Develops from transitive_over: part_of is_transitive: true go-perl-0.15/t/data/test2.ontology000644 000765 000024 00000000665 11615622157 016746 0ustar00cjmstaff000000 000000 !autogenerated-by: DAG-Edit version 1.419 rev 3 !saved-by: gocvs !date: Wed Mar 16 21:01:36 PST 2005 !version: $Revision: 1.1 $ !type: % is_a is a !type: < part_of part of !type: ^ inverse_of inverse of !type: | disjoint_from disjoint from !type: * star !type: # hash $Gene_Ontology ; GO:0003673 /dev/null")) { print <{help}) { system("perldoc $0"); exit; } my $errf = $opt->{err}; my $errhandler = Data::Stag->getformathandler('xml'); if ($errf) { $errhandler->file($errf); } else { $errhandler->fh(\*STDERR); } my @files = GO::Parser->new->normalize_files(@ARGV); while (my $fn = shift @files) { eval { summarise_file($fn); }; if ($@) { $errhandler->err_event(exception=>"$@"); } } sub summarise_file { my $fn = shift; my %h = %$opt; my $fmt; if ($fn =~ /\.obo/) { $fmt = 'obo_text'; } if ($fn =~ /\.ont/) { $fmt = 'go_ont'; } if ($fmt && !$h{format}) { $h{format} = $fmt; } $h{handler} = 'obj'; my $parser = new GO::Parser(%h); $parser->litemode(1); $parser->use_cache(1) if $opt->{use_cache}; $parser->errhandler($errhandler); $parser->parse($fn); my $g = $parser->handler->graph; my %counts = (); my %ns_h=(); foreach my $t (@{$g->get_all_terms}) { next if $t->is_obsolete; my $ns = $t->term_type; if (!$ns) { if ($fn =~ /\/(.*)\.\w+/) { $ns = $1; } else { $ns = $fn; } } $ns_h{$ns}=1; my $acc = $t->acc; $counts{term}->{$ns}++; my $parent_rels = $g->get_parent_relationships($acc); $counts{relationship}->{$ns} += scalar(@$parent_rels); my $paths = $g->paths_to_top($acc); my $n_paths = scalar(@$paths); $counts{path}->{$ns} += $n_paths; if ($n_paths >= $counts{pathmax}->{$ns}) { $counts{pathmax}->{$ns} = $n_paths; $counts{pathmaxacc}->{$ns} = $acc; $counts{pathmaxname}->{$ns} = $t->name; } } foreach my $ns (keys %ns_h) { printf "%s\n", join("\t", $fn, $ns, (map {$counts{$_}->{$ns}} qw(term relationship path)), $counts{path}->{$ns}/$counts{term}->{$ns}, (map {$counts{$_}->{$ns}} qw(pathmax pathmaxacc pathmaxname)), ); } } $errhandler->finish; exit 0; __END__ =head1 NAME go-dag-summary =head1 SYNOPSIS go-dag-summary ontology/gene_ontology.obo =head1 DESCRIPTION Summarises an ontology =head1 ARGUMENTS =head3 -e ERRFILE writes parse errors in XML - defaults to STDERR (there should be no parse errors in well formed files) =head3 -p FORMAT determines which parser to use; if left unspecified, will make a guess based on file suffix. See below for formats =head2 -use_cache If this switch is specified, then caching mode is turned on. With caching mode, the first time you parse a file, then an additional file will be exported in a special format that is fast to parse. This file will have the same filename as the original file, except it will have the ".cache" suffix. The next time you parse the file, this program will automatically check for the existence of the ".cache" file. If it exists, and is more recent than the file you specified, this is parsed instead. If it does not exist, it is rebuilt. =head1 OUTPUT One row per ontology Each row has the following columns =over =item input filename =item total no of terms =item total no of relationships =item total no of paths =item avg no of paths per term (p/t) =item maximum no of paths for any term =item ID of term with maximum no of paths NOTE: obsolete terms are not included =back =head2 DOCUMENTATION L =head2 SEE ALSO L =cut go-perl-0.15/scripts/go-export-graph.pl000755 000765 000024 00000004032 11615622160 017771 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl use strict; use GO::Basic; use GO::Dotty::Dotty; use Getopt::Long; my $w = 'text'; my $use_cache; my $fmt; GetOptions("write|w=s"=>\$w, "use_cache"=>\$use_cache, "format|parser|p=s"=>\$fmt, "help|h"=>sub{system("perldoc $0");exit 0}, ); my $graph = parse({format=>$fmt, use_cache=>$use_cache},shift @ARGV); my $subgraph = $graph->subgraph({@ARGV}); unless ($subgraph->term_count) { print STDERR "No matching terms for: @ARGV\n"; exit 1; } if ($w eq 'text') { $subgraph->to_text_output; } elsif ($w eq 'obo') { $subgraph->to_obo; } else { my $graphviz = GO::Dotty::Dotty::go_graph_to_graphviz( $subgraph, {node => {shape => 'box'}, }); print $graphviz->as_png; } exit 0; __END__ =head1 NAME go-export-graph.pl =head1 SYNOPSIS go-export-graph.pl -w png ontology/gene_ontology.obo | display - go-export-graph.pl ontology/gene_ontology.obo 'acc' GO:0007610 go-export-graph.pl ontology/so.obo 'name' 'protein' =head1 DESCRIPTION exports a graph as an indented ascii tree, PNG or OBO file =head1 ARGUMENTS after the file name you can optionally specify query constraint pairs; eg acc GO:0007610 name 'cysteine biosynthesis' =head1 OPTIONS =head3 -w EXPORT_FORMAT one of B, B or B =head2 -use_cache If this switch is specified, then caching mode is turned on. With caching mode, the first time you parse a file, then an additional file will be exported in a special format that is fast to parse. This file will have the same filename as the original file, except it will have the ".cache" suffix. The next time you parse the file, this program will automatically check for the existence of the ".cache" file. If it exists, and is more recent than the file you specified, this is parsed instead. If it does not exist, it is rebuilt. =head2 DOCUMENTATION L =head2 SEE ALSO L =cut go-perl-0.15/scripts/go-export-prolog.pl000755 000765 000024 00000001443 11615622160 020175 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w use strict; use GO::Parser; use Getopt::Long; use Data::Dumper; my $opt = {}; GetOptions($opt, "format|p=s", "handler|h=s", "force_namespace=s", "replace_underscore", "litemode|l", "multifile", "expand|e"); my @fns = @ARGV; my $fmt = $opt->{format}; my $parser = new GO::Parser (format=>$fmt, handler=>'prolog'); if ($opt->{force_namespace}) { $parser->force_namespace($opt->{force_namespace}); } if ($opt->{replace_underscore}) { $parser->replace_underscore(' '); } $parser->litemode(1) if $opt->{litemode}; if ($opt->{multifile}) { print <parse (@fns); go-perl-0.15/scripts/go-filter-subset.pl000755 000765 000024 00000010764 11615622160 020152 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl # POD docs at end of file use strict; use Getopt::Long; use FileHandle; use GO::Parser; use Data::Stag; $|=1; my $opt = {}; GetOptions($opt, "help|h", "format|p=s", "err|e=s", "subset=s", "id=s@", "partial", "to=s", "namespace=s", "filter_code=s", "use_cache", # auto pass-through ); if ($opt->{help}) { system("perldoc $0"); exit; } my $filter_sub; # functional-programming style filters if ($opt->{filter_code}) { $filter_sub = eval $opt->{filter_code}; } if ($opt->{namespace}) { die "cannot use filter_code combined with namespace option" if $filter_sub; $filter_sub = sub { shift->namespace eq $opt->{namespace}; }; } my $errf = $opt->{err}; my $errhandler = Data::Stag->getformathandler('xml'); if ($errf) { $errhandler->file($errf); } else { $errhandler->fh(\*STDERR); } my @ids = @{$opt->{id} || []}; my $subset = $opt->{subset}; my $partial = $opt->{partial}; if (!defined $partial) { $partial = 1 if $subset; } my @files = GO::Parser->new->normalize_files(@ARGV); if (!@files) { print STDERR "You must specify at least one ontology file!\n"; exit 1; } while (my $fn = shift @files) { my $fn = shift; my %h = %$opt; my $fmt; if ($fn =~ /\.obo/) { $fmt = 'obo_text'; } if ($fmt && !$h{format}) { $h{format} = $fmt; } $h{handler} = 'obj'; my $parser = new GO::Parser(%h); $parser->litemode(1) if $opt->{litemode}; $parser->errhandler($errhandler); $parser->parse($fn); my $g = $parser->handler->graph; my @terms = map {$g->get_term($_) || die("no such id:$_")} @ids; if ($subset) { my $terms_in_subset = $g->get_terms_by_subset($subset); push(@terms, @$terms_in_subset); } if ($filter_sub) { push(@terms, grep {$filter_sub->($_)} @{$g->get_all_terms}); } my $subg = $g->subgraph_by_terms(\@terms,{partial=>$partial}); $subg->export({format=>$opt->{to} || 'obo'}); } $errhandler->finish; exit 0; __END__ =head1 NAME go-filter-subset.pl - extracts a subgraph from an ontology file =head1 SYNOPSIS go-filter-subset.pl -id GO:0003767 go.obo go-filter-subset.pl -id GO:0003767 -to png go.obo | xv - go-filter-subset.pl -filter_code 'sub{shift->name =~ /transcr/}' go.obo =head1 DESCRIPTION Exports a subset of an ontology from a file. The subset can be based on a specified set of IDs, a preset "subset" filter in the ontology file (eg a GO "slim" or subset), or a user-defined filter. The subset can be exported in any format, including a graphical image =head1 ARGUMENTS =over =item -id ID ID to use as leaf node in subgraph. All ancestors of this ID are included in the exported graph (unless -partial is set) Multiple IDs can be passed -id ID1 -id ID2 -id ID3 ....etc =item -subset SUBSET_ID Extracts a named subset from the ontology file. (only works with obo format files). For example, a specific GO slim ONLY terms belonging to the subset are exported - the -partial option is automatically set =item -namespace NAMESPACE only terms in this namespace =item -filter_code SUBROUTINE B A subroutine with which the L object is tested for inclusion in the subgraph (all ancestors are automatically included) You should have an understanding of the go-perl object model before using this option Example: go-filter-subset -filter_code 'sub {shift->namespace eq 'molecular_function'}' go.obo (the same things can be achieved with the -namespace option) =item -partial If this is set, then only terms that match the user query are included. Parentage is set to the next recursive parent node in the filter For example, with the -subset option: if X and Y belong to the subset, and Z does not, and X is_a Z is_a Y, then the exported graph withh have X is_a Y =item -use_cache If this switch is specified, then caching mode is turned on. With caching mode, the first time you parse a file, then an additional file will be exported in a special format that is fast to parse. This file will have the same filename as the original file, except it will have the ".cache" suffix. The next time you parse the file, this program will automatically check for the existence of the ".cache" file. If it exists, and is more recent than the file you specified, this is parsed instead. If it does not exist, it is rebuilt. =back =head2 DOCUMENTATION L =cut go-perl-0.15/scripts/go-make-slim.pl000755 000765 000024 00000004270 11615622160 017234 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl # POD docs at end of file use strict; use Getopt::Long; use FileHandle; use GO::Parser; use Data::Stag; $|=1; my $opt = {}; GetOptions($opt, "help|h", "format|p=s", "min|m=s", "err|e=s", "id=s@", "names", "use_cache", "count", ); if ($opt->{help}) { system("perldoc $0"); exit; } my $errf = $opt->{err}; my $errhandler = Data::Stag->getformathandler('xml'); if ($errf) { $errhandler->file($errf); } else { $errhandler->fh(\*STDERR); } my $outer_parser = new GO::Parser({handler=>'obj'}); my $handler = $outer_parser->handler; my @files = GO::Parser->new->normalize_files(@ARGV); while (my $fn = shift @files) { my $fn = shift; my %h = %$opt; my $fmt; if ($fn =~ /\.obo/) { $fmt = 'obo_text'; } if ($fn =~ /\gene_assoc/) { $fmt = 'go_assoc'; } if ($fmt && !$h{format}) { $h{format} = $fmt; } my $parser = new GO::Parser(%h); $parser->handler($handler); #$parser->litemode(1); $parser->errhandler($errhandler); $parser->parse($fn); } my $g = $handler->graph; my $subg = GO::Model::Graph->new; my $min = $opt->{min} || 1; my %ok = (); foreach my $term (@{$g->get_all_terms}) { my $id = $term->acc; my $n = scalar(@{$g->deep_product_list($id)}); if ($n >= $min) { #print STDERR "OK: $id [c=$n]\n"; $ok{$id} = 1; } } foreach my $term (@{$g->get_all_terms}) { my $id = $term->acc; if($ok{$id}) { } else { #print STDERR "XX: $id\n"; $g->delete_node($id); } } $g->export({format=>$opt->{to} || 'obo'}); $errhandler->finish; exit 0; __END__ =head1 NAME go-make-slim.pl - generates a slim file based on association file =head1 SYNOPSIS go-show-assocs-by-node.pl gene_ontology.obo gene_associations.fb =head1 DESCRIPTION =head1 ARGUMENTS =head3 -m minimum number of distinct gene products a node must have attached at-or-below that node for it to be included in the slim =head3 -e ERRFILE writes parse errors in XML - defaults to STDERR (there should be no parse errors in well formed files) =head2 DOCUMENTATION L =cut go-perl-0.15/scripts/go-perl-make-pod-html.pl000755 000765 000024 00000002466 11615622160 020761 0ustar00cjmstaff000000 000000 #!/usr/bin/perl -w use strict; while (<>) { chomp; my $f = $_; my @path = split(/\//, $f); my $lf = pop @path; next unless $lf; if ($lf =~ /(.*)\.(\S+)$/) { my $n = $1; my $sfx = $2; if ($sfx eq 'pm' || $sfx eq 'pl' || $sfx eq 'pod') { print STDERR "Making pod for $lf\n"; my $dir = join('/', 'pod', @path); my $title = join('::',@path,$n); `mkdir -p $dir` unless -d $dir; my $outf = $dir . '/'. $n . '.html'; my $tmpf = "tmp"; open(OF,">$tmpf") || die ("can't open $tmpf"); open(F, $f) || die ("cannot open file:$f"); while() { s/L\<(map2slim|go2\w+|\w+)(\.pl|)\>/L\/g; print OF $_; } close(F); close(OF); system("pod2html --htmlroot /dev/pod --title $title $tmpf > $outf"); } } elsif (@path && $path[-1] eq 'scripts') { print STDERR "Making pod for $lf\n"; my $dir = join('/', 'pod', @path); my $title = join('::',@path,$lf); `mkdir -p $dir` unless -d $dir; my $outf = $dir . '/'. $lf . '.html'; system("pod2html --htmlroot /dev/pod --title $title $f > $outf"); } else { } } go-perl-0.15/scripts/go-show-assocs-by-node.pl000755 000765 000024 00000004521 11615622160 021160 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl # POD docs at end of file use strict; use Getopt::Long; use FileHandle; use GO::Parser; use Data::Stag; $|=1; my $opt = {}; GetOptions($opt, "help|h", "format|p=s", "err|e=s", "id=s@", "names", "use_cache", "count", ); if ($opt->{help}) { system("perldoc $0"); exit; } my $errf = $opt->{err}; my $errhandler = Data::Stag->getformathandler('xml'); if ($errf) { $errhandler->file($errf); } else { $errhandler->fh(\*STDERR); } my @ids = @{$opt->{id} || []}; if (!@ids) { print STDERR "specify id list with -id ID option\n"; exit 1; } my $outer_parser = new GO::Parser({handler=>'obj'}); my $handler = $outer_parser->handler; my @files = GO::Parser->new->normalize_files(@ARGV); while (my $fn = shift @files) { my $fn = shift; my %h = %$opt; my $fmt; if ($fn =~ /\.obo/) { $fmt = 'obo_text'; } if ($fn =~ /\gene_assoc/) { $fmt = 'go_assoc'; } if ($fmt && !$h{format}) { $h{format} = $fmt; } my $parser = new GO::Parser(%h); $parser->handler($handler); #$parser->litemode(1); $parser->errhandler($errhandler); $parser->parse($fn); } my $g = $handler->graph; foreach my $id (@ids) { if ($opt->{count}) { my $prods = $g->deep_product_list($id); printf STDERR "Count: %d\n", scalar(@$prods); } else { my $assocs = $g->deep_association_list($id); foreach my $assoc (@$assocs) { my $prod = $assoc->gene_product; my $evs = $assoc->evidence_list; my @codes = map {$_->code} @$evs; printf "%s %s %s\n", "@codes", $prod->xref->as_str, $prod->symbol; } } } $errhandler->finish; exit 0; __END__ =head1 NAME go-show-assocs-by-node.pl - find association for a GO term =head1 SYNOPSIS go-show-assocs-by-node.pl -id GO:0008021 gene_ontology.obo gene_associations.fb =head1 DESCRIPTION =head1 ARGUMENTS =head3 -c performs a count of gene products, rather than listing them =head3 -e ERRFILE writes parse errors in XML - defaults to STDERR (there should be no parse errors in well formed files) =head3 -p FORMAT determines which parser to use; if left unspecified, will make a guess based on file suffix. See below for formats =head2 DOCUMENTATION L =cut go-perl-0.15/scripts/go-show-paths-to-root.pl000755 000765 000024 00000005627 11615622160 021062 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl # POD docs at end of file use strict; use Getopt::Long; use FileHandle; use GO::Parser; use Data::Stag; $|=1; my $opt = {}; GetOptions($opt, "help|h", "format|p=s", "err|e=s", "id=s@", "names", "use_cache", ); if ($opt->{help}) { system("perldoc $0"); exit; } my $errf = $opt->{err}; my $errhandler = Data::Stag->getformathandler('xml'); if ($errf) { $errhandler->file($errf); } else { $errhandler->fh(\*STDERR); } my @ids = @{$opt->{id} || []}; if (!@ids) { print STDERR "specify id list with -id ID option\n"; exit 1; } my @files = GO::Parser->new->normalize_files(@ARGV); while (my $fn = shift @files) { my $fn = shift; my %h = %$opt; my $fmt; if ($fn =~ /\.obo/) { $fmt = 'obo_text'; } if ($fmt && !$h{format}) { $h{format} = $fmt; } $h{handler} = 'obj'; my $parser = new GO::Parser(%h); $parser->litemode(1); $parser->errhandler($errhandler); $parser->parse($fn); my $g = $parser->handler->graph; foreach my $id (@ids) { my $t = $g->get_term($id); if (!$t) { next; } printf "%s %s\n", $id, $t->name; my $paths = $g->paths_to_top($id) || []; foreach my $path (@$paths) { printf " PATH: %s\n", $path->to_text($opt->{names} ? () : ('acc')); } } } $errhandler->finish; exit 0; __END__ =head1 NAME go-show-paths-to-root.pl - shows all possible paths from a term to the top =head1 SYNOPSIS go-show-paths-to-root.pl -id GO:0008021 ontology/gene_ontology.obo go-show-paths-to-root.pl -names -id GO:0008021 ontology/gene_ontology.obo =head1 DESCRIPTION traverses DAG showing all paths (terms and intervening relationships) to the root This script is purely file based; it needs to parse the ontology each time Subsequent parses can be speeded up using the use_cache option If you wish to use the GO MySQL db, see the script go-db-show-paths-to-root.pl in the go-db-perl distribution =head1 ARGUMENTS =head3 -e ERRFILE writes parse errors in XML - defaults to STDERR (there should be no parse errors in well formed files) =head3 -p FORMAT determines which parser to use; if left unspecified, will make a guess based on file suffix. See below for formats =head2 -use_cache If this switch is specified, then caching mode is turned on. With caching mode, the first time you parse a file, then an additional file will be exported in a special format that is fast to parse. This file will have the same filename as the original file, except it will have the ".cache" suffix. The next time you parse the file, this program will automatically check for the existence of the ".cache" file. If it exists, and is more recent than the file you specified, this is parsed instead. If it does not exist, it is rebuilt. =head2 DOCUMENTATION L =cut go-perl-0.15/scripts/go-validate-xml000755 000765 000024 00000002044 11615622160 017327 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl use strict; use Getopt::Long; use XML::Checker; use XML::Checker::Parser; my %expat_options = (KeepCDATA => 1);#, Handlers => { Unparsed => \&my_Unparsed_handler }); my $parser = new XML::Checker::Parser (%expat_options); my %unique_h; unless (@ARGV) { usage(); exit; } local $XML::Checker::FAIL = \&fail_handler; foreach my $f (@ARGV) { $parser->parsefile ($f); } map{print STDERR "$_\n"}values %unique_h; print STDERR "DONE\n"; my $status = scalar(keys %unique_h); exit $status; # code < 200, invalid xml element/attr? # code >= 200, a warning or info message? sub fail_handler { my $code = shift; my $msg = shift; my @context = @_; my $k = "ERROR-CODE=$code: $msg"; if ($code < 200) { $unique_h{$k} = sprintf("$k\n\tContext: %s",join(", ",@context)); } } sub usage { print <{err}; my $errhandler = Data::Stag->getformathandler('xml'); if ($errf) { $errhandler->file($errf); } else { $errhandler->fh(\*STDOUT); } foreach my $f (@ARGV) { my $parser = new GO::Parser($opt); $parser->errhandler($errhandler); $parser->parse($f); } go-perl-0.15/scripts/go2fmt.pl000755 000765 000024 00000014131 11615622160 016145 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl # POD docs at end of file use strict; use Getopt::Long; use FileHandle; use Data::Stag; use GO::Parser; my $opt = {handler=>'xml'}; GetOptions($opt, "help|h", "obo_set", "litemode|l", "format|p=s", "output|o=s", "datatype|t=s", "xslt|xsl|x=s", "err|e=s", "use_cache", "handler_args|a=s%", "handler|w|writer=s", ); if ($opt->{help}) { system("perldoc $0"); exit; } my $errf = $opt->{err}; my $errhandler = Data::Stag->getformathandler('xml'); if ($errf) { $errhandler->file($errf); } else { $errhandler->fh(\*STDERR); } # create an initial parser object; we won't actually use this # to parse; we use this to get the auto-created handler object my $initial_parser = GO::Parser->new(%$opt); # user will specify handler option which makes handler object my $main_handler = $initial_parser->handler; # some handlers will do something directly (eg make objects or # write xml); others will go through a stag transform, and # then onto the user-specified handler if ($main_handler->can("is_transform") && $main_handler->is_transform) { # create handler chain; the inner handler is what the user # specifies (eg xml output) my $chain_handler = Data::Stag->chainhandlers([$main_handler->CONSUMES], $main_handler, 'xml'); # wrap initial handler inside chained handler $main_handler = $chain_handler; } $main_handler->file($opt->{output}) if $opt->{output}; # unzip etc my @files = $initial_parser->normalize_files(@ARGV); my $in_set = 0; if ($opt->{obo_set} || @files >1) { $main_handler->start_event('obo_set'); $in_set = 1; } while (my $fn = shift @files) { my %h = %$opt; my $fmt; if ($fn =~ /\.obo$/) { $fmt = 'obo_text'; } if ($fmt && !$h{format}) { $h{format} = $fmt; } my $parser = new GO::Parser(%h); $parser->handler($main_handler); $parser->litemode(1) if $opt->{litemode}; $parser->use_cache(1) if $opt->{use_cache}; $parser->errhandler($errhandler); if ($opt->{xslt}) { my $xf = $opt->{xslt}; $parser->xslt($xf); } $parser->parse($fn); $parser->handler->export if $parser->handler->can("export"); } $errhandler->finish; $main_handler->finish; exit 0; __END__ =head1 NAME go2fmt.pl go2obo_xml go2owl go2rdf_xml go2obo_text =head1 SYNOPSIS go2fmt.pl -w obo_xml -e errlog.xml ontology/*.ontology go2fmt.pl -w obo_xml -e errlog.xml ontology/gene_ontology.obo =head1 DESCRIPTION parses any GO/OBO style ontology file and writes out as a different format =head2 ARGUMENTS =head3 -e ERRFILE writes parse errors in XML - defaults to STDERR (there should be no parse errors in well formed files) =head3 -p FORMAT determines which parser to use; if left unspecified, will make a guess based on file suffix. See below for formats =head3 -w|writer FORMAT format for output - see below for list =head3 -|xslt XSLT The name or filename of an XSLT transform This can either be an absolute path to a file anywhere on the filesystem, or it can just be the name of the xslt; eg go2fmt.pl -xslt oboxml_to_owl go.obo If the name is specified, then first of all $GO_ROOT/xml/xsl/*.xsl will be searched; if GO_ROOT is not set, then the perl modules dir where GO is installed will be searched (the xslts will be installed here automatically if you follow the normal install process) =head2 -use_cache If this switch is specified, then caching mode is turned on. With caching mode, the first time you parse a file, then an additional file will be exported in a special format that is fast to parse. This file will have the same filename as the original file, except it will have the ".cache" suffix. The next time you parse the file, this program will automatically check for the existence of the ".cache" file. If it exists, and is more recent than the file you specified, this is parsed instead. If it does not exist, it is rebuilt. This will bring a speed improvement for b of the output formats below (such as pathlist). Most output formats work with event-based parsing, so caching the object brings no benefit and will in fact be slower than bypassing the cache =head2 FORMATS writable formats are =over =item go_ont Files with suffix ".ontology" These store the ontology DAGs =item go_def Files with suffix ".defs" =item go_xref External database references for GO terms Files with suffix "2go" (eg ec2go, metacyc2go) =item go_assoc Annotations of genes or gene products using GO Files with prefix "gene-association." =item obo_text Files with suffix ".obo" This is a new file format replacement for the existing GO flat file formats. It handles ontologies, definitions and xrefs (but not associations) =item obo_xml Files with suffix ".obo.xml" or ".obo-xml" This is the XML version of the OBO flat file format above =item prolog prolog facts - you will need a prolog compiler/interpreter to use these. You can reason over these facts using Obol or the forthcoming Bio-LP project =item tbl simple (lossy) tabular representation =item summary can be used on both ontology files and association files =item pathlist shows all paths to the root =item owl OWL format (default: OWL-DL) OWL is a W3C standard format for ontologies You will need the XSL files from the full go-dev distribution to run this; see the XML section in L =item obj_yaml a YAML representation of a GO::Model::Graph object =item obj_storable A dump of the perl L object. You need L from CPAN for this to work. This is intended to cache objects on the filesystem, for fast access. The obj_storable representation may not be portable =item text_html A html-ified OBO output format =item godb_prestore XML that maps directly to the GODB relational schema (can then be loaded using stag-storenode.pl) =item chadodb_prestore XML that maps directly to the Chado relational schema (can then be loaded using stag-storenode.pl) =back =head2 DOCUMENTATION L =cut go-perl-0.15/scripts/go2godb_prestore000755 000765 000024 00000000110 11615622160 017573 0ustar00cjmstaff000000 000000 #!/bin/sh go2fmt.pl -w xml $@ | go-apply-xslt oboxml_to_godb_prestore - go-perl-0.15/scripts/go2obo000755 000765 000024 00000000036 11615622160 015523 0ustar00cjmstaff000000 000000 #!/bin/sh go2fmt.pl -w obo $@ go-perl-0.15/scripts/go2obo_html000755 000765 000024 00000000043 11615622160 016545 0ustar00cjmstaff000000 000000 #!/bin/sh go2fmt.pl -w obo_html $@ go-perl-0.15/scripts/go2obo_text000755 000765 000024 00000000043 11615622160 016565 0ustar00cjmstaff000000 000000 #!/bin/sh go2fmt.pl -w obo_text $@ go-perl-0.15/scripts/go2obo_xml000755 000765 000024 00000000036 11615622160 016403 0ustar00cjmstaff000000 000000 #!/bin/sh go2fmt.pl -w xml $@ go-perl-0.15/scripts/go2owl000755 000765 000024 00000000076 11615622160 015551 0ustar00cjmstaff000000 000000 #!/bin/sh go2fmt.pl -w xml $@ | go-apply-xslt oboxml_to_owl - go-perl-0.15/scripts/go2owl_simple000755 000765 000024 00000000105 11615622160 017113 0ustar00cjmstaff000000 000000 #!/bin/sh go2fmt.pl -w xml $@ | go-apply-xslt oboxml_to_simple_owl - go-perl-0.15/scripts/go2pathlist000755 000765 000024 00000000043 11615622160 016572 0ustar00cjmstaff000000 000000 #!/bin/sh go2fmt.pl -w pathlist $@ go-perl-0.15/scripts/go2prolog000755 000765 000024 00000000041 11615622160 016242 0ustar00cjmstaff000000 000000 #!/bin/sh go2fmt.pl -w prolog $@ go-perl-0.15/scripts/go2racer000755 000765 000024 00000000100 11615622160 016030 0ustar00cjmstaff000000 000000 #!/bin/sh go2fmt.pl -w xml $1 | go-apply-xslt oboxml_to_racer - go-perl-0.15/scripts/go2rdf000755 000765 000024 00000000036 11615622160 015517 0ustar00cjmstaff000000 000000 #!/bin/sh go2fmt.pl -w rdf $@ go-perl-0.15/scripts/go2rdfxml000755 000765 000024 00000000036 11615622160 016240 0ustar00cjmstaff000000 000000 #!/bin/sh go2fmt.pl -w rdf $@ go-perl-0.15/scripts/go2summary000755 000765 000024 00000000042 11615622160 016436 0ustar00cjmstaff000000 000000 #!/bin/sh go2fmt.pl -w summary $@ go-perl-0.15/scripts/go2sxpr000755 000765 000024 00000000037 11615622160 015741 0ustar00cjmstaff000000 000000 #!/bin/sh go2fmt.pl -w sxpr $@ go-perl-0.15/scripts/go2tbl000755 000765 000024 00000000036 11615622160 015525 0ustar00cjmstaff000000 000000 #!/bin/sh go2fmt.pl -w tbl $@ go-perl-0.15/scripts/go2text_html000755 000765 000024 00000000044 11615622160 016753 0ustar00cjmstaff000000 000000 #!/bin/sh go2fmt.pl -w text_html $@ go-perl-0.15/scripts/go2xml000755 000765 000024 00000000036 11615622160 015544 0ustar00cjmstaff000000 000000 #!/bin/sh go2fmt.pl -w xml $@ go-perl-0.15/scripts/ipr2obo000755 000765 000024 00000000076 11615622160 015714 0ustar00cjmstaff000000 000000 #!/bin/sh go2fmt.pl -p obo_xml -x ipr_to_oboxml -w obo_xml $@ go-perl-0.15/scripts/ipr2obo_xml000755 000765 000024 00000000076 11615622160 016574 0ustar00cjmstaff000000 000000 #!/bin/sh go2fmt.pl -p obo_xml -x ipr_to_oboxml -w obo_xml $@ go-perl-0.15/scripts/map2slim000755 000765 000024 00000051277 11615622160 016075 0ustar00cjmstaff000000 000000 #!/usr/local/bin/perl -w # POD docs at end of file use strict; use FileHandle; use GO::Parser; if (!@ARGV) { system("perldoc $0"); exit; } if ("@ARGV" eq "-h") { system("perldoc $0"); exit; } use Getopt::Long; my $opt = {}; GetOptions($opt, "help", "dbname|d=s", "host|h=s", "out|o=s", "err|e=s", "force", "ontdir=s", "outmap=s", "shownames", "cache=s", "inmap=s", "gff", "aspect|a=s", "count|c", "tab|t", "bucket|b=s", "evcode|ev=s@", "verbose|v"); if ($opt->{help}) { system("perldoc $0"); exit; } my $verbose = $opt->{verbose}; # cached results my %memo_mapslim = (); my $slimfile = shift @ARGV; my $assocfile; $assocfile = pop @ARGV unless $opt->{outmap}; my @ontfiles = @ARGV; if ($opt->{ontdir}) { @ontfiles = glob($opt->{ontdir}."/*{obo}"); @ontfiles = glob($opt->{ontdir}."/*{ontology}") unless @ontfiles; } # parse GO-slim and get the slim graph my $parser = GO::Parser->new({handler=>'obj'}); printf STDERR "Parsing slimfile: $slimfile\n" if $verbose; $parser->parse($slimfile); my $gslim = $parser->handler->graph; # optionally add "slop" terms; eg "OTHER nucleotide binding" my $bucketf = $opt->{bucket}; if ($bucketf) { printf STDERR "Adding bucket terms to: $bucketf\n" if $verbose; $gslim->add_buckets; if (-f $bucketf && !$opt->{force}) { printf STDERR "Overwrite existing $bucketf file?\n(use -force option to skip this prompt)\n"; my $yesno = ; unless ($yesno =~ /^y/i) { printf STDERR "Will not overwrite $bucketf. Quitting!\n"; exit 1; } } my $fh = FileHandle->new(">$bucketf") || die("can't write to $bucketf"); $gslim->to_text_output(-fh=>$fh); $fh->close; } # make a hash of term objects keyed by slim term accession my $slimterms = $gslim->get_all_terms; my %slimh = map {$_->acc => $_} @$slimterms; # parse full ontology # use cache if required (secret option) my $cache = $opt->{cache}; require "Storable.pm" if $cache; my $ont; if ($cache && -f $cache) { print STDERR "Using cache: $cache\n" if $verbose; #$ont = YAML::LoadFile($cache); $ont = Storable::retrieve($cache); } else { if ($opt->{dbname}) { # secret db mode require "GO/AppHandle.pm"; my $apph = GO::AppHandle->connect(-dbname=>$opt->{dbname}, -dbhost=>$opt->{host}, ); $ont = $apph->get_graph(-template=>{terms=>{acc=>1}}); $apph->disconnect; } else { my $parser2 = GO::Parser->new({handler=>'obj'}); foreach my $ontfile (@ontfiles) { printf STDERR "Parsing ontology file: $ontfile\n" if $verbose; $parser2->litemode(1); $parser2->parse($ontfile); } $ont = $parser2->handler->graph; } if ($cache) { print STDERR "Writing to cache: $cache\n" if $verbose; #print YAML::DumpFile($cache, $ont); store($ont, $cache); } } # write output to stdout or a file my $ofh; if ($opt->{out}) { $ofh = FileHandle->new(">".$opt->{out}) || die($opt->{out}); } else { $ofh = \*STDOUT; } # initialize counts to 0 my %countleaf = map { ($_ => 0) } keys %slimh; my %countall = %countleaf; # write out slim mappings and exit if in outmap mode if ($opt->{outmap}) { printf STDERR "Writing slim mappings\n" if $verbose; my $outmap = FileHandle->new(">$opt->{outmap}") || die("cannot open $opt->{outmap} for writing"); # write slim mapping for all GO terms my $terms = $ont->get_all_terms; foreach my $t (sort {$a->acc cmp $b->acc} @$terms) { my $acc = $t->acc; my ($leaf_pnodes, $all_pnodes) = mapslim($acc); if ($opt->{shownames}) { printf $outmap "%s => %s // %s\n", fmt_acc_names($acc), fmt_acc_names(@$leaf_pnodes), fmt_acc_names(@$all_pnodes), } else { print $outmap "$acc => @$leaf_pnodes // @$all_pnodes\n"; } } $outmap->close; exit 0; } # use pre-made mappings if ($opt->{inmap}) { printf STDERR "Using predefined mappings\n" if $verbose; my $inmap = FileHandle->new(">$opt->{inmap}") || die("cannot open $opt->{inmap}"); while (<$inmap>) { chomp; if (/(\S+)\s*=\>\s*(.*)\s+\/\.\s+(.*)/) { my $acc = $1; $memo_mapslim{$acc} = [[split(' ', $2)], [split(' ', $3)]]; } else { warn("illegal slimmap line: $_"); } } $inmap->close; exit 0; } # hash of hashes - maps slim accessions to gene products # key of outer hash is slim accession # key of inner hash is gene product accession # value is boolean my %leafh = (); my %allh = (); my %counted = (); my $fh; if ($assocfile =~ /\.(Z|gz)$/) { printf STDERR "Uncompressing and mapping $assocfile to slim\n" if $verbose; $fh = FileHandle->new("gzip -dc $assocfile|") || die("cannot open assocfile: $assocfile"); } else { printf STDERR "Mapping $assocfile to slim\n" if $verbose; $fh = FileHandle->new($assocfile) || die("cannot open assocfile: $assocfile"); } my $gff = $opt->{gff}; while(<$fh>) { next if /^\!/; chomp; next unless $_; my @cols = split('\t', $_); my $is_not = $cols[3]; my $acc = $cols[4]; if ($gff) { $is_not = 0; my $type = $cols[2]; if ($type =~ /^SO:/) { $acc = $type; } else { my $term = $ont->get_term_by_name($type); if (!$term) { warn("ignoring type: $type"); next; } $acc = $term->acc; } } if (!$acc) { printf STDERR "WARNING! NO ACCESSION: $_\n" if $verbose; next; } my $prod = $cols[1]; if ($gff) { $prod = $cols[8]; } next if $is_not && $is_not =~ /^not$/i; # skip NOT assocs if ($opt->{aspect}) { next unless $cols[8] eq $opt->{aspect}; } if ($opt->{count}) { # save time - if we've encoutered this pair before # then skip it next if $counted{$acc.$prod}; $counted{$acc.$prod} = 1; } # map the annotated GO term up to the slim term(s) my ($leaf_pnodes, $all_pnodes) = mapslim($acc); # mark the gene product as belonging to that slim term $leafh{$_}->{$prod} = 1 foreach @$leaf_pnodes; $allh{$_}->{$prod} = 1 foreach @$all_pnodes; unless ($opt->{count}) { foreach my $replacement_acc (@$leaf_pnodes) { if ($gff) { $cols[2] = $replacement_acc; } else { $cols[4] = $replacement_acc; } print $ofh join("\t", @cols), "\n"; } } } close($fh) || die("problem reading $assocfile"); if ($opt->{count}) { printf STDERR "Getting gene product counts\n" if $verbose; # iterate through the slim graph, depth-first traversal, # printing out slim term accession & name, and the total # distinct gene products attached to that term or its children $gslim->iterate( sub { my $ni = shift; my $t = $ni->term; return if $t->is_relationship_type; my $acc = $t->acc; my $t2; # equivalent term in GO-full if ($acc) { $t2 = $ont->get_term($acc); } else { # no equivalent term - the slim id has been # retired and not tracked; this should # only happen with old slims $acc = "NO_ACC"; } if ($opt->{tab}) { my $depth = $ni->depth +1; printf $ofh ' ' x $depth; } my $count_leaf = scalar(keys %{$leafh{$acc} || {}}) || 0; my $count_all = scalar(keys %{$allh{$acc} || {}}) || 0; printf $ofh ("%s %s (%s)\t%d\t%d\t%s\t%s\n", $acc, $t->name, $t2 && $t2->name ? $t2->name : '?', $count_leaf || 0, $count_all || 0, $t2 && $t2->is_obsolete ? 'OBSOLETE' : '', $t->type || '', ); return; }, {no_duplicates=>1} ); } $ofh->close; printf STDERR "Done!\n" if $verbose; exit 0; # function: mapslim($acc) # # argument: accession [in full GO] # returns: slim-direct-acc-list, slim-all-acc-list # # slim-direct-acc-list is the slim accs that the input acc DIRECTLY maps to # - this corresponds to the most pertinent slim term # # slim-all-acc-list is the slim accs that the input acc maps to # DIRECT & INDIRECT # - this corresponds to ALL the slim terms that are ancestors of input term # # algorithm for finding most pertinent slim term: # # IF a GO acc has two ancestors in the slim, # AND the parents are NOT ancestors of one another # THEN the acc maps to BOTH parents # # IF an acc has two ancestors in the slim, # AND the parents ARE ancestors of one another, # THEN the MORE SPECIFIC parent acc is returned # sub mapslim { my $acc = shift; # save time - never recompute on the same accession my $memo = $memo_mapslim{$acc}; return (@$memo) if $memo; # return same result # trace the paths to root of the input acc in the full GO # (there may be multiple paths to the root) my $paths = $ont->paths_to_top($acc); my $term = $ont->get_term($acc); if (!$term) { # no such accession in GO return ([],[]); } # keep hash, keyed by slim accession, boolean value - # will have true if the slim term is an ancestor of $acc my %ancestorh = (); # ALL ancestors of $acc in slim my %pancestorh = (); # ancestors of $acc in slim for which there # is a path through another ancestor foreach my $path (@$paths) { my $terms = $path->term_list; unshift(@$terms, $term); # make path inclusive of base term # if there are "slop" terms (eg OTHER nucleotide binding) # AND there is an IMPLICIT path through this slop term, # then add this to the explicit path if ($opt->{bucket}) { my $got_leaf = 0; @$terms = map { my $slimt = $slimh{$_}; my @R = ($_); if ($slimt && !$got_leaf) { my $crs = $gslim->get_child_relationships($_); my @brels = grep {$_->type eq "bucket"} @$crs; if (@brels) { my $bterm = $gslim->get_term($brels[0]->acc2); @R = ($bterm, $_); } } if ($slimt) { $got_leaf = 1; } @R; } @$terms; } my $got_leaf = 0; # follow path from $acc up to root, checking to # see if the intermediate term is in the slim foreach my $term (@$terms) { my $pacc = $term->acc; if ($slimh{$pacc}) { # intermediate term is in the slim $ancestorh{$pacc} = 1; if ($got_leaf) { $pancestorh{$pacc} = 1; } $got_leaf = 1; } } } # find unique ancestors, ie ancestors that are not intermediates to # another anestor my @uancestors = grep {!$pancestorh{$_}} keys %ancestorh; $memo = [[@uancestors], [keys %ancestorh]]; #printf STDERR "SLIM($acc) = @{$memo->[0]} // @{$memo->[1]}\n"; $memo_mapslim{$acc} = $memo; return @$memo; } sub fmt_acc_names { my @accs = @_; return join(' ', map { my $t = $ont->get_term($_); if (!$t) { $t = $gslim->get_term($_); } sprintf('%s "%s"',$_,$t ? $t->name : '?'); } @accs); } __END__ =head1 NAME map2slim - maps gene associations to a 'slim' ontology =head1 SYNOPSIS cd go map2slim GO_slims/goslim_generic.obo ontology/gene_ontology.obo gene-associations/gene_association.fb =head1 DESCRIPTION Given a GO slim file, and a current ontology (in one or more files), this script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim. The script can be used to either create a new gene association file, containing the most pertinent GO slim accessions, or in count-mode, in which case it will give distinct gene product counts for each slim term The association file format is described here: L =head1 ARGUMENTS =over =item -b B This argument adds B to the slim ontology; see the documentation below for an explanation. The new slim ontology file, including bucket terms will be written to B =item -outmap B This will generate a mapping file for every term in the full ontology showing both the most pertinent slim term and all slim terms that are ancestors. If you use this option, do NOT supply a gene-associations file =item shownames (Only works with -outmap) Show the names of the term in the slim mapping file =item -c This will force map2slim to give counts of the assoc file, rather than map it =item -t When used in conjunction with B<-c> will tab the output so that the indentation reflects the tree hierarchy in the slim file =item -o B This will write the mapped assocs (or counts) to the specified file, rather than to the screen =back =head1 DOWNLOAD This script is part of the B package, available from CPAN L This script will not work without installing go-perl =head2 MAPPING ALGORITHM GO is a DAG, not a tree. This means that there is often more than one path from a GO term up to the root Gene_Ontology node; the path may intersect multiple terms in the slim ontology - which means that one annotation can map to multiple slim terms! (B you need to view this online to see the image below - if you are not viewing this on the http://www.geneontology.org site, you can look at the following URL: L ) =begin html =end html A hypothetical example blue circles show terms in the GO slim, and yellow circles show terms in the full ontology. The full ontology subsumes the slim, so the blue terms are also in the ontology. GO ID MAPS TO SLIM ID ALL SLIM ANCESTORS ===== =============== ================== 5 2+3 2,3,1 6 3 only 3,1 7 4 only 4,3,1 8 3 only 3,1 9 4 only 4,3,1 10 2+3 2,3,1 The 2nd column shows the most pertinent ID(s) in the slim the direct mapping. The 3rd column shows all ancestors in the slim. Note in particular the mapping of ID 9 although this has two paths to the root through the slim via 3 and 4, 3 is discarded because it is subsumed by 4. On the other hand, 10 maps to both 2 and 3 because these are both the first slim ID in the two valid paths to the root, and neither subsumes the other. The algorithm used is: to map any one term in the full ontology: find all valid paths through to the root node in the full ontology for each path, take the first slim term encountered in the path discard any redundant slim terms in this set ie slim terms subsumed by other slim terms in the set =head2 BUCKET TERMS If you run the script with the -b option, bucket terms will be added. For any term P in the slim, if P has at least one child C, a bucket term P' will be created under P. This is a catch-all term for mapping any term in the full ontology that is a descendant of P, but NOT a descendant of any child of P in the slim ontology. For example, the slim generic.0208 has the following terms and structure: %DNA binding ; GO:0003677 %chromatin binding ; GO:0003682 %transcription factor activity ; GO:0003700, GO:0000130 After adding bucket terms, it will look like this: %DNA binding ; GO:0003677 %chromatin binding ; GO:0003682 %transcription factor activity ; GO:0003700 ; synonym:GO:0000130 @bucket:Z-OTHER-DNA binding ; slim_temp_id:12 Terms from the full ontology that are other children of DNA binding, such as single-stranded DNA binding and its descendents will map to the bucket term. The bucket term has a slim ID which is transient and is there only to facilitate the mapping. It should not be used externally. The bucket term has the prefix Z-OTHER; the Z is a hack to make sure that the term is always listed last in the alphabetic ordering. The algorithm is slightly modified if bucket terms are used. The bucket term has an implicit relationship to all OTHER siblings not in the slim. =head3 Do I need bucket terms? Nowadays most slim files are entirely or nearly 'complete', that is there are no gaps. This means the the -b option will not produce noticeable different results. For example, you may see a bucket term OTHER-binding created, with nothing annotated to it: because all the children of binding in the GO are represented in the slim file. The bucket option is really only necessary for some of the older archived slim files, which are static and were generated in a fairly ad-hoc way; they tend to accumulate 'gaps' over time (eg GO will add a new child of binding, but the static slim file won't be up to date, so any gene products annotated to this new term will map to OTHER-binding in the slim) =head2 GRAPH MISMATCHES Note that the slim ontology file(s) may be out of date with respect to the current ontology. Currently map2slim does not flag graph mismatches between the slim graph and the graph in the full ontology file; it takes the full ontology as being the real graph. However, the slim ontology will be used to format the results if you select B<-t -c> as options. =head2 OUTPUT In normal mode, a standard format gene-association file will be written. The GO ID column (5) will contain GO slim IDs. The mapping corresponds to the 2nd column in the table above. Note that the output file may contain more lines that the input file. This is because some full GO IDs have more than one pertinent slim ID. =head3 COUNT MODE map2slim can be run with the -c option, which will gives the counts of distinct gene products mapped to each slim term. The columns are as follows =over =item GO Term The first column is the GO ID followed by the term name (the term name is provided as it is found in both the full GO and slim ontologies - these will usually be the same but occasionally the slim file will lage behind changes in the GO file) =item Count of gene products for which this is the most relevant slim term the number of distinct gene products for which this is the most pertinent/direct slim ID. By most direct we mean that either the association is made directly to this term, OR the association is made to a child of this slim term AND there is no child slim term which the association maps to. For most slims, this count will be equivalent to the number of associations directly mapped to this slim term. However, some older slim files are "spotty" in that they admit "gaps". For example, if the slim has all children of "biological process" with the exception of "behavior" then all annotations to "behavior" or its children will be counted here see example below =item Count of gene products inferred to be associated with slim term and the number of distinct gene products which are annotated to any descendant of this slim ID (or annotated directly to the slim ID). =item obsoletion flag =item GO ontology =back To take an example; if we use -t and -c like this: map2slim -t -c GO_slims/goslim_generic.obo ontology/gene_ontology.obo gene-associations/gene_association.fb Then part of the results may look like this: GO:0008150 biological_process (biological_process) 34 10025 biological_process GO:0007610 behavior (behavior) 632 632 biological_process GO:0000004 biological process unknown (biological process unknown) 832 832 biological_process GO:0007154 cell communication (cell communication) 333 1701 biological_process GO:0008037 cell recognition (cell recognition) 19 19 biological_process 19 products were mapped to GO:0008037 or one of its children. (GO:0008037 is a leaf node in the slim, so the two counts are identical). On the other hand, GO:0008150 only gets 34 products for which this is the most relevant term. This is because most annotations would map to some child of GO:0008150 in the slim, such as GO:0007610 (behavior). These 34 gene products are either annotated directly to GO:0008150, or to some child of this term which is not in the slim. This can point to 'gaps' in the slim. Note that running map2slim with the -b option will 'plug' these gaps with artificial filler terms. =head1 AUTHOR Chris Mungall BDGP =head1 SEE ALSO http://www.godatabase.org/dev L L =cut go-perl-0.15/GO/Basic.pm000644 000765 000024 00000007030 11615622160 014604 0ustar00cjmstaff000000 000000 # $Id: Basic.pm,v 1.4 2005/03/30 21:15:48 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself =head1 NAME GO::Basic - basic procedural interface to go-perl =head1 SYNOPSIS use GO::Basic; parse_obo(shift @ARGV); find_term(name=>"cytosol"); print $term->acc(); # OO usage print acc(); # procedural usage get_parent; print name(); =head1 DESCRIPTION =cut package GO::Basic; use Exporter; use Carp; use GO::Model::Graph; use GO::Parser; use FileHandle; use strict; use base qw(GO::Model::Root Exporter); use vars qw(@EXPORT); our $graph; our $terms; our $term; @EXPORT = qw( parse parse_obo parse_goflat parse_def parse_assoc term terms acc accs name names graph find_term find_terms get_parents get_rparents get_children get_rchildren ); sub parse_obo { parse(@_, {fmt=>'obo'}) } sub parse_goflat { parse(@_, {fmt=>'go_ont'}) } sub parse_def { parse(@_, {fmt=>'go_def'}) } sub parse_assoc { parse(@_, {fmt=>'go_assoc'}) } sub parse { my $opt = {format=>'obo'}; my @files = map { if (ref($_)) { if (ref($_) eq 'HASH') { my %h = %$_; $opt->{$_} = $h{$_} foreach keys %h; } else { throw("bad argument: $_"); } (); } else { $_; } } @_; my $parser = GO::Parser->new({format=>$opt->{fmt}, use_cache=>$opt->{use_cache}, handler=>'obj'}); $parser->parse($_) foreach @files; $graph = $parser->handler->graph; $graph; } sub find_terms { @_ < 1 && throw("must pass an argument!"); my %constr = @_==1 ? (name=>shift) : @_; check_for_graph(); $terms = $graph->term_query(\%constr); return $terms; } sub find_term { find_terms(@_); if (@$terms) { if (@$terms > 1) { message(">1 terms returned!"); } $term = $terms->[0]; return $term; } return; } sub term { check_for_term(); return $term; } sub terms { check_for_terms(); return @$terms; } sub next_term { $term = shift @$terms; } sub graph { check_for_graph(); return $graph; } sub acc { check_for_term(); return $term->acc; } sub accs { check_for_terms(); return map {$_->acc} @$terms; } sub name { check_for_term(); return $term->name; } sub names { check_for_terms(); return map {$_->name} @$terms; } sub definition { check_for_term(); return $term->definition; } sub check_for_term { $term || throw("no term selected!"); } sub check_for_terms { $terms || throw("no term set selected!"); } sub check_for_graph { $graph || throw("no graph selected!"); } sub get_parents { check_for_graph(); check_for_term(); $terms = $graph->get_parent_terms($term->acc); } sub get_rparents { check_for_graph(); check_for_term(); $terms = $graph->get_recursive_parent_terms($term->acc); } sub get_children { check_for_graph(); check_for_term(); $terms = $graph->get_child_terms($term->acc); } sub get_rchildren { check_for_graph(); check_for_term(); $terms = $graph->get_recursive_child_terms($term->acc); } sub throw { confess "@_"; } sub message { print STDERR "@_\n"; } 1; go-perl-0.15/GO/Handlers/000755 000765 000024 00000000000 12156117750 014772 5ustar00cjmstaff000000 000000 go-perl-0.15/GO/IO/000755 000765 000024 00000000000 12156117750 013541 5ustar00cjmstaff000000 000000 go-perl-0.15/GO/Metadata/000755 000765 000024 00000000000 12156117750 014752 5ustar00cjmstaff000000 000000 go-perl-0.15/GO/Model/000755 000765 000024 00000000000 12156117750 014272 5ustar00cjmstaff000000 000000 go-perl-0.15/GO/ObjCache.pm000644 000765 000024 00000005042 11615622160 015222 0ustar00cjmstaff000000 000000 # $Id: ObjCache.pm,v 1.3 2005/05/20 18:46:57 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::ObjCache; =head1 NAME GO::ObjCache; =head1 DESCRIPTION This is a kind of L - you should not need to use this method directly =cut use Carp; use strict; use Exporter; use GO::Utils qw(rearrange); #use strict; use FileHandle; use Exporter; use vars qw(@ISA); use strict; use base qw(GO::Model::Graph GO::ObjFactory); sub _valid_params { return qw(dbh); } sub _initialize { my $self = shift; $self->SUPER::_initialize(@_); } sub apph { my $self = shift; $self->{apph} = shift if @_; return $self->{apph} || $self; } sub n_deep_associations { my $self = shift; my $acc = shift; $self->extend_down([$acc]); # make sure all terms loaded $self->SUPER::n_deep_associations($acc); } sub deep_association_list { my $self = shift; my $acc = shift; $self->extend_down([$acc]); # make sure all terms loaded $self->SUPER::deep_association_list($acc); } #------ sub extend_graph_by_acc { my $self = shift; my $graph = shift; my $acc = shift; my $depth = shift; my $term = $self->get_term($acc); $self->extend_up($graph, [$acc]); $self->extend_down($graph, [$acc], $depth); } sub extend_up { my $self = shift; my $graph = shift; my @accs = @{shift || []}; my $i=0; while ($i < scalar(@accs)) { my $acc = $accs[$i]; $i++; my $term = $self->get_term($acc); $graph->add_term($term); my $parent_rels = $self->get_parent_relationships($acc); foreach my $rel (@$parent_rels) { $graph->add_relationship($rel); if (!(grep {$_ == $rel->acc1} @accs)) { # only put new accs in push(@accs, $rel->acc1); } } } @accs; } sub extend_down { my $self = shift; my $graph = shift; my @accs = @{shift || []}; my $max_depth = shift; my $i=0; while ($i < scalar(@accs)) { printf STDERR "======== %d %d %s\n", $i, $#accs, join(", ", @accs); my $acc = $accs[$i]; $i++; my $term = $self->get_term($acc); $graph->add_term($term); my $child_rels = $self->get_child_relationships($acc); foreach my $rel (@$child_rels) { $graph->add_relationship($rel); if (!(grep {$_ == $rel->acc2} @accs)) { # only put new accs in push(@accs, $rel->acc2); } } } @accs; } sub get_deep_product_count { 0 } 1; go-perl-0.15/GO/ObjFactory.pm000644 000765 000024 00000012643 11615622160 015633 0ustar00cjmstaff000000 000000 # $Id: ObjFactory.pm,v 1.6 2007/01/24 01:16:19 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::ObjFactory; =head1 NAME GO::ObjFactory - GO Object Factory =head1 SYNOPSIS You should not use this method directly =head1 DESCRIPTION You only need to be aware of this class if you are generating new objects. You should not directly create objects like this: $term = GO::Model::Term->new($h); Instead you should create them like this: $fac = GO::ObjFactory->new(); $term = $fac->create_term_obj($h); Usually you do not need to instantiate a factory, as all objects created with a factory carry around a reference to that factory, so you can do this: # $graph object was previously created via a factory $term = $graph->create_term_obj($h); If you are only using the go-perl module, then factories do not buy you much. However, if you are also using go-db-perl and GO::AppHandle, then factories can be useful - all objects generated from the database will be attached to an AppHandle which means that "lazy loading" can be used. See GO::AppHandle in go-db-perl for details =cut use strict; use Carp; use GO::Model::Seq; use GO::Model::Term; use GO::Model::Xref; use GO::Model::GeneProduct; use GO::Model::CrossProduct; use GO::Model::LogicalDefinition; use GO::Model::Graph; use GO::Model::DB; use GO::Model::Ontology; use GO::Model::Property; use GO::Model::Restriction; use GO::Model::Species; use base qw(GO::Model::Root); sub apph{ my $self = shift; $self->{apph} = shift if @_; my $apph = $self->{apph} || $self; return $apph; } =head2 create_term_obj Usage - $term = $apph->create_term_obj; Returns - L Args - =cut sub create_term_obj { my $self = shift; my $term = GO::Model::Term->new(@_); $term->apph( $self->apph ); return $term; } =head2 create_relationship_obj Usage - $relationship = $apph->create_relationship_obj; Returns - L Args - =cut sub create_relationship_obj { my $self = shift; my $term = GO::Model::Relationship->new(@_); $term->apph( $self->apph ); return $term; } =head2 create_xref_obj Usage - $xref = $apph->create_xref_obj; Returns - L Args - =cut sub create_xref_obj { my $self = shift; my $xref = GO::Model::Xref->new(@_); # $xref->apph($self); return $xref; } =head2 create_evidence_obj Usage - $evidence = $apph->create_evidence_obj; Returns - L Args - =cut sub create_evidence_obj { my $self = shift; my $ev = GO::Model::Evidence->new(@_); return $ev; } =head2 create_seq_obj Usage - $seq = $apph->create_seq_obj; Returns - L Args - =cut sub create_seq_obj { my $self = shift; my $seq = GO::Model::Seq->new(@_); $seq->apph( $self->apph ); return $seq; } =head2 create_db_obj Usage - $db = $apph->create_db_obj; Returns - L Args - =cut sub create_db_obj { my $self = shift; my $db = GO::Model::DB->new(@_); $db->apph( $self->apph ); return $db; } =head2 create_association_obj Usage - $association = $apph->create_association_obj; Returns - L Args - =cut sub create_association_obj { my $self = shift; my $association = GO::Model::Association->new(); $association->apph( $self->apph ); $association->_initialize(@_); return $association; } =head2 create_gene_product_obj Usage - $gene_product = $apph->create_gene_product_obj; Synonym - create_product_obj Returns - L Args - =cut sub create_gene_product_obj { my $self = shift; my $gene_product = GO::Model::GeneProduct->new(@_); $gene_product->apph( $self->apph ); return $gene_product; } *create_product_obj = \&create_gene_product_obj; =head2 create_species_obj Usage - $species = $apph->create_species_obj; Returns - L Args - =cut sub create_species_obj { my $self = shift; my $sp = GO::Model::Species->new(@_); $sp->apph( $self->apph ); return $sp; } =head2 create_graph_obj Usage - $graph = $apph->create_graph_obj; Returns - L Args - =cut sub create_graph_obj { my $self = shift; my $graph = GO::Model::Graph->new(@_); $graph->apph( $self->apph ); return $graph; } # deprecated synonym for Graph sub create_ontology_obj { my $self = shift; my $ontology = GO::Model::Ontology->new(@_); $ontology->apph( $self->apph ); return $ontology; } # alpha code sub create_property_obj { my $self = shift; my $property = GO::Model::Property->new(@_); $property->apph( $self->apph ); return $property; } # alpha code sub create_restriction_obj { my $self = shift; my $restriction = GO::Model::Restriction->new(@_); $restriction->apph( $self->apph ); return $restriction; } sub create_logical_definition_obj { my $self = shift; my $ldef = GO::Model::LogicalDefinition->new(@_); $ldef->apph( $self->apph ); return $ldef; } # experimental/deprecated code sub create_cross_product_obj { my $self = shift; my $cross_product = GO::Model::CrossProduct->new(@_); $cross_product->apph( $self->apph ); return $cross_product; } 1; go-perl-0.15/GO/Parser.pm000644 000765 000024 00000035245 11615622160 015030 0ustar00cjmstaff000000 000000 # $Id: Parser.pm,v 1.15 2006/04/20 22:48:23 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself =head1 NAME GO::Parser - parses all GO files formats and types =head1 SYNOPSIS fetch L objects using a parser: # Scenario 1: Getting objects from a file use GO::Parser; my $parser = new GO::Parser({handler=>'obj',use_cache=>1}); $parser->parse("function.ontology"); # ontology $parser->parse("GO.defs"); # definitions $parser->parse("ec2go"); # external refs $parser->parse("gene-associations.sgd"); # gene assocs # get GO::Model::Graph object my $graph = $parser->handler->graph; # Scenario 2: Getting OBO XML from a file use GO::Parser; my $parser = new GO::Parser({handler=>'xml'}); $parser->handler->file("output.xml"); $parser->parse("gene_ontology.obo"); # Scenario 3: Using an XSL stylesheet to convert the OBO XML use GO::Parser; my $parser = new GO::Parser({handler=>'xml'}); # xslt files are kept in in $ENV{GO_ROOT}/xml/xsl # (if $GO_ROOT is not set, defaults to install directory) $parser->xslt("oboxml_to_owl"); $parser->handler->file("output.owl-xml"); $parser->parse("gene_ontology.obo"); # Scenario 4: via scripts my $cmd = "go2xml gene_ontology.obo | xsltproc my-transform.xsl -"; my $fh = FileHandle->new("$cmd |") || die("problem initiating $cmd"); while(<$fh>) { print $_ } $fh->close || die("problem running $cmd"); =cut =head1 DESCRIPTION Module for parsing GO flat files; for examples of GO/OBO flatfile formats see: L L For a description of the various file formats, see: L L This module will generate XML events from a correctly formatted GO/OBO file =head1 SEE ALSO This module is a part of go-dev, see: L for more details =head1 PUBLIC METHODS =head2 new Title : new Usage : my $p = GO::Parser->new({format=>'obo_xml',handler=>'obj'}); $p->parse("go.obo-xml"); my $g = $p->handler->graph; Synonyms: Function: creates a parser object Example : Returns : GO::Parser Args : a hashref of arguments: format: a format for which a parser exists handler: a format for which a perl handler exists use_cache: (boolean) see caching below =head2 parse Title : parse Usage : $p->parse($file); Synonyms: Function: parses a file Example : Returns : Args : str filename =head2 handler Title : handler Usage : my $handler = $p->handler; Synonyms: Function: gets/sets a GO::Handler object Example : Returns : L Args : L =head1 FORMATS This module is a front end wrapper for a number of different GO/OBO formats - see the relevant module documentation below for details. The full list of parsers can be found in the go-perl/GO/Parsers/ directory =over =item obo_text Files with suffix ".obo" This is a new file format replacement for the existing GO flat file formats. It handles ontologies, definitions and xrefs (but not associations) =item go_ont Files with suffix ".ontology" These store the ontology DAGs =item go_def Files with suffix ".defs" =item go_xref External database references for GO terms Files with suffix "2go" (eg ec2go, metacyc2go) =item go_assoc Annotations of genes or gene products using GO Files with prefix "gene-association." =item obo_xml Files with suffix ".obo.xml" or ".obo-xml" This is the XML version of the OBO flat file format above See L =item obj_yaml A YAML dump of the perl L object. You need L from CPAN for this to work =item obj_storable A dump of the perl L object. You need L from CPAN for this to work. This is intended to cache objects on the filesystem, for fast access. The obj_storable representation may not be portable =head2 PARSING ARCHITECTURE Each parser fires XML B. The XML events are known as B. These XML events can be B by a handler written in perl, or they can be caught by an XML parser written in some other language, or by using XSL stylesheets. go-dev comes with a number of stylesheets in the go-dev/xml/xsl directory Anything that catches these XML events is known as a B go-perl comes with some standard perl XML handlers, in addition to some standard XSL stylesheets. These can be found in the B directory If you are interested in getting perl B from files then you will want the B handler, which gives back L objects The parsing architecture gives you the option of using the go-perl object model, or just parsing the XML events directly If you are using the go-db-perl library, the load-go-into-db.pl script will perform the following processes when loading files into the database =over =item Obo-XML events fired using GO::Parser::* classes =item Obo-XML transformed into godb xml using oboxml_to_godb_prestore.xsl =item godb_prestore.xml stored in database using generic loader =back =head2 Obo-XML The Obo-XML format DTD is stored in the go-dev/xml/dtd directory =head2 HOW IT WORKS Currently the various parsers and perl event handlers use the B module for this - see L for more details, or http://stag.sourceforge.net =head2 NESTED EVENTS nested events can be thought of as xml, without attributes; nested events can easily be turned into xml events have a start, a body and an end event handlers can *catch* these events and do something with them. an object handler can turn the events into objects, centred around the GO::Model::Graph object; see GO::Handlers::obj other handlers can catch the events and convert them into other formats, eg OWL or OBO Or you can bypass the handler and get output as an XML stream - to do this, just run the go2xml script a database loading event handler can catch the events and turn them into SQL statements, loading a MySQL or postgres database (see the go-db-perl library) the advantage of an event based parsing architecture is that it is easy to build lightweight parsers, and heavy weight object models can be bypassed if prefered. =head2 EXAMPLES To see examples of the events generated by the GO::Parser class, run the script go2xml; for example go2xml function.ontology on any GO-formatted flatfile This also works on OBO-formatted files: go2xml gene_ontology.obo You can also use the script "stag-parse.pl" which comes with the L distribution. for example stag-parse.pl -p GO::Parsers::go_assoc_parser gene-association.fb =head2 XSLT HANDLERS The full list can be found in the go-dev/xml/xsl directory =head2 PERL HANDLERS see GO::Handlers::* for all the different handlers possible; more can be added dynamically. you can either create the handler object yourself, and pass it as an argument, e.g. my $apph = new GO::AppHandle(-db=>"go"); my $handler = new GO::Handlers::godb({apph=>$apph}); my $parser = new GO::Parser({handler=>$handler}); $parser->parse(@files); or you can use one of the registered handlers: my $parser = new GO::Parser({handler=>'db', handler_args=>{apph=>$apph}}); or you can just do things from the command line go2fmt.pl -w oboxml function.ontology the registered perl handlers are as follows: =over =item obo_xml writes out OBO-XML (which is basically a straightforward conversion of the event stream into XML) =item obo_text =item go_ont legacy GO-ontology file format =item go_xref GO xref file, for linking GO terms to terms and dbxrefs in other ontologies =item go_defs legacy GO-definitions file format =item go_assoc GO association file format =item rdf GO XML-RDF file format =item owl OWL format (default: OWL-DL) OWL is a W3C standard format for ontologies You will need the XSL files from the full go-dev distribution to run this; see the XML section in L =item prolog prolog facts - you will need a prolog compiler/interpreter to use these. You can reason over these facts using Obol or the forthcoming Bio-LP project =item sxpr lisp style S-Expressions, conforming to the OBO-XML schema; you will need lisp to make full use of these. you can also do some nice stuff just within emacs (use lisp-mode and load an sxpr file into your buffer) =item godb this is actually part of the go-db-perl library, not the go-perl library catches events and loads them into a database conforming to the GO database schema; see the directory go-dev/sql, as part of the whole go-dev distribution; or www.godatabase.org/dev/database =item obj_yaml A YAML dump of the perl L object. You need L from CPAN for this to work =item obj_storable A dump of the perl L object. You need L from CPAN for this to work. This is intended to cache objects on the filesystem, for fast access. The obj_storable representation may not be portable =back =head1 EXAMPLES OF DATATYPE TEXT FORMATS =head2 go_ont format eg format: go_ont for storing graphs and metadata; for example: !version: $Revision: 1.15 $ !date: $Date: 2006/04/20 22:48:23 $ !editors: Michael Ashburner (FlyBase), Midori Harris (SGD), Judy Blake (MGD) $Gene_Ontology ; GO:0003673 $cellular_component ; GO:0005575 %extracellular ; GO:0005576 file z.ontology 1075164285 GO:0003673 Gene_Ontology root GO:0005575 cellular_component root GO:0003673 GO:0005576 extracellular root GO:0005575 GO:0005577 fibrinogen root part_of GO:0005576 GO:0005972 fibrinogen alpha chain root part_of GO:0005577 GO:0005973 fibrinogen beta chain root part_of GO:0005577 =head2 go_def format eg format: go_defs for storing definitions: !Gene Ontology definitions ! term: 'de novo' protein folding goid: GO:0006458 definition: Processes that assist the folding of a nascent peptide chain into its correct tertiary structure. definition_reference: Sanger:mb See GO::Parsers::go_def_parser for more details =head2 go_xref format eg format: go_xrefs for storing links between GO IDs and IDs for terms in other DBs: EC:1.-.-.- > GO:oxidoreductase ; GO:0016491 EC:1.1.-.- > GO:1-phenylethanol dehydrogenase ; GO:0018449 See GO::Parsers::go_xref_parser for more details =head2 go_assoc format eg format: go-assocs for storing gene-associations: SGD S0004660 AAC1 GO:0005743 SGD:12031|PMID:2167309 TAS C ADP/ATP translocator YMR056C gene taxon:4932 20010118 SGD S0004660 AAC1 GO:0006854 SGD:12031|PMID:2167309 IDA P ADP/ATP translocator YMR056C gene taxon:4932 20010118 See GO::Parsers::go_assoc_parser for more details =head2 obo_text format L =cut package GO::Parser; use Exporter; use Carp; use GO::Model::Term; use FileHandle; use strict qw(subs vars refs); use base qw(GO::Model::Root); # Exceptions # Constructor =head2 new Usage - my $parser = GO::Parser->new() Returns - GO::Parser creates a new parser =cut sub new { my $proto = shift; my $class = ref($proto) || $proto;; my $self = {}; bless $self, $class; my $init_h = $_[0] || {}; if (!ref($init_h)) { $init_h = {@_}; } my $fmt = $init_h->{format} || $init_h->{fmt} || ''; my $use_cache = $init_h->{use_cache}; $fmt = lc($fmt) unless $fmt =~ /::/; # $fmt = 'gotext' unless $fmt; if (!$fmt) { # this parser guesses/defers on what type it is parsing $fmt = "unknown_format"; } my $p = $self->get_parser_impl($fmt); if ($init_h) { map {$p->{$_} = $init_h->{$_}} keys %$init_h; } my $handler = $init_h->{handler} || "base"; if (UNIVERSAL::isa($handler, "GO::AppHandle")) { require "GO/Handlers/DbStoreHandler.pm"; $handler = GO::Handlers::DbStoreHandler->new({apph=>$handler}); } unless (ref($handler)) { my $hclass = $handler; if ($handler !~ /::/) { if ($handler =~ /^::/) { $hclass = $handler; $hclass =~ s/^:://; } else { $hclass = "GO::Handlers::$handler"; } } eval { $class->load_module($hclass); }; if ($@) { print STDERR $@, "\n\n\n"; $self->throw("No such handler: $handler"); } $handler = $hclass->new($init_h->{handler_args}); } $p->handler($handler); $p->use_cache($use_cache); delete $init_h->{parser}; delete $init_h->{handler}; return $p; } sub get_parser_impl { my $self = shift; my $fmt = shift; my $mod; if ($fmt =~ /::/) { $mod = $fmt; } else { $mod = "GO::Parsers::$fmt"."_parser"; } $self->load_module($mod); my $p = $mod->new(); return $p; } =head2 create_handler Usage - my $handler = GO::Parser->create_handler('obj'); Returns - L Args - handler type [str] =cut sub create_handler { my $self = shift; my $type = shift || 'obj'; my $p = $self->new({handler=>$type}); return $p->handler; } sub load_module { my $self = shift; my $classname = shift; my $mod = $classname; $mod =~ s/::/\//g; if ($main::{"_<$mod.pm"}) { } else { eval { require "$mod.pm"; }; if ($@) { $self->throw("No such module: $classname;;\n$@"); } } } 1; go-perl-0.15/GO/Parsers/000755 000765 000024 00000000000 12156117750 014651 5ustar00cjmstaff000000 000000 go-perl-0.15/GO/Utils.pm000644 000765 000024 00000022233 11615622160 014665 0ustar00cjmstaff000000 000000 # $Id: Utils.pm,v 1.2 2004/11/24 02:28:00 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Utils; use Exporter; @ISA = qw(Exporter); @EXPORT_OK = qw(rearrange remove_duplicates merge_hashes get_method_ref get_param pset2hash dd spell_greek max check_obj_graph); use strict; use Carp; use Data::Dumper; =head2 rearrange() Usage : n/a Function : Rearranges named parameters to requested order. Returns : @params - an array of parameters in the requested order. Argument : $order : a reference to an array which describes the desired order of the named parameters. @param : an array of parameters, either as a list (in which case the function simply returns the list), or as an associative array (in which case the function sorts the values according to @{$order} and returns that new array. Exceptions : carps if a non-recognised parameter is sent =cut sub rearrange { # This function was taken from CGI.pm, written by Dr. Lincoln # Stein, and adapted for use in Bio::Seq by Richard Resnick. # ...then Chris Mungall came along and adapted it for BDGP my($order,@param) = @_; # If there are no parameters, we simply wish to return # an undef array which is the size of the @{$order} array. return (undef) x $#{$order} unless @param; # If we've got parameters, we need to check to see whether # they are named or simply listed. If they are listed, we # can just return them. return @param unless (defined($param[0]) && $param[0]=~/^-/); # Now we've got to do some work on the named parameters. # The next few lines strip out the '-' characters which # preceed the keys, and capitalizes them. my $i; for ($i=0;$i<@param;$i+=2) { if (!defined($param[$i])) { carp("Hmmm in $i ".join(";", @param)." == ".join(";",@$order)."\n"); } else { $param[$i]=~s/^\-//; $param[$i]=~tr/a-z/A-Z/; } } # Now we'll convert the @params variable into an associative array. my(%param) = @param; my(@return_array); # What we intend to do is loop through the @{$order} variable, # and for each value, we use that as a key into our associative # array, pushing the value at that key onto our return array. my($key); foreach $key (@{$order}) { $key=~tr/a-z/A-Z/; my($value) = $param{$key}; delete $param{$key}; push(@return_array,$value); } # catch user misspellings resulting in unrecognized names my(@restkeys) = keys %param; if (scalar(@restkeys) > 0) { carp("@restkeys not processed in rearrange(), did you use a non-recognized parameter name ? "); } return @return_array; } =head2 get_param() Usage : get_param('name',(-att1=>'ben',-name=>'the_name')) Function : Fetches a named parameter. Returns : The value of the requested parameter. Argument : $name : The name of the the parameter desired @param : an array of parameters, as an associative array Exceptions : carps if a non-recognised parameter is sent Based on rearrange(), which is originally from CGI.pm by Lincoln Stein and BioPerl by Richard Resnick. See rearrange() for details. =cut sub get_param { # This function was taken from CGI.pm, written by Dr. Lincoln # Stein, and adapted for use in Bio::Seq by Richard Resnick. # ...then Chris Mungall came along and adapted it for BDGP # ... and ben berman added his 2 cents. my($name,@param) = @_; # If there are no parameters, we simply wish to return # false. return '' unless @param; # If we've got parameters, we need to check to see whether # they are named or simply listed. If they are listed, we # can't return anything. return '' unless (defined($param[0]) && $param[0]=~/^-/); # Now we've got to do some work on the named parameters. # The next few lines strip out the '-' characters which # preceed the keys, and capitalizes them. my $i; for ($i=0;$i<@param;$i+=2) { $param[$i]=~s/^\-//; $param[$i] = uc($param[$i]); } # Now we'll convert the @params variable into an associative array. my(%param) = @param; # We capitalize the key, and use it as a key into our # associative array my $key = uc($name); my $val = $param{$key}; return $val; } =head2 remove_duplicates remove duplicate items from an array usage: remove_duplicates(\@arr) affects the array passed in, and returns the modified array =cut sub remove_duplicates { my $arr_r = shift; my @arr = @{$arr_r}; my %h = (); my $el; foreach $el (@arr) { $h{$el} = 1; } my @new_arr = (); foreach $el (keys %h) { push (@new_arr, $el); } @{$arr_r} = @new_arr; @new_arr; } =head1 merge_hashes joins two hashes together usage: merge_hashes(\%h1, \%h2); %h1 will now contain the key/val pairs of %h2 as well. if there are key conflicts, %h2 values will take precedence. =cut sub merge_hashes { my ($h1, $h2) = @_; map { $h1->{$_} = $h2->{$_}; } keys %{$h2}; return $h1; } =head1 get_method_ref returns a pointer to a particular objects method e.g. my $length_f = get_method_ref($seq, 'length'); $len = &$length_f(); =cut sub get_method_ref { my $self = shift; my $method = shift; return sub {return $self->$method(@_)}; } =head2 pset2hash Usage - my $h = pset2hash([{name=>"id", value=>"56"}, {name=>"name", value=>"jim"}]); Returns - hashref Args - arrayref of name/value keyed hashrefs =cut sub pset2hash { my $pset = shift; my $h = {}; # printf STDERR "REF=%s;\n", ref($pset); if (ref($pset) eq "ARRAY") { map {$h->{$_->{name}} = $_->{value}} @$pset; } elsif (ref($pset) eq "HASH") { $h = $pset; } else { $h = $pset; } return $h; } sub dd { my $obj = shift; my $d= Data::Dumper->new(['obj',$obj]); print $d->Dump; } =head2 spell_greek takes a word as a parameter and spells out any greek symbols encoded within (eg s/&agr;/alpha/g) =cut sub spell_greek { my $name = shift; $name =~ s/&agr\;/alpha/g; $name =~ s/&Agr\;/Alpha/g; $name =~ s/&bgr\;/beta/g; $name =~ s/&Bgr\;/Beta/g; $name =~ s/&ggr\;/gamma/g; $name =~ s/&Ggr\;/Gamma/g; $name =~ s/&dgr\;/delta/g; $name =~ s/&Dgr\;/Delta/g; $name =~ s/&egr\;/epsilon/g; $name =~ s/&Egr\;/Epsilon/g; $name =~ s/&zgr\;/zeta/g; $name =~ s/&Zgr\;/Zeta/g; $name =~ s/&eegr\;/eta/g; $name =~ s/&EEgr\;/Eta/g; $name =~ s/&thgr\;/theta/g; $name =~ s/&THgr\;/Theta/g; $name =~ s/&igr\;/iota/g; $name =~ s/&Igr\;/Iota/g; $name =~ s/&kgr\;/kappa/g; $name =~ s/&Kgr\;/Kappa/g; $name =~ s/&lgr\;/lambda/g; $name =~ s/&Lgr\;/Lambda/g; $name =~ s/&mgr\;/mu/g; $name =~ s/&Mgr\;/Mu/g; $name =~ s/&ngr\;/nu/g; $name =~ s/&Ngr\;/Nu/g; $name =~ s/&xgr\;/xi/g; $name =~ s/&Xgr\;/Xi/g; $name =~ s/&ogr\;/omicron/g; $name =~ s/&Ogr\;/Omicron/g; $name =~ s/&pgr\;/pi/g; $name =~ s/&Pgr\;/Pi/g; $name =~ s/&rgr\;/rho/g; $name =~ s/&Rgr\;/Rho/g; $name =~ s/&sgr\;/sigma/g; $name =~ s/&Sgr\;/Sigma/g; $name =~ s/&tgr\;/tau/g; $name =~ s/&Tgr\;/Tau/g; $name =~ s/&ugr\;/upsilon/g; $name =~ s/&Ugr\;/Upsilon/g; $name =~ s/&phgr\;/phi/g; $name =~ s/&PHgr\;/Phi/g; $name =~ s/&khgr\;/chi/g; $name =~ s/&KHgr\;/Chi/g; $name =~ s/&psgr\;/psi/g; $name =~ s/&PSgr\;/Psi/g; $name =~ s/&ohgr\;/omega/g; $name =~ s/&OHgr\;/Omega/g; $name =~ s//\[/g; $name =~ s/<\/up>/\]/g; $name =~ s//\[\[/g; $name =~ s/<\/down>/\]\]/g; return $name; } =head2 check_obj_graph Usage - Returns - true if cycle detected Args - any object =cut sub check_obj_graph { my $object = shift; my $h = {}; my $cnt = 1; my @nodes = ({obj=>$object,path=>[]}); my @path = (); my $cycle = 0; while (!$cycle && @nodes) { my $node = shift @nodes; my $obj = $node->{obj}; my $id = sprintf("%s", $node->{obj}); if (ref($obj) && $id !~ /GLOB/) { if (!$h->{$id}) { $h->{$id} = $cnt; $cnt++; } # check for cycles if (grep {my $idelt = sprintf("%s", $_); $idelt eq $id} @{$node->{path}}) { $cycle = $node; } printf "* OB:%5s %20s [%s]\n", $h->{$id}, $obj, join(", ", map {$h->{$_}} @{$node->{path}}); my @newobjs = (); if (ref($obj) eq "ARRAY") { @newobjs = @$obj; } ## if (ref($obj) eq "HASH") { elsif (ref($obj) eq "GLOB") { } else { @newobjs = values %$obj; } map { my @newpath = (@{$node->{path}}, $obj); my $newnode = {obj=>$_, path=>\@newpath}; push(@nodes, $newnode); } @newobjs; } } return $cycle; } sub max { my @items = @_; my $max; my $item; foreach $item (@items) { if (!defined($max)) { $max = $item; } else { $max = $item if ($item > $max); } } return $max; } 1; go-perl-0.15/GO/xsl/000755 000765 000024 00000000000 12156117750 014040 5ustar00cjmstaff000000 000000 go-perl-0.15/GO/xsl/chadoxml_to_oboxml.xsl000644 000765 000024 00000027231 12156117741 020456 0ustar00cjmstaff000000 000000 DEPRECATED< NOT COMPLETE relationship synonym_type cvterm_property_type no contact OBO_REL no_contact internal no_contact internal cvterm_property_type cvterm_property_type comment obo_rel is_a relationship is_a 1 internal intersection_of cvterm_property_type intersection_of 1 1 obo_rel relationship 1 1 no_contact is_a relationship 1 obo_rel intersection_of internal synonym_type comment_type 0 no_contact no_contact 1 no_contact sequence no_contact ncbi_taxononmy go-perl-0.15/GO/xsl/ipr_to_oboxml.xsl000644 000765 000024 00000003312 12156117741 017443 0ustar00cjmstaff000000 000000 InterPro: InterPro: ipr:can_occur_in taxon_name: go-perl-0.15/GO/xsl/oboxml_filter.xsl000644 000765 000024 00000002374 12156117741 017443 0ustar00cjmstaff000000 000000 go-perl-0.15/GO/xsl/oboxml_to_chadoxml.xsl000644 000765 000024 00000044723 12156117741 020463 0ustar00cjmstaff000000 000000 XORT macros - we can refer to these later relationship synonym_type cvterm_property_type anonymous OBO_REL _global internal internal comment cvterm_property_type comment internal is_anonymous cvterm_property_type is_anonymous OBO_REL is_a relationship is_a 1 external cvterms that are referred to in this document dbxref__ cv/namespaces relationship types terms instances is_a relationship types other relationship types intersection_of; logical definition DAG links. you should only expect to find cvterm_relationships under here for advanced obo1.2 and owl sourced ontologies internal intersection_of cvterm_property_type intersection_of 1 is_a relationship types between typedefs cvterm metadata instance-level relations 1 (obsolete ) relationship 1 1 1 internal cvterm_property_type 1 No ID OBO_REL _default_idspace builtin__is_a intersection_of internal anonymous_cv is_anonymous 1 0 internal synonym_type cv__ comment_type 0 1 sequence ncbi_taxononmy go-perl-0.15/GO/xsl/oboxml_to_dig.xsl000644 000765 000024 00000007233 12156117741 017422 0ustar00cjmstaff000000 000000 # # go-perl-0.15/GO/xsl/oboxml_to_godb_prestore.xsl000644 000765 000024 00000050654 12156117741 021522 0ustar00cjmstaff000000 000000 type/term_synonym.synonym_type_id=term.id category/term_synonym.synonym_category_id=term.id property_key/term_property.property_key_id=term.id term1/term2term.term1_id=term.id term2/term2term.term2_id=term.id type/term2term.relationship_type_id=term.id term1/intersection_of.term1_id=term.id term2/intersection_of.term2_id=term.id type/intersection_of.relationship_type_id=term.id relation1/relation_composition.relation1_id=term.id relation2/relation_composition.relation2_id=term.id inferred_relation/relation_composition.inferred_relation_id=term.id term1/term2term_metadata.term1_id=term.id term2/term2term_metadata.term2_id=term.id type/term2term_metadata.relationship_type_id=term.id type/association_property.relationship_type_id=term.id type/gene_product.type_id=term.id source_db/association.source_db_id=db.id type/synonym.type_id=term.id parentfk:term2term.term2_id parentfk:term2term_metadata.term2_id parentfk:intersection_of.term2_id subset/term_subset.subset_id=term.id is_a is_a relationship inheritance relationship 1 consider consider metadata 1 replaced_by replaced_by metadata 1 is_a 1 1 1 subset 1 is_a obsolete_ obsolete_ 1 1 1 relationship 1 1 is_a 1 relationship 1 Requires relation_composition table, added to DDL 2008/10/27 translating transitive_over meta-property to relation_composition. P transitive_over Q is the same as P.Q->P is_a synonym_scope synonym_type synonym_type alt_id alt_id 0 1 sequence association_qualifier go-perl-0.15/GO/xsl/oboxml_to_obd_prestore.xsl000644 000765 000024 00000100660 12156117741 021344 0ustar00cjmstaff000000 000000 ]> XORT macros - we can refer to these later by stag?? OBO_REL http://www.obofoundry.org/ro# I _global OBO_REL:is_a R OBO_REL:instance_of R owl:inverseOf R oban:in_organism R oban:influences R t t relationship types terms instances annotations is_a relationship types other relationship types logical definitions (by intersection or union) instance-level relations Update policy: all links from this source are deleted and repopulated <_sql op="delete" from="link" match="loaded_from_id" pkey="link_id"> <_sql op="delete" from="tagval" match="loaded_from_id" pkey="tagval_id"> <_sql op="delete" from="sameas" match="loaded_from_id" pkey="sameas_id"> <_sql op="delete" from="alias" match="loaded_from_id" pkey="alias_id"> <_sql op="delete" from="description" match="loaded_from_id" pkey="description_id"> <_sql op="select" from="node" col="node_id" match="uid"> <_sql op="select" from="node" col="node_id" match="uid"> t C t R I _default_idspace t t I I subset t No ID __source now __source now No ID owl:inverseOf I U t is_a I t comment R oboMetaModel:description R dc:creator R dc:date R oboMetaModel:provenance R t : oboMetaModel:xref t alt_id definition R oboMetaModel:inSubset t t annotated entity : full_name synonym in_organism NCBITaxon: is_a annotations influences t the annotation is the attribution for the link t t I instance_of oban:Annotation t the annotation is the attributation for the link t I instance_of oban:Annotation I __source I instance_of obd_meta:Document obd_meta:md5 obd_meta:modification_time obd_meta:source_fullpath t C I is_a &oboContent; # _ &oboContent; _global/ go-perl-0.15/GO/xsl/oboxml_to_obotext.xsl000644 000765 000024 00000022425 12156117741 020343 0ustar00cjmstaff000000 000000 format-version: 1.2 [Term] [Typedef] id: name: namespace: subsetdef: synonymtypedef: : true intersection_of: ! : {namespaces=" "} ! : {namespaces=" "} ! synonym: " " EXACT BROAD NARROW UNSPECIFIED [] [ , ] : " " def: " " xref: xref_analog: : [Instance] id: instance_of: property_value: " " go-perl-0.15/GO/xsl/oboxml_to_owl.xsl000644 000765 000024 00000112221 12156117741 017452 0ustar00cjmstaff000000 000000 ]> obo &oboContent; oboInOwl meta-model - we must declare this here, otherwise the ontology will be OWL-Full unless we import &oboInOwl; : &xref; # _ This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi Collection Collection obo: &oboContent; # obo: &oboContent; # &oboContent; &oboContent; &xsd; _ &oboContent; # _ &oboContent; OBO_REL# &BFO; &RO; &oboContent; obo# !"#$%'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~ !'()*-.0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ_abcdefghijklmnopqrstuvwxyz~ 0123456789ABCDEF Warning: string contains a character that is out of range! Substituting "?". 63 go-perl-0.15/GO/xsl/oboxml_to_racer.xsl000644 000765 000024 00000006340 12156117741 017751 0ustar00cjmstaff000000 000000 (in-knowledge-base test x-test) (signature :atomic-concepts ( ) :roles ( ( ) )) (concept-subsumes? ) (concept-ancestors ) (equivalent (and )) (implies ) (implies (some )) (some ) go-perl-0.15/GO/xsl/oboxml_to_simple_owl.xsl000644 000765 000024 00000011673 12156117741 021034 0ustar00cjmstaff000000 000000 Collection # # go-perl-0.15/GO/xsl/oboxml_to_summary_table.xsl000644 000765 000024 00000004056 12156117741 021523 0ustar00cjmstaff000000 000000 #ID NAME NAMESPACE OBS IS_A REL DEF SYNS ALT-IDS XREFS OBSOLETE CURRENT ; = ; : ; go-perl-0.15/GO/xsl/owl_to_oboxml.xsl000644 000765 000024 00000023422 12156117741 017456 0ustar00cjmstaff000000 000000
true ignoring datatype property is_a relationship to unresolvable Cannot resolve ID: go-perl-0.15/GO/xsl/text_html.xsl000644 000765 000024 00000007610 12156117741 016604 0ustar00cjmstaff000000 000000 ontology_html.css stylesheet text/css !type: % is_a is a !type: < part_of Part of
  • $ ; part-of is_a
  • % < part-of part-of
; < % # ; ; synonym: go-perl-0.15/GO/Parsers/base_parser.pm000644 000765 000024 00000032241 11615622157 017500 0ustar00cjmstaff000000 000000 # $Id: base_parser.pm,v 1.18 2008/03/13 05:16:40 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Parsers::base_parser; =head1 NAME GO::Parsers::base_parser - base class for parsers =head1 SYNOPSIS do not use this class directly; use GO::Parser =cut =head1 DESCRIPTION =head1 AUTHOR =cut use Carp; use FileHandle; use Digest::MD5 qw(md5_hex); use GO::Parser; use Data::Stag qw(:all); use base qw(Data::Stag::BaseGenerator Exporter); use strict qw(subs vars refs); # Exceptions sub throw { my $self = shift; confess("@_"); } sub warn { my $self = shift; warn("@_"); } sub messages { my $self = shift; $self->{_messages} = shift if @_; return $self->{_messages}; } *error_list = \&messages; sub message { my $self = shift; my $msg = shift; CORE::warn 'deprecated'; $self->parse_err($msg); } =head2 show_messages Usage - Returns - Args - =cut sub show_messages { my $self = shift; my $fh = shift; $fh = \*STDERR unless $fh; foreach my $e (@{$self->error_list || []}) { printf $fh "\n===\n Line:%s [%s]\n%s\n %s\n\n", $e->{line_no} || "", $e->{file} || "", $e->{line} || "", $e->{msg} || ""; } } sub init { my $self = shift; $self->messages([]); $self->acc2name_h({}); $self; } sub parsed_ontology { my $self = shift; $self->{parsed_ontology} = shift if @_; return $self->{parsed_ontology}; } =head2 normalize_files Usage - @files = $parser->normalize_files(@files) Returns - Args - takes a list of filenames/paths, "glob"s them, uncompresses any compressed files and returns the new file list =cut sub normalize_files { my $self = shift; my $dtype; my @files = map {glob $_} @_; my @errors = (); my @nfiles = (); # uncompress any compressed files foreach my $fn (@files) { if ($fn =~ /\.gz$/) { my $nfn = $fn; $nfn =~ s/\.gz$//; my $cmd = "gzip -dc $fn > $nfn"; #print STDERR "Running $cmd\n"; my $err = system("$cmd"); if ($err) { push(@errors, "can't uncompress $fn"); next; } $fn = $nfn; } if ($fn =~ /\.Z$/) { my $nfn = $fn; $nfn =~ s/\.Z$//; my $cmd = "zcat $fn > $nfn"; print STDERR "Running $cmd\n"; my $err = system("$cmd"); if ($err) { push(@errors, "can't uncompress $fn"); next; } $fn = $nfn; } push(@nfiles, $fn); } my %done = (); @files = grep { my $d = !$done{$_}; $done{$_} = 1; $d } @nfiles; return @files; } sub fire_source_event { my $self = shift; my $file = shift || die "need to pass file argument"; my @fileparts = split(/\//, $file); my @stat = stat($file); my $mtime = $stat[9]; my $parsetime = time; my $md5 = md5_hex($fileparts[-1]); $self->event(source => [ [source_id => $file ], [source_type => 'file'], [source_fullpath => $file ], [source_path => $fileparts[-1] ], [source_md5 => $md5], [source_mtime => $mtime ], [source_parsetime => $parsetime ], ] ); return; } sub parse_assocs { my $self = shift; my $fn = shift; $self->dtype('go_assoc'); my $p = GO::Parser->get_parser_impl('go_assoc'); %$p = %$self; $p->parse($fn); return; } sub parse_to_graph { my $self = shift; my $h = GO::Parser->create_handler('obj'); $self->handler($h); $self->parse(@_); return $h->graph; } sub set_type { my ($self, $fmt) = @_; $self->dtype($fmt); my $p = GO::Parser->get_parser_impl($fmt); bless $self, ref($p); return; } sub dtype { my $self = shift; $self->{_dtype} = shift if @_; return $self->{_dtype}; } sub parse_file { my ($self, $file, $dtype) = @_; $self->dtype($dtype); $self->parse($file); } sub xslt { my $self = shift; $self->{_xslt} = shift if @_; return $self->{_xslt}; } sub force_namespace { my $self = shift; $self->{_force_namespace} = shift if @_; return $self->{_force_namespace}; } sub replace_underscore { my $self = shift; $self->{_replace_underscore} = shift if @_; return $self->{_replace_underscore}; } # EXPERIMENTAL: cache objects sub use_cache { my $self = shift; $self->{_use_cache} = shift if @_; return $self->{_use_cache}; } # EXPERIMENTAL: returns subroutine # sub maps name to cached name sub file_to_cache_sub { my $self = shift; my $lite = $self->litemode; my $suffix = $lite ? ".lcache" : ".cache"; $self->{_file_to_cache_sub} = shift if @_; return $self->{_file_to_cache_sub} || sub { my $f = shift; $f =~ s/\.\w+$//; $f .= $suffix; return $f; }; } sub cached_obj_file { my $self = shift; return $self->file_to_cache_sub->(@_); } sub parse { my ($self, @files) = @_; my $dtype = $self->dtype; foreach my $file (@files) { $file = $self->download_file_if_required($file); $self->file($file); #printf STDERR "parsing: $file %d\n", $self->use_cache; if ($self->use_cache) { my $cached_obj_file = $self->cached_obj_file($file); my $reparse; if (-f $cached_obj_file) { my @stat1 = lstat($file); my @stat2 = lstat($cached_obj_file); my $t1 = $stat1[9]; my $t2 = $stat2[9]; if ($t1 >= $t2) { $reparse = 1; } else { $reparse = 0; } } else { $reparse = 1; } if ($reparse) { # make/remake cache my $hclass = "GO::Handlers::obj_storable"; $self->load_module($hclass); my $cache_handler = $hclass->new; $self->use_cache(0); my $orig_handler = $self->handler; $self->handler($cache_handler); $cache_handler->file($cached_obj_file); $self->parse($file); my $g = $cache_handler->graph; $self->use_cache(1); my $p2 = GO::Parser->new({ format=>'GO::Parsers::obj_emitter'}); $p2->handler($orig_handler); # this is the only state we need to copy across if ($self->can('xslt')) { $p2->xslt($self->xslt); } $p2->emit_graph($g); } else { # use cache my $p2 = GO::Parser->new({format=>'obj_storable'}); $p2->handler($self->handler); # this is the only state we need to copy across if ($self->can('xslt')) { $p2->xslt($self->xslt); } $p2->parse_file($cached_obj_file); } next; } # check for XSL transform if ($self->can('xslt') && $self->xslt) { my $xsl = $self->xslt; my $xslt_file = $xsl; if (!-f $xslt_file) { # if GO_ROOT is set then this specifies the location of the xslt dir # if it is not set, assume we are using an installed version of go-perl, # in which case, the xslts will be located along with the perl modules my $GO_ROOT = $ENV{GO_ROOT}; if ($GO_ROOT) { # env var takes precedence; # developers should use this $xslt_file = "$GO_ROOT/xml/xsl/$xsl.xsl"; } # default location is with perl modules if (!$xslt_file || !-f $xslt_file) { # user-mode; xsl will be wherever the GO modules are installed require "GO/Parser.pm"; my $dir = $INC{'GO/Parser.pm'}; $dir =~ s/Parser\.pm/xsl/; $xslt_file = "$dir/$xsl.xsl"; } } if (!-f $xslt_file) { $self->throw("No such file: $xslt_file OR $xsl"); } # first parse input file to intermediate xml my $file1 = _make_temp_filename($file, "-1.xml"); my $handler = $self->handler; my $outhandler1 = Data::Stag->getformathandler("xml"); $outhandler1->file($file1); $self->handler($outhandler1); $self->SUPER::parse($file); $self->handler->finish; # transform intermediate xml using XSLT my $file2 = _make_temp_filename($file, "-2.xml"); # $results contains the post-xslt XML doc; # we either want to write this directly, or # pass it to a handler if ($handler->isa("Data::Stag::XMLWriter")) { # WRITE DIRECTLY: # if the final goal is XML, then write this # directly if ($handler->file) { # $ss->output_file($results,$handler->file); xsltproc($xslt_file,$file1,$handler->file); } else { my $fh = $handler->fh; if (!$fh) { $fh = \*STDOUT; xsltproc($xslt_file,$file1); } else { xsltproc($xslt_file,$file1,$file2); my $infh = FileHandle->new($file2) || die "cannot open $file2"; while (<$infh>) {print $fh $_} unlink($file2); } #$ss->output_fh($results,$handler->fh); } } else { # PASS TO HANDLER: # we need to do another transform, in perl. # # write $results of stylesheet transform #$ss->output_file($results,$file2); xsltproc($xslt_file,$file1,$file2); # clear memory #$ss=undef; #$xslt=undef; #$results=undef; # we pass the final XML to the handler my $load_parser = new GO::Parser ({format=>'obo_xml'}); $load_parser->handler($handler); $load_parser->errhandler($self->errhandler); $load_parser->parse($file2); unlink($file2); } # restore to previous state $self->handler($handler); } else { # no XSL transform - perform parse as normal # (use Data::Stag superclass) $self->SUPER::parse($file); } } } # applies XSLT and removes input file sub xsltproc { my ($xf,$inf,$outf) = @_; my $cmd = "xsltproc $xf $inf"; if ($outf) { $cmd .= " > $outf"; } my $err = system($cmd); unlink($inf); if ($err) { confess("problem running: $cmd"); } return; } sub _make_temp_filename { my ($base, $suffix) = @_; $base =~ s/.*\///; return "TMP.$$.$base$suffix"; } sub download_file_if_required { my $self = shift; my $f = shift; if ($f =~ /^http:/) { my $tmpf = _make_temp_filename($f,'.obo'); system("wget -O $tmpf $f"); return $tmpf; } else { return $f; } } =head2 litemode Usage - $p->litemode(1) Returns - Args - bool when set, parser will only throw the following events: id|name|is_a|relationship|namespace (optimisation for fast parsing) =cut sub litemode { my $self = shift; $self->{_litemode} = shift if @_; return $self->{_litemode}; } =head2 acc2name_h Usage - $n = $p->acc2name_h->{'GO:0003673'} Returns - hashref Args - hashref [optional] gets/sets a hash mapping IDs to names this will be automatically set by an ontology parser a non-ontology parser will use this index to verify the parsed data (see $p->acc_not_found($id), below) =cut sub acc2name_h { my $self = shift; $self->{_acc2name_h} = shift if @_; $self->{_acc2name_h} = {} unless $self->{_acc2name_h}; return $self->{_acc2name_h}; } =head2 acc_not_found Usage - if ($p->acc_not_found($go_id)) { warn("$go_id not known") } Returns - bool Args - acc string uses acc2name_h - if this hash mapping has been created AND the acc is not in the hash, THEN it is considered not found This is useful for non-ontology parsers (xref_parser, go_assoc_parser) to check whether a referenced ID is actually present in the ontology note that if acc2name_h has not been created, then accs cannot be considered not-found, and this will always return 0/false =cut sub acc_not_found { my $self = shift; my $acc = shift; my $h = $self->acc2name_h; if (scalar(keys %$h) && !$h->{$acc}) { return 1; } return 0; } sub dtd { undef; } 1; go-perl-0.15/GO/Parsers/generic_tagval_parser.pm000644 000765 000024 00000005166 11615622157 021546 0ustar00cjmstaff000000 000000 # $Id: generic_tagval_parser.pm,v 1.3 2007/02/02 05:54:11 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Parsers::generic_tagval_parser; =head1 NAME GO::Parsers::generic_tagval_parser - syntax parsing of GO .def flat files =head1 SYNOPSIS do not use this class directly; use GO::Parser =cut =head1 DESCRIPTION This generates Stag event streams from one of the various GO flat file formats (ontology, defs, xref, associations). See GO::Parser for details Examples of these files can be found at http://www.geneontology.org A description of the event streams generated follows; Stag or an XML handler can be used to catch these events =head1 GO DEFINITION FILES These have a suffix .defs or .definitions =head1 AUTHOR =cut use Exporter; use base qw(GO::Parsers::base_parser); use GO::Parsers::ParserEventNames; # declare XML constants use Carp; use FileHandle; use strict qw(subs vars refs); sub dtd { 'generic_tagval-parser-events.dtd'; } sub _class { 'generic' } sub _id_column {} sub _map_property_type { shift;@_ } sub parse_fh { my ($self, $fh) = @_; my $file = $self->file; $self->start_event(OBO); my $lnum = 0; my $in_record=0; my $class = $self->_class; my $id_column = $self->_id_column; while (my $line = <$fh>) { chomp $line; ++$lnum; next if $line =~ /^\!/; $line =~ s/^\s+$//; if (!$line) { $self->pop_stack_to_depth(1); $in_record = 0; next; } if ($line =~ /^(\S+):\s+(.*)/) { my ($t,$v) = ($1,$2); if (!$in_record) { $self->start_event(INSTANCE); $self->event(instance_of=>$class); if (!$id_column) { $t = 'id'; } $in_record = 1; } if ($id_column && $t eq $id_column) { $t = 'id'; } if ($t eq 'id') { $self->event(ID, $v); } else { my $dt = 'xsd:string'; if ($v =~ /^http:/) { $dt = 'xsd:anyURI'; } $self->event(PROPERTY_VALUE, [[TYPE,$self->_map_property_type($t)], [VALUE,$v], [DATATYPE,$dt]]); } } elsif ($line =~ /^(\S+):\s*$/) { } else { # $self->parse_err("cannot parse:\"$line\""); } } $self->pop_stack_to_depth(0); # end event obo } 1; go-perl-0.15/GO/Parsers/go_assoc_parser.pm000644 000765 000024 00000026754 11615622157 020377 0ustar00cjmstaff000000 000000 # $Id: go_assoc_parser.pm,v 1.22 2009/08/17 00:46:16 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Parsers::go_assoc_parser; =head1 NAME GO::Parsers::go_assoc_parser - syntax parsing of GO gene-association flat files =head1 SYNOPSIS =head1 DESCRIPTION do not use this class directly; use L This generates Stag/XML event streams from GO association files. Examples of these files can be found at http://www.geneontology.org, an example of lines from an association file: SGD S0004660 AAC1 GO:0005743 SGD:12031|PMID:2167309 TAS C ADP/ATP translocator YMR056C gene taxon:4932 20010118 SGD S0004660 AAC1 GO:0006854 SGD:12031|PMID:2167309 IDA P ADP/ATP translocator YMR056C gene taxon:4932 20010118 See L See L For the DTD of the event stream that is generated The following stag-schema describes the events that are generated in parsing an assoc file: (assocs (dbset+ (proddb "s") (prod+ (prodacc "s") (prodsymbol "s") (prodtype "s") (prodtaxa "i") (assoc+ (assocdate "i") (source_db "s") (termacc "s") (is_not "i") (aspect "s") (evidence+ (evcode "s") (ref "s")))))) =cut use Exporter; use base qw(GO::Parsers::base_parser Exporter); #use Text::Balanced qw(extract_bracketed); use GO::Parsers::ParserEventNames; use GO::Parser; use Carp; use FileHandle; use strict; sub dtd { 'go_assoc-parser-events.dtd'; } sub ev_filter { my $self = shift; $self->{_ev_filter} = shift if @_; return $self->{_ev_filter}; } sub skip_uncurated { my $self = shift; $self->{_skip_uncurated} = shift if @_; return $self->{_skip_uncurated}; } sub parse_fh { my ($self, $fh) = @_; my $file = $self->file; my $product; my $term; my $assoc; my $line_no = 0; my $obo_parser; # an OBO parser may be required for parsing the PROPERTIES column my @COLS = (0..16); my ($PRODDB, $PRODACC, $PRODSYMBOL, $QUALIFIER, $TERMACC, $REF, $EVCODE, $WITH, $ASPECT, $PRODNAME, $PRODSYN, $PRODTYPE, $PRODTAXA, $ASSOCDATE, $SOURCE_DB, $PROPERTIES, # GAF2.0 $ISOFORM, # GAF2.0 ) = @COLS; my @mandatory_cols = ($PRODDB, $PRODACC, $TERMACC, $EVCODE); # # # fb # # FBgn0027087 # Aats-his # gene # 7227 # ... # # GO:0004821 # # NAS # FB:FBrf0105495 # ... # # # # # $self->start_event(ASSOCS); $self->fire_source_event($file); my @last = map {''} @COLS; my $skip_uncurated = $self->skip_uncurated; my $ev = $self->ev_filter; my %evyes = (); my %evno = (); if ($ev) { if ($ev =~ /\!(.*)/) { $evno{$1} = 1; } else { $evyes{$ev} = 1; } } my $taxa_warning; my $line; my @vals; my @stack = (); while (<$fh>) { # UNICODE causes problems for XML and DB # delete 8th bit tr [\200-\377] [\000-\177]; # see 'man perlop', section on tr/ # weird ascii characters should be excluded tr/\0-\10//d; # remove weird characters; ascii 0-8 # preserve \11 (9 - tab) and \12 (10-linefeed) tr/\13\14//d; # remove weird characters; 11,12 # preserve \15 (13 - carriage return) tr/\16-\37//d; # remove 14-31 (all rest before space) tr/\177//d; # remove DEL character $line_no++; chomp; if (/^\!/) { next; } if (!$_) { next; } # some files use string NULL - we just use empty string as null s/\\NULL//g; $line = $_; $self->line($line); $self->line_no($line_no); @vals = split(/\t/, $line); # normalise columns, and set $h for (my $i=0; $i<@COLS;$i++) { if (defined($vals[$i])) { # remove trailing and # leading blanks $vals[$i] =~ s/^\s*//; $vals[$i] =~ s/\s*$//; # sometimes - is used for null $vals[$i] =~ s/^\-$//; # TAIR seem to be # doing a mysql dump... $vals[$i] =~ s/\\NULL//; } if (!defined($vals[$i]) || length ($vals[$i]) == 0) { if ( grep {$i == $_} @mandatory_cols) { $self->parse_err("no value defined for col ".($i+1)." in line_no $line_no line\n$line\n"); next; } $vals[$i] = ''; } } my ($proddb, $prodacc, $prodsymbol, $qualifier, $termacc, $ref, $evcode, $with, $aspect, $prodname, $prodsyn, $prodtype, $prodtaxa, $assocdate, $source_db, $properties, # GAF2.0 $isoform) = @vals; # GAF2.0 # backward compatibility GAF2.0 -> GAF1.0 $properties = '' unless defined $properties; $isoform = '' unless defined $isoform; $assocdate = '' unless defined $assocdate; $source_db = '' unless defined $source_db; # if (!grep {$aspect eq $_} qw(P C F)) { # $self->parse_err("Aspect column says: \"$aspect\" - aspect must be P/C/F"); # next; # } if ($self->acc_not_found($termacc)) { $self->parse_err("No such ID: $termacc"); next; } if (!($ref =~ /:/)) { # ref does not have a prefix - we assume it is medline $ref = "medline:$ref"; } if ($skip_uncurated && $evcode eq "IEA") { next; } if (%evyes && !$evyes{$evcode}) { next; } if (%evno && $evno{$evcode}) { next; } my @prodtaxa_ids = split(/\|/,$prodtaxa); @prodtaxa_ids = map { s/taxonid://gi; s/taxon://gi; if ($_ !~ /\d+/) { if (!$taxa_warning) { $taxa_warning = 1; $self->parse_err("No NCBI TAXON wrong fmt: $_"); $_ = ""; } } $_; } @prodtaxa_ids; @prodtaxa_ids = grep {$_} @prodtaxa_ids; my $main_taxon_id = shift @prodtaxa_ids; if (!$main_taxon_id) { if (!$taxa_warning) { $taxa_warning = 1; $self->parse_err("No NCBI TAXON specified; ignoring"); } } # check for new element; shift a level my $new_dbset = $proddb ne $last[$PRODDB]; my $new_prodacc = $prodacc ne $last[$PRODACC] || $new_dbset; my $new_assoc = ($termacc ne $last[$TERMACC]) || $new_prodacc || ($qualifier ne $last[$QUALIFIER]) || ($source_db ne $last[$SOURCE_DB]) || ($assocdate ne $last[$ASSOCDATE]) || ($isoform ne $last[$ISOFORM]); #if (!$new_prodacc && ($prodtaxa ne $last[$PRODTAXA])) { ## Before we declare an error, let's make sure that we're not ## talking about secondary taxons... my $chopped_taxa = $prodtaxa; my $chopped_prev_taxa = $last[$PRODTAXA]; $chopped_taxa =~ s/\|.+//; $chopped_prev_taxa =~ s/\|.+//; if (!$new_prodacc && ($chopped_taxa ne $chopped_prev_taxa)) { # two identical gene products with the same taxon # IGNORE! $self->parse_err("different taxa ($prodtaxa, $last[$PRODTAXA]) for same product $prodacc"); next; } # close finished events if ($new_assoc) { $self->pop_stack_to_depth(3) if $last[$TERMACC]; # $self->end_event("assoc") if $last[$TERMACC]; } if ($new_prodacc) { $self->pop_stack_to_depth(2) if $last[$PRODACC]; # $self->end_event("prod") if $last[$PRODACC]; } if ($new_dbset) { $self->pop_stack_to_depth(1) if $last[$PRODDB]; # $self->end_event("dbset") if $last[$PRODDB]; } # open new events if ($new_dbset) { $self->start_event(DBSET); $self->event(PRODDB, $proddb); } if ($new_prodacc) { $self->start_event(PROD); $self->event(PRODACC, $prodacc); $self->event(PRODSYMBOL, $prodsymbol); $self->event(PRODNAME, $prodname) if $prodname; $self->event(PRODTYPE, $prodtype) if $prodtype; if ($main_taxon_id) { $self->event(PRODTAXA, $main_taxon_id); } my $syn = $prodsyn; if ($syn) { my @syns = split(/\|/, $syn); my %ucheck = (); @syns = grep { if ($ucheck{lc($_)}) { 0; } else { $ucheck{lc($_)} = 1; 1; } } @syns; map { $self->event(PRODSYN, $_); } @syns; } } if ($new_assoc) { my $assocdate = $assocdate; $self->start_event(ASSOC); if ($assocdate) { if ($assocdate && length($assocdate) == 8) { $self->event(ASSOCDATE, $assocdate); } else { $self->parse_err("ASSOCDATE wrong format (must be YYYYMMDD): $assocdate"); } } $self->event(SOURCE_DB, $source_db) if $source_db; $self->event(TERMACC, $termacc); my @quals = map lc,split(/[\|]\s*/,$qualifier || ''); my $is_not = grep {/^not$/i} @quals; $self->event(IS_NOT, $is_not || '0'); $self->event(QUALIFIER, $_) foreach @quals; $self->event(SPECIES_QUALIFIER, $_) foreach @prodtaxa_ids; # all REMAINING (after "|') tax ids are qualifiers $self->event(ASPECT, $aspect); if ($isoform) { $self->event(ISOFORM, $isoform); } if ($properties) { my @properties_list = split(/\|/,$properties); if (!$obo_parser) { $obo_parser = GO::Parser->new({format=>'obo_text'}); } foreach my $p (@properties_list) { my $diffs = $obo_parser->parse_differentia($p); $self->event(PROPERTIES, $diffs); } } } $self->start_event(EVIDENCE); $self->event(EVCODE, $evcode); if ($with) { # TODO: discriminate between pipes and commas # (semicolon is there for legacy reasons - check if this can be removed) my @with_accs = split(/\s*[\|\;\,]\s*/, $with); $self->event(WITH, $_) foreach (grep (/:/, @with_accs)); # we have found errors where the : was left out, this just skips # no longer checks for cardinality errors } my @refs = split(/\|/, $ref); map { $self->event(REF, $_) } @refs; $self->end_event(EVIDENCE); #@last = @vals; @last = ( $proddb, $prodacc, $prodsymbol, $qualifier, $termacc, $ref, $evcode, $with, $aspect, $prodname, $prodsyn, $prodtype, $prodtaxa, $assocdate, $source_db, $properties, $isoform, ); } $fh->close; $self->pop_stack_to_depth(0); } 1; # 2.864 orig/handler # 2.849 opt/handler # 1.986 orig/xml # 1.310 opt/xml go-perl-0.15/GO/Parsers/go_def_parser.pm000644 000765 000024 00000005376 11615622157 020022 0ustar00cjmstaff000000 000000 # $Id: go_def_parser.pm,v 1.6 2005/03/22 22:38:32 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Parsers::go_def_parser; =head1 NAME GO::Parsers::go_def_parser - syntax parsing of GO .def flat files =head1 SYNOPSIS do not use this class directly; use GO::Parser =cut =head1 DESCRIPTION This generates Stag event streams from one of the various GO flat file formats (ontology, defs, xref, associations). See GO::Parser for details Examples of these files can be found at http://www.geneontology.org A description of the event streams generated follows; Stag or an XML handler can be used to catch these events =head1 GO DEFINITION FILES These have a suffix .defs or .definitions =head1 AUTHOR =cut use Exporter; use base qw(GO::Parsers::base_parser); use GO::Parsers::ParserEventNames; # declare XML constants use Carp; use FileHandle; use strict qw(subs vars refs); sub dtd { 'go_def-parser-events.dtd'; } sub parse_fh { my ($self, $fh) = @_; my $file = $self->file; $self->start_event(OBO); my $lnum = 0; my $in_def=0; while (my $line = <$fh>) { chomp $line; ++$lnum; next if $line =~ /^\!/; next if !$line; if ($line =~ /^term:\s+(.*)/) { $self->pop_stack_to_depth(1); $self->start_event(TERM); $self->event(NAME, $1); $in_def = 0; } elsif ($line =~ /^goid:\s+(\S+)/) { if ($in_def) { $self->parse_err("goid in definition"); } $self->event(ID,$1); } elsif ($line =~ /^(\w+):\s+(.*)/) { my ($k, $v) = ($1,$2); if (!$in_def) { $in_def = 1; $self->start_event(DEF); } if ($k eq 'definition_reference') { my ($db, $acc) = ('', $v); if ($v =~ /(.*)?:(\S+)/) { ($db,$acc) = ($1,$2); } $self->event(DBXREF,[[acc=>$acc],[dbname=>$db]]); next; } $k =~ s/^definition$/defstr/; $self->event($k=>$v); if ($k eq 'comment') { my $stag = $self->parse_comment($v); $self->event(@$stag) if $stag; } } else { $self->parse_err("trailing text"); } } $self->pop_stack_to_depth(0); # end event obo } sub parse_comment { my $self = shift; my $v = shift; my $stag; if ($v =~ /This term was made obsolete because (.*) To update annotations, (\w+) (.*)/) { my $reason = $1; my $update_type = $2; my $nu = $3; my @nu_ids = (); while ($nu =~ / ; (\S+)\'/) { push(@nu_ids, $1); $nu =~ s/ ; (\S+)\'//; } $stag = [obsolete_data=>[ [reason=>$reason], [update_type=>$update_type], (map {[id=>$_]} @nu_ids), ]]; } return $stag; } 1; go-perl-0.15/GO/Parsers/go_ids_parser.pm000644 000765 000024 00000005077 11615622157 020041 0ustar00cjmstaff000000 000000 # $Id: go_ids_parser.pm,v 1.2 2007/08/03 01:52:23 sjcarbon Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Parsers::go_ids_parser; =head1 NAME GO::Parsers::go_ids_parser - syntax parsing of flat files containing GO IDs. =head1 SYNOPSIS =head1 DESCRIPTION do not use this class directly; use L This generates Stag/XML event streams from files containing GO IDs. Lines from such a file might be: GO:0000003 GO:0000166 GO:0000228 GO:0000229 GO:0003674 GO:0003676 GO:0003677 GO:0003682 GO:0003700 GO:0003723 GO:0003774 GO:0003779 GO:0005634 GO:0005635 GO:0005654 See L For the DTD of the event stream that is generated =cut use Exporter; use base qw(GO::Parsers::base_parser Exporter); #use Text::Balanced qw(extract_bracketed); use GO::Parsers::ParserEventNames; use Carp; use FileHandle; use strict; ## sub dtd { 'go_ids-parser-events.dtd'; } ## sub parse_fh { my ($self, $fh) = @_; #my $file = $self->file; my $term; my $line_no = 0; my %done = (); # Don't bother with things already done. $self->start_event(OBO); #$self->fire_source_event($file); while (<$fh>) { $line_no++; # UNICODE causes problems for XML and DB # delete 8th bit tr [\200-\377] [\000-\177]; # see 'man perlop', section on tr/ # weird ascii characters should be excluded tr/\0-\10//d; # remove weird characters; ascii 0-8 # preserve \11 (9 - tab) and \12 (10-linefeed) tr/\13\14//d; # remove weird characters; 11,12 # preserve \15 (13 - carriage return) tr/\16-\37//d; # remove 14-31 (all rest before space) tr/\177//d; # remove DEL character ## Skip if not there or comment. next if ! $_; next if /^\!/; # some files use string NULL - we just use empty string as null s/\\NULL//g; $self->line($_); $self->line_no($line_no); ## Remove leadng and trailing whitespace. s/^[\s\n]+//; s/[\s\n]+$//; my @accs = split /\s+/; for( my $i = 0; $i < @accs; $i++ ){ my $acc = $accs[$i]; ## Massage a bit more. if( $acc ){ next if $done{$acc}; # skip if done ## if( $self->acc_not_found($acc) ){ $self->parse_err("No such ACC: $acc"); next; } $self->start_event(TERM); $self->event(ID, $acc); $self->end_event(TERM); $done{$acc} = 1; } } } # This is causing problems during direct fh access. $fh->close; $self->pop_stack_to_depth(0); } 1; go-perl-0.15/GO/Parsers/go_ont_parser.pm000644 000765 000024 00000025531 11615622157 020057 0ustar00cjmstaff000000 000000 # $Id: go_ont_parser.pm,v 1.17 2005/08/19 01:48:09 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Parsers::go_ont_parser; =head1 NAME GO::Parsers::go_ont_parser - syntax parsing of GO .ontology flat files =head1 SYNOPSIS do not use this class directly; use GO::Parser =cut =head1 DESCRIPTION This generates Stag event streams from one of the various GO flat file formats (ontology, defs, xref, associations). See GO::Parser for details Examples of these files can be found at http://www.geneontology.org A description of the event streams generated follows; Stag or an XML handler can be used to catch these events =head1 GO ONTOLOGY FILES These files have the .ontology suffix. The stag-schema for the event streams generated look like this: (ontology (source (source_type "s") (source_path "s") (source_mtime "i")) (term+ (id "s") (name "s") (is_root? "i") (relationship+ (type "s") (to "s")) (dbxref* (dbname "s") (acc "s")) (synonym* "s") (secondaryid* "s") (is_obsolete? "i"))) =head1 AUTHOR =cut use Exporter; use base qw(GO::Parsers::base_parser); use GO::Parsers::ParserEventNames; use Carp; use FileHandle; use strict qw(vars refs); sub dtd { 'go_ont-parser-events.dtd'; } sub regesc { my $code = shift; if ($code eq '|') { $code = '\|'; } if ($code eq '*') { $code = '\*'; } if ($code eq '?') { $code = '\?'; } $code; } sub reln_regexp { join("|", map {" ".regesc($_)." "} keys %{shift || {}}); } sub parse_fh { my ($self, $fh) = @_; my $file = $self->file; my $is_go; my %typemap = ('$'=>'is_a', '%'=>'is_a', '<'=>'part_of', '~'=>'derives_from', ); my $reln_regexp = reln_regexp(\%typemap); my $lnum = 0; my @stack = (); my $obs_depth; my $usc = $self->replace_underscore; $self->start_event(OBO); my %rtypenameh = (); $self->fire_source_event($file); $self->handler->{ontology_type} = $self->force_namespace; my $root_id; PARSELINE: while (<$fh>) { # UNICODE causes problems for XML and DB # delete 8th bit tr [\200-\377] [\000-\177]; # see 'man perlop', section on tr/ # weird ascii characters should be excluded tr/\0-\10//d; # remove weird characters; ascii 0-8 # preserve \11 (9 - tab) and \12 (10-linefeed) tr/\13\14//d; # remove weird characters; 11,12 # preserve \15 (13 - carriage return) tr/\16-\37//d; # remove 14-31 (all rest before space) tr/\177//d; # remove DEL character my $line = $_; $line =~ s/\r//g; chomp $line; $line =~ s/\s+$//; ++$lnum; $self->line($line); $self->line_no($lnum); if ($line =~ /^\!type:\s*(\S+)\s+(\S+)/) { my ($code, $name) = ($1, $2); $name =~ s/\s+/_/g; $name = lc($name); if ($name eq 'isa') { $name = 'is_a'; } if ($name eq 'partof') { $name = 'part_of'; } $typemap{$code} = $name unless $code eq '%'; #$code = '\\'.$code; $reln_regexp = reln_regexp(\%typemap); next; } next if $line =~ /^\s*\!/; # comment next if $line eq '\$'; # next if $line eq ''; # last if $line =~ /^\s*\$\s*$/; # end of file # get rid of SGML directives, e.g. FADH2, as these confuse the relationship syntax $line =~ s/<\/?[A-Za-z]+>//g; # $line = &spellGreek ($line); $line =~ s/&([a-z]+);/$1/g; $line =~ /( *)(.*)/; my $body = $2; my $indent = length($1); my $is_obs = 0; while ((scalar @stack) && $stack[$#stack]->[0] >= $indent) { pop @stack; if (defined($obs_depth) && $obs_depth >= $indent) { # no longer under obsolete node $obs_depth = undef; } } my $rchar; if ($body =~ /^(\@\w+\@)(.*)/) { $rchar = $self->typemap($1,\%typemap); $body = $2; $reln_regexp = ' \@\w+\@ '; } else { $rchar = $self->typemap(substr($body, 0, 1),\%typemap); $body = substr($body, 1); } # +++++++++++++++++++++++++++++++++ # parse body / main content of line # +++++++++++++++++++++++++++++++++ my $currxref; my @parts = split(/($reln_regexp)/, $body); for (my $i=0; $i < @parts; $i+=2) { my $part = $parts[$i]; my ($name, @xrefs) = split(/\s*;\s+/, $part); $name = $self->unescapego($name); if ($usc) { $name =~ s/_/$usc/g; } if ($name =~ /^obsolete/i && $i==0) { $obs_depth = $indent; } if ($name eq "Gene_Ontology") { $is_go =1; } if (defined($obs_depth)) { # set obsolete flag if we # are anywhere under the obsolete node $is_obs = 1; } if ($indent < 2 && $is_go) { $self->handler->{ontology_type} = $name unless $self->force_namespace; } elsif ($indent < 1) { $self->handler->{ontology_type} = $name unless $self->force_namespace; } elsif (!$self->handler->{ontology_type}) { $self->handler->{ontology_type} = $name; } else { } my $pxrefstr = shift @xrefs; if (!$pxrefstr) { $pxrefstr = ''; $self->parse_err("no ID"); next PARSELINE; } # get the GO id for this line my ($pxref, @secondaryids) = split(/,\s+/, $pxrefstr); if ($i==0) { $currxref = $pxref; if ($currxref =~ /\s/) { my $msg = "\"$pxref\" doesn't look valid"; $self->parse_err($msg); } my $a2t = $self->acc2name_h; my $prevname = $a2t->{$currxref}; if ($prevname && $prevname ne $name) { my $msg = "clash on $pxref; was '$prevname' now '$name'"; $self->parse_err($msg); next PARSELINE; } if ($prevname && $indent) { # seen before - no new data, skip to avoid repeats next PARSELINE; } $a2t->{$currxref} = $name; $root_id = $currxref if !$indent; $a2t->{$currxref} = $name; $self->start_event(TERM); $self->event(ID, $currxref); $self->event(NAME, $name); $self->event(IS_OBSOLETE, $is_obs) if $is_obs; $self->event(IS_ROOT, 1) if !$indent; $self->event(NAMESPACE, $self->handler->{ontology_type}) if $self->handler->{ontology_type}; map { $self->event(ALT_ID, $_); } @secondaryids; } # map { # $self->start_event("secondaryid"); # $self->event("id", $_); # $self->end_event("secondaryid"); # } @secondaryids; if ($i == 0) { # first part on line has main # info for this term foreach my $xref (@xrefs) { my ($db,@rest) = split(/:/,$xref); my $dbacc = $self->unescapego(join(":", @rest)); if ($db eq "synonym") { $self->event(SYNONYM, [[synonym_text=>$dbacc], [type=>'related']]); } # elsif ($dbacc =~ /\s/) { # # db accessions should not have # # spaces in them - this # # indicates that there is a problem; # # eg synonym spelled wrongly # # [MetaCyc accessions have spaces!] # my $msg = # "ignoring $db:$dbacc - doesn't look like accession"; # $self->parse_err({msg=>$msg, # line_no=>$lnum, # line=>$line, # file=>$file}); # } else { $self->event(XREF_ANALOG, [[dbname => $db], [acc => $dbacc]]); } } } else { # other parts on line # have redundant info, # but the relationship # part is useful my $rchar = $self->typemap($parts[$i-1],\%typemap); if (!$pxref) { $self->parse_err("problem with $name $currxref: rel $rchar has no parent/object"); } else { $self->relationship_event($rchar, $pxref); } } } #$line =~ s/\\//g; # end of parse body if (@stack) { my $up = $stack[$#stack]; my $obj = $up->[1]; if (!$obj) { $self->parse_err("problem with $currxref: rel $rchar has no parent/object [top of stack is @$up]"); } else { $self->relationship_event($rchar, $up->[1]); $rtypenameh{$rchar} = 1; } } else { # $self->event("rel", "isa", "TOP"); } $self->end_event(TERM); push(@stack, [$indent, $currxref]); } $self->pop_stack_to_depth(1); foreach my $rtypename (keys %rtypenameh) { next if $rtypename eq 'is_a'; $self->event(TYPEDEF, [ [id=>$rtypename], [name=>$rtypename], [domain=>$root_id], [range=>$root_id], ]); } $self->pop_stack_to_depth(0); $self->parsed_ontology(1); } sub relationship_event { my $self = shift; my $rchar = shift; my $to = shift; if ($rchar eq 'is_a' || $rchar eq 'isa') { $self->event(IS_A, $to); } else { $self->event(RELATIONSHIP, [[type => $rchar], [to=>$to]]); } } sub typemap { my $self = shift; my $ch = shift; my %typemap = %{shift || {}}; $ch =~ s/^ *//g; $ch =~ s/ *$//g; if ($typemap{$ch}) { $ch = $typemap{$ch}; } elsif ($typemap{'\\'.$ch}) { $ch = $typemap{$ch}; } elsif ($ch =~ /^\@(\w+)\@/) { $ch = lc($1); } else { } $ch =~ s/isa/is_a/; $ch =~ s/partof/part_of/; $ch; } sub unescapego { my $self = shift; my $ch = shift; $ch =~ s/\\//g; $ch; } 1; go-perl-0.15/GO/Parsers/go_xref_parser.pm000644 000765 000024 00000006203 11615622157 020216 0ustar00cjmstaff000000 000000 # $Id: go_xref_parser.pm,v 1.9 2010/02/15 17:34:57 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Parsers::go_xref_parser; =head1 NAME GO::Parsers::go_xref_parser - syntax parsing of GO xref flat files (eg eg2go, metacyc2go) =head1 SYNOPSIS do not use this class directly; use GO::Parser =cut =head1 DESCRIPTION This generates Stag event streams from one of the various GO flat file formats (ontology, defs, xref, associations). See GO::Parser for details Examples of these files can be found at http://www.geneontology.org A description of the event streams generated follows; Stag or an XML handler can be used to catch these events =head1 GO XREF FILES These files have a filename *2go; eg metacyc2go (dbxrefs (termdbxref+ (termacc "s") (dbxref (xref_dbname "s") (xref_key "s")))) =head1 AUTHOR =cut use Carp; use FileHandle; use strict qw(vars refs); use base qw(GO::Parsers::base_parser); use GO::Parsers::ParserEventNames; # XML constants sub dtd { 'go_xref-parser-events.dtd'; } sub parse_fh { my ($self, $fh) = @_; my $file = $self->file; my $lnum = 0; $self->start_event(OBO); while (<$fh>) { chomp; tr [\200-\377] [\000-\177]; # see 'man perlop', section on tr/ # weird ascii characters should be excluded tr/\0-\10//d; # remove weird characters; ascii 0-8 # preserve \11 (9 - tab) and \12 (10-linefeed) tr/\13\14//d; # remove weird characters; 11,12 # preserve \15 (13 - carriage return) tr/\16-\37//d; # remove 14-31 (all rest before space) tr/\177//d; # remove DEL character $lnum++; next if /^\!/; next if /^$/; $self->line($_); $self->line_no($lnum); my ($ext, @goids) = split(' > ',$_); if ($ext =~ /^([\w\-]+):?(\S+)(.*)/) { my ($db,$dbacc,$name) = ($1,$2,$3); $name =~ s/^\s+// if $name; $dbacc =~ s/\s/\%20/g; foreach my $goid (@goids) { if ($goid =~ /(.*)\s+\;\s+(.*)/) { my $goacc = $2; if ($self->acc_not_found($goacc)) { $self->parse_err("No such ID: $goacc"); next; } $self->start_event(TERM); $self->event(ID, $goacc); $self->start_event(XREF_ANALOG); $self->event(ACC, $dbacc); $self->event(DBNAME, $db); if ($name) { $self->event(NAME, $name) } $self->end_event(XREF_ANALOG); $self->end_event(TERM); } else { $self->parse_err("would not extract GO ID from: $goid"); } } } else { $self->parse_err("bad external ID: $ext in line: $_"); } } $self->end_event(OBO); } 1; go-perl-0.15/GO/Parsers/locuslink_parser.pm000644 000765 000024 00000011104 11615622157 020564 0ustar00cjmstaff000000 000000 # $Id: locuslink_parser.pm,v 1.1 2004/01/27 23:52:24 cmungall Exp $ # # Adapterd from BioPerl module for Bio::SeqIO::locuslink # # POD documentation - main docs before the code =head1 NAME GO::Parsers::locuslink_parser - =head1 SYNOPSIS =head1 DESCRIPTION =cut package GO::Parsers::locuslink_parser; use strict; use vars qw(@ISA); use base qw(GO::Parsers::base_parser); sub _initialize { my($self,@args) = @_; $self->SUPER::_initialize(@args); } sub transitions { return qw( NM transcript NG 0 CONTIG 0 EVID evidence ACCNUM accession OFFICIAL_SYMBOL 0 BUTTON url DB_DESCR dbxref /DB_LINK dbxref ); } sub compounds { return ( STS => [qw(sts_acc chr_num unk symbol type src)], GO => [qw(aspect term evcode go_acc src unk)], EXTANNOT => [qw(aspect term evcode src unk)], CDD => [qw(domain domain_acc num unk score)], NG => [qw(acc u1 u2 u3 u4)], CONTIG => [qw(contig_acc u1 u2 u3 u4 strand chr_num src)], XM => [qw(acc gi)], XP => [qw(acc gi)], XG => [qw(acc gi)], ACCNUM => [qw(acc gi)], PROT => [qw(acc gi)], MAP => [qw(map_loc link code)], SUMFUNC => [qw(descr src)], GRIF => [qw(grif_pmid descr)], COMP => [qw(comp_acc symbol2 chr_num2 map_pos2 locusacc2 chr_num1 symbol1 src)], ); } sub record_tag {'locusset'} sub parse_fh { my $self = shift; my $fh = shift; $self->start_event('locusset'); my (%record,@results,$search,$ref,$cddref); my ($PRESENT,@keep); # LOCUSLINK entries begin w/ >> local $/=">>"; # slurp in a whole entry and return if no more entries return unless my $entry = <$fh>; # if its the first entry you have to slurp it in again if ($entry eq '>>'){ #first entry return unless $entry = <$fh>; } if (!($entry=~/LOCUSID/)){ $self->throw("No LOCUSID in first line of record. ". "Not LocusLink in my book."); } my %transitions = $self->transitions; my %compounds = $self->compounds; # my %grouped = (); # foreach (keys %transitions) { # if (/\;/) { # my $t = $transitions{$_}; # my (@keylist) = split(/\;/, $_); # foreach (@keylist) { # $transitions{$_} = $t; # $grouped{$_} = $t; # } # } # } $self->start_event('locus'); my $level = 0; my @lines = split(/\n/, $entry); foreach (@lines) { if (/(\w+):\s*(.*)/) { my ($k, $v) = (uc($1), $2); my $transition = $transitions{$k}; if (defined $transition) { if (!$transition) { if ($level) { #$self->throw("uh oh $_") unless $level; $self->end_event($level); } $level = 0; } elsif ($transition eq $level) { $self->end_event($level); $self->start_event($level); } else { if ($level) { $self->end_event($level); $level = 0; } $self->start_event($transition); $level = $transition; } } # for grouped keys, every key must be part of # group to remain part of the same super-element # if ($level && # $grouped{$level}) { # if (!$grouped{$k} || # $grouped{$k} ne $grouped{$level}) { # $self->end_event($level); # $level = 0; # } # } if ($compounds{$k}) { my (@vals) = split(/\|/, $v); my @pairs = ([defline=>$v]); foreach (@{$compounds{$k}}) { my $v = shift @vals; push(@pairs, [$_ => $v]) unless $v eq 'na'; } $self->event(lc($k) => [@pairs]); } else { $self->event(lc($k), $v); } my $end = $transitions{'/'.$k}; if ($end) { $self->end_event($end); $level = 0; } } } if ($level) { $self->end_event($level); } $self->end_event('locus'); $self->end_event('locusset'); return; } 1; go-perl-0.15/GO/Parsers/mesh_parser.pm000644 000765 000024 00000005517 11615622157 017530 0ustar00cjmstaff000000 000000 # $Id: mesh_parser.pm,v 1.4 2005/03/30 21:15:48 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Parsers::mesh_parser; =head1 NAME GO::Parsers::mesh_parser - Parses Mesh ascii text files =head1 SYNOPSIS do not use this class directly; use GO::Parser =cut =head1 DESCRIPTION EXPERIMENTAL =head1 AUTHOR =cut use Exporter; use GO::Parsers::base_parser; @ISA = qw(GO::Parsers::base_parser Exporter); use Carp; use FileHandle; use strict qw(subs vars refs); sub parse_file { my ($self, $file, $dtype) = @_; $self->file($file); my $fh = new FileHandle($file); if (!$fh) {confess "Couldn't open '$file': $!"}; $/ = '*NEWRECORD'; my %treenode2acc = (); $self->start_event("subgraph"); my @accs = (); my $lnum = 0; PARSELINE: while (my $block = <$fh>) { chomp $block; next unless $block; ++$lnum; $self->line($block); $self->line_no($lnum); my @lines = split(/\n/, $block); my ($name, $acc, $def, @mn); map { if (/(\w+) = (.*)/) { my ($key, $val) = ($1, $2); if ($key eq "MH") { $name = $val; } if ($key eq "UI") { $acc = $val; } if ($key eq "MS") { $def = $val; } if ($key eq "MN") { push(@mn, $val); } } } @lines; $self->event('term', [ [name=>$name], [acc=>"Mesh:$acc"], [term_type=>"Mesh"], ] ); $self->event('def', [ ['godef-goid'=>$acc], ['godef-definition'=>$def], ] ) if $def; push(@accs, $acc); foreach (@mn) { $treenode2acc{$_} = $acc; } } foreach my $tn (keys %treenode2acc) { my $child = $treenode2acc{$tn}; my $pn = $tn; $pn =~ s/\.(\d+)$//; if ($pn ne $tn) { my $parent = $treenode2acc{$pn}; $self->event("term" => [ [acc=>$child], [rel=> [ [type => 'isa'], [obj=>$parent] ] ] ] ); } } $self->end_event("subgraph"); $self->parsed_ontology(1); # use Data::Dumper; # print Dumper $self; } 1; go-perl-0.15/GO/Parsers/mgi_assoc_parser.pm000644 000765 000024 00000007123 11615622157 020533 0ustar00cjmstaff000000 000000 # $Id: mgi_assoc_parser.pm,v 1.3 2006/08/05 20:26:12 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Parsers::mgi_assoc_parser; =head1 NAME GO::Parsers::mgi_assoc_parser - parses MGI gene assoc stanza files =head1 SYNOPSIS do not use this class directly; use GO::Parser =head1 DESCRIPTION This is an EXPERIMENTAL module for converting MGIs in-house stanza format this is richer than go_assoc files as it allows combinatorial assocs these are represented with the go-assoc xml element =head1 AUTHOR =cut use Exporter; use base qw(GO::Parsers::base_parser Exporter); use GO::Parsers::ParserEventNames; use Carp; use FileHandle; use strict; sub dtd { 'go_assoc-parser-events.dtd'; } sub ev_filter { my $self = shift; $self->{_ev_filter} = shift if @_; return $self->{_ev_filter}; } sub skip_uncurated { my $self = shift; $self->{_skip_uncurated} = shift if @_; return $self->{_skip_uncurated}; } sub _parse_ids { my $txt = shift; $txt =~ s/^:+//; $txt =~ s/^\s+//; my @parts = split(/\|/,$txt); return grep {$_} map {if (/(\w+:\S+)/){$1}else {()}} @parts; } sub parse_fh { my ($self, $fh) = @_; my $file = $self->file; $self->start_event(ASSOCS); $self->start_event(DBSET); $self->event(PRODDB, 'mgi'); my $curr_gene = ''; while (<$fh>) { # UNICODE causes problems for XML and DB # delete 8th bit tr [\200-\377] [\000-\177]; # see 'man perlop', section on tr/ # weird ascii characters should be excluded tr/\0-\10//d; # remove weird characters; ascii 0-8 # preserve \11 (9 - tab) and \12 (10-linefeed) tr/\13\14//d; # remove weird characters; 11,12 # preserve \15 (13 - carriage return) tr/\16-\37//d; # remove 14-31 (all rest before space) tr/\177//d; # remove DEL character chomp; if (/^\!/) { next; } if (!$_) { next; } if (/^MGI gene:\s(\S+);\s+(\S+)/) { if ($1 ne $curr_gene) { $self->pop_stack_to_depth(2); $self->start_event(PROD); $self->event(PRODACC, $1); $self->event(PRODSYMBOL, $2); $self->event(PRODTYPE, 'gene'); $curr_gene = $1; } } if (/^GO term:\s(.*);\s+(\S+)/) { $self->start_event(ASSOC); $self->event(TERMACC, $2); while (<>) { chomp; last unless $_; if (/^GO evidence:\s*(.*)/) { my $evtxt = $1; foreach (split(/\s+\|\s+/,$evtxt)) { $self->start_event(EVIDENCE); $self->event(EVCODE, $_); $self->end_event(EVIDENCE); } } elsif (/^anatomy:(.*)/) { my @ids = _parse_ids($1); $self->event(property_value=>[[type=>'located_in'], [to=>$_]]) foreach @ids; } elsif (/^cell type:(.*)/) { my @ids = _parse_ids($1); $self->event(property_value=>[[type=>'located_in'], [to=>$_]]) foreach @ids; } else { } } $self->end_event(ASSOC); } } $fh->close; $self->pop_stack_to_depth(0); } 1; go-perl-0.15/GO/Parsers/ncbi_taxon_names_parser.pm000644 000765 000024 00000002655 11615622157 022103 0ustar00cjmstaff000000 000000 # $Id: ncbi_taxon_names_parser.pm,v 1.2 2004/11/24 02:28:02 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Parsers::ncbi_taxon_names_parser; =head1 NAME GO::Parsers::ncbi_taxon_names_parser - OBO Flat file parser object =head1 SYNOPSIS do not use this class directly; use GO::Parser =cut =head1 DESCRIPTION =cut use Exporter; use Text::Balanced qw(extract_quotelike extract_bracketed); use base qw(GO::Parsers::base_parser); use Carp; use FileHandle; use strict qw(subs vars refs); sub parse_fh { my ($self, $fh) = @_; my @stags = (); my $curr_id; $self->start_event('taxon_set'); while (<$fh>) { chomp; my @vals = split(/\s*\|\s*/,$_); my ($id,$val,$xx,$tag) = @vals; if ($curr_id && $id != $curr_id) { $self->event(taxon=>[ [id=>$curr_id], @stags ]); @stags = (); } $tag = lc($tag); $tag =~ s/\s/_/g; $tag =~ tr/a-z0-0_//cd; push(@stags, [$tag=>$val]); if ($tag eq 'scientific_name') { # lump subspecies in with species; # eg genus=Homo, species=sapiens neanderthalensis my ($genus,$species) = ($val =~ /^(\S+)\s+(.*)/); push(@stags, [genus=>$genus],[species=>$species]); } $curr_id = $id; } $self->event(taxon=>[ [id=>$curr_id], @stags ]); $self->end_event('taxon_set'); return; } 1; go-perl-0.15/GO/Parsers/ncbi_taxonomy_parser.pm000644 000765 000024 00000014567 11671573314 021454 0ustar00cjmstaff000000 000000 # $Id: ncbi_taxonomy_parser.pm,v 1.10 2008/02/05 00:34:15 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Parsers::ncbi_taxonomy_parser; =head1 NAME GO::Parsers::ncbi_taxonomy_parser =head1 SYNOPSIS do not use this class directly; use GO::Parser =cut =head1 DESCRIPTION See L =head1 PARSER ARCHITECTURE This generates Stag event streams from one of the various GO flat file formats (ontology, defs, xref, associations). See GO::Parser for details Examples of these files can be found at http://www.geneontology.org A description of the event streams generated follows; Stag or an XML handler can be used to catch these events =cut use Exporter; use base qw(GO::Parsers::base_parser); use GO::Parsers::ParserEventNames; # declare XML constants use Carp; use FileHandle; use strict qw(subs vars refs); my %synonymtypes = ( 'genbank synonym'=>['related'], 'synonym'=>['related'], 'in-part'=>['related'], 'blast name'=>['related'], 'misnomer'=>['related'], 'misspelling'=>['related'], 'scientific name'=>['exact'], 'equivalent name'=>['exact'], 'common name'=>['exact'], 'genbank common name'=>['exact'], 'acronym'=>['broad'], 'genbank acronym'=>['broad'], 'teleomorph'=>['related'], 'anamorph'=>['related'], 'genbank anamorph'=>['related'], ); sub syn { my $name = shift; $name =~ s/\s/_/g; $name =~ s/\-/_/g; $name; } sub parse_fh { my ($self, $fh) = @_; my $file = $self->file; $self->{name_h} = {}; $self->start_event(OBO); $self->event(header=> [ ['default-namespace'=>'ncbi_taxonomy'], ['ontology'=>'ncbitaxon'], [remark=>'autogenerated via GO::Parsers::ncbi_taxonomy_parser'], (map {[synonymtypedef=>[[id=>syn($_)],[name=>$_],[scope=>$synonymtypes{$_}->[0]]]]} keys %synonymtypes), ]); $self->event(typedef=> [ [id=>'has_rank'], [name=>"has_rank"], [def=>[[defstr=>"A metadata relation between a class and its taxonomic rank (eg species, family)"]]], [is_metadata_tag=>1], [comment=>"This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored"] ]); $self->event(term=> [ [id=>_fix_id("taxonomic_rank")], [name=>"taxonomic_rank"], [def=>[[defstr=>"A level of depth within a species taxonomic tree"]]], [comment=>"This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored"] ]); my $lnum = 0; my %h = (); my $text; while (my $line = <$fh>) { chomp $line; if ($line eq '//') { $self->emit_term(\%h,$text); %h = (); $text = ''; } else { if ($line =~ /^([\w\s\-]+)\s+:\s*(.*)/) { my ($k,$v) = ($1,$2); $k = lc($k); # lowercase $k =~ s/\s+$//; # removing trailing ws push(@{$h{$k}},$v); } else { $self->parse_err("Line: $line"); } $text .= "$line\n"; } } $self->pop_stack_to_depth(0); # end event obo } sub _rank_id { my $rank = shift; $rank =~ s/\s+/_/g; _fix_id($rank); } sub _fix_id { return "NCBITaxon:$_[0]"; } sub emit_term { my ($self, $h, $text) = @_; my $id = pop @{$h->{id}}; if (!$id) { $self->parse_err("No id! in:\n$text"); return; } $id = _fix_id($id); $self->start_event(TERM); $self->event(ID,$id); my $name = pop @{$h->{'scientific name'}}; my ($gname) = @{$h->{'genbank common name'} || []}; if (!$name) { $name = $gname; pop @{$h->{'genbank common name'}} if $gname; } if ($self->{name_h}->{$name}) { $name .= " [$id]"; # force unique } $self->{name_h}->{$name} = $id; $self->event(NAME, $name); foreach my $st (keys %synonymtypes) { my $syns = $h->{$st}; next unless $syns; my $scope = $synonymtypes{$st}->[0]; foreach my $s (@$syns) { my @xrefs = (); if ($s =~ /\"(.+)\"\s*(.+)/ || $s =~ /\'(.+)\'\s*(.+)/) { my $xref = $2; $s = $1; $xref =~ s/\s+/_/g; $xref =~ tr/\(\)//d; $xref =~ tr/\[\]//d; $xref =~ s@,@\\,@g; push(@xrefs, [dbxref=>[[acc=>$xref],[dbname=>"NCBITaxonRef"]]]); } $self->event(SYNONYM,[ ['@'=>[['scope',$scope], [SYNONYM_TYPE,syn($st)]]], [SYNONYM_TEXT,$s], @xrefs]); } } my $rank = pop @{$h->{rank}}; if ($rank eq 'no rank') { $rank = undef; } if ($rank) { if (!$self->{__rank}->{$rank}) { $self->{__rank}->{$rank} = 1; $self->event(TERM,[[ID,_rank_id($rank)], [NAME,$rank], [IS_A,_rank_id('taxonomic_rank')], ]); } #this is the correct way to handle this - as annotation properties $self->event(PROPERTY_VALUE,[[TYPE,'has_rank'], [TO,_rank_id($rank)]]) if $rank; # do it this way for now until oboedit is fixed: # $self->event(RELATIONSHIP,[[TYPE,'has_rank'], # [TO,_rank_id($rank)]]) } my $gc = pop @{$h->{'gc id'}}; $self->event(XREF, "GC_ID:$gc") if $gc; my $parent_id = pop @{$h->{'parent id'}}; if ($parent_id) { $parent_id = _fix_id($parent_id); $self->event(IS_A,$parent_id); } $self->end_event(TERM); } 1; go-perl-0.15/GO/Parsers/obj_emitter.pm000644 000765 000024 00000010452 11615622157 017515 0ustar00cjmstaff000000 000000 # $Id: obj_emitter.pm,v 1.3 2006/08/13 02:02:37 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Parsers::obj_emitter; =head1 NAME GO::Parsers::obj_emitter - =head1 SYNOPSIS do not use this class directly; use GO::Parser =head1 DESCRIPTION This is not a file parser - it takes a L object as inputs and fires OBO XML events =cut use Exporter; use base qw(GO::Parsers::base_parser); use GO::Parsers::ParserEventNames; use GO::Model::Graph; use Carp; use FileHandle; use strict; our @TAGS = qw(id name alt_id* namespace comment def subset* is_a* relationship* is_root is_obsolete is_transitive synonym* xref_analog* xref_unknown* ); sub dtd { 'obo-parser-events.dtd'; } sub emit_graph { my ($self, $g) = @_; $self->start_event(OBO); $self->fire_source_event($self->file || "object"); $self->start_event(HEADER); $self->end_event(HEADER); $g->iterate(sub { my $ni = shift; $self->emit_term($ni->term, $g); return; }); $self->end_event(OBO); } sub emit_term { my ($self, $t, $g) = @_; my $stanza = TERM; if ($t->is_relationship_type) { $stanza = TYPEDEF; } $self->start_event($stanza); my $parent_rels = $g->get_parent_relationships($t->acc); foreach my $xtag (@TAGS) { my $multiple = 0; my $tag = $xtag; if ($xtag =~ /(.*)\*$/) { $tag = $1; $multiple = 1; } if ($tag eq ID) { $self->event(ID, $t->acc); } elsif ($tag eq IS_ROOT) { $self->event(IS_ROOT, 1) unless @$parent_rels; } elsif ($tag eq IS_OBSOLETE) { $self->event(IS_OBSOLETE, 1) if $t->is_obsolete; } elsif ($tag eq IS_TRANSITIVE || $tag eq IS_SYMMETRIC || $tag eq IS_ANTI_SYMMETRIC || $tag eq IS_REFLEXIVE || $tag eq INVERSE_OF) { # obo extensions - not dealt with yet } elsif ($tag eq XREF_ANALOG || $tag eq XREF_UNKNOWN) { $self->event($tag=>dbxref($_)) foreach @{$t->dbxref_list || []}; } elsif ($tag eq DEF) { my $xrefs = $t->definition_dbxref_list || []; $self->event(DEF, [[DEFSTR, $t->definition], map { [DBXREF,dbxref($_)] } @$xrefs ]); } elsif ($tag eq SYNONYM) { my $sh = $t->synonyms_by_type_idx || {}; foreach my $type (keys %$sh) { foreach my $val (@{$sh->{$type} || []}) { $self->event(SYNONYM, [['@'=>[[scope=>$type]]], [SYNONYM_TEXT,$val]]); } } } elsif ($tag eq IS_A) { foreach (grep {$_->type eq 'is_a'} @$parent_rels) { $self->event(IS_A, $_->parent_acc) } } elsif ($tag eq RELATIONSHIP) { foreach (grep {$_->type ne 'is_a'} @$parent_rels) { $self->event(RELATIONSHIP, [[TYPE,$_->type], [TO,$_->parent_acc] ]); } } else { if ($multiple) { my $method = $tag.'_list'; my $vals = $t->$method(); $self->event($tag, $_) foreach @$vals; } else { if ($t->can($tag)) { my $v = $t->$tag(); $self->event($tag, $v) if defined $v; } else { warn("no method for: $tag"); } } } } $self->end_event($stanza); } sub dbxref { my $xref = shift || confess; my $name = $xref->name; return [[acc=>$xref->acc], [dbname=>$xref->dbname], $name ? [name=>$xref->name] : () ]; } 1; go-perl-0.15/GO/Parsers/obj_storable_parser.pm000644 000765 000024 00000001220 11615622157 021224 0ustar00cjmstaff000000 000000 package GO::Parsers::obj_storable_parser; use GO::Parsers::ParserEventNames; use strict; use base qw(GO::Parsers::obj_emitter GO::Parsers::base_parser); use GO::Model::Graph; use Storable qw(fd_retrieve); sub parse_fh { my ($self, $fh) = @_; # my $t=time; # print STDERR "RETRIEVING FROM CACHE $t\n"; my $g = fd_retrieve($fh); if ($self->handler->isa("GO::Handler::obj")) { $self->handler->g($g); $self->start_event(OBO); $self->end_event(OBO); } else { $self->emit_graph($g); } # my $t2 = time; # my $td = $t2-$t; # print STDERR "GOT FROM CACHE $t2 [$td]\n"; return $g; } 1; go-perl-0.15/GO/Parsers/obj_yaml_parser.pm000644 000765 000024 00000000463 11615622157 020363 0ustar00cjmstaff000000 000000 package GO::Parsers::obj_yaml_parser; use strict; use base qw(GO::Parsers::obj_emitter GO::Parsers::base_parser); use GO::Model::Graph; use YAML; sub parse_fh { my ($self, $fh) = @_; my $str = join('',<$fh>); $fh->close; my $g = Load($str); $self->emit_graph($g); return $g; } 1; go-perl-0.15/GO/Parsers/obo_parser.pm000644 000765 000024 00000000117 11615622157 017342 0ustar00cjmstaff000000 000000 package GO::Parsers::obo_parser; use base qw(GO::Parsers::obo_text_parser); 1; go-perl-0.15/GO/Parsers/obo_text_parser.pm000644 000765 000024 00000060216 12052734745 020417 0ustar00cjmstaff000000 000000 # $Id: obo_text_parser.pm,v 1.52 2010/03/11 22:40:27 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Parsers::obo_text_parser; =head1 NAME GO::Parsers::obo_text_parser - OBO Flat file parser object =head1 SYNOPSIS do not use this class directly; use GO::Parser =cut =head1 DESCRIPTION =cut use Exporter; use Text::Balanced qw(extract_quotelike extract_bracketed); use base qw(GO::Parsers::base_parser); use GO::Parsers::ParserEventNames; use Carp; use FileHandle; use strict qw(vars refs); sub dtd { 'obo-parser-events.dtd'; } sub parse_fh { my ($self, $fh) = @_; $self->start_event(OBO); $self->parse_fh_inner($fh); $self->pop_stack_to_depth(0); $self->parsed_ontology(1); } sub parse_fh_inner { my ($self, $fh) = @_; my $file = $self->file; my $litemode = $self->litemode; my $is_go; local($_); # latest perl is more strict about modification of $_ $self->fire_source_event($file); $self->start_event(HEADER); my $stanza_count; my $in_hdr = 1; my $is_root = 1; # default my $namespace_set; my $id; my $namespace = $self->force_namespace; # default my $force_namespace = $self->force_namespace; my $usc = $self->replace_underscore; my %id_remap_h = (); my @imports = (); my $is_utf8; # temporary hack... if ($ENV{OBO_IDMAP}) { my @parts = split(/\;/,$ENV{OBO_IDMAP}); foreach (@parts) { if (/(.*)=(.*)/) { $id_remap_h{$1} = $2; } } } my $default_id_prefix; while(<$fh>) { chomp; if (/^encoding:\s*utf/) { $is_utf8 = 1; } if (!$is_utf8) { tr [\200-\377] [\000-\177]; # see 'man perlop', section on tr/ # weird ascii characters should be excluded tr/\0-\10//d; # remove weird characters; ascii 0-8 # preserve \11 (9 - tab) and \12 (10-linefeed) tr/\13\14//d; # remove weird characters; 11,12 # preserve \15 (13 - carriage return) tr/\16-\37//d; # remove 14-31 (all rest before space) tr/\177//d; # remove DEL character } s/^\!.*//; s/[^\\]\!.*//; #s/[^\\]\#.*//; s/^\s+//; s/\s+$//; next unless $_; next if ($litemode && $_ !~ /^(\[|id:|name:|is_a:|relationship:|namespace:|is_obsolete:)/ && !$in_hdr); if (/^\[(\w+)\]\s*(.*)/) { # new stanza # we are at the beginning of a new stanza # reset everything and make sure everything from # previous stanza is exported my $stanza = lc($1); my $rest = $2; if ($in_hdr) { $in_hdr = 0; $self->end_event(HEADER); } else { if (!$namespace_set) { if (!$namespace) { if ($stanza ne 'instance') { #$self->parse_err("missing namespace for ID: $id"); } } else { $self->event(NAMESPACE, $namespace); } } $self->event(IS_ROOT,1) if $is_root; $is_root = 1; # assume root by default; override if parents found $namespace_set = 0; $self->end_event; } $is_root = 0 unless $stanza eq 'term'; $self->start_event($stanza); $id = undef; $stanza_count++; } elsif ($in_hdr) { # we are in the header section if (/^([\w\-]+)\:\s*(.*)/) { # tag-val pair my ($tag, $val) = ($1,$2); if ($tag eq 'subsetdef') { if ($val =~ /(\S+)\s+(.*)/) { my $subset_id = $1; $val = $2; my ($subset_name, $parts) = extract_qstr($val); $val = [[ID,$subset_id], [NAME,$subset_name], map {dbxref($_)} @$parts]; } else { $self->parse_err("subsetdef: expect ID \"NAME\", got: $val"); } } if ($tag eq 'synonymtypedef') { if ($val =~ /(\S+)\s+\"(.*)\"\s*(.*)/) { my $stname = $1; my $stdef = $2; my $scope = $3; $val = [[ID,$stname], [NAME,$stdef], ($scope ? ['scope', $scope] : ())]; } else { $self->parse_err("synonymtypedef: expect ID \"NAME\", got: $val"); } } if ($tag eq 'idspace') { my ($idspace,$global,@rest) = split(' ',$val); if (!$global) { $self->parse_err("idspace requires two columns"); } $val = [['local',$idspace], ['global',$global], (@rest ? [COMMENT,join(' ',@rest)] : ()), ]; } if ($tag eq 'local-id-mapping') { if ($val =~ /(\S+)\s+(.*)/) { # with a local ID mapping we delay binding $val = [['local',$1], ['to',$2]]; } else { $self->parse_err("id-mapping requires two columns"); } } if ($tag eq 'import') { if ($ENV{OBO_FOLLOW_IMPORTS}) { push(@imports, $val); } else { # handled below #$self->event(import=>$val); } } $self->event($tag=>$val); # post-processing if ($tag eq 'default-namespace') { $namespace = $val unless $namespace; } if ($tag eq 'id-mapping') { if ($val =~ /(\S+)\s+(.*)/) { # bind at parse time if ($id_remap_h{$1}) { $self->parse_err("remapping $1 to $2"); } $id_remap_h{$1} = $2; } else { $self->parse_err("id-mapping requires two columns"); } } if ($tag eq 'default-id-prefix') { $default_id_prefix = $val; } } else { $self->parse_err("illegal header entry: $_"); } } # END OF IN-HEADER elsif (/^([\w\-]+)\:\s*(.*)/) { # tag-val pair my ($tag, $val) = ($1,$2); my $qh; ($val, $qh) = extract_quals($val); #$val =~ s/\\//g; my $val2 = $val; $val2 =~ s/\\,/,/g; $val2 =~ s/\\//g; if ($tag eq ID) { if ($id_remap_h{$val}) { $val = $id_remap_h{$val}; } if ($val !~ /:/) { if ($default_id_prefix) { $val = "$default_id_prefix:$val"; } } } elsif ($tag eq NAME) { # replace underscore in name $val = $val2; if ($usc) { $val =~ s/_/$usc/g; } } elsif ($tag eq RELATIONSHIP) { my ($type, @ids) = split(' ', $val2); my $id = shift @ids; if ($id_remap_h{$type}) { $type = $id_remap_h{$type}; } if ($type !~ /:/) { if ($default_id_prefix) { $type = "$default_id_prefix:$type"; } } $val = [[TYPE,$type],[TO,$id]]; push(@$val,map {['additional_argument',$_]} @ids); } elsif ($tag eq INTERSECTION_OF || $tag eq UNION_OF) { my ($type, $id) = split(' ', $val2); if ($id_remap_h{$type}) { $type = $id_remap_h{$type}; } if ($type !~ /:/) { if ($default_id_prefix) { $type = "$default_id_prefix:$type"; } } if (defined $id) { $val = [[TYPE,$type],[TO,$id]]; } else { $id = $type; $val = [[TO,$id]]; } } elsif ($tag eq INVERSE_OF || $tag eq TRANSITIVE_OVER || $tag eq IS_A) { if ($id_remap_h{$val}) { $val = $id_remap_h{$val}; } if ($val !~ /:/) { if ($default_id_prefix) { $val = "$default_id_prefix:$val"; } } } elsif ($tag eq DISJOINT_FROM) { if ($id_remap_h{$val}) { $val = $id_remap_h{$val}; } if ($val !~ /:/) { if ($default_id_prefix) { $val = "$default_id_prefix:$val"; } } } elsif ($tag eq XREF) { $tag = XREF_ANALOG; my $dbxref = dbxref($val); $val = $dbxref->[1]; } elsif ($tag eq XREF_ANALOG) { my $dbxref = dbxref($val); $val = $dbxref->[1]; } elsif ($tag eq XREF_UNKNOWN) { my $dbxref = dbxref($val); $val = $dbxref->[1]; } elsif ($tag eq PROPERTY_VALUE) { if ($val =~ /^(\S+)\s+(\".*)/) { # first form # property_value: relation "literal value" xsd:datatype my $type = $1; my $rest = $2; my ($to, $datatype) = extract_quotelike($rest); $to =~ s/^\"//; $to =~ s/\"$//; $datatype =~ s/^\s+//; $val = [[TYPE,$type], [VALUE,$to], [DATATYPE,$datatype]]; } else { # second form # property_value: relation ToID my ($type,$to) = split(' ',$val); $val = [[TYPE,$type], [TO,$to]]; } } elsif ($tag eq NAMESPACE) { if ($force_namespace) { # override whatever namespace was provided $val = $force_namespace; } else { # do nothing - we will export later } $namespace_set = $val; } elsif ($tag eq DEF) { my ($defstr, $parts) = extract_qstr($val); $val = [[DEFSTR,$defstr], map {dbxref($_)} @$parts]; } elsif ($tag =~ /(\w*)synonym/) { my $scope = $1 || ''; if ($scope) { $tag = SYNONYM; if ($scope =~ /(\w+)_$/) { $scope = $1; } else { $self->parse_err("bad synonym type: $scope"); $scope = ''; } } my ($syn, $parts, $extra_quals) = extract_qstr($val2); if (@$extra_quals) { $scope = shift @$extra_quals; $scope = lc($scope); $qh->{synonym_type} = shift @$extra_quals if @$extra_quals; } if ($qh->{scope}) { if ($scope) { if ($scope ne $qh->{scope}) { $self->parse_err("inconsistent scope: $scope/$qh->{scope}"); } else { $self->parse_err("redundant scope: $scope"); } } } else { $qh->{scope} = $scope; } $val = [[SYNONYM_TEXT,$syn], (map {dbxref($_)} @$parts)]; } elsif ($tag =~ /formula/) { my ($formula, $parts, $extra_quals) = extract_qstr($val2); my $lang = 'CLIF'; if (@$extra_quals) { $lang = shift @$extra_quals; } $qh->{format} = $lang; $val = [['formula_text',$formula], (map {dbxref($_)} @$parts)]; } elsif ($tag eq 'holds_temporally_between' || # experimental support for obof1.3 $tag eq 'holds_atemporally_between' || $tag eq 'holds_on_class_level_between') { my ($sub, $ob) = split(' ', $val2); if ($id_remap_h{$sub}) { $sub = $id_remap_h{$sub}; } if ($id_remap_h{$ob}) { $ob = $id_remap_h{$ob}; } $val = [[subject=>$sub],[object=>$ob]]; } elsif ($tag eq 'holds_over_chain' || $tag eq 'equivalent_to_chain') { # obof1.3 my @rels = split(' ', $val2); @rels = map { my $rel = $_; if ($id_remap_h{$_}) { $rel = $id_remap_h{$_} } if ($rel !~ /:/) { if ($default_id_prefix) { $rel = "$default_id_prefix:$rel"; } } $rel; } @rels; $val = [map {[relation=>$_]} @rels]; } elsif ($tag =~ /^expand/) { my ($template, $parts) = extract_qstr($val); $val = $template; } else { $val = $val2; # normal tag:val } if (!ref($val) && $val eq 'true') { $val = 1; } if (!ref($val) && $val eq 'false') { $val = 0; } if (%$qh) { # note that if attributes are used for # terminal nodes then we effectively have # to 'push the node down' a level; # eg # x # ==> [is_a=>'x'] # x # ==> [is_a=>[[@=>[[t=>v]]],[.=>x]]] my $data = ref $val ? $val : [['.'=>$val]]; my @quals = map {[$_=>$qh->{$_}]} keys %$qh; $self->event($tag=>[['@'=>[@quals]], @$data, ]); } else { $self->event($tag=>$val); } if ($tag eq IS_A || $tag eq RELATIONSHIP) { $is_root = 0; } if ($tag eq IS_OBSOLETE && $val) { $is_root = 0; } if ($tag eq ID) { $id = $val; } if ($tag eq NAME) { if (!$id) { $self->parse_err("missing id!") } else { $self->acc2name_h->{$id} = $val; } } } else { $self->throw("uh oh: $_"); } } # duplicated code! check final event if (!$namespace_set) { if (!$namespace && $stanza_count) { #$self->parse_err("missing namespace for ID: $id"); } else { $self->event(NAMESPACE, $namespace); } } $self->event(IS_ROOT,1) if $is_root; foreach my $import_file (@imports) { $import_file = $self->download_file_if_required($import_file); $self->file($import_file); $self->pop_stack_to_depth(1); #$self->end_event(HEADER); my $ifh = FileHandle->new($import_file); $self->parse_fh_inner($ifh); #$self->pop_stack_to_depth(1); $ifh->close(); } return; } # each tag line can have trailing qualifiers in {}s at the end sub extract_quals { my $str = shift; my %q = (); if ($str =~ /(.*[^\s])\s+(\{.*)\}\s*$/) { my $return_str = $1; my $extr = $2; if ($extr) { my @qparts = split_on_comma($extr); foreach (@qparts) { if (/(\w+)=\"(.*)\"/) { $q{$1} = $2; } elsif (/(\w+)=\'(.*)\'/) { $q{$1} = $2; } elsif (/(\w+)=(\S+)/) { # current 1.2 standard; non-quoted $q{$1} = $2; } else { warn("$_ in $str"); } } } return ($return_str, \%q); } else { return ($str, {}); } } sub extract_qstr { my $str = shift; my ($extr, $rem, $prefix) = extract_quotelike($str); my $txt = $extr; $txt =~ s/^\"// if $txt; $txt =~ s/\"$// if $txt; if ($prefix) { warn("illegal prefix: $prefix in: $str"); } my @extra = (); # synonyms can have two words following quoted part # before dbxref section # - two if ($rem =~ /(\w+)\s+(\w+)\s+(\[.*)/) { $rem = $3; push(@extra,$1,$2); } elsif ($rem =~ /(\w+)\s+(\[.*)/) { $rem = $2; push(@extra,$1); } else { } my @parts = (); while (($extr, $rem, $prefix) = extract_bracketed($rem, '[]')) { last unless $extr; $extr =~ s/^\[//; $extr =~ s/\]$//; push(@parts, $extr) if $extr; } @parts = map {split_on_comma($_)} @parts; $txt =~ s/\\//g if $txt; return ($txt, \@parts, \@extra); } sub split_on_comma { my $str = shift; my @parts = (); while ($str =~ /(.*[^\\],\s*)(.*)/) { $str = $1; my $part = $2; unshift(@parts, $part); $str =~ s/,\s*$//; } unshift(@parts, $str); return map {s/\\//g;$_} @parts; } # turns a DB:ACC string into an obo-xml dbxref element sub dbxref { my $str = shift; $str =~ s/\\//g; my $name; if ($str =~ /(.*)\s+\"(.*)\"$/) { $str = $1; $name = $2; } my ($db, @rest) = split(/:/, $str); my $acc = join(':',@rest); $db =~ s/^\s+//; if ($db eq 'http' && $acc =~ /^\/\//) { # dbxref is actually a URI $db = 'URL'; $acc = simple_escape($acc); $acc =~ s/\s/\%20/g; $acc = "http:$acc"; } else { # $db=escape($db); # $acc=escape($acc); } $db =~ s/\s+/_/g; # HumanDO.obo has spaces in xref $acc =~ s/\s+/_/g; $db = 'NULL' unless $db; $acc = 'NULL' unless $acc; [DBXREF,[[ACC,$acc], [DBNAME,$db], defined $name ? [NAME,$name] : () ]]; } sub parse_term_expression { my $self = shift; my $expr = shift; my ($te,$rest) = $self->parse_term_expression_with_rest($expr); if ($rest) { $self->parse_err("trailing: $rest"); } return Data::Stag->nodify($te); } sub parse_term_expression_with_rest { my $self = shift; my $expr = shift; if ($expr =~ /^\((.*)/) { my $genus_expr = $1; my ($genus,$diff_expr) = $self->parse_term_expression_with_rest($genus_expr); my $next_c = substr($diff_expr,0,1,''); if ($next_c eq ')') { my ($diffs,$rest) = $self->parse_differentia_with_rest($diff_expr); my $stag = [intersection=>[ [link=>[[to=>[$genus]]]], @$diffs]]; return ($stag,$rest); } else { $self->parse_err("expected ) at end of genus. Got: $next_c followed by $diff_expr"); } } elsif ($expr =~ /^([\w\:\.\-]+)\^(.*)/) { my $genus = $1; my $diff_expr = $2; my ($diffs,$rest) = $self->parse_differentia_with_rest($diff_expr); my $stag = [intersection=>[ [link=>[[to=>$genus]]], @$diffs]]; return ($stag,$rest); } elsif ($expr =~ /^([\w\:\.\-]+)(.*)/) { return ($1,$2); } else { $self->parse_err("could not parse: $expr"); } } sub parse_differentia { my $self = shift; my $expr = shift; my ($diffs,$rest) = $self->parse_differentia_with_rest($expr); if ($rest) { $self->parse_err("trailing: $rest"); } Data::Stag->nodify($_) foreach @$diffs; return $diffs; } sub parse_differentia_with_rest { my $self = shift; my $expr = shift; if ($expr =~ /^(.+?)\((.*)/) { my $rel = $1; my $term_expr = $2; my ($term,$rest) = $self->parse_term_expression_with_rest($term_expr); my $diff = [link=>[[type=>$rel], [to=>(ref($term) ? [$term] : $term)]]]; if ($rest) { my $next_c = substr($rest,0,1,''); if ($next_c eq ')') { $next_c = substr($rest,0,1); if ($next_c eq '^' || $next_c eq ',') { my ($next_diffs,$next_rest) = $self->parse_differentia_with_rest(substr($rest,1)); if (!$next_diffs) { $self->parse_err("problem parsing differentia: $rest. Expr: $term_expr"); return ([$diff],$rest); } return ([$diff,@$next_diffs],$next_rest); } elsif ($next_c eq '') { return ([$diff],$rest); } elsif ($next_c eq ')') { return ([$diff],$rest); } else { $self->parse_err("expected ^ or ) in differentium. Got: $next_c followed_by: $rest. Expr: $term_expr"); } } else { $self->parse_err("expected ) to close differentium. Got: $next_c followed by: $rest. Expr: $term_expr"); } } else { $self->parse_err("expected ). Got: \"\". Expr: $term_expr"); } } else { $self->parse_err("expect relation(...). Got: $expr. "); } } # lifted from CGI::Util our $EBCDIC = "\t" ne "\011"; # (ord('^') == 95) for codepage 1047 as on os390, vmesa our @E2A = ( 0, 1, 2, 3,156, 9,134,127,151,141,142, 11, 12, 13, 14, 15, 16, 17, 18, 19,157, 10, 8,135, 24, 25,146,143, 28, 29, 30, 31, 128,129,130,131,132,133, 23, 27,136,137,138,139,140, 5, 6, 7, 144,145, 22,147,148,149,150, 4,152,153,154,155, 20, 21,158, 26, 32,160,226,228,224,225,227,229,231,241,162, 46, 60, 40, 43,124, 38,233,234,235,232,237,238,239,236,223, 33, 36, 42, 41, 59, 94, 45, 47,194,196,192,193,195,197,199,209,166, 44, 37, 95, 62, 63, 248,201,202,203,200,205,206,207,204, 96, 58, 35, 64, 39, 61, 34, 216, 97, 98, 99,100,101,102,103,104,105,171,187,240,253,254,177, 176,106,107,108,109,110,111,112,113,114,170,186,230,184,198,164, 181,126,115,116,117,118,119,120,121,122,161,191,208, 91,222,174, 172,163,165,183,169,167,182,188,189,190,221,168,175, 93,180,215, 123, 65, 66, 67, 68, 69, 70, 71, 72, 73,173,244,246,242,243,245, 125, 74, 75, 76, 77, 78, 79, 80, 81, 82,185,251,252,249,250,255, 92,247, 83, 84, 85, 86, 87, 88, 89, 90,178,212,214,210,211,213, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57,179,219,220,217,218,159 ); sub escape { shift() if @_ > 1 and ( ref($_[0]) || (defined $_[1] && $_[0] eq $CGI::DefaultClass)); my $toencode = shift; return undef unless defined($toencode); # force bytes while preserving backward compatibility -- dankogai $toencode = pack("C*", unpack("C*", $toencode)); if ($EBCDIC) { $toencode=~s/([^a-zA-Z0-9_.-])/uc sprintf("%%%02x",$E2A[ord($1)])/eg; } else { $toencode=~s/([^a-zA-Z0-9_.-])/uc sprintf("%%%02x",ord($1))/eg; } return $toencode; } sub simple_escape { return unless defined(my $toencode = shift); $toencode =~ s{&}{&}gso; $toencode =~ s{<}{<}gso; $toencode =~ s{>}{>}gso; $toencode =~ s{\"}{"}gso; # Doesn't work. Can't work. forget it. # $toencode =~ s{\x8b}{‹}gso; # $toencode =~ s{\x9b}{›}gso; $toencode; } 1; go-perl-0.15/GO/Parsers/obo_xml_parser.pm000644 000765 000024 00000001317 11615622157 020225 0ustar00cjmstaff000000 000000 # $Id: obo_xml_parser.pm,v 1.3 2004/11/24 02:28:02 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Parsers::obo_xml_parser; =head1 NAME GO::Parsers::obo_xml_parser.pm - Parses xml made from events =head1 SYNOPSIS do not use this class directly; use GO::Parser =cut =head1 DESCRIPTION this parser does a direct translation of XML to events, passed on to the handler the XML used should be the attribute-less xml generated by the GO::Handlers::XmlOutHandler class =head1 AUTHOR =cut use Exporter; use base qw(GO::Parsers::base_parser Data::Stag::XMLParser); 1; go-perl-0.15/GO/Parsers/owl_parser.pm000644 000765 000024 00000001203 11615622157 017361 0ustar00cjmstaff000000 000000 # $Id: owl_parser.pm,v 1.3 2005/04/19 04:35:50 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Parsers::owl_parser; =head1 NAME GO::Parsers::owl_parser.pm - turns OWL XML into event stream =head1 SYNOPSIS do not use this class directly; use GO::Parser =cut =head1 DESCRIPTION this parser does a direct translation of XML to events, passed on to the handler =head1 AUTHOR =cut use Exporter; use base qw(GO::Parsers::base_parser Data::Stag::XMLParser); sub xslt { 'owl_to_oboxml' } 1; go-perl-0.15/GO/Parsers/ParserEventNames.pm000644 000765 000024 00000011707 11615622157 020440 0ustar00cjmstaff000000 000000 =head1 NAME GO::Parsers::ParserEventNames - exports constants corresponding to XML =head1 SYNOPSIS use GO::Parsers::ParserEventNames; =cut =head1 DESCRIPTION =head1 AUTHOR =cut package GO::Parsers::ParserEventNames; use strict; use base qw(Exporter); use vars qw(@EXPORT); use constant OBO => 'obo'; use constant HEADER => 'header'; use constant SUBSETDEF => 'subsetdef'; use constant TYPEDEF => 'typedef'; use constant IS_CYCLIC => 'is_cyclic'; use constant IS_TRANSITIVE => 'is_transitive'; use constant IS_SYMMETRIC => 'is_symmetric'; use constant IS_ANTI_SYMMETRIC => 'is_anti_symmetric'; use constant IS_REFLEXIVE => 'is_reflexive'; use constant IS_METADATA_TAG => 'is_metadata_tag'; use constant DISJOINT_FROM => 'disjoint_from'; use constant INVERSE_OF => 'inverse_of'; use constant TRANSITIVE_OVER => 'transitive_over'; use constant DOMAIN => 'domain'; use constant RANGE => 'range'; use constant TERM => 'term'; use constant ID => 'id'; use constant IS_ANONYMOUS => 'is_anonymous'; use constant ACC => 'acc'; use constant NAMESPACE => 'namespace'; use constant NAME => 'name'; use constant SUBSET => 'subset'; use constant DEF => 'def'; use constant DEFSTR => 'defstr'; use constant IS_ROOT => 'is_root'; use constant IS_OBSOLETE => 'is_obsolete'; use constant BUILTIN => 'builtin'; use constant IS_A => 'is_a'; use constant INSTANCE_OF => 'instance_of'; use constant RELATIONSHIP => 'relationship'; use constant INTERSECTION_OF => 'intersection_of'; use constant UNION_OF => 'union_of'; use constant ALT_ID => 'alt_id'; use constant SYNONYM => 'synonym'; use constant COMMENT => 'comment'; use constant TO => 'to'; use constant TYPE => 'type'; use constant XREF => 'xref'; use constant XREF_ANALOG => 'xref_analog'; use constant XREF_UNKNOWN => 'xref_unknown'; use constant DBXREF => 'dbxref'; use constant TERM_DBXREF => 'term_dbxref'; use constant SYNONYM_TEXT => 'synonym_text'; use constant SYNONYM_TYPE => 'synonym_type'; use constant CONSIDER => 'consider'; use constant REPLACED_BY => 'replaced_by'; use constant INSTANCE => 'instance'; use constant PROPERTY_VALUE => 'property_value'; use constant VALUE => 'value'; use constant DATATYPE => 'datatype'; use constant DBSET => 'dbset'; use constant DBNAME => 'dbname'; use constant PROD => 'prod'; use constant PRODDB => 'proddb'; use constant PRODNAME => 'prodname'; use constant PRODSYMBOL => 'prodsymbol'; use constant PRODACC => 'prodacc'; use constant PRODTAXA => 'prodtaxa'; use constant PRODTYPE => 'prodtype'; use constant SECONDARY_PRODTAXA => 'secondary_prodtaxa'; # DEPRECATED use constant PRODSYN => 'prodsyn'; use constant ISOFORM => 'isoform'; use constant ASSOCS => 'assocs'; use constant ASSOC => 'assoc'; use constant QUALIFIER => 'qualifier'; use constant SPECIES_QUALIFIER => 'species_qualifier'; use constant PROPERTIES => 'properties'; use constant ASPECT => 'aspect'; use constant SOURCE_DB => 'source_db'; use constant TERMACC => 'termacc'; use constant IS_NOT => 'is_not'; use constant ASSOCDATE => 'assocdate'; use constant WITH => 'with'; use constant REF => 'ref'; use constant EVIDENCE => 'evidence'; use constant EVCODE => 'evcode'; use constant DBXREFS => 'dbxrefs'; @EXPORT = qw( OBO HEADER SUBSETDEF TYPEDEF IS_CYCLIC IS_TRANSITIVE IS_SYMMETRIC IS_ANTI_SYMMETRIC IS_REFLEXIVE IS_METADATA_TAG DISJOINT_FROM INVERSE_OF TRANSITIVE_OVER DOMAIN RANGE TERM ID IS_ANONYMOUS ACC NAMESPACE NAME SUBSET DEF DEFSTR IS_OBSOLETE IS_ROOT IS_A BUILTIN RELATIONSHIP TO TYPE INTERSECTION_OF UNION_OF SYNONYM SYNONYM_TYPE SYNONYM_TEXT ALT_ID CONSIDER REPLACED_BY COMMENT XREF XREF_ANALOG XREF_UNKNOWN DBXREF TERM_DBXREF INSTANCE INSTANCE_OF PROPERTY_VALUE VALUE DATATYPE ASSOCS DBSET DBNAME PROD PRODDB PRODNAME PRODSYMBOL PRODACC PRODTAXA PRODTYPE SECONDARY_PRODTAXA PRODSYN ISOFORM ASSOC QUALIFIER SPECIES_QUALIFIER PROPERTIES ASPECT SOURCE_DB TERMACC IS_NOT ASSOCDATE EVIDENCE EVCODE WITH REF DBXREFS ); 1; go-perl-0.15/GO/Parsers/references_parser.pm000644 000765 000024 00000001263 11615622157 020707 0ustar00cjmstaff000000 000000 # $Id: references_parser.pm,v 1.1 2006/12/06 02:59:07 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Parsers::references_parser; =head1 NAME GO::Parsers::references_parser - syntax parsing of GO.refences files =head1 SYNOPSIS do not use this class directly; use GO::Parser =cut =head1 DESCRIPTION Parses this file: L =cut use Exporter; use base qw(GO::Parsers::generic_tagval_parser); use strict qw(subs vars refs); sub _class { 'GOModel:References' } sub _id_column {'go_ref_id'} 1; go-perl-0.15/GO/Parsers/refgenomes_parser.pm000644 000765 000024 00000005733 11615622157 020726 0ustar00cjmstaff000000 000000 # $Id: refgenomes_parser.pm,v 1.1 2007/01/24 01:16:20 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Parsers::refgenomes_parser; =head1 NAME GO::Parsers::refgenomes_parser - syntax parsing of GO .def flat files =head1 SYNOPSIS do not use this class directly; use GO::Parser =cut =head1 DESCRIPTION =head1 GO DEFINITION FILES =head1 AUTHOR =cut use Exporter; use base qw(GO::Parsers::base_parser); use GO::Parsers::ParserEventNames; # declare XML constants use Carp; use FileHandle; use strict qw(subs vars refs); sub dtd { 'refgenomes-parser-events.dtd'; } sub _class { 'generic' } sub _id_column {} sub _map_property_type { shift;@_ } our %DB_LOOKUP = (dictybase=>'DDB', flybase=>'FB', wormbase=>'WB', goa=>'UniProt', chicken=>'UniProt', zfin=>'ZFIN', pombase=>'GeneDB_Spombe', ); sub parse_fh { my ($self, $fh) = @_; my $file = $self->file; my $LAST_COL = 'completion target'; my @hdr = (); $self->start_event('refgenomeset'); my $lnum = 0; my $in_record=0; my $class = $self->_class; my $id_column = $self->_id_column; while (my $line = <$fh>) { chomp $line; ++$lnum; next if $line =~ /^\!/; $line =~ s/^\s+$//; if (!$line) { $self->pop_stack_to_depth(1); $in_record = 0; next; } my @vals = split(/\t/,$line); if (!@hdr) { @hdr = @vals; next; } $self->start_event('homologset'); my %valh = (); for (my $i=0; $i<@hdr; $i++) { my $col = $hdr[$i]; $col =~ s/\s/_/g; $col =~ s/\W//g; $valh{$col} = $vals[$i]; } my $id = $valh{OMIM_ID}; $id =~ s/\W//g; $self->event('@'=>[[id=>"MIM:$id"]]); my $in_genes = 0; my $i=-1; while ($i<@vals) { $i++; my $col = $hdr[$i]; my $val = $vals[$i]; if ($in_genes) { my ($sp, @extra) = split(' ',$col); if (!@extra) { # ignore anything with annoying chatty text next if $val =~ / /i; next unless $val; next if $val =~ /\"/; my $sp2 = $DB_LOOKUP{lc($sp)}; $sp = $sp2 if ($sp2); my $fid = "$sp:$val"; $self->event('member',[['@'=>[[ref=>$fid]]]]); } } else { if ($col eq $LAST_COL) { $in_genes = 1; } $col =~ s/\s/_/g; $col =~ s/\W//g; $self->event(tagval=>[['@'=>[[type=>$col]]],['.'=>$val]]) if $val; } } $self->end_event('homologset'); } $self->pop_stack_to_depth(0); # end event obo } 1; go-perl-0.15/GO/Parsers/unknown_format_parser.pm000644 000765 000024 00000006106 11615622157 021636 0ustar00cjmstaff000000 000000 # $Id: unknown_format_parser.pm,v 1.9 2005/08/18 21:23:11 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Parsers::unknown_format_parser; =head1 NAME GO::Parsers::unknown_format_parser - base class for parsers =head1 SYNOPSIS do not use this class directly; use GO::Parser =cut =head1 DESCRIPTION =head1 AUTHOR =cut use Carp; use FileHandle; use GO::Parser; use base qw(GO::Parsers::base_parser Exporter); use strict qw(subs vars refs); sub parse_file_by_type { shift->parse_file(@_); } sub parse_file { my ($self, $file, $dtype) = @_; $self->file($file); my $fmt; # input file format my $p; # determine format based on dtype # (legacy code - dtypes should switch to standard formars) if ($dtype) { # convert legacy types if ($dtype =~ /ontology$/) { $fmt = "go_ont"; } elsif ($dtype =~ /defs$/) { $fmt = "go_def"; } elsif ($dtype =~ /xrefs$/) { $fmt = "go_xref"; } elsif ($dtype =~ /assocs$/) { $fmt = "go_assoc"; } else { $fmt = $dtype; } } if (!$p) { # no default parser, or it has been overwritten if (!$fmt) { # messy guessing of format from file extension if ($file =~ /\.go$/) { $fmt = "go_ont"; } if ($file =~ /\.ontology$/) { $fmt = "go_ont"; } if ($file =~ /defs$/) { $fmt = "go_def"; } if ($file =~ /2go$/) { $fmt = "go_xref"; } if ($file =~ /gene_association/) { $fmt = "go_assoc"; } if ($file =~ /\.obo$/ || $file =~ /\.obo[\.\-_]text$/) { $fmt = "obo_text"; } if ($file =~ /\.obo\W*xml$/) { $fmt = "obo_xml"; } if (!$fmt) { # if suffix is a known parser module, use it if ($file =~ /\.(\w+)$/) { my $suffix = $1; my $mod = "GO/Parsers/$suffix"."_parser.pm"; eval { require "$mod"; }; if ($@) { } else { $fmt = $suffix; } } } if (!$fmt) { #$self->throw("I have no idea how to parse: $file\n"); open(F,$file) || $self->throw("Cannot open $file"); my $first_line = ; if ($first_line =~ /^format/) { $fmt = 'obo_text'; } else { $fmt = 'go_ont'; } close(F); } } $p = GO::Parser->get_parser_impl($fmt); } %$p = %$self; $p->parse($file); %$self = %$p; $self->parser($p); $self; } sub parser { my $self = shift; $self->{_parser} = shift if @_; return $self->{_parser}; } sub parse { my $self = shift; my $filename; foreach $filename (@_) { $self->parse_file($filename); } return; } # deprecated! sub parse_ontology { my ($self, $file) = @_; $self->parse_file($file, 'go_ont'); } 1; go-perl-0.15/GO/Parsers/xrf_abbs_parser.pm000644 000765 000024 00000001363 11615622157 020355 0ustar00cjmstaff000000 000000 # $Id: xrf_abbs_parser.pm,v 1.2 2007/01/24 01:16:20 cmungall Exp $ # # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Parsers::xrf_abbs_parser; =head1 NAME GO::Parsers::xrf_abbs_parser - syntax parsing of GO xrf_abbs flat files =head1 SYNOPSIS do not use this class directly; use GO::Parser =cut =head1 DESCRIPTION Parses this file: L =cut use Exporter; use base qw(GO::Parsers::generic_tagval_parser); use strict qw(subs vars refs); sub _class { 'GOMetaModel:Database' } sub _id_column {'abbreviation'} sub _map_property_type { shift;return "GOMetaModel:".shift } 1; go-perl-0.15/GO/Model/Association.pm000644 000765 000024 00000020625 11615622160 017104 0ustar00cjmstaff000000 000000 # $Id: Association.pm,v 1.7 2007/03/27 22:36:16 sjcarbon Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.fruitfly.org/annot/go # # You may distribute this module under the same terms as perl itself package GO::Model::Association; =head1 NAME GO::Model::Association; =head1 SYNOPSIS # print all gene products associated with a GO::Model::Term my $assoc_l = $term->association_list; foreach my $assoc (@$assoc_l) { printf "gene product:%s %s %s (evidence: %s)\n", $assoc->gene_product->symbol, $assoc->is_not ? "IS NOT" : "IS", $term->name, map {$_->code} @{$assoc->evidence_list}; } =head1 DESCRIPTION Represents an association between a GO term (GO::Model::Term) and a gene product (GO::Model::GeneProduct) =cut use Carp; use Exporter; use GO::Utils qw(rearrange); use GO::Model::Root; use GO::Model::Evidence; use strict; use vars qw(@ISA); use Data::Dumper; use base qw(GO::Model::Root Exporter); sub _valid_params { return qw(id gene_product evidence_list is_not role_group qualifier_list source_db_id assigned_by assocdate); } sub _initialize { my $self = shift; my $paramh = shift; # an association is a compound obj of both Association and # GeneProduct; both objs created together from same hash # sometimes this is from the external world and sometimes from the db my $product_h = {}; my $ev_h = {}; # SHULY Nov 28, 04 - added the gene product type to the product hash if (defined ($paramh->{gene_product_id})) { $product_h->{speciesdb} = $paramh->{xref_dbname}; $product_h->{acc} = $paramh->{xref_key}; $product_h->{id} = $paramh->{gene_product_id}; $product_h->{symbol} = $paramh->{symbol}; $product_h->{full_name} = $paramh->{full_name} if defined ($paramh->{full_name}); # SHULY - added the type to the hash #$product_h->{type} = $paramh->{type_id}; $product_h->{type_id} = $paramh->{type_id}; if (!$self->apph) { confess("ASSERTION ERROR"); } my $product = $self->apph->create_gene_product_obj($product_h); $product->{species_id} = $paramh->{species_id}; $self->gene_product($product); delete $paramh->{xref_dbname}; delete $paramh->{xref_key}; delete $paramh->{gene_product_id}; delete $paramh->{symbol}; delete $paramh->{full_name}; # SHULY - added the type to the hash delete $paramh->{type_id}; delete $paramh->{species_id}; } $self->SUPER::_initialize($paramh); } =head2 go_public_acc Usage - Returns - Args - =cut sub go_public_acc { my $self = shift; $self->{go_public_acc} = shift if @_; return $self->{go_public_acc} || ''; } =head2 add_evidence Usage - $assoc->add_evidence($my_evid); Returns - Args - GO::Model::Evidence =cut sub add_evidence { my $self = shift; if (!$self->{evidence_list}) { $self->{evidence_list} = []; } push(@{$self->{evidence_list}}, (shift)); return $self->{evidence_list}; } =head2 evidence_list Usage - my $ev_l = $assoc->evidence_list; Returns - Args - gets/sets arrayref of GO::Model::Evidence =cut sub evidence_list { my $self = shift; $self->{evidence_list} = shift if @_; return $self->{evidence_list}; } =head2 evidence_as_str Usage - print $assoc->evidence_as_str Usage - print $assoc->evidence_as_str(1); #verbose Returns - Args - verbose concatenates evcodes together, for display =cut sub evidence_as_str { my $self = shift; my $v = shift; if ($v) { return join("; ", map { sprintf("%s %s %s", $_->code, $_->seq_acc ? $_->seq_acc->as_str : "", $_->xref ? $_->xref->as_str : "") } @{$self->evidence_list || []}); } else { return join("; ", map {$_->code} @{$self->evidence_list || []}); } } =head2 has_evcode Usage - if $assoc->has_evcode("IEA"); Returns - boolean Args - evcode [string] =cut sub has_evcode { my $self = shift; my $code = shift; return grep {$_->code eq $code} @{$self->evidence_list || []}; } =head2 remove_evcode Usage - $assoc->remove_evcode("IEA"); Returns - Args - evcode [string] removes all evidence of the specified type from the association; useful for filtering =cut sub remove_evcode { my $self = shift; my $code = shift; my @ok_ev = grep {$_->code ne $code} @{$self->evidence_list || []}; $self->evidence_list(\@ok_ev); } =head2 evidence_score Usage - my $score = $assoc->evidence_score Returns - 0 <= float <= 1 Args - returns a score for the association based on the evidence; This is an EXPERIMENTAL method; it may be removed in future versions. The evidence fields can be thought of in a loose hierachy: TAS IDA IMP/IGI/IPI ISS NAS see http://www.geneontology.org/GO.evidence.html =cut sub evidence_score { my $self = shift; my %probs = qw(IEA 0.1 NAS 0.3 NR 0.3 ISS 0.4 IMP 0.6 IGI 0.6 IPI 0.6 IDA 0.8 TAS 0.9); my $np = 1; map {$np *= (1 - $probs{$_}) } @{$self->evcodes||[]}; return 1 - $np; } =head2 gene_product Usage - my $gp = $assoc->gene_product Returns - Args - gets sets GO::Model::GeneProduct =cut sub gene_product { my $self = shift; $self->{gene_product} = shift if @_; return $self->{gene_product}; } =head2 assigned_by Usage - Returns - Args - =cut #autoloaded =head2 is_not Usage - Returns - Args - gets/sets boolean representing whether this relationship is negated =cut sub is_not { my $self = shift; $self->{is_not} = shift if @_; return $self->{is_not}; } =head2 assocdate Usage - Returns - Args - =cut #autoloaded =head2 assocdate Usage - Returns - Args - gets/sets integer representing the date of the association (YYYYMMDD format) =cut sub assocdate { my $self = shift; $self->{assocdate} = shift if @_; return $self->{assocdate}; } =head2 role_group Usage - Returns - Args - gets/sets integer to indicate which associations go together =cut sub role_group { my $self = shift; $self->{role_group} = shift if @_; return $self->{role_group}; } sub from_idl { my $class = shift; my $h = shift; map { $_ = GO::Model::Evidence->from_idl($_); } @{$h->{"evidence_list"}}; $h->{"gene_product"} = GO::Model::GeneProduct->from_idl($h->{"gene_product"}); return $class->new($h); } sub to_idl_struct { my $self = shift; my $struct; eval { $struct = { "evidence_list"=>[map {$_->to_idl_struct} @{$self->evidence_list()}], "gene_product"=>$self->gene_product->to_idl_struct, "reference"=>"" }; }; if ($@) { print $self->dump; print $@; throw POA_GO::ProcessError(); } return $struct; } sub to_ptuples { my $self = shift; my ($term, $th) = rearrange([qw(term tuples)], @_); my @s = (); foreach my $e (@{$self->evidence_list()}) { my @xids = (); foreach my $x (@{$e->xref_list || []}) { push(@s, $x->to_ptuples(-tuples=>$th) ); push(@xids, $x->as_str); } push(@s, ["assoc", $term->acc, $self->gene_product->xref->as_str, $e->code, "[".join(", ", @xids)."]", ], $self->gene_product->to_ptuples(-tuples=>$th), ); } @s; } # **** EXPERIMENTAL CODE **** # the idea is to be homogeneous and use graphs for # everything; eg gene products are nodes in a graph, # associations are arcs # cf rdf, daml+oil etc # args - optional graph to add to sub graphify { my $self = shift; my ($term, $subg, $opts) = rearrange([qw(term graph opts)], @_); $opts = {} unless $opts; $subg = $self->apph->create_graph_obj unless $subg; my $acc = sprintf("%s", $self); my $t = $self->apph->create_term_obj({name=>$acc, acc=>$acc}); $subg->add_node($t); $subg->add_arc($t, $term, "hasAssociation") if $term; foreach my $ev (@{$self->evidence_list || []}) { $ev->apph($self->apph); $ev->graphify($t, $subg); } my $gp = $self->gene_product; $gp->graphify($t, $subg); $subg; } 1; go-perl-0.15/GO/Model/CrossProduct.pm000644 000765 000024 00000006332 11615622160 017261 0ustar00cjmstaff000000 000000 # $Id: CrossProduct.pm,v 1.2 2004/11/24 02:28:01 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Model::CrossProduct; =head1 NAME GO::Model::CrossProduct; =head1 SYNOPSIS =head1 DESCRIPTION for cross products - an intersection between another class/term and a list of anonymous subclass over some restrictions =cut use Carp qw(cluck confess); use Exporter; use GO::Utils qw(rearrange); use GO::Model::Root; use strict; use vars qw(@ISA); @ISA = qw(GO::Model::Root Exporter); sub _valid_params { return qw(xp_acc parent_acc restriction_list); } sub get_restriction_values_for_property { my $self = shift; my $prop = shift; my @vals = map {$_->value} grep {$_->property_name eq $prop} @{$self->restriction_list||[]}; return \@vals; } sub add_restriction { my $self = shift; my $r = shift; if (!ref($r)) { $r = $self->apph->create_restriction_obj({property_name=>$r, value=>shift}); } my $rl = $self->restriction_list || []; $self->restriction_list([@$rl, $r]); $r; } sub all_parent_accs { my $self = shift; my $restrs = $self->restriction_list; return [ $self->parent_acc, map { $_->value } @$restrs ]; } sub all_parent_relationships { my $self = shift; my $restrs = $self->restriction_list; my $xp_acc = $self->xp_acc; my @hashes = ( {acc1=>$self->parent_acc, acc2=>$xp_acc, type=>'is_a' }, map { ({ acc1=>$_->value, acc2=>$xp_acc, type=>$_->property_name }) } @$restrs ); return [ map { $self->apph->create_relationship_obj($_) } @hashes ]; } sub to_obo { my $self = shift; my $restrs = $self->restriction_list; return sprintf("cross_product: %s %s\n", $self->parent_acc, join(' ', map {sprintf("(%s %s)", $_->property_name, $_->value)} @$restrs)); } sub equals { my $self = shift; my $xp = shift; # printf "TESTING FOR EQUALITY (%s):\n", $xp->xp_acc; # print $self->to_obo; # print $xp->to_obo; return 0 unless $self->parent_acc eq $xp->parent_acc; my @r1 = @{$self->restriction_list || []}; my @r2 = @{$xp->restriction_list || []}; return 0 unless scalar(@r1) == scalar(@r2); my @propnames = map {$_->property_name} @{$self->restriction_list||[]}, @{$xp->restriction_list||[]}; my %uniqpropnames = map{$_=>1} @propnames; my $ok = 1; foreach my $pn (keys %uniqpropnames) { my @vals1 = sort @{$self->get_restriction_values_for_property($pn)}; my @vals2 = sort @{$xp->get_restriction_values_for_property($pn)}; while (@vals1) { if (shift @vals1 ne shift @vals2) { $ok = 0; } } if (@vals2) { $ok = 0; } last unless $ok; } return $ok; } 1; go-perl-0.15/GO/Model/DB.pm000644 000765 000024 00000001307 11615622160 015111 0ustar00cjmstaff000000 000000 # $Id: DB.pm,v 1.1 2007/01/24 01:16:20 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Model::DB; =head1 NAME GO::Model::DB; =head1 SYNOPSIS =head1 DESCRIPTION Fields: name fullname datatype generic_url url_syntax url_example =cut use Carp qw(cluck confess); use Exporter; use GO::Utils qw(rearrange); use GO::Model::Root; use strict; use vars qw(@ISA); @ISA = qw(GO::Model::Root Exporter); sub _valid_params { return qw(name fullname datatype generic_url url_syntax url_example); } 1; go-perl-0.15/GO/Model/Evidence.pm000644 000765 000024 00000017677 11615622160 016367 0ustar00cjmstaff000000 000000 # $Id: Evidence.pm,v 1.5 2009/05/22 23:06:40 sjcarbon Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Model::Evidence; =head1 NAME GO::Model::Evidence; =head1 SYNOPSIS my $ev_l = $association->evidence_list; foreach my $ev (@$ev_l) { print "Evidence for association %s : %s\n", $association->gene_product->symbol, $ev->code; } =head1 DESCRIPTION evidence for an association see http://www.geneontology.org/GO.evidence.html for a list of evidence codes =cut use Carp qw(confess cluck); use Exporter; use GO::Utils qw(rearrange); use GO::Model::Root; use strict; use vars qw(@ISA); @ISA = qw(GO::Model::Root Exporter); sub _valid_params { return qw(id code seq_acc xref seq_xref_list pub_xref_list); } =head2 code Usage - $ev->code("IEA"); Returns - Args - gets/sets the evidence code see http://www.geneontology.org/GO.evidence.html =cut # dynamic method =head2 seq_acc Usage - Returns - Args - gets/sets the sequence accesion GO::Model::Xref ALPHA CODE - API may change used to set the GO::Model::Xref list from a text string. eg $ev->seq_acc("SGD:RRP41; SGDID:L0003550"); will actually add two GO::Model::Xref objects This method doesnt really belong in the GO::Model::* hierarchy as it contains parsing code. Its a minor hack mainly due to the fact that this data is still denormalized in the database. =cut sub seq_acc { my $self = shift; if (@_) { my $acc = shift; if (ref($acc)) { if (ref($acc) eq "ARRAY") { foreach (@$acc) { $self->add_seq_xref($_); } } else { if (UNIVERSAL::isa($acc, "GO::Model::Xref")) { $self->add_seq_xref($acc) } else { confess("$acc is not a valid argument for $self -> seq_acc()"); } } } else { # it's a string my @accs = split(/\;/, $acc); foreach my $acc (@accs) { $self->add_seq_xref($acc); } } } return join("; ", map {$_->as_str} @{$self->seq_xref_list || []}); } =head2 add_seq_xref Usage - Returns - Args - equivalent to WITH column in gene_association files, and evidence_dbxref tables in db =cut sub add_seq_xref { my $self = shift; my $xref = shift; if (ref($xref)) { if (UNIVERSAL::isa($xref, "GO::Model::Xref")) { $self->{seq_xref_list} = [] unless $self->{seq_xref_list}; push(@{$self->{seq_xref_list}}, $xref); } else { confess("$xref is not a valid argument for $self -> add_seq_xref()"); } } else { # string maybe in db:acc format if ($xref =~ /\s*(\S+?):(\S+)/) { my ($db, $acc) = ($1, $2); $acc =~ s/ *$//; $xref = GO::Model::Xref->new({xref_dbname=>$db, xref_key=>$acc}); } else { $xref = GO::Model::Xref->new({xref_dbname=>"UNKNOWN", xref_key=>"$xref"}); } confess("Assertion error") unless $xref->isa("GO::Model::Xref"); $self->add_seq_xref($xref); } } =head2 add_pub_xref Usage - Returns - Args - =cut sub add_pub_xref { my $self = shift; my $xref = shift; if (ref($xref)) { if (UNIVERSAL::isa($xref, "GO::Model::Xref")) { $self->{pub_xref_list} = [] unless $self->{pub_xref_list}; push(@{$self->{pub_xref_list}}, $xref); } else { confess("$xref is not a valid argument for $self -> add_pub_xref()"); } } else { # string maybe in db:acc format if ($xref =~ /\s*(\S+?):(\S+)/) { my ($db, $acc) = ($1, $2); $acc =~ s/ *$//; $xref = GO::Model::Xref->new({xref_dbname=>$db, xref_key=>$acc}); } else { $xref = GO::Model::Xref->new({xref_dbname=>"UNKNOWN", xref_key=>"$xref"}); } confess("Assertion error") unless $xref->isa("GO::Model::Xref"); $self->add_pub_xref($xref); } } =head2 xref Usage - Returns - Args - gets/sets the literature or sequence reference GO::Model::Xref NOTE: at some point we may want to deprecate this method and persuade API client code to call $ev->literature_xref instead, to make explicit the fact that this is a literature reference as opposed to a sequence reference =cut # dynamic method =head2 xref_list Usage - Returns - GO::Model::Xref listref Args - returns all (sequence and literature) references =cut sub xref_list { my $self = shift; if (@_) { confess("get only"); } my @x = @{$self->pub_xref_list || []}; push(@x, @{$self->seq_xref_list || []}); return \@x; } =head2 xref Usage - Returns - Args - deprected - sets first pub_xref_list =cut sub xref { my $self = shift; if (@_) { $self->pub_xref_list([@_]); } $self->pub_xref_list && $self->pub_xref_list->[0]; } =head2 valid_codes Usage - print join("; ", GO::Model::Evidence->valid_codes); Returns - string array Args - list of valid evidence codes =cut ## TODO: This should be fixed to get the values from the live DB. sub valid_codes { #qw(IMP IGI IPI ISS IDA IEP IEA TAS NAS ND NR); #qw(IC IDA IEP IGC IGI IMP IPI ISS NAS ND NR RCA TAS); ## Latest scraped version: qw(EXP IC IDA IEA IEP IGC IGI IMP IPI ISA ISM ISO ISS NAS ND NR RCA TAS); } sub _initialize { my $self = shift; my $paramh = shift; if (!ref($paramh)) { confess("init param must be hash"); } if ($paramh->{reference}) { my ($db, @keyparts) = split (/:/, $paramh->{reference}); # usually there is only one : in the dbxref, but # MGI includes the dbname in the id, so their # dbxrefs look like this: # MGI:MGI:00000001 my $key = join(":", @keyparts); if (!$key) { $key = $db; $db = "U"; } else { ($db) =~ tr/A-Z/a-z/; } my $xref = GO::Model::Xref->new({xref_key=>$key, xref_dbname=>$db}); $self->xref($xref); delete $paramh->{reference}; } $self->SUPER::_initialize($paramh); } sub to_idl_struct { my $self = shift; if (!$self->xref) { confess("$self has no xref"); } return { code=>$self->code, seq_acc=>$self->seq_acc, dbxref=>$self->xref->to_idl_struct, }; } sub from_idl { my $class = shift; my $h = shift; $h->{dbxref} = GO::Model::Xref->from_idl($h->{dbxref}); return $class->new($h); } # **** EXPERIMENTAL CODE **** # the idea is to be homogeneous and use graphs for # everything; eg gene products are nodes in a graph, # associations are arcs # cf rdf, daml+oil etc # args - optional graph to add to sub graphify { my $self = shift; my ($ref, $subg, $opts) = rearrange([qw(ref graph opts)], @_); $opts = {} unless $opts; $subg = $self->apph->create_graph_obj unless $subg; my $acc = sprintf("%s", $self); my $t = $self->apph->create_term_obj({name=>$acc, acc=>$acc}); $subg->add_node($t); $subg->add_arc($t, $ref, "hasEvidence") if $ref; foreach my $xr (@{$self->xref_list || []}) { $xr->apph($self->apph); $xr->graphify($t, $subg); } my $code = $self->code; my $cn = $subg->get_node($code); if (!$cn) { $cn = $self->apph->create_term_obj({name=>$code, acc=>$code}); $subg->add_node($cn); } $subg->add_arc($cn, $t, "hasCode"); $subg; } 1; go-perl-0.15/GO/Model/GeneProduct.pm000644 000765 000024 00000020332 11615622160 017042 0ustar00cjmstaff000000 000000 # $Id: GeneProduct.pm,v 1.11 2007/09/13 12:44:47 girlwithglasses Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Model::GeneProduct; =head1 NAME GO::Model::GeneProduct; =head1 DESCRIPTION represents a gene product in a particular species (this will effectively always be refered to implicitly by the gene symbol even though a gene may have >1 product) =cut use Carp; use Exporter; use GO::Utils qw(rearrange); use GO::Model::Root; use strict; use vars qw(@ISA); use Data::Dumper; @ISA = qw(GO::Model::Root Exporter); sub _valid_params { return qw(id acc symbol properties full_name type_id type xref speciesdb synonym_list seq_list species); } sub _initialize { my $self = shift; my $paramh = shift; my $db; if ($paramh->{speciesdb}) { $db = $paramh->{speciesdb}; } else { $db = $paramh->{xref_dbname}; } my $xref = GO::Model::Xref->new({xref_key=>$paramh->{acc}, xref_keytype=>"acc", xref_dbname=>$db}); $self->xref($xref); delete $paramh->{acc}; delete $paramh->{speciesdb}; $self->SUPER::_initialize($paramh); } =head2 acc Usage - Returns - Args - =cut sub acc { my $self = shift; my $acc = shift; if ($acc) { $self->xref->xref_key($acc); } return $self->xref->xref_key; } =head2 symbol Usage - Returns - Args - =cut # AUTOGENERATED =head2 type Usage - Returns - Args - =cut # AUTOGENERATED =head2 full_name Usage - Returns - Args - =cut # AUTOGENERATED =head2 as_str Usage - Returns - Args - =cut sub as_str { my $self = shift; return "GP-".$self->xref->as_str; } =head2 add_synonym =cut sub add_synonym { my $self = shift; if (!$self->{synonym_list}) { $self->{synonym_list} = []; } push(@{$self->{synonym_list}}, (shift)); return $self->{synonym_list}; } =head2 synonym_list accessor: gets/set list of synonyms [array reference] =cut # AUTOGENERATED =head2 speciesdb Usage - Returns - Args - =cut sub speciesdb { my $self = shift; my $db = shift; if ($db) { $self->xref->xref_dbname ($db); } return $self->xref->xref_dbname; } =head2 add_seq Usage - Returns - Args - GO::Model::Seq =cut sub add_seq { my $self = shift; my $seq = shift; if ($seq->isa("Bio::SeqI")) { my $bpseq = $seq; $seq = GO::Model::Seq->new; $seq->pseq($bpseq); } $seq->isa("GO::Model::Seq") or confess ("Not a seq object"); $self->{seq_list} = [] unless $self->{seq_list}; push(@{$self->{seq_list}}, $seq); $self->{seq_list}; } #indicate fetching seqs has been done: no need to try even if no seq (see seq_list) sub _seqs_obtained { my $self = shift; $self->{_seqs_obtained} = shift if @_; return $self->{_seqs_obtained}; } =head2 seq_list Usage - Returns - GO::Model::Seq listref Args - =cut sub seq_list { my $self = shift; if (@_) { $self->{seq_list} = shift; } else { if (!defined($self->{seq_list})) { $self->{seq_list} = $self->apph->get_seqs({product=>$self}) unless ($self->_seqs_obtained); } } return $self->{seq_list}; } =head2 seq Usage - Returns - GO::Model::Seq Args - returns representative sequence object for this product =cut sub seq { my $self = shift; my $seqs = $self->seq_list; my $str = ""; # longest by default my $longest; foreach my $seq (@$seqs) { if (!defined($longest) || $seq->length > $longest->length) { $longest = $seq; } } return $longest; } =head2 properties Usage - Returns - hashref Args - hashref =cut =head2 set_property Usage - $sf->set_property("wibble", "on"); Returns - Args - property key, property scalar note: the property is assumed to be multivalued, therefore $sf->set_property($k, $scalar) will add to the array, and $sf->set_property($k, $arrayref) will set the array =cut sub set_property { my $self = shift; my $p = shift; my $v = shift; if (!$self->properties) { $self->properties({}); } if (ref($v) eq 'ARRAY') { confess("@$v is not all scalar") if grep {ref($_)} @$v; $self->properties->{$p} = $v; } else { push(@{$self->properties->{$p}}, $v); } # uniqify my @vals = @{$self->properties->{$p}}; my %h = (); my @nu_vals = (); foreach (@vals) { next if $h{$_}; $h{$_} = 1; push(@nu_vals, $_); } $self->properties->{$p} = \@nu_vals; $v; } =head2 get_property Usage - Returns - first element of the property Args - property key =cut sub get_property { my $self = shift; my $p = shift; if (!$self->properties) { $self->properties({}); } my $val = $self->properties->{$p}; if ($val) { $val = $val->[0]; } return $val; } =head2 get_property_list Usage - Returns - the property arrayref Args - property key =cut sub get_property_list { my $self = shift; my $p = shift; if (!$self->properties) { $self->properties({}); } $self->properties->{$p}; } =head2 to_fasta Usage - Returns - Args - returns the longest seq by default =cut sub to_fasta { my $self = shift; my ($fullhdr, $hdrinfo, $gethdr) = rearrange([qw(fullheader headerinfo getheader)], @_); $hdrinfo = " " . ($hdrinfo || ""); my $seqs = $self->seq_list; my $str = ""; # longest by default my $longest; return "" unless @{$seqs || []}; foreach my $seq (@$seqs) { if (!defined($longest) || $seq->length > $longest->length) { $longest = $seq; } } $seqs = [$longest]; if ($gethdr) { my $apph = $self->get_apph; my $terms = $apph->get_terms({product=>$self}); my @h_elts = (); foreach my $term (@$terms) { my $al = $term->selected_association_list; my %codes = (); map { $codes{$_->code} = 1 } map { @{$_->evidence_list} } @$al; push(@h_elts, sprintf("%s evidence=%s", $term->public_acc, join(";", keys %codes), ) ); } $hdrinfo = join(", ", @h_elts); } foreach my $seq (@$seqs) { my $desc; if ($fullhdr) { $desc = $fullhdr; } else { $desc = sprintf("%s|%s symbol:%s %s %s %s", uc($self->xref->xref_dbname), $self->xref->xref_key, $self->symbol, $self->species ? sprintf("species:%s \"%s\"", $self->species->ncbi_taxa_id, $self->species->binomial) : '-', $hdrinfo, join(" ", map {$_->as_str} @{$seq->xref_list || []}) ); } $seq->description($desc); $str.= $seq->to_fasta; } return $str; } sub to_idl_struct { my $self = shift; return { "symbol"=>$self->symbol, "full_name"=>$self->full_name, "acc"=>$self->xref->xref_key, "speciesdb"=>$self->xref->xref_dbname, }; } sub to_ptuples { my $self = shift; my ($th) = rearrange([qw(tuples)], @_); my @s = (); push(@s, ["product", $self->xref->as_str, $self->symbol, $self->full_name, ]); push(@s, $self->xref->to_ptuples(-tuples=>$th)); @s; } # **** EXPERIMENTAL CODE **** # the idea is to be homogeneous and use graphs for # everything; eg gene products are nodes in a graph, # associations are arcs # cf rdf, daml+oil etc # args - optional graph to add to sub graphify { my $self = shift; my ($ref, $subg, $opts) = rearrange([qw(ref graph opts)], @_); $opts = {} unless $opts; $subg = $self->apph->create_graph_obj unless $subg; my $t = $self->apph->create_term_obj({name=>$self->as_str, acc=>$self->as_str}); $subg->add_node($t); $subg->add_arc($t, $ref, "hasProduct"); return $subg; } 1; go-perl-0.15/GO/Model/Graph.pm000644 000765 000024 00000212466 11615622160 015677 0ustar00cjmstaff000000 000000 # $Id: Graph.pm,v 1.25 2008/03/27 01:48:43 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Model::Graph; =head1 NAME GO::Model::Graph - a collection of relationships over terms =head1 SYNOPSIS # FETCHING GRAPH FROM FILES use GO::Parser; my $parser = new GO::Parser({handler=>'obj'}); $parser->parse("gene_ontology.obo"); # ontology $parser->parse("gene-associations.sgd"); # gene assocs # get L object my $graph = $parser->handler->graph; my $terms = $graph->term_query("/transmembrane/"); # matching terms foreach my $term (@$terms) { # find gene products associated to this term my $assocs = $graph->deep_association_list($term->acc); printf "Term: %s %s\n", $term->acc, $term->name; print " Associations (direct and via transitive closure_\n"; foreach my $assoc (@$assocs) { next if $assoc->is_not; printf " Assoc evidence: %s to: %s %s\n", join(';', map {$_->code} @{$assoc->evidence_list}), $assoc->gene_product->xref->as_str, $assoc->gene_product->symbol; } } # -- alternatively, use this code... -- # FETCHING FROM DATABASE (requires go-db-perl library) # pretty-printing a subgraph from "nuclear pore" $apph = GO::AppHandle->connect(-dbname=>"$dbname"); $term = $apph->get_term({name=>"nuclear pore"}); $graph = $apph->get_graph_by_terms([$term], $depth); $it = $graph->create_iterator; # returns a GO::Model::GraphIterator object while (my $ni = $it->next_node_instance) { $depth = $ni->depth; $term = $ni->term; $reltype = $ni->parent_rel->type; printf "%s %8s Term = %s (%s) // number_of_association=%s // depth=%d\n", "----" x $depth, $reltype, $term->name, $term->public_acc, $term->n_associations || 0, $depth; } =head1 DESCRIPTION Object containing Nodes (L objects) and relationships (: objects) this may be either the whole ontology tree, or a subgraph, depending on how the object is instantiated. =head2 ONTOLOGY GRAPH MODEL relationships can be thought of as B or sentences of the form SUBJECT-TERM PREDICATE OBJECT-TERM for example, "dog" IS_A "animal" "G-Protein coupled receptor" IS_A "transmembrane receptor" Statements have a B (i.e. the subject of the sentence/statement), a predicate/relationship-type and an B (i.e. the object of the sentence/statement) Relationships can also be seen as arcs in a directed graph, with the subject being equivalent to the child, and the object equivalent to the parent. The arc is labeled with the predicate/relationship-type. perl doesnt handle bidirectional links between objects too well, so rather than having the relationship object know about the terms or the term know about the realtionships, all the graph info is in the Graph object the Relationship object gives you the accessions of the related terms, use the Graph methods to fetch these actual terms. The idea is to keep the Term & Relationship objects lightweight, and keep the Graph logic in the Graph object. The Graph object is responsible for stuff like making sure that a Term object is not instantiated twice if it can be reached by two different paths. Currently all graphs are acyclic, cyclic graphs may be allowed in the future when such relationships are added to GO/OBOA =head2 TRANSITIVE CLOSURES graph object will calculate transitive closures for you - that is it will follow the path in the graph to the root or to all leafs =head2 ITERATORS Using the create_iterator and iterate methods, you can create "visitors" that will traverse the graph, performing actions along the way. Functional-style programming is encouraged, as the iterature() method allows for the passing of lexical closures: $graph->iterate(sub {$term=shift->term; printf "%s %s\n", $term->acc,$term->name}, {direction=>'up', acc=>"GO:0008045"}) =head2 SEE ALSO L L L L =cut use Carp; use strict; use Exporter; use GO::Utils qw(rearrange max); use GO::ObjFactory; use GO::Model::Root; use GO::Model::Term; use GO::Model::Path; use GO::Model::Relationship; use GO::Model::GraphIterator; use FileHandle; use Exporter; use Data::Dumper; use vars qw(@ISA @EXPORT_OK %EXPORT_TAGS $AUTOLOAD); use base qw(GO::Model::Root Exporter); sub _valid_params { return qw(); } =head2 new Usage - $g = GO::Model::Graph->new; Returns - GO::Model::Graph; Args - Normally you would not create a graph object yourself - this is typically done for you by either a L object or a L object =cut sub _initialize { my $self = shift; $self->SUPER::_initialize(@_); $self->{nodes_h} = {}; $self->{nodes_a} = {}; $self->{n_children_h} = {}; $self->{n_parents_h} = {}; $self->{child_relationships_h} = {}; $self->{parent_relationships_h} = {}; $self->apph(GO::ObjFactory->new) unless $self->apph; return; } sub clone { my ($self) = @_; my $new_g = GO::Model::Graph->new(); foreach my $key (keys(%$self)) { my $val = $self->{$key}; my $val_ref = ref($val); my $new_val; if ($val_ref =~ /HASH/i) { my %new_obj = %$val; $new_val = \%new_obj; } elsif ($val_ref =~ /ARRAY/i) { my @new_obj = @$val; $new_val = \@new_obj; } else { $new_val = $val; } $new_g->{$key} = $new_val; } return $new_g; } =head2 create_iterator Usage - $it = $graph->create_iterator("GO:0003677") Usage - $it = $graph->create_iterator({acc=>"GO:0008045", direction=>"up"}); Returns - GO::Model::GraphIterator; Args - accession no [optional] or GO::Model::Term [optional] makes a L, an object which traverses the graph =cut sub create_iterator { my $self = shift; my $arg = shift; my $h = ref($arg) ? ($arg || {}) : {acc=>$arg}; my $it = GO::Model::GraphIterator->new({graph=>$self, %$h}); if ($h->{acc}) { $it->reset_cursor($h->{acc}); } return $it; } =head2 iterate Usage - $graph->iterate(sub {$ni=shift;printf "%s\n", $ni->term->name}); Usage - sub mysub {...}; $graph->iterate(\&mysub); Returns - Args - CODE iterates through the graph executing CODE on every L object =cut sub iterate { my $self = shift; my $sub = shift; my @args = @_; if (!ref($sub)) { $sub = eval("sub{$sub}"); } if (!ref($sub) eq "CODE") { confess("argument must be CODE not $sub"); } my $it = $self->create_iterator(@args); $it->no_duplicates(1); while (my $ni = $it->next_node_instance) { &$sub($ni); } } =head2 term_filter Alias - node_filter Usage - $terms = $graph->term_filter(sub {shift->term->name =~ /transmembrane/}); Usage - sub mysub {...}; $graph->iterate(\&mysub); Returns - ref to an array of GO::Model::Term objects Args - CODE iterates through the graph executing CODE on every L object. If CODE returns true, that node will be returned =cut sub node_filter { my $self = shift; my $sub = shift; my @args = @_; if (!ref($sub)) { $sub = eval("sub{$sub}"); } if (!ref($sub) eq "CODE") { confess("argument must be CODE not $sub"); } my $it = $self->create_iterator(@args); $it->compact(1); my @nodes = (); while (my $ni = $it->next_node_instance) { if (&$sub($ni)) { push(@nodes, $ni->term); } } return \@nodes; } *term_filter = \&node_filter; =head2 term_query Usage - $terms = $graph->term_query({name=>'/transmembrane/'}); Usage - $terms = $graph->term_query({acc=>'GO:0008045'}); Usage - $terms = $graph->term_query('/transmembrane/'); Returns - ref to an array of GO::Model::Term objects Args - hashref of constraints OR name constraint as string returns a set of terms matching query constraints. If the constraint value is enclosed in // a regexp match will be performed constraints are ANDed. For more complex queries, use node_filter() =cut sub term_query { my $self = shift; my $constr = shift; if (!ref($constr)) { $constr = {name=>$constr}; } # compile code for speed my $code = join(' && ', map { my $v = $constr->{$_}; my $op = 'eq'; if ($v =~ /^\/.*\/$/) { $op = '=~'; } else { $v =~ s/\'/\\\'/g; $v = "'$v'"; } if (GO::Model::Term->new->can($_."_list")) { sprintf('grep {$_ %s %s} @{$term->%s_list || []}', $op, $v, $_); } else { sprintf('$term->%s %s %s', $_, $op, $v); } } keys %$constr); my $sub = eval "sub { my \$term=shift->term; $code}"; return $self->node_filter($sub); } =head2 subgraph Usage - my $subgraph = $graph->subgraph({acc=>"GO:0008045"}); Returns - GO::Model::Graph Args - as term_query() creates a subgraph of the current graph containing the terms returned by a term_query() call and all paths to the root =cut sub subgraph { my $self = shift; my $terms = $self->term_query(@_); my $subgraph = $self->subgraph_by_terms($terms); return $subgraph; } =head2 subgraph_by_terms Usage - my $subgraph = $graph->subgraph_by_terms($terms); Usage - my $subgraph = $graph->subgraph_by_terms($terms,{partial=>1}); Returns - GO::Model::Graph Args - GO::Model::Term listref creates a subgraph of the current graph containing the specified terms The path-to-top will be calculated for all terms and added to the subgraph, UNLESS the partial option is set; in this case a relationship between =cut sub subgraph_by_terms { my $self = shift; my $terms = shift || []; my $opt = shift || {}; my $g = $self->apph->create_graph_obj; my %done = (); my %in_set = map {$_->acc=>1} @$terms; my $partial = $opt->{partial}; foreach my $term (@$terms) { my $it = $self->create_iterator($term->acc); if ($partial) { $it->subset_h(\%in_set); } $it->direction('up'); while (my $ni = $it->next_node_instance) { my $t = $ni->term; my $rel = $ni->parent_rel; $g->add_relationship($rel) if $rel; # don't add term twice (but do add rel to term) # don't continue past already-visited term next if $done{$t->acc}; $done{$t->acc} = 1; $g->add_term($t); } } return $g; } =head2 get_all_nodes Usage - my $node_listref = $graph->get_all_nodes(); Synonyms- get_all_terms Returns - ref to an array of GO::Model::Term objects Args - none The returned array is UNORDERED If you want the returned list ordered (eg breadth first or depth first) use the create_iterator() method to get a GO::Model::GraphIterator See also L =cut sub get_all_nodes { my $self = shift; my ($order) = rearrange([qw(order)], @_); my @nodes; if (!$order) { @nodes = values %{$self->{nodes_h}}; # @nodes = @{$self->{nodes_a}}; } else { confess("not implemented yet!"); } return \@nodes; } *get_all_terms = \&get_all_nodes; =head2 get_term Usage - my $term = $graph->get_term($acc); Synonyms- get_node Returns - GO::Model::Term Args - id returns a GO::Model::Term object for an accession no. the term must be in the Graph object See also L =cut sub get_term { my $self = shift; my $acc = shift || confess "you need to provide an accession ID"; # be liberal in what we accept - id, hashref or object if (ref($acc)) { if (ref($acc) eq "HASH") { $acc = $acc->{acc}; } else { $acc = $acc->acc; } } return $self->{nodes_a}->{$acc}; } *get_node = \&get_term; =head2 get_term_by_name Usage - my $term = $graph->get_term_by_name("blah"); Returns - GO::Model::Term Args - string returns a GO::Model::Term object for a name the term must be in the Graph object CASE INSENSITIVE See also L =cut sub get_term_by_name { my $self = shift; my $name = shift || confess; my @terms = grep { lc($_->name) eq lc($name) } @{$self->get_all_terms}; if (!@terms > 1) { confess(">1 term: @terms"); } return $terms[0]; } *get_node_by_name = \&get_term_by_name; =head2 get_terms_by_subset Usage - my $term = $graph->get_terms_by_subset("goslim_plant"); Returns - GO::Model::Term Args - string returns a GO::Model::Term object for a subset the term must be in the Graph object CASE INSENSITIVE See also L =cut sub get_terms_by_subset { my $self = shift; my $subset = shift || confess; my @terms = grep { $_->in_subset($subset) } @{$self->get_all_terms}; return \@terms; } *get_nodes_by_subset = \&get_terms_by_subset; =head2 get_top_nodes Usage - my $node_listref = $graph->get_top_nodes(); Synonyms- get_top_terms Returns - ref to an array of GO::Model::Term objects Args - none usually returns 1 node - the root term See also L =cut sub get_top_nodes { my $self = shift; if ($self->{_top_nodes}) { return $self->{_top_nodes}; } my @topnodes = (); foreach my $node (@{$self->get_all_nodes}) { my $parent_rels = $self->get_parent_relationships($node->acc); my @parent_nodes = (); foreach my $rel (@$parent_rels) { my $node = $self->get_term($rel->acc1); if ($node) { push(@parent_nodes, $node); } } if (!@parent_nodes) { push(@topnodes, $node); } } $self->{_top_nodes} = \@topnodes; return \@topnodes; } *get_top_terms = \&get_top_nodes; =head2 get_leaf_nodes Usage - my $node_listref = $graph->get_top_nodes(); Synonyms- get_leaf_terms Returns - ref to an array of GO::Model::Term objects Args - none See also L =cut sub get_leaf_nodes { my $self = shift; if ($self->{_leaf_nodes}) { return $self->{_leaf_nodes}; } my @leafnodes = (); foreach my $node (@{$self->get_all_nodes}) { my $child_rels = $self->get_child_relationships($node->acc); if (!@$child_rels) { push(@leafnodes, $node); } } $self->{_leaf_nodes} = \@leafnodes; return \@leafnodes; } *get_leaf_terms = \&get_leaf_nodes; =head2 is_leaf_node Usage - if ($graph->is_leaf_node($acc)) {...} Returns - bool Args - accession str See also L =cut sub is_leaf_node { my $self = shift; my $acc = shift; my $child_rels = $self->get_child_relationships($acc); return !@$child_rels; } *is_leaf_term = \&is_leaf_node; =head2 seed_nodes Usage - $nodes = $graph->seed_nodes; Returns - GO::Model::Term listref Args - GO::Model::Term listref [optional] gets/sets the "seed" nodes/terms - these are the terms the Graph is started from, e.g. for building a node ancestory graph, the seed term would be the leaf of this graph, but not term that are expanded or collpased from the ancestory graph. This is mostly relevant if you are fetching your graphs from a database via go-db-perl See also L =cut sub seed_nodes { my $self = shift; $self->{_seed_nodes} = shift if @_; return $self->{_seed_nodes}; } =head2 focus_nodes Usage - $nodes = $graph->focus_nodes; Synonyms- focus_terms Returns - GO::Model::Term listref Args - GO::Model::Term listref [optional] gets/sets the "focus" nodes/terms - these are the terms the Graph is centred around; for instance, if the graph was built around a query to "endoplasmic*" all the terms matching this string would be focused This is mostly relevant if you are fetching your graphs from a database via go-db-perl See also L =cut sub focus_nodes { my $self = shift; $self->{_focus_nodes} = shift if @_; return $self->{_focus_nodes}; } *focus_terms = \&focus_nodes; =head2 is_focus_node Usage - if ($g->is_focus_node($term)) {..} Returns - bool Args - GO::Model::Term =cut sub is_focus_node { my $self = shift; my $term = shift; if (grep {$_->acc eq $term->acc} @{$self->focus_nodes || []}) { return 1; } return 0; } *is_focus_term = \&is_focus_node; =head2 add_focus_node Usage - $g->add_focus_node($term) Returns - Args - GO::Model::Term See also L =cut sub add_focus_node { my $self = shift; my $term = shift; if (!$self->is_focus_node($term)) { push(@{$self->{_focus_nodes}}, $term); } } *add_focus_term = \&add_focus_node; =head2 paths_to_top Usage - my $paths = $graph->paths_to_top("GO:0005045"); Returns - arrayref of GO::Model::Path objects Args - See also L =cut #sub FAST_paths_to_top { # my $self= shift; # my $acc = shift; # my %is_ancestor_h = (); # $self->iterate(sub { # my $ni = shift; # $is_ancestor_h->{$ni->term->acc}=1; # return; # }, # {acc=>$acc, # direction=>'up'} # ); # print "$_\n" foreach keys %is_ancestor_h; # my @root_accs = # grep {!$self->n_parents($_)} (keys %is_ancestor_h); # if (!@root_accs) { # confess("ASSERTION ERROR: No root accs for $acc"); # } # if (@root_accs > 1) { # confess("ONTOLOGY ERROR: >1 root for $acc"); # } # my $root_acc = shift @root_accs; # my @nodes = ( {acc=>$root_acc,paths=>[]} ); # while (@nodes) { # my $node = shift @nodes; # my $curr_acc = $node->{acc}; # my $child_rels = $self->get_child_relationships($curr_acc); # foreach my $child_rel (@$child_rels) { # my $child_term = $self->get_term($child_rel->acc2); # my $child_acc = $child_term->acc; # next unless $is_ancestor_h{$child_acc}; # } # } # die 'todo'; #} sub paths_to_top { my $self= shift; require GO::Model::Path; my $acc=shift; my $path = GO::Model::Path->new; my @nodes = ({path=>$path, acc=>$acc}); my @paths = (); while (@nodes) { my $node = shift @nodes; my $parent_rels = $self->get_parent_relationships($node->{acc}); # printf # "$node->{acc} has parents: %s\n", # join("; ", map {$_->acc} @$parents); if (!@$parent_rels) { # print "PUSING PATH $node->{path}\n"; push(@paths, $node->{path}); } else { foreach my $parent_rel (@$parent_rels) { my $parent = $self->get_term($parent_rel->acc1); if (!$parent) { # dangling parent - do nothing } else { my $new_path = $node->{path}->duplicate; $new_path->add_link($parent_rel->type, $parent); push(@nodes, {path=>$new_path, acc=>$parent->acc}); } } } } return \@paths; } =head2 node_count Usage - my $count = $g->node_count Synonyms- term_count Returns - int Args - returns the number of terms/nodes in the graph See also L =cut sub node_count { my $self = shift; return scalar(@{$self->get_all_nodes}); } *term_count = \&node_count; =head2 n_associations Usage - my $count = $g->n_associations($acc); Returns - int Args - if you parsed an association file into this graph, this will return the number of instances attached directly to acc See also L See also L =cut sub n_associations { my $self = shift; my $acc = shift; my $term = $self->get_term($acc); if ($term) { return $term->n_associations } else { confess("Don't have $acc in $self"); } } =head2 n_deep_associations Usage - my $count = $g->n_deep_associations($acc); Returns - int Args - if you parsed an association file into this graph, this will return the number of instances attached directly to acc OR to a node subsumed by acc See also L See also L =cut sub n_deep_associations { my $self = shift; my $acc = shift; my $rcterms = $self->get_recursive_child_terms($acc); my $cnt = 0; foreach (@$rcterms){ $cnt+= $self->n_associations($_->acc) } return $cnt; } =head2 n_children Usage - $n = $graph->n_children('GO:0003677'); Synonyms- n_sterms, n_subj_terms, n_subject_terms Returns - int Args - returns the number of DIRECT children/subject/subordinate terms beneath this one =cut sub n_children { my $self = shift; my $acc = shift; if (ref($acc)) { if (ref($acc) eq "HASH") { confess("illegal argument: $acc"); } $acc = $acc->acc; } my @tl = @{$self->get_child_terms($acc) || []}; if (@tl) { return scalar(@tl); } # if ($self->{trailing_edges}) { # my $edgeh = $self->{trailing_edges}->{$acc}; # if ($edgeh) { # return scalar(keys %$edgeh); # } # return 0; # } # else { if (!defined($self->{n_children_h}->{$acc})) { my $term = $self->get_term($acc); $term || confess("$acc not in graph $self"); my $tl = $term->apph->get_child_terms($term, {acc=>1}); $self->{n_children_h}->{$acc} = scalar(@$tl); } return $self->{n_children_h}->{$acc}; # } } *n_sterms = \&n_children; *n_subj_terms = \&n_children; *n_subject_terms = \&n_children; =head2 n_parents Usage - $n = $graph->n_parents(3677); Synonyms- n_oterms, n_obj_terms, n_object_terms Returns - int Args - returns the number of DIRECT parent/object/superordinate terms above this one =cut sub n_parents { my $self = shift; my $acc = shift; if (ref($acc)) { if (ref($acc) eq "HASH") { confess("illegal argument: $acc"); } $acc = $acc->acc; } if (!defined($self->{n_parents_h}->{$acc})) { my $term = $self->get_term($acc); $term || confess("$acc not in graph $self"); my $tl = $term->apph->get_parent_terms($term, {acc=>1}); $self->{n_parents_h}->{$acc} = scalar(@$tl); } return $self->{n_parents_h}->{$acc}; } *n_oterms = \&n_parents; *n_obj_terms = \&n_parents; *n_object_terms = \&n_parents; =head2 association_list Usage - $assocs = $g->association_list('GO:0003677') Returns - listref of GO::Model::Association Args - acc (string) returns a list of association objects B attached to the specified term See also L =cut sub association_list { my $self = shift; my $acc = shift; my $term = $self->get_term($acc); if (!$term) { # use Data::Dumper; # print Dumper [keys %{$self->{nodes_a}}]; # die "no term with acc $acc"; return undef; } return $term->association_list(); } =head2 get_direct_associations Usage - Returns - Args - See also L =cut sub get_direct_associations { my $self = shift; my $acc = shift; $acc = $acc->acc if ref $acc; $self->association_list($acc); } =head2 deep_association_list Usage - $assocs = $g->association_list('GO:0003677') Returns - listref of GO::Model::Association Args - acc (string) returns a list of association objects B attached to the specified term. (ie assocs attached to the term or to terms subsumed by the specified term). See also L =cut sub deep_association_list { my $self = shift; my $acc = shift; my @accs = @{$self->association_list($acc) || []}; push(@accs, map {@{$self->deep_association_list($_->acc)||[]}} @{$self->get_child_terms($acc) || []}); return \@accs; } =head2 product_list Usage - $prods = $g->product_list('GO:0003677') Returns - listref of GO::Model::GeneProduct Args - acc (string) returns a list of distinct gene product objects B attached to the specified term. See also L =cut sub product_list { my $self = shift; my $acc = shift; my $assocs = $self->association_list($acc) || []; my @prods = (); my %ph = (); foreach my $assoc (@$assocs) { my $gp = $assoc->gene_product; if (!$ph{$gp->xref->as_str}) { push(@prods, $gp); $ph{$gp->xref->as_str} = 1; } } return [@prods]; } =head2 deep_product_list Usage - $prods = $g->deep_product_list('GO:0003677') Returns - listref of GO::Model::GeneProduct Args - acc (string) returns a list of distinct gene product objects B attached to the specified term. (ie assocs attached to the term or to terms subsumed by the specified term). See also L =cut sub deep_product_list { my $self = shift; my $acc = shift; my $assocs = $self->deep_association_list($acc) || []; my @prods = (); my %ph = (); foreach my $assoc (@$assocs) { my $gp = $assoc->gene_product; if (!$ph{$gp->xref->as_str}) { push(@prods, $gp); $ph{$gp->xref->as_str} = 1; } } return [@prods]; } =head2 deep_product_count Usage - $n_prods = $g->deep_product_count('GO:0003677') Returns - int Args - acc (string) returns a count of distinct gene product objects B attached to the specified term. performs transitive closure. will not count gene products twice See also L =cut sub deep_product_count { my $self = shift; my $acc = shift; return scalar(@{$self->deep_product_list($acc)}); } =head2 get_relationships Usage - my $rel_listref = $graph->get_relationships('GO:0003677'); Returns - ref to an array of GO::Model::Relationship objects Args - identifier/acc (string) returns relationships which concern the specified term; the specified term can be the subject or object term in the relationship (ie child or parent) See also L =cut sub get_relationships { my $self = shift; my $acc = shift || confess("You must specify an acc"); my $child_rel_l = $self->get_child_relationships($acc); my $parent_rel_l = $self->get_parent_relationships($acc); return [@{$child_rel_l}, @{$parent_rel_l}]; } *get_rels = \&get_relationships; =head2 get_parent_relationships Usage - my $rel_listref = $graph->get_parent_relationships('GO:0003677'); Synonym - get_relationships_by_child Synonym - get_relationships_by_subj Synonym - get_relationships_by_subject Synonym - get_obj_relationships Synonym - get_object_relationships Returns - ref to an array of GO::Model::Relationship objects Args - identifier/acc (string) See also L =cut sub get_parent_relationships { my $self = shift; my $acc = shift || confess("You must specify an acc"); # if a term object is specified instead of ascc no, use the acc no if (ref($acc) && $acc->isa("GO::Model::Term")) { $acc = $acc->acc; } my $rel_h = $self->{parent_relationships_h}->{$acc}; return $self->get_acc_relationships ($rel_h); } *get_relationships_by_child = \&get_parent_relationships; *get_relationships_by_subj = \&get_parent_relationships; *get_relationships_by_subject = \&get_parent_relationships; *get_obj_relationships = \&get_parent_relationships; *get_object_relationships = \&get_parent_relationships; =head2 get_child_relationships Usage - my $rel_listref = $graph->get_child_relationships('GO:0003677'); Synonym - get_relationships_by_parent Synonym - get_relationships_by_obj Synonym - get_relationships_by_object Synonym - get_subj_relationships Synonym - get_subject_relationships Returns - ref to an array of GO::Model::Relationship objects Args - identifier/acc (string) See also L =cut sub get_child_relationships { my $self = shift; my $acc = shift || confess("You must specify an acc"); # if a term object is specified instead of ascc no, use the acc no if (ref($acc) && $acc->isa("GO::Model::Term")) { $acc = $acc->acc; } my $rel_h = $self->{child_relationships_h}->{$acc}; return $self->get_acc_relationships ($rel_h); } *get_relationships_by_parent = \&get_child_relationships; *get_relationships_by_obj = \&get_child_relationships; *get_relationships_by_object = \&get_child_relationships; *get_subj_relationships = \&get_child_relationships; *get_subject_relationships = \&get_child_relationships; =head2 get_all_relationships Usage - Returns - GO::Model::Relationship list Args - returns all the relationships/statements in this graph See also L =cut sub get_all_relationships { my $self = shift; my $nl = $self->get_all_nodes; [ map { values %{$self->{child_relationships_h}->{$_->acc}} } @$nl ]; } sub get_acc_relationships { my $self = shift; my $rel_h = shift; my $rels = []; foreach my $acc (keys (%{$rel_h})) { push (@{$rels}, $rel_h->{$acc}); } return $rels; } =head2 get_parent_terms Usage - my $term_lref = $graph->get_parent_terms($parent_term->acc); Synonym - get_obj_terms Synonym - get_object_terms Returns - ref to array of GO::Model::Term objs Args - the accession of the query term See also L =cut sub get_parent_terms { return shift->_get_related_terms_by_type("parent",@_); } *get_obj_terms = \&get_parent_terms; *get_object_terms = \&get_parent_terms; =head2 get_parent_terms_by_type Usage - Synonym - get_obj_terms_by_type Synonym - get_object_terms_by_type Returns - ref to array of GO::Model::Term objs Args - the accession of the query term - the type by which to constrain relationships See also L =cut sub get_parent_terms_by_type { return shift->_get_related_terms_by_type("parent",@_); } *get_obj_terms_by_type = \&get_parent_terms_by_type; *get_object_terms_by_type = \&get_parent_terms_by_type; =head2 get_recursive_parent_terms Title : get_recursive_parent_terms Usage : Synonyms: get_recursive_obj_terms Synonyms: get_recursive_object_terms Function: Example : Returns : Args : accession of query term See also L =cut sub get_recursive_parent_terms{ my $self = shift; my $acc = shift; $self->get_recursive_parent_terms_by_type($acc, undef, @_); } *get_recursive_obj_terms = \&get_recursive_parent_terms; *get_recursive_object_terms = \&get_recursive_parent_terms; =head2 get_recursive_parent_terms_by_type Title : get_recursive_parent_terms_by_type Usage : Synonyms: get_recursive_obj_terms_by_type Synonyms: get_recursive_object_terms_by_type Function: Example : Returns : Args : if type is blank, gets all See also L =cut sub get_recursive_parent_terms_by_type { return shift->_get_recursive_related_terms_by_type("parent",@_); } *get_recursive_obj_terms_by_type = \&get_recursive_parent_terms_by_type; *get_recursive_object_terms_by_type = \&get_recursive_parent_terms_by_type; =head2 get_reflexive_parent_terms Title : get_reflexive_parent_terms Usage : Function: Example : Returns : Args : acc returns parent terms plus the term (for acc) itself [reflexive transitive closure of relationships in upward direction] See also L =cut sub get_reflexive_parent_terms { my ($self, $acc) = @_; my $terms = $self->get_recursive_parent_terms($acc); unshift(@$terms, $self->get_term($acc)); return $terms; } =head2 get_reflexive_parent_terms_by_type Title : get_reflexive_parent_terms_by_type Usage : Function: Example : Returns : listref of terms Args : acc, type closure of relationship including the term itself See also L =cut sub get_reflexive_parent_terms_by_type{ my ($self,$acc, $type) = @_; my $terms = $self->get_recursive_parent_terms_by_type($acc, $type); return [$self->get_term($acc), @$terms]; } =head2 get_child_terms Usage - my $term_lref = $graph->get_child_terms($parent_term->acc); Synonym - get_subj_terms Synonym - get_subject_terms Returns - ref to array of GO::Model::Term objs Args - See also L =cut sub get_child_terms { return shift->_get_related_terms_by_type("child",@_); } *get_subj_terms = \&get_child_terms; *get_subject_terms = \&get_child_terms; =head2 get_child_terms_by_type Synonym - get_subj_terms_by_type Synonym - get_subject_terms_by_type Returns - ref to array of GO::Model::Term objs Args - the accession of the query term - the type by which to constrain relationships See also L =cut sub get_child_terms_by_type { return shift->_get_related_terms_by_type("child",@_); } *get_subj_terms_by_type = \&get_child_terms_by_type; *get_subject_terms_by_type = \&get_child_terms_by_type; =head2 get_recursive_child_terms Title : get_recursive_child_terms Usage : Synonyms: get_recursive_subj_terms Synonyms: get_recursive_subject_terms Function: Example : Returns : a reference to an array of L objects Args : the accession of the query term See also L =cut sub get_recursive_child_terms{ my ($self,$acc, $refl) = @_; $self->get_recursive_child_terms_by_type($acc, undef, $refl); } *get_recursive_subj_terms = \&get_recursive_child_terms; *get_recursive_subject_terms = \&get_recursive_child_terms; =head2 get_recursive_child_terms_by_type Title : get_recursive_child_terms_by_type Usage : Synonyms: get_recursive_subj_terms_by_type Synonyms: get_recursive_subject_terms_by_type Function: Example : Returns : a reference to an array of L objects Args : accession, type if type is blank, gets all See also L =cut sub get_recursive_child_terms_by_type{ return shift->_get_recursive_related_terms_by_type("child",@_); } *get_recursive_subj_terms_by_type = \&get_recursive_child_terms_by_type; *get_recursive_subject_terms_by_type = \&get_recursive_child_terms_by_type; =head2 _get_recursive_related_terms_by_type Title : _get_recursive_related_terms_by_type Usage : Function: Obtain all relationships of the given kind and type for the term identified by its accession, and recursively repeat this with all parents and children as query for parent and child relationships, respectively. This is an internal method. Example : Returns : A reference to an array of L objects. Args : - the kind of relationship, either "child" or "parent" - the accession of the term with which to query - the type to which to constrain relationships (optional, all types if left undef) - TRUE if reflexive and FALSE otherwise (default FALSE) See also L =cut sub _get_recursive_related_terms_by_type{ my ($self, $relkind, $acc, $type, $refl) = @_; # if a term object is specified instead of ascc no, use the acc no if (ref($acc) && $acc->isa("GO::Model::Term")) { $acc = $acc->acc; } my $rels = ($relkind eq "child") ? $self->get_child_relationships($acc) : $self->get_parent_relationships($acc); if ($type) { @$rels = grep { $_->type eq $type; } @$rels; } my $relmethod = $relkind."_acc"; my @pterms = map { my $term = $self->get_term($_->$relmethod()); my $rps = $self->_get_recursive_related_terms_by_type($relkind, $_->$relmethod(), $type); ($term, @$rps); } @$rels; if ($refl) { @pterms = ($self->get_term($acc), @pterms); } return \@pterms; } =head2 _get_related_terms_by_type Usage - my $term_lref = $graph->_get_related_terms_by_type("child",$acc); Returns - ref to array of GO::Model::Term objs Args - the kind of relationship, either "child" or "parent" - the accession of the term for which to obtain rel.ships - the type by which to constrain relationships (optional, defaults to all terms if left undef) This is an internal method. =cut sub _get_related_terms_by_type { my ($self,$relkind,$acc,$type) = @_; # if a term object is specified instead of ascc no, use the acc no if (ref($acc) && $acc->isa("GO::Model::Term")) { $acc = $acc->acc; } my $rels = ($relkind eq "child") ? $self->get_child_relationships($acc) : $self->get_parent_relationships($acc); if ($type) { @$rels = grep { $_->type eq $type; } @$rels; } my $relmethod = $relkind."_acc"; my @term_l = (); foreach my $r (@$rels) { my $t = $self->get_term($r->$relmethod()); if ($t) { push(@term_l, $t); } } return \@term_l; } =head2 get_parent_accs_by_type Usage - Returns - Args - acc, type =cut sub get_parent_accs_by_type { my $self = shift; my $term = shift; my $type = shift; my $rels = $self->get_parent_relationships($term); return [map {$_->acc1} grep {lc($_->type) eq lc($type) } @$rels]; } =head2 get_reflexive_parent_accs_by_type Title : get_reflexive_parent_accs_by_type Usage : Function: Example : Returns : listref of terms Args : acc, type closure of relationship including the term itself See also L =cut sub get_reflexive_parent_accs_by_type{ my ($self,$acc, $type) = @_; my $terms = $self->get_recursive_parent_accs_by_type($acc, $type); return [$acc, @$terms]; } =head2 get_relationships_between_terms Title : get_relationships_between_terms Usage : Function: Example : Returns : [] of relationships Args : parent id, child id See also L =cut sub get_relationships_between_terms{ my ($self, $acc1, $acc2) = @_; my $child_rels = $self->get_child_relationships($acc1); return [grep {$_->acc2 eq $acc2} @$child_rels]; } =head2 get_parent_closure_hash_by_type Title : get_parent_closure_hash_by_type Usage : Function: given a term-acc and relationship type, will give a hash that can be used to check if a term X is a parent of term Y Example : Returns : Args : keys will be lower-cased =cut sub get_parent_closure_hash_by_type{ my ($self, $acc, $type) = @_; my $parents = $self->get_reflexive_parent_terms_by_type($acc, $type); return {map {lc($_->name)=>1} @$parents}; } =head2 add_child_relationship See also L =cut sub add_child_relationship { my $self = shift; confess("deprecated"); my ($rel) = rearrange([qw(term)], @_); } =head2 add_parent_relationship parent relationships are as valued as child relationships See also L =cut sub add_parent_relationship { my $self = shift; confess("deprecated"); my ($rel) = rearrange([qw(term)], @_); } =head2 close_below Usage - $graph->close_below(3677); Returns - Args - term (as acc or GO::Model::Term object) gets rid of everything below a node used by AmiGO for when a user closes a term in the graph =cut sub close_below { my $self = shift; my $node = shift; my $if_no_parent_to_delete = shift; my $acc; if (ref($node)) { if (ref($node) eq "ARRAY") { map { $self->close_below($_) } @$node; return; } elsif ($node->isa('GO::Model::Term')) { $acc = $node->acc; } else { $acc = $node->{acc}; } } else { $acc = $node; } my $iter = $self->create_iterator($acc); my @togo = (); while (my $n = $iter->next_node) { unless ($n->acc eq $acc) { push(@togo, $n); } } my $p = $if_no_parent_to_delete ? $acc : undef; foreach my $n (@togo) { $self->delete_node($n->acc, $p); } } # add 2nd optional arg: parent acc for checking if to delete the node -- Shu # if there are other parent(s), do not delete the node sub delete_node { my $self = shift; my $acc = shift; my $p_acc = shift; # delete $self->{parent_relationships_h}->{$acc}; # delete $self->{child_relationships_h}->{$acc}; # Remove the parent relationship, first from our parents... my $par_rel_hashes = $self->{parent_relationships_h}->{$acc} || {}; my $par_rels = [grep {$_} values(%$par_rel_hashes)]; my $par_rel; my $other_p = 0; foreach $par_rel (@$par_rels) { my $par_acc = $par_rel->acc1; if (!$p_acc || $par_acc && $par_acc eq $p_acc) { $self->{child_relationships_h}->{$par_acc}->{$acc} = undef; delete $self->{child_relationships_h}->{$par_acc}->{$acc}; } else { $other_p++; } } # ... then from ourself $self->{parent_relationships_h}->{$acc} = undef unless ($other_p); # Remove the child relationship, first from our children... my $child_rel_hashes = $self->{child_relationships_h}->{$acc} || {}; my $child_rels = [grep {$_} values(%$child_rel_hashes)]; my $child_rel; foreach $child_rel (@$child_rels) { my $child_acc = $child_rel->acc2; unless ($other_p) { $self->{parent_relationships_h}->{$child_acc}->{$acc} = undef; delete $self->{parent_relationships_h}->{$child_acc}->{$acc}; } } # ... then from ourself $self->{child_relationships_h}->{$acc} = undef unless ($other_p); # Now delete ourself unless ($other_p) { delete $self->{nodes_h}->{$acc}; $self->{nodes_a}->{$acc} = undef; } # This could change the top and leaf nodes, so # remove the cached values $self->{_top_nodes} = undef; $self->{_leaf_nodes} = undef; } sub category_term { my $self= shift; my $acc=shift; my $paths = $self->paths_to_top($acc); my $path = $paths->[0]; if (!$path || !$path->term_list) { return; } if ($path->length < 2) { return $path->term_list->[-1]; } return $path->term_list->[-2]; } =head2 find_roots Usage - my $terms = $graph->find_roots; Returns - arrayref of GO::Model::Term objects Args - All terms withOUT a parent See also L =cut sub find_roots { my $self= shift; require GO::Model::Path; my $nodes = $self->get_all_nodes; my @roots = (); foreach my $node (@$nodes) { my $ps = $self->get_parent_terms($node->acc); if (!@$ps) { push(@roots, $node); } } return \@roots; } =head2 get_all_products Usage - Returns - Args - See also L =cut sub get_all_products { my $self = shift; my $nodes = $self->get_all_nodes; my @prod_index = (); my @prods = (); foreach my $n (@$nodes) { foreach my $p (@{$n->product_list}) { if (!$prod_index[$p->id]) { } } } } sub find_path { confess; } sub build_matrix { my $self = shift; my %node_lookup = (); my $terms = $self->get_all_nodes; foreach my $t (@$terms) { $node_lookup{$t->acc} = {$t->acc => 0}; my $parents = $self->get_parent_terms($t->acc); # foreach my $p (@$parents) { # $node_lookup[$t->acc]->{$p->acc} = 1; # } my %h = $self->parent_dist($t->acc); foreach my $k (keys %h) { $node_lookup{$t->acc}->{$k} = $h{$k}; } } return %node_lookup; } sub parent_dist { my $self = shift; my $acc = shift; my $dist = shift || 0; $dist ++; my $parents = $self->get_parent_terms($acc); my %h = (); foreach my $p (@$parents) { $h{$p->acc} = $dist; my %rh = $self->parent_dist($p->acc, $dist); foreach my $k (keys %rh) { # multiple parentage; take the shortest path if (!defined($h{$k}) || $h{$k} > $rh{$k}) { $h{$k} = $rh{$k}; } } } return %h; } =head2 merge Usage - $g->merge($g2); Returns - Args - GO::Model::Graph merges two graphs =cut sub merge { my $self = shift; my $g2 = shift; foreach my $t (@{$g2->get_all_nodes}) { if ($self->get_term($t->acc)) { } else { $self->add_term($t); } } foreach my $t (@{$g2->focus_nodes || []}) { $self->add_focus_node($t); } foreach my $r (@{$g2->get_all_relationships}) { # don't need to worry about duplicates, # add_relationship unqiuifies $self->add_relationship($r); } } sub to_lisp { my $self = shift; my $term = shift; my @parent_rels = @{$self->get_parent_relationships($term->acc) || []}; my @parents = (); my @lisp_isa = (); my @lisp_partof = (); map { if ($_->is_inheritance) { push(@lisp_isa, $self->get_term($_->acc1)); } else { push(@lisp_partof, $self->get_term($_->acc1)); } push(@parents, $self->get_term($_->acc1)); } @parent_rels; my $lisp = ["|".$term->lisp_acc."| T ", [ ["OCELOT::PARENTS ". (@parents ? join("", (map {"|".$_->lisp_acc."| "} @parents)) : "OCELOT::FRAMES") ], ["DESCRIPTION \"".$term->name."\""], # ["DEFINITION \"".$term->description."\""], @lisp_isa ? ["IS-A ".join("",map{"|".$_->lisp_acc."| "} @lisp_isa)] : "", @lisp_partof ? ["PART-OF ".join("",map{"|".$_->lisp_acc."| "} @lisp_partof)] : "", ], "NIL", ]; my $lisp_term = lisp2text($lisp); } sub lisp2text { my $arr = shift; my $text = ""; for (my $i=0; $i<@$arr; $i++) { if (ref($arr->[$i])) { $text.= lisp2text($arr->[$i]); } else { $text.= $arr->[$i]; } } return "($text)\n"; } sub to_ptuples { my $self = shift; my ($th, $include, $sort) = rearrange([qw(tuples include sort)], @_); my $it = $self->create_iterator; my @stmts = (); my %done = (); while (my $ni = $it->next_node_instance) { my $term = $ni->term; next if $done{$term->acc}; push(@stmts, $term->to_ptuples(-tuples=>$th)); $done{$term->acc} = $term; } my $rels = $self->get_all_relationships; push(@stmts, map { $_->to_ptuples(-tuples=>$th) } @$rels); unless ($include && $include->{'-assocs'}) { map { printf "$_:$include->{$_};;;\n"; } keys %$include; foreach my $t (values %done) { my $assocs = $t->association_list || []; push(@stmts, map {$_->to_ptuples(-term=>$t, -tuples=>$th) } @$assocs); } } return @stmts; } =head2 export Usage - $graph->export({format=>$format}); Returns - Args - opt hash writes out the graph in any export format, including obo, go_ont, owl, png (graphviz) etc =cut sub export { my $self = shift; my $opt = shift || {}; my $format = $opt->{format} || 'obo'; delete $opt->{format}; # todo: filehandles/files if ($format eq 'png') { require "GO/IO/Dotty.pm"; my $graphviz = GO::IO::Dotty::go_graph_to_graphviz( $self, {node => {shape => 'box'}, %$opt, }); print $graphviz->as_png; } elsif ($format eq 'go_ont') { # todo: tidy this up $self->to_text_output(-fmt=>'gotext'); } else { my $p = GO::Parser->new({format=>"GO::Parsers::obj_emitter", handler=>$format}); $p->emit_graph($self); } return; } =head2 to_xml Usage - Returns - Args - =cut sub to_xml { my $self = shift; my $fh = shift; require "GO/IO/RDFXML.pm"; my $out = GO::IO::RDFXML->new(-output=>$fh); $out->start_document(); $out->draw_node_graph($self, @_); $out->end_document(); } sub to_obo { my $self = shift; my $fh = shift; require "GO/Handlers/OboOutHandler.pm"; my $out = GO::Handlers::OboOutHandler->new(-output=>$fh); $out->g($self); $out->out; } sub add_path { my $self = shift; my $path = shift; die 'TODO'; my $links = $path->link_list; for (my $i=0; $i<@$links; $i+=2) { my $t = $links->[$i+1]; $self->add_term($t); $self->add_relationship(); # TODO } } =head2 add_term Usage - $g->add_term($term) Returns - Args - GO::Model::Term =cut sub add_term { my $self = shift; my $term = shift; if (!ref($term)) { confess("Term must be either hashref or Term object"); } if (ref($term) eq 'HASH') { # $term = $self->apph->create_term_obj($term); $term = GO::Model::Term->new($term); } my $acc = $term->acc; $acc or confess ("$term has no acc"); $self->{nodes_a}->{$acc} = $term; $self->{nodes_h}->{$acc} = $self->{nodes_a}->{$acc}; $term; } =head2 add_node Usage - Returns - Args - synonym for add_term =cut *add_node = \&add_term; =head2 add_relationship Usage - $graph->add_relationship({acc1=>from_id, acc2=>to_id}); Usage - $graph->add_relationship($from_id, $to_id, $type}); Usage - $graph->add_relationship($obj, $subj, $type}); Returns - Args - only one relationship between id1 and id2 is allowed See also L =cut sub add_relationship { my $self = shift; my ($rel) = @_; if (ref($rel) eq "HASH") { $rel = GO::Model::Relationship->new($rel); } if (UNIVERSAL::isa($rel, "GO::Model::Relationship")) { } else { my ($from_id, $to_id, $type) = @_; if (ref($from_id)) { if (UNIVERSAL::isa($from_id, "GO::Model::Term")) { my $term1 = $from_id; if ($term1->acc) { $from_id = $term1->acc; } else { $from_id = sprintf("%s", $term1); } } } if (ref($to_id)) { if (UNIVERSAL::isa($to_id, "GO::Model::Term")) { my $term2 = $to_id; if ($term2->acc) { $to_id = $term2->acc; } else { $to_id = sprintf("%s", $term2); } } } $from_id || confess("did not specify a from id, only @_"); $to_id || confess("did not specify a to id, only @_"); $rel = GO::Model::Relationship->new({acc1=>$from_id, acc2=>$to_id}); $rel->type($type || 'is_a'); } # if (!ref($rel)) { # my ($from_id, $to_id, $type) = @_; # $rel = GO::Model::Relationship->new({acc1=>$from_id, acc2=>$to_id}); # $rel->type($type); # } # if (ref($rel) eq "HASH") { # $rel = GO::Model::Relationship->new($rel); # } $rel->acc1 || confess($rel); $rel->acc2 || confess($rel); if (0 && $rel->complete) { # EXPERIMENTAL: # an OWL/DL style logical definition (N+S conditions) is stored in the DAG as # normal Relationships but with the 'completes' tag set to true # # e.g. for a logical def of "larval locomotory behaviour" # genus: locomotory behavior # differentia: during larval_stage # # we would have 2 Relationships, one an is_a link to locomotory behavior # the other a during link to larval_stage (eg from fly_anatomy) # both these would be tagged complete=1 # - note this is in *addition* to existing links (N conditions) # # calling this method removes the logical def links and creates # a logical definition object my $term = $self->get_term($rel->acc2); my $ldef = $term->logical_definition; if (!$ldef) { $ldef = $self->apph->create_logical_definition_obj; $term->logical_definition($ldef); } my $oacc = $rel->acc1; my $type = $rel->type; if ($type ne 'is_a') { $ldef->add_intersection([$type,$oacc]); } else { $ldef->add_intersection([$oacc]); } return; } # add an index going from parent to child if (!$self->{child_relationships_h}->{$rel->acc1}) { $self->{child_relationships_h}->{$rel->acc1} = {}; } $self->{child_relationships_h}->{$rel->acc1}->{$rel->acc2} = $rel; # add an index going from child to parent if (!$self->{parent_relationships_h}->{$rel->acc2}) { $self->{parent_relationships_h}->{$rel->acc2} = {}; } $self->{parent_relationships_h}->{$rel->acc2}->{$rel->acc1} = $rel; } *add_arc = \&add_relationship; sub get_term_properties { my $self = shift; my $acc = shift; if (ref($acc)) { # term obj? $acc = $acc->acc; } my $parents = $self->get_recursive_parent_terms_by_type($acc, 'is_a', 1); return [map {@{$_->property_list || []}} @$parents]; } sub get_all_properties { my $self = shift; my $terms = $self->get_all_terms; my @props = map {@{$_->property_list || []}} @$terms; my %ph = map {$_->name => $_} @props; return [values %ph]; } sub cross_product_index { my $self = shift; $self->{_cross_product_index} = shift if @_; $self->{_cross_product_index} = {} unless $self->{_cross_product_index}; return $self->{_cross_product_index}; } sub add_cross_product { my $self = shift; my $xp_acc = shift; my $xp; if (ref($xp_acc)) { $xp = $xp_acc; $xp_acc = $xp->xp_acc; } else { my $parent_acc = shift; my $restrs = shift; $xp = $self->apph->create_cross_product_obj({xp_acc=>$xp_acc, parent_acc=>$parent_acc, restriction_list=>$restrs}); } $self->cross_product_index->{$xp_acc} = $xp; return $xp; } sub get_cross_product { my $self = shift; my $xp_acc = shift; return $self->cross_product_index->{$xp_acc}; } sub get_term_by_cross_product { my $self = shift; my $xp = shift; my $cpi = $self->cross_product_index; my @xp_accs = keys %$cpi; my $term; foreach my $xp_acc (@xp_accs) { my $curr_xp = $cpi->{$xp_acc}; if ($xp->equals($curr_xp)) { $term = $self->get_term($xp_acc); last; } } return $term; } sub create_subgraph_by_term_type { my $self = shift; my $tt = shift; my $g = $self->apph->create_graph_obj; my $terms = $self->get_all_terms; foreach my $t (@$terms) { next unless $t->type eq $tt; $g->add_term($t); $g->add_relationship($_) foreach @{$self->get_relationships($t->acc)}; my $xp = $self->get_cross_product($t->acc); $g->add_cross_product($xp) if $xp; } return $g; } sub add_trailing_edge { my $self = shift; my $acc = shift; my $id = shift; if (!$self->{trailing_edges}) { $self->{trailing_edges} = {}; } if (!$self->{trailing_edges}->{$acc}) { $self->{trailing_edges}->{$acc} = {}; } $self->{trailing_edges}->{$acc}->{$id} = 1; } sub infer_logical_definitions { my $self = shift; my $terms = $self->get_all_terms; $self->infer_logical_definition_for_term($_->acc) foreach @$terms; } # EXPERIMENTAL: # an OWL/DL style logical definition (N+S conditions) is stored in the DAG as # normal Relationships but with the 'completes' tag set to true # # e.g. for a logical def of "larval locomotory behaviour" # genus: locomotory behavior # differentia: during larval_stage # # we would have 2 Relationships, one an is_a link to locomotory behavior # the other a during link to larval_stage (eg from fly_anatomy) # both these would be tagged complete=1 # - note this is in *addition* to existing links (N conditions) # # calling this method removes the logical def links and creates # a logical definition object sub infer_logical_definition_for_term { my $self = shift; my $acc = shift; my $term = $self->get_term($acc); my $parent_rels = $self->get_parent_relationships($acc); my @isects = grep {$_->complete} @$parent_rels; warn("assertion warning: $acc has 1 logical def link") if @isects == 1; return unless @isects > 1; my $ldef; if (@isects) { $ldef = $self->apph->create_logical_definition_obj; $term->logical_definition($ldef); foreach my $isect (@isects) { # hack: todo; test if genuinely anonymous my $oacc = $isect->object_acc; my $rel = $isect->type; if ($rel ne 'is_a') { $ldef->add_intersection([$_->type,$oacc]); } else { $ldef->add_intersection([$oacc]); } } } return $ldef; } sub set_category { my ($self, $id, $category) = @_; } sub add_obsolete_pointer { my ($self, $id, $obsolete_id) = @_; } sub add_synonym { my ($self, $id, $synonym) = @_; } sub add_dbxref { my ($self, $id, $dbxref) = @_; } sub tab { my $tab = shift; my $tc = shift || " "; print $tc x $tab; } sub _rel_prefix { my $self = shift; my $rel = shift; my %th = qw(is_a % part_of < develops_from ~ isa % partof < developsfrom ~); return $th{lc($rel->type)} || '@'.$rel->type.":"; } =head2 add_buckets Usage - Returns - Args - adds bucket terms to non-leaf nodes this is useful for making GO slims =cut sub add_buckets { my $self = shift; my ($idspace) = rearrange([qw(idpsace)], @_); my $terms = $self->get_all_nodes; my $id = 1; $idspace = $idspace || "slim_temp_id"; foreach my $term (@$terms) { if (!$self->is_leaf_node($term->acc)) { #printf STDERR "adding bucket for %s\n", $term->acc; my $t = $self->apph->create_term_obj; # start name with Z to force last alphabetic placement $t->name("Z-OTHER-".$term->name); $t->acc("$idspace:$id"); $id++; $self->add_term($t); $self->add_relationship($term, $t, "bucket"); } } return; } =head2 to_text_output Usage - Returns - Args - fmt, assocs [bool] hacky text output this method should probably move out of the model code into output adapters =cut sub to_text_output { my $self = shift; my ($fmt, $show_assocs, $fh, $disp_filter, $it, $opts, $suppress) = rearrange([qw(fmt assocs fh disp_filter it opts suppress)], @_); $fmt = $fmt || "gotext"; $fh = $fh || \*STDOUT; $opts = {} unless $opts; $it = $self->create_iterator unless $it; $it->no_duplicates(1); if ($opts->{isa_only}) { $it->reltype_filter("is_a"); } if ($fmt eq "gotext") { while (my $ni = $it->next_node_instance) { my $depth = $ni->depth; my $term = $ni->term; next if $term->is_relationship_type; my $parent_rel = $ni->parent_rel; my $line = " " x $depth; my $prefix = $ni->parent_rel ? $self->_rel_prefix($ni->parent_rel) : "\$"; $line .= $term->to_text(-prefix=>$prefix, -escape=>1, -suppress=>$suppress, ); my $parents = $self->get_parent_relationships($term->acc); my @others = @$parents; if ($parent_rel) { @others = grep {$_->acc1 ne $parent_rel->acc1} @$parents; if ($disp_filter) { my %filh = (); $disp_filter = [$disp_filter] unless ref($disp_filter); %filh = map {lc($_)=>1} @$disp_filter; @others = grep { $filh{lc($_->type)} } @others; } } foreach my $rel (@others) { my $prefix = $self->_rel_prefix($rel); my $n = $self->get_term($rel->acc1); next unless $n; # not in graph horizon $line .= sprintf(" %s %s ; %s", $prefix, $n->name, $n->public_acc); } if ($opts->{show_counts}) { $line.= " [gps: ".$term->n_deep_products."]"; if ($opts->{grouped_by_taxid}) { my $sh = $opts->{species_hash} || {}; my $n_by_tax = $term->n_deep_products_grouped_by_taxid; my @taxids = sort {$n_by_tax->{$b} <=> $n_by_tax->{$a}} keys %$n_by_tax; # arbitrarily select first 10... my @staxids = splice(@taxids,0,10); $line .= " by_tax="; foreach (@staxids) { my $sn = $_; my $sp = $sh->{$_}; if ($sp && $sp->binomial) { $sn = $sp->binomial; } $line .= " $sn:$n_by_tax->{$_}" } } } $line .= "\n"; if ($show_assocs && $self->is_focus_node($term)) { my $al = $term->association_list; foreach my $a (@$al) { $line .= " " x $depth; $line.= sprintf(" * %s %s %s %s\n", $a->gene_product->symbol, $a->gene_product->full_name, $a->gene_product->acc, join("; ", map {$_->code} @{$a->evidence_list}) ), } } print $fh "$line"; } } elsif ($fmt eq 'tree') { while (my $ni = $it->next_node_instance) { my $depth = $ni->depth; my $term = $ni->term; my $rtype = $ni->parent_rel ? $ni->parent_rel->type : " "; my $line = " " x $depth; $line .= sprintf("[%s] ", uc(substr($rtype,0,1))); $line .= $term->name; print $fh "$line\n"; } } elsif ($fmt eq "triples") { my @nodes = @{$self->get_all_nodes}; my $line = ""; while (my $term = shift @nodes) { my $parents = $self->get_parent_relationships($term->acc); foreach my $rel (@$parents) { my $p = $self->get_term($rel->acc1); next unless $p; # not in graph horizon $line .= sprintf("(\"%s\" %s \"%s\")\n", $term->name, $rel->type, $p->name); } print $fh "$line"; } } else { while (my $ni = $it->next_node_instance) { my $term = $ni->term; next if $term->is_relationship_type; my $depth = $ni->depth; my $parent_rel = $ni->parent_rel; tab($depth, $self->is_focus_node($term) ? "->" : " "); my %th = qw(isa % partof < developsfrom ~); printf $fh "%2s Term = %s (%s) // products=%s // $depth\n", $ni->parent_rel ? $th{$ni->parent_rel->type} : "", $term->name, $term->public_acc, $term->n_deep_products || 0, $depth, ; if ($show_assocs && $self->is_focus_node($term)) { my $al = $term->association_list; foreach my $a (@$al) { tab $depth; printf $fh "\t* %s %s %s\n", $a->gene_product->symbol, $a->gene_product->full_name, $a->gene_product->acc, join("; ", map {$_->code} @{$a->evidence_list}), } } } } } #Removes a node and connects the parents directly #to the children. It is a tricky question which #rel_type to use for the new connection (the parent #and childs rel_types might be different). For #now I just use the childs, but this may need to #be revisited. sub delete_node_with_reconnect { my $self = shift; my $acc = shift; #print "
\t\t=-=-= Removing $acc
\n"; # First adjust the child and parent relationships my $par_rel_hashes = $self->{parent_relationships_h}->{$acc} || {}; my $par_rels = [grep {$_} values(%$par_rel_hashes)]; my $child_rel_hashes = $self->{child_relationships_h}->{$acc} || {}; my $child_rels = [grep {$_} values(%$child_rel_hashes)]; my ($par_rel, $child_rel); foreach $par_rel (@$par_rels) { my $par_acc = $par_rel->acc1; my $par_type = $par_rel->type; foreach $child_rel (@$child_rels) { my $child_acc = $child_rel->acc2; my $child_type = $child_rel->type; # There's a heirarchy of types my $rel_type = $child_type; #qw(isa partof developsfrom); #print "
\t\t=-=-=\t\t  Adding $par_acc -> $child_acc ($rel_type)
\n"; $self->add_relationship({acc1=>$par_acc, acc2=>$child_acc, type=>$rel_type}); } } # And get rid of the node itself $self->delete_node($acc); } sub DEPRECATED_sub_graph { my ($self, $terms) = @_; # Output a clone of the graph my $subg = $self->clone; my $it = $subg->create_iterator(); my $ni; while ($ni = $it->next_node_instance) { my $term = $ni->term; my $term_name = $term->name; my $acc = $term->public_acc; $subg->delete_node_with_reconnect($acc) unless (grep {$_->public_acc eq $term->public_acc} @$terms); #print_debug_line("Keeping term \"$term_name\" in graph") if (grep {$_->public_acc eq $term->public_acc} @$terms); } return $subg; } sub max_depth { my ($self) = @_; my $it = $self->create_iterator(); my $max_d = 0; my $ni; while ($ni = $it->next_node_instance) { my $depth = $ni->depth; $max_d = max($max_d, $depth); } return $max_d; } sub split_graph_by_re { my ($acc, $re, $rtype, $orthogroot) = rearrange([qw(acc re rtype re orthogroot)], @_); my $func = sub {$_=shift->name;/$re/;print STDERR "$re on $_;xx=$1\n";($1)}; shift->split_graph_by_func($acc,$func,$rtype,$orthogroot); } sub split_graph_by_func { my $self = shift; my ($acc, $func, $rtype, $orthogroot) = rearrange([qw(acc func rtype re orthogroot)], @_); # my $ng = ref($self)->new; my $ng = $self->apph->create_graph_obj; my $new_acc = $self->apph->new_acc; my $root = $self->get_term($acc); # $ng->add_term($root); my $it = $self->create_iterator($acc); my %h = (); while (my $ni = $it->next_node_instance) { my $term = $ni->term; my $rel = $ni->parent_rel; next unless !$rel || lc($rel->type) eq "is_a"; my ($n) = &$func($term); # my $t1 = GO::Model::Term->new({name=>$n1}); # my $t2 = GO::Model::Term->new({name=>$n}); my $t2; $t2 = $self->apph->get_term({search=>$n}); if (!$t2) { print STDERR "$n not found; checking graph\n"; my $all = $ng->get_all_nodes; ($t2) = grep { $_->name eq $n } @$all; } if (!$t2) { print STDERR "$n not found; creating new\n"; $t2 = $self->apph->create_term_obj({name=>$n}); $t2->type("new"); $t2->acc($new_acc++); } $h{$term->acc} = $t2; # original term now gets flattened in main graph $ng->add_term($term); # $ng->add_relationship($root->acc, $term->acc, $rel->type) if $rel; if ($rel) { $ng->add_relationship($rel->acc1, $term->acc, $rel->type) if $rel->acc1; } # this part gets externalised and the relationship # gets preserved here $ng->add_term($t2); if ($rel) { my $np = $h{$rel->acc1}; if ($np) { # new externalised ontology $ng->add_relationship($np->acc, $t2->acc, $rel->type); # x-product $ng->add_relationship($t2->acc, $term->acc, $rtype); } } } return $ng; } sub store { my $self = shift; foreach my $t (@{$self->get_all_nodes}) { $self->apph->add_term($t); } foreach my $r (@{$self->get_all_relationships}) { $self->apph->add_relationship($r); } } # **** EXPERIMENTAL CODE **** # the idea is to be homogeneous and use graphs for # everything; eg gene products are nodes in a graph, # associations are arcs # cf rdf, daml+oil etc sub graphify { my $self = shift; my ($subg, $opts) = rearrange([qw(graph opts)], @_); $opts = {} unless $opts; $subg = $self unless $subg; foreach my $term (@{$self->get_all_nodes}) { $term->graphify($subg); } $subg; } 1; go-perl-0.15/GO/Model/GraphIterator.pm000644 000765 000024 00000024406 11615622160 017404 0ustar00cjmstaff000000 000000 # $Id: GraphIterator.pm,v 1.11 2008/01/22 23:54:46 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Model::GraphIterator; =head1 NAME GO::Model::GraphIterator; =head1 SYNOPSIS $it = $graph->create_iterator; # returns a GO::Model::GraphIterator object while (my $ni = $it->next_node_instance) { $depth = $ni->depth; $term = $ni->term; $reltype = $ni->parent_rel->type; printf "%s %8s Term = %s (%s) // depth=%d\n", "----" x $depth, $reltype, $term->name, $term->public_acc, $depth; } =head1 DESCRIPTION =head1 SEE ALSO L L =cut use Carp; use strict; use Exporter; use GO::Utils qw(rearrange); use GO::Model::Graph; use GO::Model::GraphNodeInstance; use FileHandle; use Exporter; use Data::Dumper; use vars qw(@EXPORT_OK %EXPORT_TAGS); use base qw(GO::Model::Root Exporter); sub _valid_params { return qw(graph acc order sort_by sort_by_list noderefs direction no_duplicates reltype_filter visited arcs_visited compact subset_h); } =head2 order Usage - $graphiter->order("breadth"); Returns - string Args - string gets/sets traversal order; breadth or depth; default is depth =cut =head2 direction Usage - $graphiter->direction("up"); Returns - string Args - string gets/sets direction; default is "down" =cut =head2 compact Usage - $graphiter->compact(1); Returns - bool Args - bool set this if you dont want relationships to be traversed twice; this gives a more compact tree representation of the graph =cut =head2 reltype_filter Usage - $graphiter->reltype_filter(qw(is_a part_of)) Returns - array Args - array by default, all relationship types are treated as transitive, and will be traversed by the iterator sometimes you dont want to traverse all relations, even if they are transitive. For example, when answering the query "find all genes expressed in the embryo" you way want subtypes of embryo and parts of the embryo but not things that develop_from the embryo. For more details, see L =cut sub _initialize { my $self = shift; my $acc; if (!ref($_[0])) { $acc = shift; } $self->SUPER::_initialize(@_); $acc = $self->acc unless $acc; $self->reset_cursor($acc); } =head2 reset_cursor Usage - Returns - Args - =cut sub reset_cursor { my $self = shift; my $acc = shift; $self->visited({}); $self->arcs_visited({}); my $terms; if ($acc) { $terms = [$self->graph->get_term($acc) || confess("$acc not in graph")]; } else { if (!$self->direction || $self->direction ne "up") { $terms = $self->graph->get_top_nodes; # foreach (@$terms) { # printf "TOP: %s\n", $_->acc; # } } else { $terms = $self->graph->get_leaf_nodes; } } my $sort_by = $self->sort_by || "alphabetical"; my $sort_by_list = $self->sort_by_list || []; # print "
sort_by_list has ".scalar(@$sort_by_list)." elements , number of terms to sort = ".scalar(@$terms)."
\n" # if ($sort_by eq 'pos_in_list'); my %fh = ( "alphabetical" => sub {lc($a->name) cmp lc($b->name)}, "pos_in_list" => sub {_sortby_pos_in_list($sort_by_list, $a, $b)} ); my $sortf = $fh{$sort_by}; confess("Dont know $sort_by") unless $sortf; my @sorted_terms = sort $sortf @$terms; my @noderefs = map { GO::Model::GraphNodeInstance->new({term=>$_, depth=>0}) } @sorted_terms; $self->noderefs(\@noderefs); } =head2 next_node Usage - Returns - GO::Model::Term Args - =cut sub next_node { my $self = shift; my $ni = $self->next_node_instance; return $ni ? $ni->term : undef; } =head2 next_node_instance Usage - Returns - GO::Model::GraphNodeInstance Args - =cut sub next_node_instance { my $self = shift; if (!$self->noderefs) { $self->reset_cursor; } my $noderefs = $self->noderefs; if (!@$noderefs) { return; } my $order = $self->order || "depth"; my $noderef = shift @$noderefs; my $term = $noderef->term; my $depth = $noderef->depth; my @child_relns = (); my $dir = (!$self->direction || $self->direction ne "up") ? "down" : "up"; # default is to traverse a distance of 1 in the DAG # however, if subset_h is set, we want to traverse the # transitive distance to the next node in the specified subset my $subset_h = $self->subset_h; my @accs = ($term->acc); # current IDs # iterate to next node - usually just 1 iteration, unless subset_h is set while (@accs) { my @this_child_relns = (); my $acc = shift @accs; if ($dir eq "down") { @this_child_relns = @{$self->graph->get_child_relationships($acc)}; if ($subset_h) { @this_child_relns = grep { if ($subset_h->{$_->acc2}) { $_->acc1($term->acc); 1; } else { push(@accs, $_->acc2); 0; } } @this_child_relns; } } elsif ($dir eq "up") { @this_child_relns = @{$self->graph->get_parent_relationships($acc)}; if ($subset_h) { @this_child_relns = grep { my $keep; if ($subset_h->{$_->acc1}) { $_->acc2($term->acc); $keep=1; } else { push(@accs, $_->acc1); $keep=0; } $keep; } @this_child_relns; } } else { die $dir; } push(@child_relns, @this_child_relns); } if ($self->reltype_filter) { my %filh = (); my $fs = $self->reltype_filter; $fs = [$fs] unless ref($fs); %filh = map {lc($_)=>1} @$fs; @child_relns = grep { $filh{lc($_->type)} } @child_relns; } if ($self->compact) { @child_relns = grep { !$self->arcs_visited->{$_->as_str} } @child_relns; } my @new = (); foreach (@child_relns) { $self->arcs_visited->{$_->as_str} = 1; my $t = $self->graph->get_term($dir ne "up" ? $_->acc2 : $_->acc1); if ($t) { my $h = { term=>$t, depth=>($depth+1), parent_rel=>$_, }; push(@new, GO::Model::GraphNodeInstance->new($h)); } } my $sort_by = $self->sort_by || "alphabetical"; my $sort_by_list = $self->sort_by_list || []; my %fh = ( "alphabetical" => sub {lc($a->term->name) cmp lc($b->term->name)}, "pos_in_list" => sub {_sortby_pos_in_list($sort_by_list, $a->term, $b->term)} ); my $sortf = $fh{$sort_by}; confess("Dont know $sort_by") unless $sortf; @new = sort $sortf @new; my $visited = $self->visited; if ($self->no_duplicates) { # don't visit nodes twice @new = grep {!$visited->{$_->term->acc}} @new; } foreach (@new) { $visited->{$_->term->acc} = 1; } if ($order eq "breadth") { push(@$noderefs, @new); } else { # depth first: splice(@$noderefs, 0, 0, @new); } return $noderef; } =head2 flatten Usage - Returns - Args - =cut sub flatten { my $self = shift; my ($bracket, $fmt) = rearrange([qw(bracket fmt)], @_); my $str = ""; $fmt ||= "%s"; my $depth = 0; my $ob = $bracket ? substr($bracket, 0, 1) : "("; my $cb = $bracket ? substr($bracket, -1, 1) : ")"; sub diffchr { my ($dd, $ob, $cb) = @_; my $ch; if ($dd < 0) { $ch = "$cb" x -$dd; } elsif ($dd > 0) { $ch = "$ob" x $dd; } else { $ch = ""; } } while (my $ni = $self->next_node_instance) { my $dd = $ni->depth - $depth; my $ch = diffchr($dd, $ob, $cb); $depth = $ni->depth; $str .= sprintf(" $ch $fmt", $ni->term->public_acc, $ni->term->name, $ni->term->definition); } $str .= diffchr(-$depth, $ob, $cb); return $str; } =head2 _sortby_pos_in_list Careful, this sort function work on Term objects, not GraphNodeInstance objects. Comparison is done by the name of the term. =cut sub _sortby_pos_in_list { my ($t_list, $t_a, $t_b) = @_; # print "
_sortby called (".join(",",map {$_->name} @$t_list).") // ".$t_a->name." // ".$t_b->name."
\n"; my $inf = 100000000; # First see which is first in list my $a_pos = _term_pos_in_list($t_list, $t_a); my $b_pos = _term_pos_in_list($t_list, $t_b); # If one is bigger than the other, return the bigger one. my $res = 0; my $name_cmp = lc($t_a->name) cmp lc($t_b->name); if (($a_pos >= 0) && ($b_pos >= 0)) { # Both are in list if ($a_pos != $b_pos) { $res = ($a_pos <=> $b_pos); } else { $res = $name_cmp; } } elsif (($a_pos < 0) && ($b_pos < 0)) { # Neither are in the list $res = $name_cmp; } else { # One is in the list and the other isn't $res = ($a_pos >= 0) ? 1 : -1; } return $res; } sub _term_pos_in_list { my ($t_list, $t) = @_; # First see which is first in list my $out = -1; my $num_terms = scalar(@$t_list); for (my $i = 0; $i < $num_terms; $i++) { my $cur_t = @{$t_list}[$i]; return $i if (lc($cur_t->name) eq lc($t->name)); } return $out; } 1; go-perl-0.15/GO/Model/GraphNodeInstance.pm000644 000765 000024 00000003261 11615622160 020161 0ustar00cjmstaff000000 000000 # $Id: GraphNodeInstance.pm,v 1.4 2004/11/29 20:18:16 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Model::GraphNodeInstance; =head1 NAME GO::Model::GraphNodeInstance - a graph node located in a tree =head1 SYNOPSIS $it = $graph->create_iterator; # returns a GO::Model::GraphIterator object while (my $ni = $it->next_node_instance) { $depth = $ni->depth; $term = $ni->term; $reltype = $ni->parent_rel->type; printf "%s %8s Term = %s (%s) // depth=%d\n", "----" x $depth, $reltype, $term->name, $term->public_acc, $depth; } =head1 DESCRIPTION see GO::Model::Graph =cut use Carp; use strict; use Exporter; use GO::Utils qw(rearrange); use GO::Model::Term; use FileHandle; use Exporter; use Data::Dumper; use vars qw(@EXPORT_OK %EXPORT_TAGS); use base qw(GO::Model::Root Exporter); sub _valid_params { return qw(term path depth parent_rel blocked); } =head2 term Usage - Returns - GO::Model::Term Args - see L =cut =head2 depth Usage - Returns - int Args - =cut =head2 parent_rel Usage - Returns - GO::Model::Relationship Args - see L =cut #=head2 block # Usage - # Returns - # Args - #blocking a node instance will stop the graph iterator going below this one #=cut #sub block { # my $self = shift; # $self->blocked(1); #} sub _initialize { my $self = shift; $self->SUPER::_initialize(@_); } 1; go-perl-0.15/GO/Model/LogicalDefinition.pm000644 000765 000024 00000003472 11615622160 020214 0ustar00cjmstaff000000 000000 # $Id: LogicalDefinition.pm,v 1.1 2006/04/05 22:47:57 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Model::LogicalDefinition; =head1 NAME GO::Model::LogicalDefinition; =head1 SYNOPSIS =head1 DESCRIPTION =cut use Carp qw(cluck confess); use Exporter; use GO::Utils qw(rearrange); use GO::Model::Root; use strict; use vars qw(@ISA); @ISA = qw(GO::Model::Root Exporter); sub _valid_params { return qw(intersection_list); } =head2 intersection_list Usage - Returns - Args - Each element of the list is itself a list This list is of length 1 or 2. [$generic_term_acc] [$relation,$differentiating_term_acc] =cut =head2 generic_term_acc Usage - Synonyms - genus_acc Returns - Args - the ID of the generic term, also known as 'genus' =cut sub generic_term_acc { my $self = shift; if (@_) { my $acc = shift; my $diffs = $self->differentia; push(@{$self->intersection_list},$acc); return $acc; } my @direct_accs = grep {scalar(@$_) == 1} @{$self->intersection_list}; if (@direct_accs > 1) { $self->throw("multiple generic terms"); } if (@direct_accs) { return $direct_accs[0]->[0]; } # no genus return; } *genus_acc = \&generic_term_acc; =head2 differentia Usage - Returns - Args - =cut sub differentia { my $self = shift; if (@_) { my $diffs = shift; my $genus = $self->generic_term_acc; $self->intersection_list([$genus, $diffs]); return $diffs; } my @diffs = grep {scalar(@$_) > 1} @{$self->intersection_list}; return \@diffs; } 1; go-perl-0.15/GO/Model/Modification.pm000644 000765 000024 00000003541 11615622160 017233 0ustar00cjmstaff000000 000000 # $Id: Modification.pm,v 1.2 2004/11/24 02:28:01 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Model::Modification; =head1 NAME GO::Model::Modification; =head1 DESCRIPTION represents a cross reference to an external database =cut use Carp; use Exporter; use GO::Utils qw(rearrange); use GO::Model::Root; use strict; use vars qw(@ISA); @ISA = qw(GO::Model::Root Exporter); sub _valid_params { return qw(id type person mod_time rank); } =head2 mod_time Usage - Returns - Args - time in seconds > 1970 =cut =head2 person Usage - Returns - Args - =cut =head2 type Usage - Returns - Args - =cut =head2 time_gmtstr Usage - Returns - Args - =cut sub time_gmtstr { my $self=shift; my $t = gmtime($self->mod_time); return $t; } =head2 pre_term_list Usage - Returns - Args - =cut sub pre_term_list { my $self = shift; $self->{pre_term_list} = shift if @_; return $self->{pre_term_list}; } =head2 post_term_list Usage - Returns - Args - =cut sub post_term_list { my $self = shift; $self->{post_term_list} = shift if @_; return $self->{post_term_list}; } =head2 add_pre_term Usage - Returns - Args - =cut sub add_pre_term { my $self = shift; if (!$self->pre_term_list) { $self->pre_term_list([]); } push(@{$self->pre_term_list}, shift); $self->pre_term_list; } =head2 add_post_term Usage - Returns - Args - =cut sub add_post_term { my $self = shift; if (!$self->post_term_list) { $self->post_term_list([]); } push(@{$self->post_term_list}, shift); $self->post_term_list; } 1; go-perl-0.15/GO/Model/Ontology.pm000644 000765 000024 00000000733 11615622160 016440 0ustar00cjmstaff000000 000000 # $Id: Ontology.pm,v 1.2 2004/11/24 02:28:01 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Model::Ontology; =head1 NAME GO::Model::Ontology; =head1 SYNOPSIS this is a synonym for GO::Model::Graph =head1 DESCRIPTION =cut use base qw(GO::Model::Graph); 1; go-perl-0.15/GO/Model/Path.pm000644 000765 000024 00000004105 11615622160 015517 0ustar00cjmstaff000000 000000 # $Id: Path.pm,v 1.5 2004/11/29 20:18:17 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Model::Path; =head1 NAME GO::Model::Path; =head1 SYNOPSIS =head1 DESCRIPTION represents a path between two nodes in a graph TODO: have the path be built of relationships rather than terms, so we can get the edgetypes in here =cut use Carp; use Exporter; use GO::Utils qw(rearrange); use GO::Model::Root; use strict; use vars qw(@ISA); @ISA = qw(GO::Model::Root Exporter); sub _valid_params { return qw(link_list); } =head2 link_list Usage - Returns - arrayref of alternating type, GO::Model::Term Args - =cut =head2 term_list Usage - Returns - arrayref of GO::Model::Term Args - gets/sets an ordered list of terms in the path L =cut sub term_list { my $self = shift; my $links = $self->link_list || []; my @terms = (); for (my $i=1; $i<@$links; $i+=2) { push(@terms, $links->[$i]); } \@terms; } # add_link - private sub add_link { my $self = shift; if (!$self->{link_list}) { $self->{link_list} = []; } push(@{$self->{link_list}}, shift, shift) if @_; $self->{link_list}; } =head2 length Usage - print $path->length Returns - int Args - =cut sub length { my $self = shift; return scalar(@{$self->{link_list} || []})/2; } =head2 to_text Usage - Returns - Args - =cut sub to_text { my $self = shift; my $use = shift; my $links = $self->link_list || []; my @parts = (); for (my $i=0; $i<@$links; $i+=2) { my $t = $links->[$i+1]; push(@parts, "[$links->[$i]]", $use && $use eq 'acc' ? $t->acc : $t->name); } return join(' ', @parts); } =head2 duplicate Usage - Returns - Args - =cut sub duplicate { my $self = shift; my $dup = $self->new; $dup->link_list([@{$self->link_list || []}]); $dup; } 1; go-perl-0.15/GO/Model/Property.pm000644 000765 000024 00000001204 11615622160 016444 0ustar00cjmstaff000000 000000 # $Id: Property.pm,v 1.2 2004/11/24 02:28:02 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Model::Property; =head1 NAME GO::Model::Property; =head1 SYNOPSIS =head1 DESCRIPTION =cut use Carp qw(cluck confess); use Exporter; use GO::Utils qw(rearrange); use GO::Model::Root; use strict; use vars qw(@ISA); @ISA = qw(GO::Model::Root Exporter); sub _valid_params { return qw(acc name domain_acc range_acc textrule); } 1; go-perl-0.15/GO/Model/Relationship.pm000644 000765 000024 00000010246 11615622160 017267 0ustar00cjmstaff000000 000000 # $Id: Relationship.pm,v 1.6 2006/10/19 18:38:28 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Model::Relationship; =head1 NAME GO::Model::Relationship =head1 SYNOPSIS =head1 DESCRIPTION a relationship between two GO::Model::Terms relationships can be thought of as B or sentences of the form SUBJECT-TERM PREDICATE OBJECT-TERM for example, "dog" IS_A "animal" "G-Protein coupled receptor" IS_A "transmembrane receptor" Statements have a B (i.e. the subject of the sentence/statement), a predicate/relationship-type and an B (i.e. the object of the sentence/statement) Relationships can also be seen as arcs in a directed graph, with the subject being equivalent to the child, and the object equivalent to the parent. The arc is labeled with the predicate/relationship-type. A Relationship object currently does not contain an actual pointer to a GO::Model::Term object. Instead it stores the ID of that term. This is intended to be used in conjunction with the Graph object, or with the database. =cut use Carp; use Exporter; use GO::Utils qw(rearrange); use GO::Model::Root; use strict; use vars qw(@ISA); @ISA = qw(GO::Model::Root Exporter); sub _valid_params { return qw(acc1 acc2 is_inheritance complete type); } sub _initialize { my $self = shift; $self->SUPER::_initialize(@_); } sub acc1 { my $self = shift; $self->{"acc1"} = shift if @_; return $self->{"acc1"}; } *obj_acc = \&acc1; *object_acc = \&acc1; *parent_acc = \&acc1; sub acc2 { my $self = shift; $self->{"acc2"} = shift if @_; return $self->{"acc2"}; } *subj_acc = \&acc2; *subject_acc = \&acc2; *child_acc = \&acc2; =head2 subject_acc Title : subject_acc Usage : $obj->subject_acc($newid) Usage : $currid = $obj->subject_acc() Synonyms: subj_acc, acc2, child_acc Function: gets or sets the identifier for the child/subject term Example : Returns : value of subject_acc (string) Args : on set, new value (string) All Relationships can be thought of "subject-predicate-object" statements. The statement is *about* the subject, and states something about the relationship *to* the object. For example, the if we have a Relationship: cell ^ | | [part_of] | cell nucleus This is a statement about cell nuclei in general, so "cell nucleus" is the subject (sometimes called the child node). The Relationship tells us that all cell nuclei are part_of some cell, so the object of the relationship (sometimes called the parent node) is "cell" =cut =head2 object_acc Title : object_acc Usage : $obj->object_acc($newid) Usage : $currid = $obj->object_acc() Synonyms: obj_acc, acc1, parent_acc Function: gets or sets the identifier for the parent/object term Example : Returns : value of object_acc (string) Args : on set, new value (string) See Also: subj_acc =cut =head2 type Title : type Usage : $obj->type($newval) Usage : $currval = $obj->type() Synonyms: Function: gets or sets the relationship type (a string) Example : Returns : value of type (string) Args : on set, new value (string) Currently any string is allowed; in future the type string may be constrained to come from a controlled vocabulary of relationship types =cut sub type { my $self = shift; if (@_) { my $type = shift; if ($type) { $self->{type} = $type; } } return $self->{type} || "unknown"; } sub is_obsolete { my $self = shift; $self->{is_obsolete} = shift if @_; return $self->{is_obsolete} ? 1:0; } sub as_str { my $self = shift; sprintf("%s:%s:%s", $self->type, $self->acc1, $self->acc2); } sub to_ptuples { my $self = shift; warn("deprecated"); my ($th) = rearrange([qw(tuples)], @_); (["rel", $self->type, $self->acc1, $self->acc2]); } sub is_inheritance { my $self = shift; warn("deprecated"); if (@_) { my $is = shift; $is && $self->type("isa"); !$is && $self->type("partof"); } return $self->type eq "isa"; } 1; go-perl-0.15/GO/Model/Restriction.pm000644 000765 000024 00000001172 11615622160 017131 0ustar00cjmstaff000000 000000 # $Id: Restriction.pm,v 1.2 2004/11/24 02:28:02 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Model::Restriction; =head1 NAME GO::Model::Restriction; =head1 SYNOPSIS =head1 DESCRIPTION =cut use Carp qw(cluck confess); use Exporter; use GO::Utils qw(rearrange); use GO::Model::Root; use strict; use vars qw(@ISA); @ISA = qw(GO::Model::Root Exporter); sub _valid_params { return qw(property_name value); } 1; go-perl-0.15/GO/Model/Root.pm000644 000765 000024 00000014562 12031063461 015552 0ustar00cjmstaff000000 000000 # $Id: Root.pm,v 1.6 2007/08/07 21:43:37 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Model::Root; =head1 NAME GO::Model::Root =head1 DESCRIPTION base class for all GO::Model objects =cut use strict; use Carp; use Exporter; use Data::Dumper; use vars qw(@ISA $AUTOLOAD); my @ISA = qw(Exporter); # - - - - - - - - - - Public functions - - - - - - - - - - - - =head1 Constructors =head2 new Constructor: Basically just calls L<_initialize>(). Most subclasses should not need to override new, but instead should override L<_initialize>(). If L<_initialize>() fails , the procedure will die WARNING: This procedure will die if initialization is unsuccessful. Use an eval statement to catch such exceptions. =cut sub new { my $proto = shift; my $class = ref($proto) || $proto;; my $self = {}; bless $self, $class; $self->_initialize(@_); if ($ENV{PERL_MEMORY_TRACE}) { print STDERR "NEW: ".$self->sprint_self."\n"; } return $self; } sub throw { my $self = shift; my @msg = @_; confess("@msg"); } sub warn { my $self = shift; my @msg = @_; warn("@msg"); } =head2 obj_factory Usage - $obj->obj_factory->create_new_term_object($h); Alias - apph Returns - L Args - none =cut sub apph { my $self = shift; $self->{apph} = shift if @_; return $self->{apph}; } *obj_factory = \&apph; =head2 sprint_self Prints out a description of the object to a string. =cut sub sprint_self { my $self = shift; my $str = $self; if ($self->can("name") && $self->name) { $str.= " ".$self->name; } return $str; } =head2 dump dumps the object (can be read back in with eval) =cut sub dump { my $self = shift; my $ob = shift || $self; my $d = Data::Dumper->new(["obj", $ob]); return $d->Dump; } sub _initialize { my $self = shift; $self->init if $self->can("init"); my @valid_params = $self->_valid_params; my ($paramh) = @_; # first arg # arguments passed as hash? if (ref($paramh)) { map { if (defined($paramh->{$_})) { $self->$_($paramh->{$_}); } } @valid_params; } else { # arguments passed as array for (my $i=0; $i<@_; $i++) { my $m = $valid_params[$i]; $self->$m($_[$i]); } } } sub _valid_params { (); } sub is_valid_param { my $self = shift; my $param = shift; return scalar(grep {$_ eq $param} $self->_valid_params); } sub id { my $self = shift; $self->{id} = shift if @_; return $self->{id}; } =head2 namespace Usage - print $term->namespace(); # getting the type Usage - $term->namespace("molecular_function"); # setting the type Alias - type Alias - term_type Alias - category Alias - ontology Returns - string representing type Args - string represnting type [optional] The OBO namespace for the L or L =cut sub namespace { my $self = shift; $self->{namespace} = shift if @_; return $self->{namespace}; } # synonyms sub term_type { shift->namespace(@_) } sub category { shift->namespace(@_) } sub ontology { shift->namespace(@_) } sub type { shift->namespace(@_) } =head2 _cleanup Called at object destruction time. Should be overridden to perform cleanup tasks. =cut #sub _cleanup #{ # my $self = shift; # # The best we can do here is clean up references left # # in our hash table. We'll also drop debugging alerts. # my $attribute; # foreach $attribute (keys %$self) # { # if(ref($self->{$attribute})) # { # undef $self->{$attribute}; # } # } #} sub _initialize_attributes { my $self = shift; my @att_name_arr = @{shift || []}; my $param_ref = shift; my @param = @{$param_ref}; if (defined($param[0]) && $param[0]=~/^-/) { # attributes specified as '-key=>val' list my $i; for ($i=0;$i<@param;$i+=2) { $param[$i]=~tr/A-Z/a-z/; } # Now we'll convert the @params variable into an associative array. my(%param) = @param; my(@return_array); my $key; foreach $key (@att_name_arr) { my $orig_key = $key; $key=~tr/A-Z/a-z/; if (defined($param{"-".$key})) { my($value) = $param{"-".$key}; delete $param{"-".$key}; $self->{"_$orig_key"} = $value; } } # catch user misspellings resulting in unrecognized names my(@restkeys) = keys %param; @{$param_ref} = %param; if (scalar(@restkeys) > 0) { ###### carp("@restkeys not processed in _rearrange(), did you use a non-recognized parameter name ? "); } } else { # attributes specified as basic array my $i; for ($i=0; $i<@param; $i++) { if ($i >= @att_name_arr) { confess("Too many params"); } my $att_name = $att_name_arr[$i]; $self->{"_$att_name"} = $param[$i]; } } } sub from_idl { my $class = shift; my $h = shift; foreach my $k (%$h) { if (ref($h->{$k}) eq "HASH") { confess("must be dealth with in subclass of this"); } } return $class->new($h); } sub to_prolog { my $self = shift; my @t = $self->to_ptuples(@_); my @s = map { sprintf("%s(%s).\n", shift @$_, join(", ", map {$self->prolog_quote($_)} @$_ )); } @t; my %h=(); # uniquify @s = grep {(!$h{$_}) and ($h{$_} = 1)} @s; return join("", @s); } sub prolog_quote { my $self = shift; my $s = shift; $s = '' unless defined $s; $s =~ s/\'/\\\'/g; "'$s'"; } # auto-declare accessors sub AUTOLOAD { my $self = shift; my $name = $AUTOLOAD; $name =~ s/.*://; # strip fully-qualified portion if ($name eq "DESTROY") { # we dont want to propagate this!! return; } confess("$self") unless ref($self); my $add; if ($name =~ /add_(.+)/) { $add = $1."_list"; } if ($self->can($name)) { confess("assertion error!"); } if ($self->is_valid_param($name)) { $self->{$name} = shift if @_; return $self->{$name}; } if ($add && $self->is_valid_param($add)) { push(@{$self->{$add}}, @_); return $self->{$add}; } else { confess("can't do $name on $self"); } } 1; go-perl-0.15/GO/Model/Seq.pm000644 000765 000024 00000010133 11615622160 015351 0ustar00cjmstaff000000 000000 # $Id: Seq.pm,v 1.4 2005/01/25 06:17:28 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Model::Seq; =head1 NAME GO::Model::Seq; =head1 SYNOPSIS print $gene_product->seq->seq; =head1 DESCRIPTION represents a biological sequence; uses the bioperl Bio::PrimarySeq class any call that you can do on a bioperl sequence object, you can do here, with the addition of the calls below to get bioperl, see http://www.bioperl.org =cut use Carp; use Exporter; use GO::Utils qw(rearrange); use GO::Model::Root; use strict; use vars qw(@ISA $AUTOLOAD); @ISA = qw(GO::Model::Root Exporter); sub _valid_params { return qw(id xref_list pseq description); } sub _initialize { my $self = shift; my ($paramh) = @_; my @bpargs = @_; my %h = (); if (ref($paramh) eq "HASH") { @bpargs = (); foreach my $k (keys %$paramh) { if (grep {$k eq $_} $self->_valid_params) { $h{$k} = $paramh->{$k}; } else { push(@bpargs, "-".$k, $paramh->{$k}); } } } require "Bio/PrimarySeq.pm"; my $pseq = Bio::PrimarySeq->new(@bpargs); $self->pseq($pseq); $self->SUPER::_initialize(\%h); } =head2 pseq Usage - Returns - Bio::PrimarySeq Args - =cut sub pseq { my $self = shift; if (@_) { $self->{pseq} = shift; if ($self->{pseq}->isa("Bio::Seq::RichSeqI")) { my $annot = $self->{pseq}->annotation; # foreach my $link ( $annot->each_DBLink ) { foreach my $link ( $annot->get_Annotations('dblink') ) { my $xref = GO::Model::Xref->new; $xref->xref_key($link->primary_id); $xref->xref_dbname($link->database); $self->add_xref($xref); } } } return $self->{pseq}; } sub id { my $self = shift; $self->{id} = shift if @_; return $self->{id}; } sub residues {shift->pseq->seq(@_)} =head2 md5checksum Usage - my $md5 = $seq->md5checksum() OR $seq->md5checksum($md5) Returns - 32 char hex string Args - 32 char hex string [optional] checksum for seq - easy way to check if it has been changed etc (requires Digest::MD5 module from CPAN) =cut sub md5checksum { my $self = shift; # we want to be able to manipulte the checksum # even if the actual residues are not in memory at this time if (@_) { $self->{md5checksum} = shift; } my $res = $self->pseq->seq(); if (!$res) { return $self->{md5checksum}; } require "Digest/MD5.pm"; my $md5 = Digest::MD5->new; $md5->add($self->residues); my $hex = $md5->hexdigest; $self->{md5checksum} = $hex; return $self->{md5checksum}; } =head2 to_fasta Usage - Returns - Args - =cut sub to_fasta { my $self = shift; my $res = $self->seq; $res =~ s/(.{50})/$1\n/g; my $hdr = $self->description || $self->display_id; # my $hdr = $self->display_id; return sprintf(">%s\n%s\n", $hdr, $res); } =head2 add_xref - Usage : $term->add_xref($xref); - Args : GO::Term::Xref =cut sub add_xref { my $self = shift; if (@_) { my $xref = shift; $self->xref_list([]) unless $self->xref_list; $xref->isa("GO::Model::Xref") || confess("Not an Xref"); push(@{$self->xref_list}, $xref); } } # delegate calls to Bio::Seq object sub AUTOLOAD { my $self = shift || confess; my $name = $AUTOLOAD; $name =~ s/.*://; # strip fully-qualified portion if ($name eq "DESTROY") { # we dont want to propagate this!! return; } if (!$self->pseq) { confess("assertion error") } if ($self->pseq->can($name)) { return $self->pseq->$name(@_); } if ($self->is_valid_param($name)) { $self->{$name} = shift if @_; return $self->{$name}; } else { confess("can't do $name on $self"); } } 1; go-perl-0.15/GO/Model/Species.pm000644 000765 000024 00000002254 11615622160 016221 0ustar00cjmstaff000000 000000 # $Id: Species.pm,v 1.3 2005/06/29 18:40:19 sshu Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Model::Species; =head1 NAME GO::Model::Species; =head1 DESCRIPTION represents a gene product in a particular species (this will effectively always be refered to implicitly by the gene symbol even though a gene may have >1 product) =cut use Carp; use Exporter; use GO::Utils qw(rearrange); use GO::Model::Root; use strict; use vars qw(@ISA); @ISA = qw(GO::Model::Root Exporter); sub _valid_params { return qw(id ncbi_taxa_id genus species common_name lineage_string apph); } sub from_bpspecies { my $class = shift; my $species = shift; my $division = shift; my $taxon = $class->new; $taxon->common_name($species->common_name); $taxon->genus($species->genus); $taxon->species($species->species); # $taxon->taxon_code($division) if $division; $taxon; } sub binomial { my $self = shift; return ($self->genus || "")." ".($self->species || ""); } go-perl-0.15/GO/Model/Term.pm000644 000765 000024 00000065174 11615622160 015547 0ustar00cjmstaff000000 000000 # $Id: Term.pm,v 1.24 2008/01/17 20:08:14 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Model::Term; =head1 NAME GO::Model::Term - a term or concept in an ontology =head1 SYNOPSIS # From a file use GO::Parser; my $parser = new GO::Parser({handler=>'obj'}); # create parser object $parser->parse("gene_ontology.obo"); # parse file -> objects my $graph = $parser->handler->graph; # get L object my $term = $graph->get_term("GO:0001303"); # fetch a term by ID printf "Term %s %s\n", $term->name, $term->acc; # From a GO Database (requires go-db-perl) my apph = GO::AppHandle->connect(-dbname=>$dbname); my $term = $apph->get_term({acc=>00003677}); printf "Term:%s (%s)\nDefinition:%s\nSynonyms:%s\n", $term->name, $term->public_acc, $term->definition, join(", ", @{$term->synonym_list}); =head1 DESCRIPTION Represents an Ontology term; the same class is used for process, compartment and function currently, a Term is not aware of its Relationships; to find out how a term is related to other terms, use the a L object, which will give you the GO::Model::Relationship objects; for example $rels = $graph->get_parent_relationships($term->acc); =head1 SEE ALSO L L L L =head1 NOTES Like all the GO::Model::* classes, this uses accessor methods to get or set the attributes. by using the accessor method without any arguments gets the value of the attribute. if you pass in an argument, then the attribuet will be set according to that argument. for single-valued attributes # this sets the value of the attribute $my_object->attribute_name("my value"); # this gets the value of the attribute $my_value = $my_object->attribute_name(); for lists: # this sets the values of the attribute $my_object->attribute_name(\@my_values); # this gets the values of the attribute $my_values = $my_object->attribute_name(); =cut use Carp; use Exporter; use GO::Utils qw(rearrange); use GO::Model::Root; use GO::Model::Association; use GO::Model::Xref; use GO::Model::GeneProduct; use strict; use vars qw(@ISA); use base qw(GO::Model::Root Exporter); our %code_to_namespace = ('F'=>'molecular_function', 'P'=>'biological_process', 'C'=>'cellular_component'); sub _valid_params { return qw(id name description term_type is_obsolete is_relationship_type public_acc acc definition synonym_list association_list selected_association_list association_hash n_associations dbxref_list property_list subset_list equivalent_to_union_of_term_list disjoint_from_term_list consider_list replaced_by_list is_instance stag is_anonymous is_cyclic is_transitive is_symmetric is_anti_symmetric is_reflexive inverse_of transitive_over domain range logical_definition); } =head2 acc Usage - print $term->acc() Alias - public_acc Returns - Args - accessor: gets/sets GO ID/accession [as an integer] throws: exception if you try to pass in a non-integer if you want to use IDs in the format GO:0000nnn, then use the method public_acc() =cut sub acc { my $self = shift; if (@_) { my $acc = shift; $self->{acc} = $acc; } return $self->{acc}; } *public_acc = \&acc; =head2 name Usage - print $term->name; Returns - Args - accessor: gets/sets "name" attribute =cut sub name { my $self = shift; $self->{name} = shift if @_; my $name = $self->{name}; return $name; } sub description { my $self = shift; warn('deprecated'); $self->name(@_); } =head2 subset_list Usage - foreach (@{$term->subset_list || []}) { printf " $_\n" } Returns - list of strings Args - list of strings [optional] List of subset Accs for a term Subsets are also known as GO Slims =cut =head2 in_subset Usage - if ($term->in_subset('goslim_prok'); Returns - bool Args - subset-name str Tests if the term belongs to a subset =cut sub in_subset { my $self = shift; my $subset = shift; return 1 if grep {$_ eq $subset} @{$self->subset_list || []}; return 0; } =head2 definition Usage - print $term->definition; Returns - Args - accessor: gets/sets "definition" attribute =cut sub definition { my $self = shift; $self->{definition} = shift if @_; return $self->{definition}; } =head2 primary_xref Title : primary_xref Usage : Function: Example : Returns : GO::Model::Xref Args : The same as acc(), except the ID is returned as a L rather than a string =cut sub primary_xref{ my ($self,@args) = @_; my ($dbname, $acc) = split(/\:/, $self->acc); return GO::Model::Xref->new({xref_key=>$acc, xref_dbname=>$dbname}); } =head2 comment Title : comment Usage : $obj->comment($newval) Function: Example : Returns : value of comment (a scalar) Args : on set, new value (a scalar or undef, optional) =cut sub comment{ my $self = shift; return $self->{'comment'} = shift if @_; return $self->{'comment'}; } =head2 definition_dbxref_list Title : definition_dbxref_list Usage : $obj->definition_dbxref(\@xrefs) Function: Example : Returns : definition_dbxref_list hashlist (of GO::Model::Xref) Args : on set, new values (GO::Model::Xref hashlist) L =cut sub definition_dbxref_list{ my $self = shift; return $self->{'definition_dbxref_list'} = shift if @_; return $self->{'definition_dbxref_list'}; } =head2 add_definition_dbxref - Usage : $term->add_definition_dbxref($xref); - Args : GO::Term::Xref L =cut sub add_definition_dbxref { my $self = shift; foreach my $dbxref (@_) { if (!ref($dbxref)) { my ($db, @rest) = split(/:/, $dbxref); confess "$dbxref not a dbxref" unless @rest; my $acc = join(":", @rest); $dbxref = $self->apph->create_xref_obj({xref_key=>$acc, xref_dbname=>$db}); } UNIVERSAL::isa($dbxref, "GO::Model::Xref") or confess($dbxref." not a xref"); $self->definition_dbxref_list([]) unless $self->definition_dbxref_list; push(@{$self->definition_dbxref_list}, $dbxref); } $self->definition_dbxref_list; } sub lisp_acc { my $self = shift; return sprintf "Go%07d", $self->acc; } =head2 has_synonym Usage - if ($term->has_synonym("autotrophy") {...} Returns - bool Args - string =cut sub has_synonym { my $self = shift; my $str = shift; my @syns = @{$self->synonym_list || []}; if (grep {$_ eq $str} @syns) { return 1; } return 0; } =head2 add_synonym Usage - $term->add_synonym("calcineurin"); Usage - $term->add_synonym(@synonym_strings); Returns - Args - Adds a synonym; loses type information (the synonym type in blank) =cut sub add_synonym { my $self = shift; $self->add_synonym_by_type('', $_) foreach @_; } =head2 synonym_list Usage - my $syn_l = $term->synonym_list; Usage - $term->synonym_list([$syn1, $syn2]); Returns - arrayref Args - arrayref [optional] accessor: gets/set list of synonyms [array reference] each synonym is represented as a string - this method loses synonym typing information. If used as a setter, will set the type for each synonym to null =cut sub synonym_list { my $self = shift; if (@_) { my $syns = shift; $self->synonyms_by_type_idx({}); $self->add_synonym(@$syns); } my $sbt = $self->synonyms_by_type_idx; my @syns = map { @{$sbt->{$_} || []} } keys %$sbt; return \@syns; } sub synonym_type_list { return [keys %{shift->{_synonyms_by_type_idx} || {}}]; } # private: lookup table indexed by type, value is syn string arrayref sub synonyms_by_type_idx { my $self = shift; if (@_) { $self->{_synonyms_by_type_idx} = shift; } else { $self->{_synonyms_by_type_idx} = {} unless $self->{_synonyms_by_type_idx}; } return $self->{_synonyms_by_type_idx}; } =head2 add_synonym_by_type Usage - $term->add_synonym_by_type('exact', $syn); Returns - Args - =cut sub add_synonym_by_type { my $self = shift; my $type = shift || ''; my $syn = shift; push(@{$self->synonyms_by_type_idx->{$type}}, $syn); } =head2 synonyms_by_type Usage - $synstrs = $term->synonyms_by_type('exact'); Usage - $term->synonyms_by_type('exact', \@exact_syns); Returns - arrayref of strings Args - type string, arrayref of strings [optional] in getter mode, gets a list of synonyms of a particular type in setter mode, sets a list of synonyms for a particular type =cut sub synonyms_by_type { my $self = shift; my $type = shift; if (@_) { $self->synonyms_by_type_idx->{$type} = shift; } return $self->synonyms_by_type_idx->{$type} || []; } =head2 alt_id_list Usage - my $syn_l = $term->alt_id_list; Usage - $term->alt_id_list([$syn1, $syn2]); Returns - arrayref Args - arrayref [optional] accessor: gets/set list of synonyms [array reference] =cut sub alt_id_list { my $self = shift; if (@_) { $self->add_alt_id(@_); } $self->synonyms_by_type('alt_id'); } =head2 add_alt_id Usage - $term->add_alt_id('GO:0000001'); Returns - Args - id string, or list of id strings =cut sub add_alt_id { my $self = shift; my @alt_ids = @_; $self->add_synonym_by_type('alt_id',$_) foreach @_; } *add_secondaryid = \&add_alt_id; =head2 namespace (INHERITED) Usage - print $term->namespace(); # getting the type Usage - $term->namespace("molecular_function"); # setting the type Alias - type Alias - term_type Alias - category Alias - ontology Returns - string representing type Args - string represnting type [optional] The OBO namespace for the L or L This method is inherited from the superclass =cut # DEFINED IN SUPERCLASS # documentation repeated here to make things easier to find =head2 set_namespace_by_code Usage - $term->set_namespace_by_code("P"); Returns - Args - String: M, P or C Currently the mapping is hardcoded ('F'=>'molecular_function', 'P'=>'biological_process', 'C'=>'cellular_component'); =cut sub set_namespace_by_code { my $self = shift; my $code = shift; my $ns = $code_to_namespace{$code}; if (!$ns) { $self->throw("Unknown code: $code"); } $self->namespace($ns); return $code; } =head2 get_code_from_namespace Usage - $code = $term->get_code_from_namespace; Returns - String: M, P or F Args - String (if omitted will use current namespace) Returns the code for the current namespace (or any given namespace if supplied) =cut sub get_code_from_namespace { my $self = shift; my $ns = shift || $self->namespace || ''; my %m = reverse %code_to_namespace; # assumes 1-1 bijective mapping my $code = $m{$ns}; # if (!$code) { # $self->throw("Unknown namespace: $ns"); # } return $code; } # DEPCRECATED sub add_obsolete { my $self = shift; if (@_) { my $obs = shift; $self->{obsolete_h}->{$obs->acc} = $obs; } return $self->obsolete_list; } # deprecated sub obsolete_list { my $self = shift; while (shift @_) { $self->add_obsolete ($_); } my @obs = values %{$self->{obsolete_h}}; return \@obs; } =head2 add_dbxref - Usage : $term->add_dbxref($xref); - Args : GO::Term::Xref L =cut sub add_dbxref { my $self = shift; foreach my $dbxref (@_) { if (!ref($dbxref)) { my ($db, @rest) = split(/:/, $dbxref); confess "$dbxref not a dbxref" unless @rest; my $acc = join(":", @rest); $dbxref = $self->apph->create_xref_obj({xref_key=>$acc, xref_dbname=>$db}); } UNIVERSAL::isa($dbxref, "GO::Model::Xref") or confess($dbxref." not a xref"); $self->dbxref_list([]) unless $self->dbxref_list; push(@{$self->dbxref_list}, $dbxref); } $self->dbxref_list; } *add_xref = \&add_dbxref; =head2 dbxref_list - Usage : $term->dbxref_list($xref); - Args : optional listref of GO::Term::Xref - Returns : listref of GO::Term::Xref accessor: gets/sets list of dbxref [array reference] =cut # autodefined =head2 is_obsolete accessor: gets/set obsolete flag [boolean =cut sub is_obsolete { my $self = shift; $self->{is_obsolete} = shift if @_; return $self->{is_obsolete} ? 1:0; } =head2 is_root accessor: gets/set is_root flag [boolean] =cut sub is_root { my $self = shift; $self->{is_root} = shift if @_; return $self->{is_root} ? 1:0; } =head1 TERM ASSOCIATION METHODS =head2 association_list Usage - $assoc_l = $term->association_list Returns - arrayref of GO::Model::Association Args - arrayref of GO::Model::Association [optional] accessor: gets/set list of associations [array reference] if this is undefined, the datasource will be queried for the associations =cut sub association_list { my $self = shift; my ($al, $sort_by) = rearrange([qw(associations sort_by)], @_); if ($al) { if (!ref($al) eq "ARRAY") { confess("$al is not an array ref"); } $self->{"association_list"} = $al; foreach my $assoc (@{$self->{"association_list"} || []}) { my $gene = $assoc->gene_product; $self->{association_hash}->{$gene->acc} = $assoc; } } if (!defined($self->{"association_list"})) { if (!defined($self->apph)) { # print $self->dump; } else { $self->{"association_list"} = $self->apph->get_direct_associations($self); foreach my $assoc (@{$self->{"association_list"} || []}) { my $gene = $assoc->gene_product; if (!$gene) { confess("no gene for assoc $assoc"); } if (!$self->{association_hash}->{$gene->acc}) { $self->{association_hash}->{$gene->acc} = []; } push(@{$self->{association_hash}->{$gene->acc}}, $assoc); } } } if ($sort_by && (!$self->{"association_list_sort_by"} || $self->{"association_list_sort_by"} ne $sort_by)) { my @sortlist = ref($sort_by) ? @$sort_by : ($sort_by); my @al = sort { my $as1 = $a; my $as2 = $b; my $i=0; my $cmp; while (!defined($cmp) && $i < @sortlist) { my $sortk = $sortlist[$i]; $i++; if ($sortk eq "gene_product") { $cmp = $as1->gene_product->symbol cmp $as2->gene_product->symbol; } elsif ($sortk eq "ev_code") { confess("cant sort on evcode yet"); } else { confess("dont know $sortk"); } } $cmp; } @{$self->{association_list} || []}; $self->{"association_list"} = \@al; $self->{"association_list_sort_by"} = $sort_by; } return $self->{"association_list"}; } =head2 selected_association_list Usage - $assoc_l = $term->selected_association_list Returns - arrayref of GO::Model::Association Args - arrayref of GO::Model::Association [optional] accessor: gets list of SELECTED associations [array reference] [this method is only of use if you are using it in conjunction with L in the go-db-perl distro] this in not the total list of all associations associated with a term; if the term was created via a query on products, this will include those associations L =cut # done by AUTOLOAD =head2 add_association Usage - $term->add_association($assoc); Returns - Args - GO::Model::Association L =cut sub add_association { my $self = shift; if (!$self->{"association_list"}) { $self->{"association_list"} = []; } my $assoc = shift; if (ref($assoc) ne "GO::Model::Association") { # it's a hashref - create obj from hashref my $assoc2 = $self->apph->create_association_obj($assoc); $assoc = $assoc2; } push(@{$self->{"association_list"}}, ($assoc)); my $gene = $assoc->gene_product; if (!$self->{association_hash}->{$gene->acc}) { $self->{association_hash}->{$gene->acc} = []; } push(@{$self->{association_hash}->{$gene->acc}}, $assoc); return $self->{"association_list"}; } =head2 add_selected_association Usage - Returns - Args - L =cut sub add_selected_association { my $self = shift; my $assoc = shift; $assoc->isa("GO::Model::Association") || confess; if (!$self->{"selected_association_list"}) { $self->{"selected_association_list"} = []; } push(@{$self->{"selected_association_list"}}, $assoc); } =head2 association_hash returns associations as listref of unique GeneProduct objects L =cut sub association_hash { my $self = shift; if (!defined($self->{"association_list"})) { $self->association_list; } $self->{"association_hash"} = shift if @_; return $self->{"association_hash"}; } =head2 get_all_associations Usage - my $al = $term->get_all_associations Returns - GO::Model::Association list Args - returns all associations for the term and the terms beneath it in the GO DAG same as $apph->get_all_associations($term) L =cut sub get_all_associations { my $self = shift; $self->apph->get_all_associations($self); } =head2 n_associations Usage - my $n = $term->n_associations Returns - Args - =cut sub n_associations { my $self = shift; if (!@{$self->{"association_list"} || []}) { # association count can be get/set even if the actual # list is not present $self->{n_associations} = shift if @_; } if (!defined($self->{n_associations}) && $self->{association_list}) { # we have already loaded the # association list $self->{n_associations} = scalar(@{$self->association_list || []}); } if (!defined($self->{n_associations})) { $self->{n_associations} = $self->apph->get_association_count($self); } return $self->{n_associations}; } =head2 product_list Usage - $prods = $term->product_list Returns - L listref Args - Returns a reference to an array of gene products that are attached directly to this term. (if the products have not been fetched, this method will call $term->association_list, cache the results, and use the associations to build the product list. succeeding calls of product_list to this term will hence be faster) See L =cut sub product_list { my $self = shift; my $assocs = $self->association_list; my @prods = (); my %ph = (); foreach my $assoc (@$assocs) { my $gp = $assoc->gene_product; if (!$ph{$gp->id}) { push(@prods, $gp); $ph{$gp->id} = 1; } } return [@prods]; } =head2 deep_product_list Usage - Returns - GO::Model::GeneProduct listref Args - finds all products attached to this term and all terms below in the graph L =cut sub deep_product_list { my $self = shift; my $prods = $self->apph->get_products({deep=>1, term=>$self}); return $prods; } =head2 n_deep_products Usage - my $count = $term->n_deep_products; Returns - int Args - filter (hashref) - or string "recount" gets the count for the *dsitinct* number of GO::Model::GeneProduct entries annotated at OR BELOW this level. if you have set the filters in GO::AppHandle then these filters will be used in determining the count. Remember, if you did not explicitly set the filters, then the default filter will be used, which is [!IEA] (i.e. curated associations only, see www.geneontology.org for a discussion of evidence codes). Note: currently only the speciesdb filter is respected. It turns out to be very expensive to do the set arithmetic for distinct recursive gene counts with different evidence combinations. Because each product belongs to one speciesdb only, the speciesdb counts are mutually exclusive, which makes this easier. # get the number of gene products that have been annotated # as transcription factors in worm and fly discounting # uncurated automatic annotations $apph->filters({evcodes=>["!IEA"], speciesdbs=>["SGD", "FB"]}); $term = $apph->get_term({name=>"transcription factor"}); print $term->n_deep_products; The count will be cached, so if you alter the filter parameters be sure to get a recount like this: my $count = $term->n_deep_products("recount"); TODO: make the recount automatic if the filter is changed PERFORMANCE NOTE 1: When you ask the AppHandle to give you a list of GO::Model::Term objects, it may decide to populate this attribute when building the terms in a fast and efficient way. Therefore you should avoid setting the filters *after* you have created the objects otherwise it will have to refetch all these values slowing things down. PERFORMANCE NOTE 2: If you are using the SQL GO::AppHandle implementation, then this call will probably involve a query to the *gene_produc_count* table. If you populated the database you are using yourself, make sure this table is filled otherwise this will be an expensive query. L =cut sub n_deep_products { my $self = shift; $self->{n_deep_products} = shift if @_; if (!defined($self->{n_deep_products}) || $self->{n_deep_products} eq "recount") { $self->{n_deep_products} = $self->apph->get_deep_product_count({term=>$self}); } else { } return $self->{n_deep_products}; } # EXPERIMENTAL sub n_deep_products_grouped_by_taxid { my $self = shift; $self->{n_deep_products_grouped_by_taxid} = shift if @_; if (!defined($self->{n_deep_products_grouped_by_taxid}) || $self->{n_deep_products_grouped_by_taxid} eq "recount") { $self->{n_deep_products_grouped_by_taxid} = $self->apph->get_deep_product_count({term=>$self,group_by=>'taxid'}); } else { } return $self->{n_deep_products_grouped_by_taxid}; } =head2 n_products Usage - as n_deep_products Returns - Args - see docs for n_deep_products gets a count of products AT THIS LEVEL ONLY L =cut sub n_products { my $self = shift; $self->{n_products} = shift if @_; if (!defined($self->{n_products}) || $self->{n_products} eq "recount") { $self->{n_products} = $self->apph->get_product_count({term=>$self}); } return $self->{n_products}; } sub n_unique_associations { my $self = shift; return scalar(keys %{$self->association_hash || {}}); } sub get_child_terms { my $self = shift; return $self->apph->get_child_terms($self, @_); } sub get_parent_terms { my $self = shift; return $self->apph->get_parent_terms($self, @_); } =head2 loadtime Title : loadtime Usage : Function: Example : Returns : time term was loaded into datasource Args : none =cut sub loadtime{ my ($self) = @_; return $self->apph->get_term_loadtime($self->acc); } sub show { my $self = shift; print $self->as_str; } sub as_str { my $self = shift; sprintf("%s (%s)", $self->name, $self->public_acc); } # --- EXPERIMENTAL METHOD --- # not yet public sub namerule { my $self = shift; $self->{_namerule} = shift if @_; return $self->{_namerule}; } sub defrule { my $self = shift; $self->{_defrule} = shift if @_; return $self->{_defrule}; } # --- EXPERIMENTAL METHOD --- # not yet public sub stag { my $self = shift; $self->{_stag} = shift if @_; if (!$self->{_stag}) { require "Data/Stag.pm"; $self->{_stag} = Data::Stag->new(stag=>[]); } return $self->{_stag}; } # pseudo-private method # available to query classes; # a template is a specification from a client to a query server # showing how much data should be transferred across. # the template is an instance of the object that is being returned; # there are a few premade templates available; eg shallow sub get_template { my $class = shift; my $template = shift || {}; if ($template eq "shallow") { # shallow template, just get term attributes, no other # structs $template = GO::Model::Term->new({"name"=>"", "acc"=>-1, "definition"=>"", "n_associations"=>0, "synonym_list"=>[], "dbxref_list"=>undef}); } if ($template =~ /no.*assoc/) { # everything bar associations $template = GO::Model::Term->new({"name"=>"", "acc"=>-1, "definition"=>1, "n_associations"=>0, "synonym_list"=>[]}); $template->{dbxref_h} = 1; } if ($template eq "all") { # everything $template = GO::Model::Term->new({"name"=>"", "acc"=>-1, "definition"=>1, "association_list"=>[], "synonym_list"=>[]}); $template->{dbxref_h} = 1; } return $template; } sub to_text { my $self = shift; my ($prefix, $escape, $obs_l, $suppress) = rearrange([qw(prefix escape obs suppress)], @_); my @syns = @{$self->synonym_list || [] }; my @xrefs = @{$self->dbxref_list || [] }; if ($suppress) { if (!ref($suppress)) { $suppress = {$suppress => 1}; } @xrefs = grep {!$suppress->{$_->xref_dbname}} @xrefs; } else { @xrefs = grep {$_->xref_dbname eq 'EC'} @xrefs; } my $sub = sub { @_ }; if ($escape) { $sub = sub {map{s/\,/\\\,/g;$_}@_}; } my $text = sprintf("%s%s ; %s%s%s%s", &$sub($prefix || ""), &$sub($self->name), $self->public_acc, (($obs_l && @$obs_l) ? join ("", map {", ".$_->public_acc } @$obs_l ) : '' ), ((@xrefs) ? join("", map {&$sub(" ; ".($_->as_str || ''))} @xrefs ) : '' ), ((@syns) ? join("", map {&$sub(" ; synonym:$_")} @syns ):"" ), ); return $text; } sub to_ptuples { my $self = shift; my ($th, $include, $sort) = rearrange([qw(tuples include sort)], @_); my @s = (); push(@s, ["term", $self->acc, $self->name, ]); foreach my $x (@{$self->dbxref_list || []}) { push(@s, $x->to_ptuples(-tuples=>$th)); push(@s, ["term_dbxref", $self->acc, $x->as_str]); } @s; } 1; go-perl-0.15/GO/Model/TreeIterator.pm000644 000765 000024 00000014643 11615622160 017244 0ustar00cjmstaff000000 000000 # $Id: TreeIterator.pm,v 1.7 2007/08/21 12:25:35 girlwithglasses Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself # package GO::Model::TreeIterator; =head1 NAME GO::Model::GraphIterator; =head1 SYNOPSIS =head1 DESCRIPTION This is a hack. It wraps GO::Model::GraphIterator and provides a tree like iteration, rather than a graph-like iteration. This is done by giving TreeIterator a template array. The array looks like this : [ [3674, 'isa', 3673], [9277, 'isa', 5618] ] 3674 is selected iff it is the child of 3673. 9277 is selected iff it is the child of 5618. =cut use Carp; use strict; use Exporter; use GO::Utils qw(rearrange); use GO::Model::Graph; use GO::Model::GraphNodeInstance; use FileHandle; use Exporter; use Data::Dumper; use vars qw(@EXPORT_OK %EXPORT_TAGS); use base qw(GO::Model::Root Exporter); sub _valid_params { return qw(graph order sort_by noderefs direction no_duplicates reltype_filter visited arcs_visited); } =head2 order Usage - $graphiter->order("breadth"); Returns - string Args - string gets/sets traversal order; breadth or depth; default is depth =cut =head2 direction Usage - $graphiter->direction("up"); Returns - string Args - string gets/sets direction; default is "down" =cut #sub _initialize { # my $self = shift; # my $acc; # if (!ref($_[0])) { # $acc = shift; # } # $self->SUPER::_initialize(@_); # $self->reset_cursor($acc); #} sub new { my $class = shift; my $self = {}; bless $self, $class; $self->{'graph'} = shift || $self->throw("no graph passed in to constructor"); $self->{'selected_array'} = shift; $self->{'show_kids'} = shift; $self->{'closed_below'} = shift; my $compact = shift || 0; $self->{'nit'} = $self->{'graph'}->create_iterator({compact=>$compact}); $self->{'bootstrap_mode'} = 0; # $self->SUPER::_initialize(@_); # $self->{'current_path'}; $self->{'nit'}->reset_cursor(); return $self; } =head2 reset_cursor Usage - Returns - GO::Model::Term Args - =cut sub reset_cursor { my $self = shift; $self->{'nit'}->reset_cursor(); } =head2 next_node Usage - Returns - GO::Model::Term Args - =cut sub next_node { my $self = shift; my $ni = $self->next_node_instance; return $ni ? $ni->term : undef; } =head2 set_bootstrap_mode Usage - Returns - Args - =cut sub set_bootstrap_mode { my $self = shift; $self->{'bootstrap_mode'} = 1; } =head2 get_bootstrap_mode Usage - Returns - Args - =cut sub get_bootstrap_mode { my $self = shift; return $self->{'bootstrap_mode'}; } =head2 get_current_path Usage - Returns - array ref Args - none =cut sub get_current_path { my $self = shift; return $self->{'current_path'}; } =head2 next_node_instance Usage - Returns - GO::Model::GraphNodeInstance Args - =cut sub next_node_instance { my $self = shift; my $current_coords = $self->{'current_coords'} || []; my $nit = $self->{'nit'}; my $previous_depth = $self->{'previous_depth'} || 1; my $parent_array = $self->{'current_path'}; my $ni = $nit->next_node_instance; if ($ni) { my $depth = $ni->depth; if ($previous_depth == $depth) { $parent_array->[$depth] = $ni->term->public_acc; } elsif ($previous_depth > $depth) { while ($previous_depth > $depth) { $previous_depth -= 1; pop @$parent_array; } $parent_array->[$depth] = $ni->term->public_acc; } elsif ($previous_depth < $depth) { push @$parent_array, $ni->term->public_acc; } $self->{'previous_depth'} = $ni->depth; $self->{'current_path'} = $parent_array; if ($self->get_bootstrap_mode) { return $ni; } if ($self->should_draw_below($parent_array)) { return $ni; } else { $self->next_node_instance; } } else { return 0; } } sub should_draw_below { my $self = shift; my $current_coords = shift; my $coord_list = $self->{'selected_array'}; foreach my $coords (@$coord_list) { if (scalar(@$current_coords) <= scalar(@$coords)) { my $result = 1; my $i = 0; my $length; while ($i < scalar(@$current_coords)) { if ($coords->[$i] ne $current_coords->[$i]) { $result = 0; } } continue { $i++; } if ($result == 1) { return 1; } } elsif (scalar(@$current_coords) > scalar(@$coords)) { my $i = 0; my $test = 1; while ($i < scalar(@$coords)) { if ($current_coords->[$i] ne $coords->[$i]) { $test = 0; } } continue { $i++; } if ($test) { my $parent_coords; foreach my $anc(@$current_coords) { push @$parent_coords, $anc; } pop @$parent_coords; if ($self->is_selected($parent_coords, 'show_kids')) { return 1; } } } } return 0; } sub close_below { my $self = shift; my $closed_array = $self->{"closed_below"}; foreach my $closed (@$closed_array) { $self->{'selected_array'} = $self->delete_array($closed); } foreach my $closed (@$closed_array) { $self->{'show_kids'} = $self->delete_array($closed, 'show_kids'); } } sub delete_array { my $self = shift; my $parent_array = shift; my $array_to_test_against = shift || 'selected_array'; my $selected_array = $self->{$array_to_test_against}; my @two_d_array; foreach my $arr(@$selected_array) { my $test = 1; if (scalar(@$arr) >= scalar(@$parent_array)) { my $i = 0; while ($i < scalar(@$parent_array)) { if ($parent_array->[$i] ne $arr->[$i]) { $test = 0; } } continue { $i++; } } else { $test = 0; } if ($test != 1) { push @two_d_array, $arr; } else { } } return \@two_d_array; } sub is_selected { my $self = shift; my $parent_array = shift; my $array_to_test_against = shift || 'selected_array'; my $selected_array = $self->{$array_to_test_against}; foreach my $arr(@$selected_array) { if (scalar(@$arr) eq scalar(@$parent_array)) { my $i = 0; my $test = 1; while ($i < scalar(@$arr)) { if ($parent_array->[$i] ne $arr->[$i]) { $test = 0; } } continue { $i++; } if ($test == 1) { return 1; } } } return 0; } sub reltype_filter { my $self = shift; $self->{'nit'}->reltype_filter(@_); } 1; go-perl-0.15/GO/Model/Xref.pm000644 000765 000024 00000012524 11615622160 015533 0ustar00cjmstaff000000 000000 # $Id: Xref.pm,v 1.3 2005/02/11 05:44:56 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::Model::Xref; =head1 NAME GO::Model::Xref; =head1 SYNOPSIS my $xrefs = $term->dbxref_list(); foreach my $xref (@$xrefs) P printf "Term %s has an xref %s:%s\n", $term->name, $xref->xref_key, $xref->dbname; } =head1 DESCRIPTION represents a cross reference to an external database. an Xref is made up of a key (ie the accession number, or whatever the value of the unique field being keyed off of is) and a database name. this should theorerically be enough to uniquely identify any databased entity. =head1 NOTES Like all the GO::Model::* classes, this uses accessor methods to get or set the attributes. by using the accessor method without any arguments gets the value of the attribute. if you pass in an argument, then the attribuet will be set according to that argument. for instance # this sets the value of the attribute $my_object->attribute_name("my value"); # this gets the value of the attribute $my_value = $my_object->attribute_name(); =cut use Carp qw(cluck confess); use Exporter; use GO::Utils qw(rearrange); use GO::Model::Root; use strict; use vars qw(@ISA); @ISA = qw(GO::Model::Root Exporter); sub _valid_params { return qw(id xref_key xref_keytype xref_dbname xref_desc name); } sub _valid_dbnames { return qw(go gxd sgd tair mgi fb sp sp_kw egad ec medline pmid isbn omim embl publication U); } =head2 xref_key Alias - acc Alias - accession Usage - Returns - Args - accessor: gets/sets the key/id of the cross reference =cut sub xref_key { my $self = shift; $self->{xref_key} = shift if @_; if ($self->{xref_dbname} && $self->{xref_dbname} =~ /interpro/i) { if ($self->{xref_key} && $self->{xref_key} =~ /(\S+) (.*)/) { $self->{xref_key} = $1; $self->{xref_desc} = $2; } } return $self->{xref_key}; } *accession = \&xref_key; *acc = \&xref_key; =head2 xref_keytype Usage - Returns - Args - accessor: gets/sets the key/id type of the cross reference =cut sub xref_keytype { my $self = shift; $self->{xref_keytype} = shift if @_; return $self->{xref_keytype}; } =head2 as_str Usage - Returns - Args - =cut sub as_str { my $self=shift; # cluck unless defined $self->xref_dbname; # cluck unless defined $self->xref_key; return $self->xref_dbname().":".$self->xref_key(); } =head2 xref_dbname Alias - dbname Usage - Returns - Args - accessor: gets/sets the database name of the cross reference must be a valid database name =cut sub xref_dbname { my $self = shift; $self->{xref_dbname} = shift if @_; return $self->{xref_dbname}; } *dbname = \&xref_dbname; =head2 xref_desc Alias - name Usage - Returns - Args - accessor: gets/sets the description of the accession no useful for interpro =cut sub xref_desc { my $self = shift; $self->{xref_desc} = shift if @_; return $self->{xref_desc}; } *name = \&xref_desc; sub to_idl_struct { my $self = shift; return { dbname=>$self->xref_dbname, keyvalue=>$self->xref_key, }; } =head2 to_xml Usage - print $xref->to_xml() Returns - string Args - indent [integer] XML representation; you probably shouldnt call this directly, this will be called by entities that own xrefs =cut sub to_xml { my $self = shift; my $indent = shift || ""; my $text = $indent."\n"; $text .= $indent." ". $self->xref_dbname."\n"; if ( $self->xref_keytype ) { if ( $self->xref_keytype =~ /personal communication/ ) { $text .= $indent." ". $self->xref_keytype."\n"; $text .= $indent." ". $self->xref_key."\n"; } else { if ($self->xref_keytype !~ /acc/) { $text .= $indent." ". $self->xref_keytype."\n"; } $text .= $indent." ". $self->xref_key."\n"; } } else { $text .= $indent." ".$self->xref_key."\n"; } $text .= $indent."\n"; return $text; } sub to_ptuples { my $self = shift; my ($th) = rearrange([qw(tuples)], @_); my @s = (); my @desc = ($self->xref_desc); pop @desc unless $desc[0]; push(@s, ["xref", $self->as_str, $self->xref_dbname, $self->xref_key, @desc, ]); @s; } # **** EXPERIMENTAL CODE **** # the idea is to be homogeneous and use graphs for # everything; eg gene products are nodes in a graph, # associations are arcs # cf rdf, daml+oil etc # args - optional graph to add to sub graphify { my $self = shift; my ($ref, $subg, $opts) = rearrange([qw(ref graph opts)], @_); $opts = {} unless $opts; $subg = $self->apph->create_graph_obj unless $subg; my $t = $self->apph->create_term_obj({name=>$self->as_str, acc=>$self->as_str}); $subg->add_node($t); $subg->add_arc($t, $ref, "hasXref"); return $subg; } 1; go-perl-0.15/GO/Metadata/Panther.pm000644 000765 000024 00000015476 11615622160 016721 0ustar00cjmstaff000000 000000 package GO::Metadata::Panther; use strict; use warnings; use Exporter; use Memoize; use List::Util qw/sum first/; use Data::Dumper; use Carp; use base qw/GO::Metadata::UniProt::Species Exporter/; our @EXPORT_OK = qw/panther_codes panther_all valid_panther_codes/; =head1 NAME GO::Metadata::Panther - Species info for data used by Panther Clusters =head1 SYNOPSIS use GO::Metadata::Panther; my $s = GO::Metadata::Panther->code('YEAST'); =head1 DESCRIPTION Inherits functions from L. Accesses information related to species in the Panther F file. This file can be fetched from: L =cut # Information needed but not provided by UniProt's speclist.txt file. our %species = ( # # A # ANOGA => { prefer => [ qw/ENSEMBL UniProtKB/ ] }, ARATH => { id_filter => sub { if ($_[0] eq 'gene') { return ('TAIR', "locus:$_[1]"); } return @_; } }, AQUAE => {}, ASHGO => { also_node => [ 284811 ] }, # # B # BACSU => {}, BACTN => {}, BOVIN => { prefer => [ 'UniProtKB', 'ENSEMBL' ] }, BRAJA => {}, # # C # CAEBR => {}, CAEEL => { prefer => [ 'WB' ], id_filter => sub { $_[0] = 'WB' if ($_[1] =~ m/^WB/); return @_; } }, CANFA => { prefer => [ 'ENSEMBL' ] }, CHLTA => {}, CHLRE => {}, CHLAA => {}, CIOIN => { prefer => [ 'ENSEMBL' ] }, # # D # DANRE => { prefer => [ 'ZFIN', 'ENSEMBL', 'UniProtKB' ] }, DEIRA => {}, DICDI => {}, DROME => { prefer => [ 'FB' ], id_filter => sub { $_[0] = 'FB' if ($_[1] =~ m/^FB/); return @_; } }, # # E # EMENI => {}, ENTHI => {}, ECOLI => { also_node => [ 562, 511145 ], prefer => [ 'EcoCyc', 'UniProtKB' ] }, # # G # CHICK => { prefer => [ 'UniProtKB', 'ENSEMBL', 'NCBI' ] }, GEOSL => {}, GLOVI => { also_node => [ 251221 ] }, # # H # HUMAN => { prefer => [ 'UniProtKB', 'ENSEMBL' ] }, # # L # LEIMA => { also_node => [ 347515 ] }, LEPIN => {}, # # M # MACMU => { prefer => [ 'UniProtKB', 'ENSEMBL' ] }, METAC => {}, MONDO => { prefer => [ 'ENSEMBL' ] }, MOUSE => { prefer => [ 'MGI', 'UniProtKB', 'ENSEMBL' ], id_filter => sub { if (($_[0] eq 'MGI') and ($_[1] !~ m/^MGI:/)) { return ('MGI', "MGI:$_[1]"); } return @_; } }, # # N # NEUCR => {}, # # O # ORNAN => { prefer => [ 'ENSEMBL' ] }, ORYSJ => {}, # # P # PANTR => { prefer => [ 'ENSEMBL', 'UniProtKB' ] }, PLAYO => {}, PSEA7 => {}, # # R # RAT => { prefer => [ 'RGD', 'UniProtKB', 'ENSEMBL' ] }, # # S # YEAST => {}, SCHPO => {}, STRCO => {}, STRPU => {}, SULSO => {}, # # T # FUGRU => { is => 'TAKRU' }, TAKRU => { was => 'FUGRU', prefer => [ 'ENSEMBL' ], }, TETTH => { also_node => [ 312017 ] }, THEMA => {}, # # X # XENTR => { prefer => [ 'UniProtKB', 'ENSEMBL' ] }, ); =head2 Exportable Subroutines =over =item panther_codes() Returns the list of UniProt species codes that are used in Panther clusters. =cut sub panther_codes{ return map { defined $species{$_}->{is} ? () : $_; } keys %species; } sub codes{ carp "Please use panther_codes() instead of codes()"; panther_codes(@_); } =item GO::Metadata::Panther->panther_all() Returns a list of C objects that are used in Panther clusters. =cut sub panther_all{ my $c = shift; return $c->new(panther_codes()); } sub all { carp 'Please panther_all() instead if all()'; return shift()->panther_all(@_); } =item valid_codes(...) Returns a true value in every argument is a UniProt species code used in Panther cluster. Otherwise returns false. =cut sub valid_panther_codes{ for my $code (@_) { return undef if (!exists $species{$code}); } return '1'; } =back =head2 OO Function =over =item GO::Metadata::Panther-Enew(...); This basically hands things off to L's new function. Populates that with other Panther/GO specific information, and does some error correction. =cut our %_new_cache; sub new{ my $c = shift; my @have; my @all = map { if ($_new_cache{$_}) { push @have, $_new_cache{$_}; (); } else { $_; } } @_; ########## # Fix up also_node entries (see ECOLI) @all = map { my $all = $_; my $out = $all; if ($all =~ m/^\d+$/) { BLA: for my $code (keys %species) { for my $node (@{ $species{$code}->{also_node} }) { if ($all eq $node) { $out = $code; last BLA; } } } } $out; } @all; # This bugs me ########## @all = map { if (!$_->ncbi_taxon_id()) { warn 'Skipping unknown NCBI taxon ID, check: SELECT * FROM species WHERE ncbi_taxa_id=0'; (); } else { $_; } } $c->SUPER::new(map { if ($species{$_} && $species{$_}->{is}) { warn "$_ -> $species{$_}->{is}"; $species{$_}->{is}; } else { $_; } } @all) if (scalar @all); for (@all) { if ($species{$_->code()}) { while (my ($k,$v) = each %{ $species{$_->code} }) { $_->{$k} = $v; } } else { warn $_->code . ' Not a Panther family.'; } } for my $all (@all) { $_new_cache{$all->{node}} = $all; $_new_cache{$all->{code}} = $all; } push @all, @have; return undef if (0 == scalar @all); return $all[0] if (1 == scalar @all); return @all; } =item $s->ncbi_taxa_ids() Returns the list of NCBI taxa identifiers associated with the UniProt species code. In a perfect word this will only every return one value. In any case, the first value will be the actual numeric identifier associated. =cut sub ncbi_ids{ my $s = shift; my @out = ($s->{node}); push @out, @{ $s->{also_node} } if ($s->{also_node}); return @out; } =item $s->prefers() Returns a list of id types (generally to be populated in C) in order of preference of use. If a null list, we have never encountered a conflict that needed resolving. =cut sub prefers{ my $s = shift; if ($s->{prefer}) { return @{ $s->{prefer} }; } return qw/UniProtKB/; } # this is not fully in use. sub reject{ my $s = shift; if ($s->{reject}) { return @{ $s->{reject} }; } return qw/GeneID/; } # sub prefered{ # my $s = shift; # my $v = shift # return first { $v eq $_ } $s->preferes(); # } sub id_filter{ my $s = shift; my ($k, $v) = (shift, shift); $k = 'UniProtKB' if ($k =~ m/UniProt/i); if ($s->{id_filter}) { return &{ $s->{id_filter} }($k, $v); } return ($k, $v); } =back =head2 SEE ALSO L =head2 AUTHOR Sven Heinicke Esven@genomics.princeton.edu =cut 1; go-perl-0.15/GO/IO/Analysis.pm000644 000765 000024 00000004504 11615622160 015660 0ustar00cjmstaff000000 000000 # $Id: Analysis.pm,v 1.2 2004/11/24 02:28:00 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::IO::Analysis; =head1 NAME GO::IO::Analysis - preliminary analysis object =head1 SYNOPSIS =cut =head1 DESCRIPTION top level module for doing analyses eg clustalw on the fly =head1 CREDITS =head1 PUBLIC METHODS =cut use strict; use base qw(GO::Model::Root); use GO::Utils qw(rearrange); #use GO::IO::Blast; sub _valid_params { qw() }; sub clustalw { my $self = shift; my ($products, $seqs, $seqf) = rearrange([qw(products seqs file)], @_); my $leave = $seqf ? 1 : 0; if (!$seqs) { $seqs = []; my %h = (); foreach my $p (@$products) { push(@$seqs, grep { !$h{$_->display_id} && ($h{$_->display_id} = 1) } @{$p->seq_list}); } } # TODO : use displatcher class to allow # other ways of calling programs my $seqf = $seqf || "/tmp/$$.clustalin.fa"; my $outf = $seqf; $outf =~ s/fa$/aln/; open(F, ">$seqf") || die; map {print F $_->to_fasta} @$seqs; close(F); my $cmd = "clustalw -infile=$seqf -outfile=$outf"; print "cmd=$cmd\n"; print `$cmd`; open(F, "$outf") || die; my $out = join("", ); close(F); unless ($leave) { unlink $seqf; unlink $outf; } return $out; } #sub blastp { # my $self = shift; # my ($fn) = rearrange([qw(file)], @_); # # TODO : use displatcher class to allow # # other ways of calling programs # #HARDCODE ALERT!!!!!!!!!!!!!!!!!!!! # # this is a still a VERY preliminary module # my $db = "/www/whitefly_80/WWW/annot/go/fasta/go_pep.fa"; # my $outf = "/tmp/$$.blastout.fa"; ## my $cmd = "blastp $db $fn -filter SEG+XNU > $outf"; # my $cmd = "blastp $db $fn > $outf"; # print "cmd=$cmd\n"; # print `$cmd`; # my $blast = # GO::IO::Blast->new({apph=>$self->apph, # file=>"$outf"}); # return $blast; #} =head1 FEEDBACK Email cjm@fruitfly.berkeley.edu This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself =cut 1; go-perl-0.15/GO/IO/Blast.pm000644 000765 000024 00000020375 11615622160 015146 0ustar00cjmstaff000000 000000 # $Id: Blast.pm,v 1.2 2004/11/24 02:28:00 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::IO::Blast; =head1 NAME GO::IO::Blast - Gene Ontology Blast Reports DEPRECATED =head1 SYNOPSIS =cut =head1 DESCRIPTION parses a blast report (must be a a blast that was performed on a seqdb that can with headers that can be mapped to go terms via the go database) takes the blast hits, and finds the corresponding GO terms (currently it requires the fasta to have "genename:" in header but we should make it configurable) using the GO terms, a GO::Model::Graph is built, with the blast hits attached according to product<->term links. Any blast hit H that corresponds to a term T implicitly corresponds to all the terms above T in the DAG; eg a hit to a G-protein coupled receptor is implicitly a hit to a transmembrane receptor. At every node, all the scores (including implicit scores from hits further down) are combined. Currently we are playing with this as the scording scheme: log2( 2 ** score1 + 2 ** score2 +.... 2** scoreN) Hits are only counted once at each node. TODO - use bioperl to parse full report if required (currently parses summary) TODO - configurable ways to go from fasta header to GO terms TODO - different scoring schemes TODO - result object =head1 PUBLIC METHODS - Blast =cut use strict; use Carp; use base qw(GO::Model::Root); use GO::Utils qw(rearrange); sub _valid_params { qw(apph output file raw) }; sub load_file { my $self = shift; my $file = shift || $self->file; my $fh = FileHandle->new($file); my $raw = join("", <$fh>); $self->raw($raw); $raw; } sub showgraph { my $self = shift; $self->getgraph(@_); print $self->output; } sub getTermListByGPs { my $self = shift; my ($raw, $apph) = @_; if (!$raw) { $raw = $self->load_file; } my @lines = split(/\n/, $raw); my $in_summary = 0; my @symbols = (); my $symbol_h = {}; foreach (@lines) { chomp; if (!$_) { next; } if (/^\>/) { $in_summary = 0; } if (/^\>/) { $in_summary = 0; } if (/Sequences producing/) { $in_summary = 1; next; } else { if ($in_summary) { my @w = split; my ($n, $p, $score, @rest) = reverse @w; # if ($p >= 0.1) { # next; # } my $hit = join(" ", @rest); if ($hit =~ /genename:(\S+)/) { my $s = $1; push(@symbols, $s); $symbol_h->{$s} = {score=>$score}; } } } } # my $terms = # $apph->get_terms({products=>[@symbols], type=>"function"}); my $terms = $apph->get_terms({products=>[@symbols]}); #my $graph = $apph->get_graph_by_terms($terms, 0); return $terms; } sub getgraph { my $self = shift; my ($raw, $apph) = @_; # print '
';
#    print $raw;
#    print '
'; if (!$raw) { $raw = $self->load_file; } my @lines = split(/\n/, $raw); my $in_summary = 0; my @symbols = (); my $symbol_h = {}; foreach (@lines) { chomp; if (!$_) { next; } if (/^\>/) { $in_summary = 0; } if (/^\>/) { $in_summary = 0; } if (/Sequences producing/) { $in_summary = 1; next; } else { if ($in_summary) { my @w = split; my ($n, $p, $score, @rest) = reverse @w; # if ($p >= 0.1) { # next; # } my $hit = join(" ", @rest); if ($hit =~ /symbol:(\S+)/) { # if ($hit =~ /genename:(\S+)/) { my $s = $1; push(@symbols, $s); # if (!$symbol_h->{$s}) { # $symbol_h->{$s} = []; # } # push(@{$symbol_h->{$s}}, {score=>$score}); $symbol_h->{$s} = {score=>$score}; } } } } # printf "

SYMBOLS meeting threshold:%s\n

", join(" ", @symbols); # my $apph = $self->apph; # my $terms = # $apph->get_terms({products=>[@symbols], type=>"function"}); $apph->filters({}); my $terms = $apph->get_terms({products=>[@symbols]}); # print $terms; # foreach my $term (@$terms) { # $self->out(" ".$term->public_acc); # } my $graph = $apph->get_graph_by_terms($terms, 0); return $graph, \@symbols; # return $symbol_h;; ################################################### # ---------------- # associate every product in graph with # all the nodes at or above the current position, # counting each product only once at each node # look up a hash of products (explicit and implict) by term my @term_lookup = (); # recurse down graph to get implicit products # from node beneath sub myrecurse { my $terms = shift; foreach my $term (@$terms) { # get the list of nodes below this one my $children = $graph->get_child_terms($term); if (@$children) { # not a leaf node # recurse further myrecurse($children); foreach my $child (@$children) { my $ph = $term_lookup[$child->acc]; foreach (keys %{$ph || {}}) { $term_lookup[$term->acc]->{$_} = $ph->{$_}; } } } if (!$term_lookup[$term->acc]) { $term_lookup[$term->acc] = {}; } # count all the products at this point in the DAG foreach (@{$term->selected_association_list || []}) { $term_lookup[$term->acc]->{$_->gene_product->id} = $_->gene_product; } } } myrecurse($graph->get_top_nodes); sub shownode { my $ni = shift; my $depth = $ni->depth; my $term = $ni->term; my $reltype = $ni->parent_rel ? $ni->parent_rel->type : ""; my $tab = $graph->is_focus_node($term) ? "->->" : " "; my $ph = $term_lookup[$term->acc]; # all the products by symbol at this node or below my @allsymbols = map {$_->symbol} values %$ph; # my $logsum = 0; # map { $logsum += 2 ** $symbol_h->{$_}->{score} } @allsymbols; # my $score = log($logsum)/log(2); my $logsum = 0; my $score = 0; if (@allsymbols) { map { $logsum += 2 ** $symbol_h->{$_}->{score} } @allsymbols; $score = log($logsum)/log(2); } # fudgefactor: (assumes 90% of prod2term assoc being correct) # prod2terms aren't independent but we treat them like # they are $score *= 1 - (0.1 ** scalar(@allsymbols)); # my $score = 0; # map { $score += $symbol_h->{$_}->{score} } @allsymbols; my $out = sprintf "%s %2s Term = %s (%s); SCORE=%.2f\n", " . " x $depth, $reltype eq "isa" ? "%" : "<", $term->name, $term->public_acc, $score, ; foreach (@{$term->selected_association_list || []}) { my $sym = $_->gene_product->symbol; $out.= $tab x $depth . " :: " . $sym; $out.= " ".$_->gene_product->xref->as_str; $out.= " ".$_->evidence_as_str(1)." "; $out.= " ".$symbol_h->{$sym}->{score}.";"; $out.= "\n"; } $self->out("$out"); } # my $it = $graph->create_iterator; # returns a GO::Model::GraphIterator object #$graph->iterate(\&shownode); return $graph; } sub out { my $self = shift; my $str = shift; $self->output($self->output().$str); } sub parse { } =head1 FEEDBACK Email cjm@fruitfly.berkeley.edu This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself =cut 1; go-perl-0.15/GO/IO/Dotty.pm000644 000765 000024 00000006327 11615622160 015205 0ustar00cjmstaff000000 000000 # $Id: Dotty.pm,v 1.1 2005/02/11 05:44:56 cmungall Exp $ package GO::IO::Dotty; =head1 NAME GO::IO::Dotty; =head1 SYNOPSIS Utility functions for producing Dotty diagrams from GO graphs Contributed to the go-database list by Philip Lord =head1 REQUIREMENTS http://www.research.att.com/sw/tools/graphviz/ http://search.cpan.org/search?dist=GraphViz =cut use strict; use Exporter; use GraphViz; my @ISA=qw{Exporter}; my %labellednodes; sub graphviz_to_dotty{ my $graphviz = shift; open( DOTTY, "|dotty -" ); print DOTTY $graphviz->as_text; close( DOTTY ); } sub go_graph_to_graphviz { my $graph = shift; my %gopts = %{shift || {}}; my %opts = %{shift || {}}; my $it = $graph->create_iterator; my %relationships; my %labellednodes; my $graphviz = GraphViz->new(%gopts); while (my $ni = $it->next_node_instance ){ my $term = $ni->term; my $rel = $ni->parent_rel; my $parents = $graph->get_parent_terms($term->acc); _graphviz_label( $term, $graph, \%labellednodes, $graphviz, \%opts ); foreach my $p (@$parents){ _graphviz_label( $p, $graph->is_focus_node( $p ), \%labellednodes, $graphviz, \%opts ); my $identifier = $p->acc . " " . $term->acc; unless( $relationships{ $identifier } ){ ## for some reason graphviz assumes that a number is only a ## label, and not a node name which is irritating. my $node = "acc" . $term->acc; my $pnode = "acc" . $p->acc; my $apph = $term->apph; $graphviz->add_edge($node=>$pnode, label=>$rel->type); $relationships{ $identifier } = 1; } } if ($opts{selected_assocs}) { my @prs = map {$_->gene_product } @{$term->selected_association_list || []}; my $node = "acc" . $term->acc; foreach my $pr (@prs) { my $nid = $pr->xref->as_str; unless($labellednodes{$nid}) { $graphviz->add_node($nid, label=>$pr->symbol, color=>'red'); $labellednodes{$nid} = 1; } $graphviz->add_edge( $nid=>$node, label=>"annotated_to"); } } } return $graphviz; } sub _graphviz_label{ my $term = shift; my $graph = shift; my $labellednodes = shift; my $graphviz = shift; my %opts = %{ shift || {}}; my $acc = $term->acc; my $node = "acc" . $term->acc; unless( $labellednodes->{$acc} ){ if ($opts{sub}) { $graphviz->add_node($opts{sub}->($node, $term)); } else { $graphviz->add_node ( $node, label=>$term->name . " " . $term->acc , URL=>%opts->{'base_url'}.$term->acc, fontname=>'Courier' ); } $labellednodes->{$acc} = 1; } } sub label_nodes_with_colour{ my $graphviz = shift; my $terms = shift; my $colour = shift; foreach my $term (@$terms){ my $node = "acc" . $term->public_acc; $graphviz->add_node ( $node, style=>"filled", color=>$colour , fontname=>'Courier'); } } # support US spelling *label_nodes_with_color = \&label_nodes_with_colour; 1; go-perl-0.15/GO/IO/go_assoc.pm000644 000765 000024 00000030341 11615622160 015670 0ustar00cjmstaff000000 000000 # $Id: go_assoc.pm,v 1.6 2008/06/02 22:00:44 sjcarbon Exp $ # # This GO module is maintained by Seth Carbon # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself. ## ## TODO: Fix documentation. ## package GO::IO::go_assoc; =head1 NAME GO::IO::go_assoc; =head1 SYNOPSIS my $apph = GO::AppHandle->connect(-d=>$go, -dbhost=>$dbhost); my $term = $apph->get_term({acc=>00003677}); #### ">-" is STDOUT my $out = new FileHandle(">-"); my $ga_out = GO::IO::go_assoc->new(-output=>$out); $ga_out->write_term($term); OR: my $apph = GO::AppHandle->connect(-d=>$go, -dbhost=>$dbhost); my $graph = $apph->get_node_graph(-acc=>00003677, -depth=>2); my $out = new FileHandle(">-"); my $ga_out = GO::IO::go_assoc->new(-output=>$out); $ga_out->write_graph($graph); =head1 DESCRIPTION Utility class to dump GO terms as OBD XML. Currently, you just call start_document, write_term for each term, then end_document. =cut use strict; use GO::Utils qw(rearrange); #################### =head2 new Usage - my $ga_out = new GO::IO::go_assoc(-output=>$out); Returns - Output emitter. Args - Output FileHandle Initializes the writer object. To write to standard out, do: my $out = new FileHandle(">-"); my $ga_out = new GO::IO::go_assoc($out); =cut sub new { my $class = shift; my $self = {}; #my $outhandle = rearrange([qw(output)], @_); my $outhandle = shift; $self->{OUT} = $outhandle; bless $self, $class; return $self; } #################### =head2 cgi_header Usage - $ga_out->cgi_header; Returns - None Args - None cgi_header prints the "Content-type: text/plain" statement. If creating a CGI script, you should call this before further action. =cut sub cgi_header { my $self = shift; my $fh = $self->{OUT}; print $fh "Content-type: text/plain\n\n"; } #################### =head2 write_graph Usage - $ga_out->write_graph(-graph=>$graph); Returns - None Args -graph=>$graph, -deep=>1 or 0, # optional, default 0. -qualifier=>1 or 0, # optional, default 1. -with=>1 or 0, # optional, default 1. -object_name=>1 or 0, # optional, default 1. -object_synonym=>1 or 0, # optional, default 1. =cut ## sub write_graph { my $self = shift; my ($graph, $deep, $qualifier, $with, $object_name, $object_synonym) = rearrange([qw(graph deep qualifier with object_name object_synonym)], @_); my $term_list = $graph->get_all_nodes; $self->write_term_list(-term_listref=>$term_list, -deep=>$deep, -qualifier=>$qualifier, -with=>$with, -object_name=>$object_name, -object_synonym=>$object_synonym ); } #################### =head2 write_term_list Usage - $ga_out->write_term_list(); Returns - None Args -term_listref=>$term_listref, -deep=>1 or 0, # optional, default 0. -qualifier=>1 or 0, # optional, default 1. -with=>1 or 0, # optional, default 1. -object_name=>1 or 0, # optional, default 1. -object_synonym=>1 or 0, # optional, default 1. =cut ## sub write_term_list { my $self = shift; my ($term_listref, $deep, $qualifier, $with, $object_name, $object_synonym) = rearrange([qw(term_listref deep qualifier with object_name object_synonym)], @_); #print STDERR "\n\n" . @$term_listref . "\n\n"; #print STDERR "\n\n" . $term->acc . "\n\n"; #sleep 1; ## foreach my $term (@$term_listref) { $self->write_term(-term=>$term, -deep=>$deep, -qualifier=>$qualifier, -with=>$with, -object_name=>$object_name, -object_synonym=>$object_synonym); } } #################### =head2 write_term Usage - $ga_out->write_term(); Returns - None Args -term=>$term, -deep=>1 or 0, # optional, default 0. -qualifier=>1 or 0, # optional, default 1. -with=>1 or 0, # optional, default 1. -object_name=>1 or 0, # optional, default 1. -object_synonym=>1 or 0, # optional, default 1. =cut sub write_term{ my $self = shift; my ($term, $deep, $qualifier, $with, $object_name, $object_synonym) = rearrange([qw(term deep qualifier with object_name object_synonym)], @_); $deep = $deep || 0; $qualifier = $qualifier || 1; $with = $with || 1; $object_name = $object_name || 1; $object_synonym = $object_synonym || 1; my @output = (); my $assoc_listref; if( $deep ){ $assoc_listref = $term->get_all_associations || []; }else{ #$assoc_listref = $term->selected_association_list || []; $assoc_listref = $term->association_list; } foreach my $assoc (@$assoc_listref) { ## Get evidence info. my $ev_listref = $assoc->evidence_list; foreach my $ev (@$ev_listref) { ## Get gp info. my $gp = $assoc->gene_product; ## 1 DB gene_product x dbxref.xref_dbname push @output, $gp->speciesdb; push @output, "\t"; ## 2 DB_Object_ID gene_product x dbxref.xref_xref_key push @output, $gp->acc; push @output, "\t"; ## 3 DB_Object_Symbol gene_product.symbol push @output, $gp->symbol; push @output, "\t"; ## 4 NOT association.is_not ## Qualifiers association_qualifier if ( $qualifier ) { if ( $assoc->is_not ) { push @output, 'NOT'; #}else{ #push @output, 'IS'; } } push @output, "\t"; ## 5 GOid association x term.acc push @output, $term->acc; push @output, "\t"; ## 6 DB:Reference association x evidence.dbxref_id my $xref_listref = $ev->xref_list; foreach my $xref ( @$xref_listref ) { push @output, $xref->dbname . ':' . $xref->xref_key; push @output, '|'; } ## Get rid of trailing '|'. pop @output if $output[$#output] eq '|'; push @output, "\t"; ## 7 Evidence association x evidence.code push @output, $ev->code; push @output, "\t"; ## 8 With/From evidence.seq_acc [DENORMALIZED] ## evidence x evidence_dbxref x dbxref [NORMALIZED] if ( $with && $ev->seq_acc ) { push @output, $ev->seq_acc; push @output, '|'; } ## Get rid of trailing '|'. pop @output if $output[$#output] eq '|'; push @output, "\t"; ## 9 Aspect association x term.term_type my $aspect = $term->type; if ( $aspect eq 'cellular_component' || $aspect eq 'C' || $aspect eq 'c' ) { push @output, 'C'; } elsif ( $aspect eq 'molecular_function' || $aspect eq 'F' || $aspect eq 'f' ) { push @output, 'F'; } elsif ( $aspect eq 'biological_process' || $aspect eq 'P' || $aspect eq 'p' ) { push @output, 'P'; } push @output, "\t"; ## 10 DB_Object_Name gene_product.full_name if ( $object_name && $gp->full_name ) { push @output, $gp->full_name; } push @output, "\t"; ## 11 Synonym gene_product x gene_product_synonym my $syn_listref = $gp->synonym_list; if ( $syn_listref && @$syn_listref && $object_synonym ) { foreach my $syn (@$syn_listref) { push @output, $syn; push @output, '|'; } ## Get rid of trailing '|'. pop @output if $output[$#output] eq '|'; } push @output, "\t"; ## 12 DB_Object_type gene_product.type_id x term.name [TBA] push @output, $gp->type; push @output, "\t"; ## 13 Taxon gene_product x species.ncbi_taxa_id push @output, 'taxon:'; push @output, $gp->species->ncbi_taxa_id; push @output, "\t"; ## 14 Date association.assoc_date push @output, $assoc->assocdate; push @output, "\t"; ## 15 Assigned_by association.source_db_id x db.name ## TODO/NOTE: Hidden API. push @output, $assoc->assigned_by || ''; push @output, "\n"; } } my $fh = $self->{OUT} || undef; if( defined($fh) && scalar(@output) > 0 ){ print $fh join '', @output; } } # #################### # =head2 write_association_list # Usage - $ga_out->write_association(); # Returns - None # Args -term=>$term, # -qualifier=>1 or 0, # optional, default 1. # -with=>1 or 0, # optional, default 1. # -object_name=>1 or 0, # optional, default 1. # -object_synonym=>1 or 0, # optional, default 1. # =cut # sub write_association_list{ # my $self = shift; # my ($assoc_listref, # $qualifier, $with, $object_name, $object_synonym) = # rearrange([qw(assoc_listref # qualifier with object_name object_synonym)], @_); # $qualifier = $qualifier || 1; # $with = $with || 1; # $object_name = $object_name || 1; # $object_synonym = $object_synonym || 1; # my @output = (); # foreach my $assoc (@$assoc_listref) { # ## Get evidence info. # my $ev_listref = $assoc->evidence_list; # foreach my $ev (@$ev_listref) { # ## Get gp info. # my $gp = $assoc->gene_product; # ## 1 DB gene_product x dbxref.xref_dbname # push @output, $gp->speciesdb; # push @output, "\t"; # ## 2 DB_Object_ID gene_product x dbxref.xref_xref_key # push @output, $gp->acc; # push @output, "\t"; # ## 3 DB_Object_Symbol gene_product.symbol # push @output, $gp->symbol; # push @output, "\t"; # ## 4 NOT association.is_not # ## Qualifiers association_qualifier # if ( $qualifier ) { # if ( $assoc->is_not ) { # push @output, 'NOT'; # #}else{ # #push @output, 'IS'; # } # } # push @output, "\t"; # ## 5 GOid association x term.acc # #push @output, $term->acc; # push @output, "\t"; # ## 6 DB:Reference association x evidence.dbxref_id # my $xref_listref = $ev->xref_list; # foreach my $xref ( @$xref_listref ) { # push @output, $xref->dbname . ':' . $xref->xref_key; # push @output, '|'; # } # ## Get rid of trailing '|'. # pop @output if $output[$#output] eq '|'; # push @output, "\t"; # ## 7 Evidence association x evidence.code # push @output, $ev->code; # push @output, "\t"; # ## 8 With/From evidence.seq_acc [DENORMALIZED] # ## evidence x evidence_dbxref x dbxref [NORMALIZED] # if ( $with && $ev->seq_acc ) { # push @output, $ev->seq_acc; # push @output, '|'; # } # ## Get rid of trailing '|'. # pop @output if $output[$#output] eq '|'; # push @output, "\t"; # ## 9 Aspect association x term.term_type # #my $aspect = $term->type; # my $aspect = 'foo'; # if ( $aspect eq 'cellular_component' || # $aspect eq 'C' || $aspect eq 'c' ) { # push @output, 'C'; # } elsif ( $aspect eq 'molecular_function' || # $aspect eq 'F' || $aspect eq 'f' ) { # push @output, 'F'; # } elsif ( $aspect eq 'biological_process' || # $aspect eq 'P' || $aspect eq 'p' ) { # push @output, 'P'; # } # push @output, "\t"; # ## 10 DB_Object_Name gene_product.full_name # if ( $object_name && $gp->full_name ) { # push @output, $gp->full_name; # } # push @output, "\t"; # ## 11 Synonym gene_product x gene_product_synonym # my $syn_listref = $gp->synonym_list; # if ( $syn_listref && @$syn_listref && $object_synonym ) { # foreach my $syn (@$syn_listref) { # push @output, $syn; # push @output, '|'; # } # ## Get rid of trailing '|'. # pop @output if $output[$#output] eq '|'; # } # push @output, "\t"; # ## 12 DB_Object_type gene_product.type_id x term.name [TBA] # push @output, $gp->type; # push @output, "\t"; # ## 13 Taxon gene_product x species.ncbi_taxa_id # push @output, 'taxon:'; # push @output, $gp->species->ncbi_taxa_id; # push @output, "\t"; # ## 14 Date association.assoc_date # push @output, $assoc->assocdate; # push @output, "\t"; # ## 15 Assigned_by association.source_db_id x db.name # ## TODO/NOTE: Hidden API. # push @output, $assoc->assigned_by; # push @output, "\n"; # } # } # my $fh = $self->{OUT}; # print $fh join '', @output; # } 1; go-perl-0.15/GO/IO/ObanOwl.pm000644 000765 000024 00000027730 11615622160 015444 0ustar00cjmstaff000000 000000 # $Id: ObanOwl.pm,v 1.1 2007/05/14 18:29:39 cmungall Exp $ # # This GO module is maintained by Brad Marshall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::IO::ObanOwl; =head1 NAME GO::IO::ObanOwl; =head1 SYNOPSIS my $apph = GO::AppHandle->connect(-d=>$go, -dbhost=>$dbhost); my $term = $apph->get_term({acc=>00003677}); #### ">-" is STDOUT my $out = new FileHandle(">-"); my $xml_out = GO::IO::XML->new(-output=>$out); $xml_out->start_document(); $xml_out->draw_term($term); $xml_out->end_document(); OR: my $apph = GO::AppHandle->connect(-d=>$go, -dbhost=>$dbhost); my $term = $apph->get_node_graph(-acc=>00003677, -depth=>2); my $out = new FileHandle(">-"); my $xml_out = GO::IO::XML(-output=>$out); $xml_out->start_document(); $xml_out->draw_node_graph($term, 3677); $xml_out->end_document(); =head1 DESCRIPTION Utility class to dump GO terms as xml. Currently you just call start_ducument, then draw_term for each term, then end_document. If there's a need I'll add draw_node_graph, draw_node_list, etc. =cut use strict; use GO::Utils qw(rearrange); use XML::Writer; =head2 new Usage - my $xml_out = GO::IO::XML->new(-output=>$out); Returns - None Args - Output FileHandle Initializes the writer object. To write to standard out, do: my $out = new FileHandle(">-"); my $xml_out = new GO::IO::XML(-output=>$out); =cut sub new { my $class = shift; my $self = {}; bless $self, $class; my ($out) = rearrange([qw(output)], @_); $out = new FileHandle(">-") unless $out; my $gen = new XML::Writer(OUTPUT=>$out); $self->{writer} = $gen; $gen->setDataMode(1); $gen->setDataIndent(4); return $self; } =head2 xml_header Usage - $xml_out->xml_header; Returns - None Args - None start_document prints the "Content-type: text/xml" statement. If creating a cgi script, you should call this before start_document. =cut sub xml_header { my $self = shift; print "Content-type: text/xml\n\n"; } =head2 start_document Usage - $xml_out->start_document(-timestamp=>$time); Returns - None Args - optional: timestamp string, pre-formatted start_ducument takes care of the fiddly bits like xml declarations, namespaces, etc. It draws the initial tags and leaves the document ready to add go:term nodes. =cut sub start_document { my $self = shift; my ($timestamp) = rearrange([qw(timestamp)], @_); $self->{writer}->xmlDecl("UTF-8"); $self->{writer}->startTag('rdf:RDF', 'xmlns:oban'=>'http://www.berkeleybop.org/ontologies/oban/alpha#', 'xmlns:rdf'=>'http://www.w3.org/1999/02/22-rdf-syntax-ns#', 'xmlns:rdfs' => 'http://www.w3.org/2000/01/rdf-schema#', 'xmlns:owl' => 'http://www.w3.org/2002/07/owl#', 'xmlns:xsd' => 'http://www.w3.org/2001/XMLSchema#', 'xmlns:obo_rel' => 'http://www.obofoundry.org/ro/ro.owl#', 'xmlns:obo' => 'http://purl.org/obo/owl'); } =head2 end_document Usage - $xml_out->end_document(); Call this when done. =cut sub end_document{ my $self = shift; $self->{writer}->endTag('rdf:RDF'); } =head2 draw_node_graph Usage - $xml_out->draw_node_graph(-graph=>$graph); Returns - None Args -graph=>$node_graph, -focus=>$acc, ## optional -show_associations=>"yes" or "no" ## optional =cut sub draw_node_graph { my $self = shift; my ($graph, $focus, $show_associations, $show_terms, $show_xrefs) = rearrange([qw(graph focus show_associations show_terms show_xrefs)], @_); foreach my $term (@{$graph->get_all_nodes}) { $self->draw_term(-term=>$term, -graph=>$graph, # -focus=>$is_focus, -show_associations=>$show_associations, -show_terms=>$show_terms, -show_xrefs=>$show_xrefs ); } } sub write_all { my $self = shift; my ($terms, $graph, $focus, $show_associations, $show_terms, $show_xrefs) = rearrange([qw(terms graph focus show_associations show_terms show_xrefs)], @_); $self->start_document; if (!$terms) { $terms = $graph->get_all_terms; } foreach my $term (@$terms) { $self->draw_term(-term=>$term, -graph=>$graph, # -focus=>$is_focus, -show_associations=>$show_associations, -show_terms=>$show_terms, -show_xrefs=>$show_xrefs ); } } sub __is_focus { my $self = shift; my ($node_list, $term) = rearrange([qw(node_list term)], @_); foreach my $node (@$node_list) { if ($node->acc eq $term->acc) { return "yes"; } } return "no"; } =head2 draw_term Usage - $xml_out->draw_term(); Returns - None Args -term=>$term, -graph=>$graph, -is_focus=>"yes" or "no", ## optional -show_associations=>"yes" or "no", ## optional -show_terms=>"yes" or "no", ## optional, just draws associations =cut sub draw_term { my $self = shift; my ($term, $graph, $is_focus, $show_associations, $show_terms, $show_xrefs) = rearrange([qw(term graph focus show_associations show_terms show_xrefs)], @_); $show_terms = $show_terms || ""; $is_focus = $is_focus || ""; $show_xrefs = $show_xrefs || ""; if ($show_terms ne 'no') { $self->startTag('owl:Class', #'focus'=>'yes', 'rdf:about'=>$self->class_uri($term->public_acc), ); $self->dataElement('oboInOwl:identifier', $term->acc); $self->dataElement('rdfs:label', $term->name); my $syn_idx = $term->synonyms_by_type_idx || {}; foreach my $scope (keys %$syn_idx) { my $syn_prop = $self->_synonym_property($scope); foreach my $syn (@{$syn_idx->{$scope}}) { $self->startTag($syn_prop); $self->startTag('oboInOwl:Synonym'); $self->dataElement('rdfs:label', $syn); $self->endTag; $self->endTag; } } if ($term->definition) { $self->startTag('oboInOwl:hasDefinition'); $self->startTag('oboInOwl:Definition'); $self->dataElement('rdfs:label', $term->definition ); $self->dataElement('go:definition', $term->definition); $self->draw_dbxref($_) foreach @{$self->definition_dbxref_list || []}; $self->endTag; $self->endTag; }; if ($term->comment) { $self->dataElement('rdfs:comment', $term->comment); }; if (defined $graph) { foreach my $rel (sort by_acc1 @{$graph->get_parent_relationships($term->acc)}) { my $to = $rel->acc1; if (lc($rel->type) eq 'is_a') { $self->emptyTag('rdfs:subClassOf', 'rdf:resource'=>$self->class_uri($to)); } else { $self->startTag('rdfs:subClassOf'); $self->startTag('owl:Restriction'); $self->emptyTag('owl:onProperty', 'rdf:resource'=>$self->class_uri($to)); # assume OBO REL defs; always existential $self->emptyTag('owl:someValuesFrom', 'rdf:resource'=>$self->class_uri($to)); $self->endTag; $self->endTag; } } } if ($show_xrefs ne 'no') { if ($term->dbxref_list) { $self->draw_dbxref($_) foreach @{$self->dbxref_list || []}; } } $self->endTag('owl:Class'); if (defined ($term->selected_association_list)) { foreach my $selected_ass (sort by_gene_product_symbol @{$term->selected_association_list}) { $self->__draw_association($selected_ass, 1, $term); } } if ($show_associations && $show_associations eq 'yes') { foreach my $ass (sort by_gene_product_symbol @{$term->association_list}) { $self->__draw_association($ass, 0, $term); } } } else { if (defined ($term->selected_association_list)) { foreach my $selected_ass (sort by_gene_product_symbol @{$term->selected_association_list}) { $self->__draw_association($selected_ass, 1, $term); } } } } sub by_acc1 { lc($a->acc1) cmp lc($b->acc1); } sub by_xref_key { lc($a->xref_key) cmp lc($b->xref_key); } sub by_gene_product_symbol { lc($a->gene_product->symbol) cmp lc($b->gene_product->symbol); } sub draw_dbxref { my $self = shift; my $dbxref = shift; $self->startTag('oboInOwl:hasDbXref'); $self->startTag('oboInOwl:DbXref'); $self->dataElement('rdfs:label',$dbxref->as_str); $self->endTag; $self->endTag; } sub __draw_association { my $self = shift; my $ass = shift; my $term = shift; my $rdf_id = 'http://www.geneontology.org/go#'.$ass->go_public_acc; $self->startTag('oban:Annotation'); # bNode foreach my $ev (@{$ass->evidence_list}) { $self->startTag('oban:has_evidence'); $self->startTag('rdf:Description'); $self->dataElement('rdf:type', 'rdf:about'=>$self->class_uri($ev->code)); foreach my $with (@{$ev->seq_xref_list || []}) { $self->dataElement('oban:with', 'rdf:about'=>$self->class_uri($with->as_str)); } foreach my $pub (@{$ev->pub_xref_list || []}) { $self->dataElement('oban:has_source', 'rdf:about'=>$self->class_uri($pub->as_str)); } $self->startTag('oban:posits'); $self->startTag('rdf:Statement'); $self->dataElement('rdf:subject', 'rdf:about'=>$self->data_uri($ass->gene_product->dbxref->as_str)); $self->dataElement('rdf:predicate', 'rdf:about'=>'oban:has_role'); # TODO $self->dataElement('rdf:object', 'rdf:about'=>$self->class_uri($term->public_acc)); $self->endTag; $self->endTag; $self->endTag; $self->endTag; } $self->endTag; } sub class_uri { my $self = shift; my $id = shift; my ($db,@rest) = split(/:/,$id); if (@rest) { my $local = join(':',@rest); return sprintf("http://purl.org/obo/owl/%s#%s_%s",$db,$db,$local); } } =head2 sub characters This is simply a wrapper to XML::Writer->characters which strips out any non-ascii characters. =cut sub characters { my $self = shift; my $string = shift; if ($string) { $self->{writer}->characters($self->__strip_non_ascii($string)); } } =head2 sub dataElement This is simply a wrapper to XML::Writer->dataElement which strips out any non-ascii characters. =cut sub dataElement { my $self = shift; my $tag = shift; my $content = shift; $self->{writer}->dataElement($tag, $self->__strip_non_ascii($content)); } sub startTag { my $self = shift; $self->{writer}->startTag(@_); } sub endTag { my $self = shift; $self->{writer}->endTag(@_); } sub emptyTag { my $self = shift; $self->{writer}->emptyTag(@_); } sub __strip_non_ascii { my $self = shift; my $string = shift; $string =~ s/\P{IsASCII}//g; return $string; } sub __make_go_from_acc { my $self = shift; my $acc = shift; return $acc; } 1; go-perl-0.15/GO/IO/OBDXML.pm000644 000765 000024 00000024554 11615622160 015071 0ustar00cjmstaff000000 000000 # $Id: OBDXML.pm,v 1.3 2006/11/28 01:08:46 sjcarbon Exp $ # # This GO module is maintained by Seth Carbon # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself. ## ## TODO: Should the links to classes from instances be put in? ## TODO: Should I add the links to 'obd:with' from the ev instances? ## WARNING: Written using version XML::Writer 6.0.1. Earlier version ## may not work. ## package GO::IO::OBDXML; =head1 NAME GO::IO::OBDXML; =head1 SYNOPSIS my $apph = GO::AppHandle->connect(-d=>$go, -dbhost=>$dbhost); my $term = $apph->get_term({acc=>00003677}); #### ">-" is STDOUT my $out = new FileHandle(">-"); my $xml_out = GO::IO::OBDXML->new(-output=>$out); $xml_out->start_document(); $xml_out->draw_term($term); $xml_out->end_document(); OR: my $apph = GO::AppHandle->connect(-d=>$go, -dbhost=>$dbhost); my $term = $apph->get_node_graph(-acc=>00003677, -depth=>2); my $out = new FileHandle(">-"); my $xml_out = GO::IO::OBDXML(-output=>$out); $xml_out->start_document(); $xml_out->draw_graph($term, 3677); $xml_out->end_document(); =head1 DESCRIPTION Utility class to dump GO terms as OBD XML. Currently you just call start_ducument, then draw_term for each term, then end_document. =cut use strict; use GO::Utils qw(rearrange); use XML::Writer; #################### =head2 new Usage - my $xml_out = GO::IO::OBDXML->new(-output=>$out); Returns - None Args - Output FileHandle Initializes the writer object. To write to standard out, do: my $out = new FileHandle(">-"); my $xml_out = new GO::IO::OBDXML(-output=>$out); =cut sub new { my $class = shift; my $self = {}; bless $self, $class; my ($out) = rearrange([qw(output)], @_); $out = new FileHandle(">-") unless $out; my $gen = new XML::Writer(OUTPUT=>$out); $self->{writer} = $gen; $gen->setDataMode(1); $gen->setDataIndent(2); return $self; } #################### =head2 cgi_header Usage - $xml_out->cgi_header; Returns - None Args - None cgi_header prints the "Content-type: text/xml" statement. If creating a CGI script, you should call this before start_document. =cut sub cgi_header { my $self = shift; print "Content-type: text/xml\n\n"; } #################### =head2 start_document Usage - $xml_out->start_document; Returns - None Args - None start_document takes care of the fiddly bits like xml declarations, namespaces, etc. It draws the initial tags and leaves the document ready to add go:term nodes. =cut sub start_document { my $self = shift; $self->{writer}->xmlDecl('utf-8'); $self->{writer}->startTag('graphset', 'xmlns'=> 'http://www.bioontology.org/obd/schema/obd-generic'); } #################### =head2 start_graph Usage - $xml_out->start_graph; Returns - None Args - None start_graph opens a new graph segment. =cut sub start_graph { my $self = shift; $self->{writer}->startTag('graph'); } #################### =head2 end_document Usage - $xml_out->end_document; Call this when done. =cut sub end_document{ my $self = shift; $self->{writer}->endTag('graphset'); } #################### =head2 end_graph Usage - $xml_out->end_graph; Call this when done a graph segment. =cut sub end_graph { my $self = shift; $self->{writer}->endTag('graph'); } #################### =head2 draw_node_graph Usage - $xml_out->draw_node_graph(-graph=>$graph); Returns - None Args -graph=>$graph, -show_associations=>'yes' or 'no', # optional, default 'yes'. -show_terms=>'yes' or 'no', # optional, default 'yes'. -show_xrefs=>'yes' or 'no', # optional, default 'yes'. -show_evidence=>'yes' or 'no', # optional, default 'yes'. =cut ## sub draw_graph { my $self = shift; my ($graph, $show_associations, $show_evidence, $show_terms, $show_xrefs) = rearrange([qw(graph show_associations show_evidence show_terms show_xrefs)], @_); foreach my $term (@{$graph->get_all_nodes}) { $self->draw_term(-term=>$term, -graph=>$graph, -show_associations=>$show_associations, -show_terms=>$show_terms, -show_xrefs=>$show_xrefs, -show_evidence=>$show_evidence ); } } #################### =head2 draw_term Usage - $xml_out->draw_term(); Returns - None Args -term=>$term, -graph=>$graph, # optional -show_associations=>'yes' or 'no', # optional, default 'yes'. -show_terms=>'yes' or 'no', # optional, default 'yes'. -show_xrefs=>'yes' or 'no', # optional, default 'yes'. -show_evidence=>'yes' or 'no', # optional, default 'yes'. =cut sub draw_term { my $self = shift; my ($term, $graph, $show_associations, $show_terms, $show_xrefs, $show_evidence) = rearrange([qw(term graph show_associations show_terms show_xrefs show_evidence)], @_); $show_terms = $show_terms || 'yes'; $show_xrefs = $show_xrefs || 'yes'; $show_associations = $show_associations || 'yes'; $show_evidence = $show_evidence || 'yes'; ## We are going to show the terms in the graph. if ($show_terms eq 'yes') { ## Draw term node. Way of drawing depends on $show_ xrefs. if( $show_xrefs eq 'yes'){ $self->__draw_node(-id=>$term->acc, -metadata=>'class', -label=>$term->name, -source=>$term->type, -description=>$term->definition, -aliases=>$term->synonym_list, -xrefs=>$term->dbxref_list); }else{ $self->__draw_node(-id=>$term->acc, -metadata=>'class', -label=>$term->name, -source=>$term->type, -description=>$term->definition, -aliases=>$term->synonym_list); } ## Write out the links from the term if a graph was given. if( defined $graph ){ my $rel_list = $graph->get_relationships($term->acc); foreach my $rel ( @$rel_list ){ $self->__draw_link(-subject=>$rel->subject_acc, -object=>$rel->object_acc, -predicate=>$rel->type); } } } ## Write out associations if not nixed. if( $show_associations eq 'yes') { my $assoc_list = $term->association_list; foreach my $assoc (@$assoc_list) { ## Get gp and draw gp node. my $gp = $assoc->gene_product; $self->__draw_node(-id=>$gp->acc, -metadata=>'class', -label=>$gp->symbol, -source=>$gp->type, -description=>$gp->full_name, -aliases=>$gp->synonym_list); ## Link the gp to the term. $self->__draw_link(-subject=>$gp->acc, -object=>$term->acc, -predicate=>'obd:has_role', -id=>$gp->acc . '_obd:has_role_' . $term->acc); ## Make an ID for the node. my $ann_inst_id = 'AIID:' . $assoc->id; ## Create an annotation instance node. $self->__draw_node(-id=>$ann_inst_id, -metadata=>'instance'); ## Link annotation node to gp/term link. $self->__draw_link(-subject=>$ann_inst_id, -object=>$gp->acc . '_obd:has_role_' . $term->acc, -predicate=>'obd:posits', -id=>$ann_inst_id . '_obd:posits_assoc'); ## Now we'll deal with all the evidence... if( $show_evidence eq 'yes') { my $ev_list = $assoc->evidence_list; foreach my $ev (@$ev_list) { ## Make an ID for the node. #my $ev_node_id = $ev->xref->xref_key; my $ev_node_id = 'ENID:' . $ev->id; ## Draw term node. Way of drawing depends on $show_ xrefs. if( $show_xrefs eq 'yes'){ $self->__draw_node(-id=>$ev_node_id, -metadata=>'instance', -label=>$ev->code, -xrefs=>$ev->xref_list); }else{ ## Create evidence instance node w/o xrefs. $self->__draw_node(-id=>$ev_node_id, -metadata=>'instance', -label=>$ev->code); } ## Create link from annotation instance to evidence instance. $self->__draw_link(-subject=>$ann_inst_id, -object=>$ev_node_id, -predicate=>'obd:has_evidence'); } } } } } ## sub __draw_node { my $self = shift; my ($id, $metadata, $label, $source, $description, $aliases, $xrefs) = rearrange([qw(id metadata label source description aliases xrefs)], @_); # Open node. if( $metadata ){ $self->{writer}->startTag('node', 'id'=>$id, 'metadata'=>$metadata); }else{ $self->{writer}->startTag('node', 'id'=>$id); } # Populate the node with: label, source, and description. if( $label ){ $self->{writer}->startTag('label'); $self->{writer}->cdata($label); $self->{writer}->endTag('label'); } if( $source ){ $self->{writer}->emptyTag('source', 'about'=>$source); } if( $description ){ $self->__draw_sit(-tag=>'description', -label=>$description); } # Add any aliases. if( $aliases ){ foreach my $alias ( @$aliases ) { $self->__draw_sit(-tag=>'alias', -label=>$alias, -scope=>'exact'); } } # Add any xrefs. if( $xrefs ){ foreach my $xref ( @$xrefs ) { $self->__draw_xref(-about=>$xref->xref_key, -context=>$xref->dbname); } } # Close node. $self->{writer}->endTag('node'); } ## sub __draw_link { my $self = shift; my ($subject, $object, $predicate, $id) = rearrange([qw(subject object predicate id)], @_); if( $id ){ $self->{writer}->startTag('link', 'id'=>$id); }else{ $self->{writer}->startTag('link'); } $self->{writer}->emptyTag('predicate', 'about'=>$predicate); $self->{writer}->emptyTag('subject', 'about'=>$subject); $self->{writer}->emptyTag('object', 'about'=>$object); $self->{writer}->endTag('link'); } ## BUG: xrefs not implemented here. sub __draw_sit { my $self = shift; my ($tag, $label, $id, $scope, $type) = rearrange([qw(tag label id scope type)], @_); my %attr_hash; if( $id ){ $attr_hash{'id'} = $id; } if( $scope ){ $attr_hash{'scope'} = $scope; } if( $type ){ $attr_hash{'type'} = $type; } $self->{writer}->startTag($tag, %attr_hash); $self->{writer}->startTag('label'); $self->{writer}->cdata($label); $self->{writer}->endTag('label'); $self->{writer}->endTag($tag); } ## sub __draw_xref { my $self = shift; my ($about, $context) = rearrange([qw(about context)], @_); if( $context ){ $self->{writer}->startTag('xref', 'context'=>$context); }else{ $self->{writer}->startTag('xref'); } $self->{writer}->emptyTag('linkref', 'about'=>$about); $self->{writer}->endTag('xref'); } 1; go-perl-0.15/GO/IO/RDFXML.pm000644 000765 000024 00000027745 11615622160 015105 0ustar00cjmstaff000000 000000 # $Id: RDFXML.pm,v 1.12 2008/08/14 19:02:00 girlwithglasses Exp $ # # This GO module is maintained by Brad Marshall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself package GO::IO::RDFXML; =head1 NAME GO::IO::RDFXML; =head1 SYNOPSIS my $apph = GO::AppHandle->connect(-d=>$go, -dbhost=>$dbhost); my $term = $apph->get_term({acc=>00003677}); #### ">-" is STDOUT my $out = new FileHandle(">-"); my $xml_out = GO::IO::XML->new(-output=>$out); $xml_out->start_document(); $xml_out->draw_term($term); $xml_out->end_document(); OR: my $apph = GO::AppHandle->connect(-d=>$go, -dbhost=>$dbhost); my $term = $apph->get_node_graph(-acc=>00003677, -depth=>2); my $out = new FileHandle(">-"); my $xml_out = GO::IO::XML(-output=>$out); $xml_out->start_document(); $xml_out->draw_node_graph($term, 3677); $xml_out->end_document(); =head1 DESCRIPTION Utility class to dump GO terms as xml. Currently you just call start_ducument, then draw_term for each term, then end_document. If there's a need I'll add draw_node_graph, draw_node_list, etc. =cut use strict; use GO::Utils qw(rearrange); use XML::Writer; =head2 new Usage - my $xml_out = GO::IO::XML->new(-output=>$out); Returns - None Args - Output FileHandle Initializes the writer object. To write to standard out, do: my $out = new FileHandle(">-"); my $xml_out = new GO::IO::XML(-output=>$out); =cut sub new { my $class = shift; my $self = {}; bless $self, $class; my ($out) = rearrange([qw(output)], @_); $out = new FileHandle(">-") unless $out; my $gen = new XML::Writer(OUTPUT=>$out); $self->{writer} = $gen; $gen->setDataMode(1); $gen->setDataIndent(4); return $self; } =head2 xml_header Usage - $xml_out->xml_header; Returns - None Args - None start_document prints the "Content-type: text/xml" statement. If creating a cgi script, you should call this before start_document. =cut sub xml_header { my $self = shift; print "Content-type: text/xml\n\n"; } =head2 start_document Usage - $xml_out->start_document(-timestamp=>$time); Returns - None Args - optional: timestamp string, pre-formatted start_ducument takes care of the fiddly bits like xml declarations, namespaces, etc. It draws the initial tags and leaves the document ready to add go:term nodes. =cut sub start_document { my $self = shift; my ($timestamp) = rearrange([qw(timestamp)], @_); $self->{writer}->xmlDecl("UTF-8"); $self->{writer}->doctype("go:go", '-//Gene Ontology//Custom XML/RDF Version 2.0//EN', 'http://www.geneontology.org/dtd/go.dtd'); $self->{writer}->startTag('go:go', 'xmlns:go'=>'http://www.geneontology.org/dtds/go.dtd#', 'xmlns:rdf'=>'http://www.w3.org/1999/02/22-rdf-syntax-ns#'); if (defined ($timestamp)) { #$self->{writer}->emptyTag('go:version', 'timestamp'=>$timestamp); } $self->{writer}->startTag('rdf:RDF'); } =head2 end_document Usage - $xml_out->end_document(); Call this when done. =cut sub end_document{ my $self = shift; $self->{writer}->endTag('rdf:RDF'); $self->{writer}->endTag('go:go'); } =head2 draw_node_graph Usage - $xml_out->draw_node_graph(-graph=>$graph); Returns - None Args -graph=>$node_graph, -focus=>$acc, ## optional -show_associations=>"yes" or "no" ## optional =cut sub draw_node_graph { my $self = shift; my ($graph, $focus, $show_associations, $show_terms, $show_xrefs) = rearrange([qw(graph focus show_associations show_terms show_xrefs)], @_); my $is_focus; foreach my $term (@{$graph->get_all_nodes}) { $is_focus = $self->__is_focus(-node_list=>$graph->focus_nodes, -term=>$term ); $self->draw_term(-term=>$term, -graph=>$graph, -focus=>$is_focus, -show_associations=>$show_associations, -show_terms=>$show_terms, -show_xrefs=>$show_xrefs ); } } sub __is_focus { my $self = shift; my ($node_list, $term) = rearrange([qw(node_list term)], @_); foreach my $node (@$node_list) { if ($node->acc eq $term->acc) { return "yes"; } } return "no"; } =head2 draw_term Usage - $xml_out->draw_term(); Returns - None Args -term=>$term, -graph=>$graph, -is_focus=>"yes" or "no", ## optional -show_associations=>"yes" or "no", ## optional -show_terms=>"yes" or "no", ## optional, just draws associations =cut sub draw_term { my $self = shift; my ($term, $graph, $is_focus, $show_associations, $show_terms, $show_xrefs) = rearrange([qw(term graph focus show_associations show_terms show_xrefs)], @_); $show_terms = $show_terms || ""; $is_focus = $is_focus || ""; $show_xrefs = $show_xrefs || ""; if ($show_terms ne 'no') { if ($is_focus eq "yes") { $self->{writer}->startTag('go:term', 'focus'=>'yes', 'rdf:about'=>'http://www.geneontology.org/go#'.$term->public_acc, # 'n_associations'=>$term->n_deep_products ); } else { $self->{writer}->startTag('go:term', 'rdf:about'=>'http://www.geneontology.org/go#'.$term->public_acc, #'n_associations'=>$term->n_deep_products ); } $self->{writer}->startTag('go:accession'); $self->characters($term->acc); $self->{writer}->endTag('go:accession'); $self->dataElement('go:name', $term->name); if ($term->synonym_list) { foreach my $syn (sort @{$term->synonym_list}) { $self->{writer}->startTag('go:synonym'); $self->characters($syn); $self->{writer}->endTag('go:synonym'); } } if ($term->definition) { $self->dataElement('go:definition', $term->definition); }; if ($term->comment) { $self->dataElement('go:comment', $term->comment); }; if (defined $graph) { foreach my $rel (sort by_acc1 @{$graph->get_parent_relationships($term->acc)}) { if (lc($rel->type) eq 'partof') { $self->{writer}->emptyTag('go:part-of', 'rdf:resource'=>"http://www.geneontology.org/go#" .$self->__make_go_from_acc($rel->acc1)); } else { $self->{writer}->emptyTag("go:".$rel->type, 'rdf:resource'=>"http://www.geneontology.org/go#" .$self->__make_go_from_acc($rel->acc1)); } } } if ($show_xrefs ne 'no') { if ($term->dbxref_list) { if (scalar(@{$term->dbxref_list}) > 0) { foreach my $xref (sort by_xref_key @{$term->dbxref_list}) { $self->{writer}->startTag('go:dbxref', 'rdf:parseType'=>'Resource'); $self->{writer}->startTag('go:database_symbol'); $self->characters($xref->xref_dbname); $self->{writer}->endTag('go:database_symbol'); $self->{writer}->startTag('go:reference'); $self->characters($xref->xref_key); $self->{writer}->endTag('go:reference'); $self->{writer}->endTag('go:dbxref'); } } } } } if (defined ($term->selected_association_list)) { foreach my $selected_ass (sort by_gene_product_symbol @{$term->selected_association_list}) { # next if $selected_ass->is_not(); # skip negative associations $self->__draw_association($selected_ass, 1); } } if ($show_associations && $show_associations eq 'yes') { foreach my $ass (sort by_gene_product_symbol @{$term->association_list}) { # next if $selected_ass->is_not(); # skip negative associations $self->__draw_association($ass, 0); } } if ($show_terms ne 'no') { $self->{writer}->endTag('go:term'); } } sub by_acc1 { lc($a->acc1) cmp lc($b->acc1); } sub by_xref_key { lc($a->xref_key) cmp lc($b->xref_key); } sub by_gene_product_symbol { lc($a->gene_product->symbol) cmp lc($b->gene_product->symbol); } sub __draw_association { my $self = shift; my $ass = shift; my $is_selected = shift; my $rdf_id = 'http://www.geneontology.org/go#'.$ass->go_public_acc; # if the association is a 'NOT' one, use the tag 'negative_association' my $ass_type = 'go:association'; if ( $ass->is_not() ) { $ass_type = 'go:negative_association'; } if ($is_selected) { $self->{writer}->startTag($ass_type, 'selected'=>'yes', 'rdf:parseType'=>'Resource' ); } else { $self->{writer}->startTag($ass_type, 'rdf:parseType'=>'Resource' ); } foreach my $ev (@{$ass->evidence_list}) { $self->{writer}->startTag('go:evidence', 'evidence_code'=>$ev->code); if (defined($ev->xref)) { $self->{writer}->startTag('go:dbxref', 'rdf:parseType'=>'Resource'); $self->{writer}->startTag('go:database_symbol'); $self->characters($ev->xref->xref_dbname); $self->{writer}->endTag('go:database_symbol'); $self->{writer}->startTag('go:reference');##, 'type'=>$ev->xref->xref_keytype); $self->characters($ev->xref->xref_key); $self->{writer}->endTag('go:reference'); $self->{writer}->endTag('go:dbxref'); } $self->{writer}->endTag('go:evidence'); } $self->{writer}->startTag('go:gene_product', 'rdf:parseType'=>'Resource'); $self->dataElement('go:name', $ass->gene_product->symbol); $self->{writer}->startTag('go:dbxref', 'rdf:parseType'=>'Resource'); $self->dataElement('go:database_symbol', $ass->gene_product->speciesdb); $self->dataElement('go:reference', $ass->gene_product->acc); $self->{writer}->endTag('go:dbxref'); $self->{writer}->endTag('go:gene_product'); # add the qualifiers (if any) if ($ass->qualifier_list) { foreach my $q (@{$ass->qualifier_list}) { $self->{writer}->startTag('go:association_qualifier','rdf:parseType'=>'Resource'); $self->dataElement('go:qualifier_name', $q->name); $self->{writer}->endTag('go:association_qualifier'); } } $self->{writer}->endTag($ass_type); } =head2 sub characters This is simply a wrapper to XML::Writer->characters which strips out any non-ascii characters. =cut sub characters { my $self = shift; my $string = shift; if ($string) { $self->{writer}->characters($self->__strip_non_ascii($string)); } } =head2 sub dataElement This is simply a wrapper to XML::Writer->dataElement which strips out any non-ascii characters. =cut sub dataElement { my $self = shift; my $tag = shift; my $content = shift; $self->{writer}->dataElement($tag, $self->__strip_non_ascii($content)); } ## WARNING: it is though that this code does not correctly get all ## problem encoded characters; deprecated for __strip_non_ascii. sub __strip_non_ascii_old { my $self = shift; my $string = shift; $string =~ s/\P{IsASCII}//g; return $string; } ## NOTE: taken from GO::Parsers::go_assoc_parser ## Meant to solve slippery encoding issues, see: ## "Re: [Software-group] RDF XML go full" ## As demonstrated in the code below, this does not actually remove unicode ## characters, but rather seems to force them down. # push @INC, "/home/sjcarbon/local/src/svn/geneontology/go-dev/trunk/go-perl"; # use GO::IO::RDFXML; # use FileHandle; # $out = new FileHandle(">-"); # $x = GO::IO::RDFXML->new(-output=>$out); # $foo = "asdf" # $bar = "okテストay" # print $x->__strip_non_ascii($foo); # print $x->__strip_non_ascii($bar); sub __strip_non_ascii { my $self = shift; $_ = shift; # UNICODE causes problems for XML and DB # delete 8th bit tr [\200-\377] [\000-\177]; # see 'man perlop', section on tr/ # weird ascii characters should be excluded tr/\0-\10//d; # remove weird characters; ascii 0-8 # preserve \11 (9 - tab) and \12 (10-linefeed) tr/\13\14//d; # remove weird characters; 11,12 # preserve \15 (13 - carriage return) tr/\16-\37//d; # remove 14-31 (all rest before space) tr/\177//d; # remove DEL character return $_; } sub __make_go_from_acc { my $self = shift; my $acc = shift; return $acc; } 1; go-perl-0.15/GO/IO/XML.pm000644 000765 000024 00000000071 11615622160 014530 0ustar00cjmstaff000000 000000 package GO::IO::XML; use base qw(GO::IO::RDFXML); 1; go-perl-0.15/GO/Handlers/abstract_prolog_writer.pm000644 000765 000024 00000003040 11615622160 022101 0ustar00cjmstaff000000 000000 package GO::Handlers::abstract_prolog_writer; use base qw(GO::Handlers::base Exporter); use strict; sub out { my $self = shift; $self->print("@_"); } sub cmt { my $self = shift; my $cmt = shift; $self->out(" % $cmt") if $cmt; return; } sub prologquote { my $s = shift; my $force = shift; if (ref($s)) { if (ref($s) ne 'HASH') { sprintf("[%s]", join(',',map{prologquote($_)} @$s)); } else { my @keys = keys %$s; if (@keys == 1) { my $functor = $keys[0]; my $args = $s->{$functor}; sprintf("$functor(%s)", join(', ', map {prologquote($_)} @$args)); } else { warn "@keys != 1 - ignoring"; } } } else { $s = '' unless defined $s; if ($s =~ /^[\-]?[0-9]+$/ && !$force) { return $s; } $s =~ s/\'/\'\'/g; "'$s'"; } } sub nl { shift->print("\n"); } sub fact { my $self = shift; my $pred = shift; my @args = @{shift||[]}; my $cmt = shift; $self->out(sprintf("$pred(%s).", join(', ', map {prologquote($_)} @args))); $self->cmt($cmt); $self->nl; } # ensure all fields are quoted sub factq { my $self = shift; my $pred = shift; my @args = @{shift||[]}; my $cmt = shift; $self->out(sprintf("$pred(%s).", join(', ', map {prologquote($_,1)} @args))); $self->cmt($cmt); $self->nl; } 1; go-perl-0.15/GO/Handlers/abstract_sql_writer.pm000644 000765 000024 00000001151 11615622160 021377 0ustar00cjmstaff000000 000000 package GO::Handlers::abstract_sql_writer; use base qw(Data::Stag::Writer Exporter); use strict; sub out { my $self = shift; print "@_"; } sub cmt { my $self = shift; my $cmt = shift; $self->out(" % $cmt") if $cmt; return; } sub sqlquote { my $s = shift; $s =~ s/\'/\\\'/g; "'$s'"; } sub nl { shift->print("\n"); } sub fact { my $self = shift; my $pred = shift; my @args = @{shift||[]}; my $cmt = shift; $self->out(sprintf("INSERT INTO $pred VALUES (%s); ", join(', ', map {sqlquote($_)} @args))); $self->cmt($cmt); $self->nl; } 1; go-perl-0.15/GO/Handlers/base.pm000644 000765 000024 00000005267 11615622160 016247 0ustar00cjmstaff000000 000000 # $Id: base.pm,v 1.5 2004/11/24 02:28:00 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself =head1 NAME GO::Handlers::base - =head1 SYNOPSIS use GO::Handlers::base =cut =head1 DESCRIPTION Default Handler, other handlers inherit from this class this class catches events (start, end and body) and allows the subclassing module to intercept these. unintercepted events get pushed into a tree See GO::Parser for details on parser/handler architecture =head1 PUBLIC METHODS - =cut package GO::Handlers::base; use strict; use Exporter; use Carp; use GO::Model::Root; use vars qw(@ISA @EXPORT_OK @EXPORT); use base qw(Data::Stag::Writer Exporter); @EXPORT_OK = qw(lookup); sub EMITS { () } sub CONSUMES { qw( header source term typedef prod ) } sub is_transform { 0 } =head2 strictorder Usage - $handler->strictorder(1); Returns - Args - boolean accessor; if set, then terms passed must be in order =cut sub strictorder { my $self = shift; $self->{_strictorder} = shift if @_; return $self->{_strictorder}; } sub proddb { my $self = shift; $self->{_proddb} = shift if @_; return $self->{_proddb}; } sub ontology_type { my $self = shift; $self->{_ontology_type} = shift if @_; return $self->{_ontology_type}; } sub root_to_be_added { my $self = shift; $self->{_root_to_be_added} = shift if @_; return $self->{_root_to_be_added}; } # DEPRECATED sub messages { my $self = shift; $self->{_messages} = shift if @_; return $self->{_messages}; } *error_list = \&messages; sub message { my $self = shift; push(@{$self->messages}, shift); } sub lookup { my $tree = shift; my $k = shift; # use Data::Dumper; # print Dumper $tree; # confess; if (!ref($tree)) { confess($tree); } my @v = map {$_->[1]} grep {$_->[0] eq $k} @$tree; if (wantarray) { return @v; } $v[0]; } #sub print { # my $self = shift; # print "@_"; #} sub print {shift->addtext(@_)} sub printf { my $self = shift; my $fmt = shift; $self->addtext(sprintf($fmt, @_)); } sub throw { my $self = shift; my @msg = @_; confess("@msg"); } sub warn { my $self = shift; my @msg = @_; warn("@msg"); } sub dbxref2str { my $self = shift; my $dbxref = shift; return $dbxref->sget_dbname . ':' . $dbxref->sget_acc; } sub xslt { my $self = shift; $self->{_xslt} = shift if @_; return $self->{_xslt}; } 1; go-perl-0.15/GO/Handlers/go_def.pm000644 000765 000024 00000002325 11615622160 016550 0ustar00cjmstaff000000 000000 # $Id: go_def.pm,v 1.3 2005/03/22 04:51:08 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself =head1 NAME GO::Handlers::go_def - =head1 SYNOPSIS use GO::Handlers::go_def =cut =head1 DESCRIPTION =head1 PUBLIC METHODS - =cut # makes objects from parser events package GO::Handlers::go_def; use GO::Parsers::ParserEventNames; use Data::Stag qw(:all); use base qw(GO::Handlers::base); use strict; sub e_term { my $self = shift; my $t = shift; my $n = stag_get($t, NAME); my $def = stag_get($t, DEF); if ($def) { $self->tag(term => $n); $self->tag(goid => stag_sget($t, ID)); $self->tag(definition => stag_sget($def, DEFSTR)); $self->tag(definition_reference => stag_sget($_,DBNAME).':'.stag_sget($_,ACC)) foreach stag_get($def, DBXREF); $self->tag(comment => stag_sget($t, COMMENT)); $self->print("\n"); } return; } sub tag { my $self = shift; my ($t, $v) = @_; return unless $v; $self->printf("%s: %s\n", $t, $v); return; } 1; go-perl-0.15/GO/Handlers/go_ont.pm000644 000765 000024 00000001256 11615622160 016614 0ustar00cjmstaff000000 000000 # $Id: go_ont.pm,v 1.1 2004/01/27 23:52:24 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself =head1 NAME GO::Handlers::go_ont - =head1 SYNOPSIS use GO::Handlers::go_ont =cut =head1 DESCRIPTION =head1 PUBLIC METHODS - =cut # makes objects from parser events package GO::Handlers::go_ont; use base qw(GO::Handlers::obj); use strict; sub e_obo { my $self = shift; my $g = $self->g; $g->to_text_output(-fmt=>'gotext', -fh=>$self->safe_fh, ); } 1; go-perl-0.15/GO/Handlers/go_xref.pm000644 000765 000024 00000001440 11615622160 016753 0ustar00cjmstaff000000 000000 # $Id: go_xref.pm,v 1.1 2004/01/27 23:52:24 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself =head1 NAME GO::Handlers::go_xref - =head1 SYNOPSIS use GO::Handlers::go_xref =cut =head1 DESCRIPTION =head1 PUBLIC METHODS - =cut # makes objects from parser events package GO::Handlers::go_xref; use base qw(GO::Handlers::base); use strict; sub e_term { my $self = shift; my $t = shift; my $name = $t->sget_name; my $id = $t->sget_id; foreach ($t->get_xref_analog) { $self->printf("%s:%s > $name ; $id\n", $_->sget_dbname, $_->sget_acc); } return; } 1; go-perl-0.15/GO/Handlers/godb_prestore.pm000644 000765 000024 00000022771 11615622160 020172 0ustar00cjmstaff000000 000000 # $Id: godb_prestore.pm,v 1.9 2005/03/22 22:38:11 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself =head1 NAME GO::Handlers::godb_prestore - transforms OBO XML to GODB XML =head1 SYNOPSIS =head1 DESCRIPTION This is a transform for turning OBO XML events into XML events that are isomorphic to the GO Database (ie XML element names match GO DB table and column names). This transformation is suitable for direct loading into a db using the generic DBIx::DBStag loader (see http://stag.sourceforge.net) This perl transform may later be replaced by an XSL transform (for speed) =head1 PUBLIC METHODS - =cut # makes objects from parser events package GO::Handlers::godb_prestore; use Data::Stag qw(:all); use base qw(GO::Handlers::base); use strict; use Carp; use Data::Dumper; use Data::Stag qw(:all); use GO::Parsers::ParserEventNames; # XML constants for elements sub EMITS { qw( dbstag_metadata source_audit term gene_product ) } sub is_transform { 1 } sub dbstag_mapping { return([ "type/term_synonym.synonym_type_id=term.id", "term1/term2term.term1_id=term.id", "term2/term2term.term2_id=term.id", "type/term2term.relationship_type_id=term.id", "type/gene_product.type_id=term.id", "source_db/association.source_db_id=db.id", ] ); } sub e_source { my $self = shift; my $source = shift; stag_name($source, 'source_audit'); return $source; } sub e_header { my ($self, $hdr) = @_; [dbstag_metadata=>[ map {[map=>$_]} @{$self->dbstag_mapping} ] ]; } sub e_term { my ($self, $term) = @_; my $id = stag_get($term, ID) || $self->throw($term->sxpr); warn("DEPRECATED - use XSL instead"); stag_set($term, ACC, $id); my $name_h = $self->{name_h}; my $name = stag_get($term, NAME); my $ont = stag_get($term, NAMESPACE); my $is_obs = stag_get($term, IS_OBSOLETE); my @extra_events = (); my @is_as = stag_get($term, IS_A); my @rels = (stag_get($term, RELATIONSHIP), map {[relationship=>[[to=>$_],[type=>'is_a']]]} @is_as); if ($is_obs) { my $obs = "obsolete_$ont"; @rels = ([relationship=>[[to=>$obs], [type=>'is_a']]]); if ($obs eq $id) { # place root obs under root @rels = ([relationship=>[[to=>$self->{__added_root} || 'all'], [type=>'is_a']]]); } if (!$self->{"__added_obsnode_$ont"}) { $self->{"__added_obsnode_$ont"} = $obs; push(@extra_events, $self->e_term(Data::Stag->new(term=>[[id=>$obs], [name=>$obs], [namespace=>$ont], [is_obsolete=>1], ] ) ) ); } # in go format, obsolete nodes may have 'fake' parentage; # either to root (for root obsolete term) or to root # obsolete term; # here we replace this with $obs } my @cvrels = map { my $to = stag_get($_=>TO); my $type = stag_get($_=>TYPE); Data::Stag->new(term2term=>[ [term1=>[[term=>[[acc=>$to]]]]], [term2=>[[term=>[[acc=>$id]]]]], _type($type, 'relationship'), ] ); } @rels; if ($name && !@cvrels) { # add 'all' node; # only for named node (to avoid adding root when parsing defs) # and when there are no parents # GO DB relies on having one single root node my $all = $self->{__added_root}; if ($all) { } else { my $alldef = 'This term is the most general term possible.'; $all = 'all'; $self->{__added_root} = $all; @cvrels = (Data::Stag->new(term=>[ [acc=>'all'], [name=>'all'], [term_definition=>[ [term_definition=>$alldef], ]], [is_root=>1], [term_type=>'universal'], ]) ); } push(@cvrels, Data::Stag->new(term2term=>[ [term1=>[[term=>[[acc=>$all]]]]], [term2=>[[term=>[[acc=>$id]]]]], _type('is_a', 'relationship'), ] ) ); } my $def = stag_get($term, DEF); my @alt_ids = stag_get($term, ALT_ID); my @syns = stag_get($term, SYNONYM); my $comment = stag_find($term, COMMENT); # comment can be under term or def my $t = time; my $nuterm = Data::Stag->new(term=> [ [acc=>$id], $name ? [NAME=>$name] : (),, $ont ? [term_type=>$ont] : (), defined $is_obs ? [is_obsolete=>$is_obs && $is_obs ne 'false' ? 1:0] : (), $name ? [term_audit=>[ [term_loadtime=>$t] ]] : (), ] ); my @term_dbxrefs = map { Data::Stag->new(term_dbxref=>[[dbxref=>[_xref_stags($_)]]]) } stag_get($term, XREF_ANALOG); if ($def || $comment) { stag_set($nuterm, term_definition=> [ ($def ? [term_definition=>stag_sget($def, DEFSTR)]:()), ($comment ? [term_comment=>$comment] : ()), ]); if ($def) { push(@term_dbxrefs, Data::Stag->new(term_dbxref=>[[is_for_definition=>1], [dbxref=>[_xref_stags($_)]]])) foreach stag_get($def, DBXREF); } } stag_add($nuterm, TERM_DBXREF, $_) foreach @term_dbxrefs; stag_add($nuterm, term_synonym=> [ [acc_synonym=>$_], [term_synonym=>$_], _type('acc','synonym'), ]) foreach @alt_ids; foreach (@syns) { my $type = stag_sget($_, TYPE); stag_add($nuterm, term_synonym=> [ $type ? _type($type,'synonym') : (), [term_synonym=>stag_sget($_, SYNONYM_TEXT)] ]); } return (@extra_events,$nuterm,@cvrels); } sub e_typedef { my ($self, $t) = @_; my $id = stag_get($t, ID); return Data::Stag->new(term=>[ [acc=>$id], [name=>$id] ]); } sub e_prod { my ($self, $prod) = @_; my $proddb = stag_sget($self->up(1), PRODDB); my $full_name = stag_sget($prod, PRODNAME); my @gpstags = ( [symbol=>stag_sget($prod, PRODSYMBOL)], ($full_name ? [full_name=>$full_name] : ()), [dbxref=>[[xref_dbname=>$proddb], [xref_key=>stag_sget($prod, PRODACC)]]], [species=>[[ncbi_taxa_id=>stag_sget($prod, PRODTAXA)]]], _type(stag_sget($prod,TYPE) || 'gene', 'gene_product'), (map { [gene_product_synonym=>[[product_synonym=>$_]]] } stag_get($prod,PRODSYN)), ); my @assocs = stag_get($prod,ASSOC); foreach my $assoc (@assocs) { my @quals = stag_sget($assoc,QUALIFIER); my $source_db = stag_sget($assoc, SOURCE_DB); push(@gpstags, [association=>[ [term=>[[acc=>stag_sget($assoc,TERMACC)]]], [is_not=>stag_sget($assoc,IS_NOT)], (map { [association_qualifier=>[[term=>[[acc=>$_]]]]] } @quals), # ($qual ? [qualifier=>[[term=>[[acc=>$qual]]]]]: ()), ($source_db ? [source_db=>[[db=>[[name=>$source_db]]]]] : ()), [assocdate=>stag_sget($assoc,ASSOCDATE)], (map { my @withs = stag_get($_,WITH); [evidence=>[ [code=>stag_sget($_,EVCODE)], (scalar(@withs) ? [seq_acc=>join('|',@withs)] : ()), _xref(stag_sget($_,REF)), scalar(@withs) ? [evidence_dbxref=>[ (map { _xref($_) } @withs) ]] : (), ]] } stag_get($assoc,EVIDENCE)) ] ] ); } return Data::Stag->new(gene_product=>[@gpstags]); } sub _xref_stags { my $x = shift; ([xref_key=>stag_sget($x,ACC)], [xref_dbname=>stag_sget($x,DBNAME)]); } sub _type { my $type = shift; my $ont = shift; [type=>[[term=>[ [acc=>$type], [name=>$type], [term_type=>$ont], ] ]] ]; } sub _xref { my $id = shift; my ($dbname,$acc); if ($id =~ /(\w+):(\S+)/) { $dbname = $1; $acc = $2; } else { $dbname = ''; $acc = $id; } return [dbxref=>[ [xref_dbname=>$dbname], [xref_key=>$acc] ] ]; } 1; go-perl-0.15/GO/Handlers/lexanalysis.pm000644 000765 000024 00000002275 11615622160 017665 0ustar00cjmstaff000000 000000 # stag-handle.pl -p GO::Parsers::GoOntParser -m function/function.ontology package GO::Handlers::lexanalysis; use base qw(Data::Stag::Writer Exporter); use strict; sub e_term { my ($self, $term) = @_; my $name = $term->get_name; my $ont = $term->get_ontology; return if $term->get_is_obsolete; my @words = split(/[\W_]/, $name); for (my $i=0; $i < @words; $i++) { # my $w = $words[$i]; # $self->fact(windex => [$ont, $i, ($i-@words)+1, $w, $name]); for (my $j = 0; $j<3; $j++) { if ($i+$j < @words) { my @set = @words[($i..($i+$j))]; my $size = $j+1; $self->fact("w$size"=> [$i, ($i+$j+1)-@words, @set, $ont, $name]); } } } $self->nl; return; } sub out { my $self = shift; print "@_"; } sub cmt { my $self = shift; my $cmt = shift; $self->out(" % $cmt") if $cmt; return; } sub prologquote { my $s = shift; $s =~ s/\'/\\\'/g; "'$s'"; } sub nl { shift->print("\n"); } sub fact { my $self = shift; my $pred = shift; my @args = @{shift||[]}; my $cmt = shift; $self->out(sprintf("$pred(%s).", join(', ', map {prologquote($_)} @args))); $self->cmt($cmt); $self->nl; } 1; go-perl-0.15/GO/Handlers/lexanalysis2sql.pm000644 000765 000024 00000000202 11615622160 020453 0ustar00cjmstaff000000 000000 package GO::Handlers::lexanalysis2sql; use base qw(GO::Handlers::abstract_sql_writer GO::Handlers::lexanalysis); use strict; 1; go-perl-0.15/GO/Handlers/obj.pm000644 000765 000024 00000024406 12043562446 016111 0ustar00cjmstaff000000 000000 # $Id: obj.pm,v 1.24 2008/01/17 20:08:14 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself =head1 NAME GO::Handlers::obj - parses GO files into GO object model =head1 SYNOPSIS use GO::Handlers::obj =cut =head1 DESCRIPTION =head1 PUBLIC METHODS =cut # makes objects from parser events package GO::Handlers::obj; use Data::Stag qw(:all); use GO::Parsers::ParserEventNames; use base qw(GO::Handlers::base); use strict qw(vars refs); my $TRACE = $ENV{GO_TRACE}; sub init { my $self = shift; $self->SUPER::init; use GO::ObjCache; my $apph = GO::ObjCache->new; $self->{apph} = $apph; use GO::Model::Graph; my $g = $self->apph->create_graph_obj; $self->{g} = $g; return; } =head2 graph Usage - my $terms = $obj_handler->graph->get_all_terms; Synonym - g Synonym - ontology Returns - GO::Model::Graph object Args - as files are parsed, objects are created; depending on what kind of datatype is being parsed, the classes of the created objects will be different - eg GO::Model::Term, GO::Model::Association etc the way to access all of thses is through the top level graph object eg $parser = GO::Parser->new({handler=>'obj'}); $parser->parse(@files); my $graph = $parser->graph; =cut sub g { my $self = shift; $self->{g} = shift if @_; return $self->{g}; } *graph = \&g; *ontology = \&g; sub apph { my $self = shift; $self->{apph} = shift if @_; return $self->{apph}; } sub root_term { my $self = shift; $self->{_root_term} = shift if @_; return $self->{_root_term}; } # 20041029 - not currently used sub add_root { my $self = shift; my $g = $self->g; my $root = $self->apph->create_term_obj; $root->name('root'); $root->acc('root'); $g->add_term($root); $self->root_term($root); $self->root_to_be_added(1); $root; } # -- HANDLER METHODS -- sub e_obo { my $self = shift; my $g = $self->g; return (); } sub e_typedef { my $self = shift; my $t = shift; $self->stanza('Typedef', $t); } sub e_term { my $self = shift; my $t = shift; $self->stanza('Term', $t); } sub e_instance { my $self = shift; my $t = shift; $self->stanza('Instance', $t); } sub stanza { my $self = shift; my $stanza = lc(shift); my $tree = shift; my $acc = stag_get($tree, ID); if (!$acc) { $self->throw( "NO ACC: $@\n" ); } my $term; eval { $term = $self->g->get_term($acc); }; if ($@) { $self->throw( "ARG:$@" ); } # no point adding term twice; we # assume the details are the same return $term if $term && $self->strictorder; $term = $self->apph->create_term_obj; if ($stanza eq 'typedef') { $term->is_relationship_type(1); } if ($stanza eq 'instance') { $term->is_instance(1); } my %h = (); foreach my $sn (stag_kids($tree)) { my $k = $sn->name; my $v = $sn->data; if ($k eq RELATIONSHIP) { my $obj = stag_get($sn, TO); $self->g->add_relationship($obj, $term->acc, stag_get($sn, TYPE)); } elsif ($k eq IS_A) { $self->g->add_relationship($v, $term->acc, IS_A); } elsif ($k eq INSTANCE_OF) { $self->g->add_relationship($v, $term->acc, INSTANCE_OF); } elsif ($k eq DEF) { my $defstr = stag_get($sn, DEFSTR); my @xrefs = stag_get($sn, DBXREF); $term->definition($defstr); $term->add_definition_dbxref($self->dbxref($_)) foreach @xrefs; } elsif ($k eq SYNONYM) { my $synstr = stag_get($sn, SYNONYM_TEXT); my $type = stag_find($sn, 'scope'); my @xrefs = stag_get($sn, DBXREF); $term->add_synonym_by_type($type ? lc($type) : '', $synstr); # $term->add_definition_dbxref($_) foreach @xrefs; } elsif ($k eq ALT_ID) { $term->add_alt_id($v); } elsif ($k eq CONSIDER) { $term->add_consider($v); } elsif ($k eq REPLACED_BY) { $term->add_replaced_by($v); } elsif ($k eq ALT_ID) { $term->add_alt_id($v); } elsif ($k eq XREF_ANALOG || $k eq XREF) { my $xref = $self->apph->create_xref_obj(stag_pairs($sn)); $term->add_dbxref($xref); } elsif ($k eq XREF_UNKNOWN) { my $xref = $self->apph->create_xref_obj(stag_pairs($sn)); $term->add_dbxref($xref); } elsif ($k eq ID) { $term->acc($v); } elsif ($k eq NAMESPACE) { $term->namespace($v); } elsif ($k eq NAME) { $term->name($v); } elsif ($k eq SUBSET) { $term->add_subset($v); } elsif ($k eq COMMENT) { $term->comment($v); } elsif ($k eq IS_ROOT) { $term->is_root($v); } elsif ($k eq BUILTIN) { # ignore } elsif ($k eq PROPERTY_VALUE) { # ignore } elsif ($k eq IS_METADATA_TAG) { # ignore } elsif ($k eq IS_OBSOLETE) { $term->is_obsolete($v); } elsif ($k eq IS_TRANSITIVE || $k eq IS_SYMMETRIC || $k eq IS_ANTI_SYMMETRIC || $k eq IS_REFLEXIVE || $k eq INVERSE_OF || $k eq TRANSITIVE_OVER || $k eq DOMAIN || $k eq RANGE) { my $m = lc($k); $term->$m($v); } elsif ($term->can("add_$k")) { # CONVENIENCE METHOD - map directly to object method warn("add method for $k"); my $m = "add_$k"; $term->$m($v); } elsif ($term->can($k)) { warn("add method for $k"); # CONVENIENCE METHOD - map directly to object method $term->$k($v); } elsif ($k eq INTERSECTION_OF) { my $rel = stag_get($sn, TYPE); my $obj = stag_get($sn, TO); my $isect = [$rel,$obj]; my $ns = stag_find($sn, 'namespace'); if (!$rel) { shift @$isect; } my $ldef = $term->logical_definition; if (!$ldef) { $ldef = $self->apph->create_logical_definition_obj(); $term->logical_definition($ldef); } $ldef->namespace($ns) if ($ns); $ldef->add_intersection($isect); } elsif ($k eq UNION_OF) { my $obj = stag_get($sn, TO); $term->add_equivalent_to_union_of_term($obj); } elsif ($k eq DISJOINT_FROM) { $term->add_disjoint_from_term($v); } else { # warn("add method for $k"); $term->stag->add($k, $v); # $self->throw("don't know what to do with $k"); # print "no $k\n"; } } if ($self->root_to_be_added && !$term->is_obsolete && $stanza eq 'term') { my $parents = $self->g->get_parent_relationships($term->acc); if (!@$parents) { my $root = $self->root_term || $self->throw("no root term"); $self->g->add_relationship($root, $term->acc, IS_A); } } # $term->type($self->{ontology_type}) unless $term->type; if (!$term->name) { # warn("no name; using acc ".$term->acc); # $term->name($term->acc); } $self->g->add_term($term); printf STDERR "Added term %s %s\n", $term->acc, $term->name if $TRACE; # $term; return (); } sub dbxref { my $self = shift; my $x = shift; $self->apph->create_xref_obj(stag_pairs($x)) } sub e_proddb { my $self = shift; $self->proddb(shift->data); return; } sub e_prod { my $self = shift; my $tree = shift; my $g = $self->g; my $prod = $self->apph->create_gene_product_obj({symbol=>stag_sget($tree, PRODSYMBOL), type=>stag_sget($tree, PRODTYPE), full_name=>stag_sget($tree, PRODNAME), speciesdb=>$self->proddb, }); my @syns = stag_get($tree, PRODSYN); $prod->xref->xref_key(stag_sget($tree, PRODACC)); $prod->synonym_list(\@syns); my @assocs = stag_get($tree, ASSOC); my $taxid = stag_get($tree, PRODTAXA); my $species; if ($taxid) { $species = $self->apph->create_species_obj({ncbi_taxa_id=>$taxid}); $prod->species($species); } foreach my $assoc (@assocs) { my $acc = stag_get($assoc, TERMACC); if (!$acc) { $self->message("no accession given"); next; } my $t = $g->get_term($acc); if (!$t) { if (!$self->strictorder) { $t = $self->apph->create_term_obj({acc=>$acc}); $self->g->add_term($t); } else { $self->message("no such term $acc"); next; } } my $aspect = stag_get($assoc, ASPECT); if ($aspect) { $t->set_namespace_by_code($aspect); } my @evs = stag_get($assoc, EVIDENCE); my $ao = $self->apph->create_association_obj({gene_product=>$prod, is_not=>stag_sget($assoc, IS_NOT), }); my $date = stag_get($assoc,ASSOCDATE); $ao->assocdate($date) if $date; my $assigned_by = stag_get($assoc,SOURCE_DB); $ao->assigned_by($assigned_by) if $assigned_by; foreach my $ev (@evs) { my $eo = $self->apph->create_evidence_obj({ code=>stag_sget($ev, EVCODE), }); my @seq_xrefs = stag_get($ev, WITH), my @refs = stag_get($ev, REF); map { $eo->add_seq_xref($_) } @seq_xrefs; map { $eo->add_pub_xref($_) } @refs; $ao->add_evidence($eo); } $t->add_association($ao); } return; } 1; go-perl-0.15/GO/Handlers/obj_storable.pm000644 000765 000024 00000000762 11615622160 017775 0ustar00cjmstaff000000 000000 package GO::Handlers::obj_storable; use base qw(GO::Handlers::obj); use strict; use FileHandle; use Storable qw(store_fd); sub e_obo { my $self = shift; my $fh = $self->fh; if (!$fh) { my $f = $self->file; if ($f) { $fh = FileHandle->new(">$f") || $self->throw("cannot write to: $f"); } else { $self->throw("$self requires file or fh"); } } my $g = $self->g; store_fd $g, $fh; return; } 1; go-perl-0.15/GO/Handlers/obj_yaml.pm000644 000765 000024 00000000274 11615622160 017122 0ustar00cjmstaff000000 000000 package GO::Handlers::obj_yaml; use base qw(GO::Handlers::obj); use strict; use YAML; sub e_obo { my $self = shift; my $g = $self->g; $self->print(Dump $g); return; } 1; go-perl-0.15/GO/Handlers/obo.pm000644 000765 000024 00000000103 11615622160 016074 0ustar00cjmstaff000000 000000 package GO::Handlers::obo; use base qw(GO::Handlers::obo_text); 1; go-perl-0.15/GO/Handlers/obo_godb_flat.pm000644 000765 000024 00000024655 11615622160 020117 0ustar00cjmstaff000000 000000 # $Id: obo_godb_flat.pm,v 1.13 2008/10/30 17:50:55 benhitz Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself =head1 NAME GO::Handlers::obo_godb_flat - =head1 SYNOPSIS use GO::Handlers::obo_godb_flat =cut =head1 DESCRIPTION transforms OBO XML events into flat tables for mysql to load part of the association bulk loading pipeline =head1 PUBLIC METHODS - =cut # makes objects from parser events package GO::Handlers::obo_godb_flat; use Data::Stag qw(:all); use Data::Dumper; use GO::Parsers::ParserEventNames; use base qw(GO::Handlers::base); use strict qw(vars refs); use constant DELIMITER => "\t"; # separates fields sub init { my $self = shift; $self->SUPER::init(); $self->{tables} = { dbxref => [ qw(id xref_dbname xref_key xref_keytype xref_desc) ], # must append many dbxrefs term => [ qw(id name term_type acc is_obsolete is_root is_relation) ], # must append SO terms, qualifiers gene_product => [ qw(id symbol dbxref_id species_id type_id full_name) ], association => [ qw(id term_id gene_product_id is_not role_group assocdate source_db_id) ], db => [ qw(id name fullname datatype generic_url url_syntax url_example uri_prefix) ], # last 4 all null in current load evidence => [ qw(id code association_id dbxref_id seq_acc) ], association_qualifier => [ qw(id association_id term_id value) ], # must append species => [ qw(id ncbi_taxa_id common_name lineage_string genus species parent_id left_value right_value taxonomic_rank) ], # linking tables gene_product_synonym => [ qw(gene_product_id product_synonym)], evidence_dbxref => [ qw(evidence_id dbxref_id) ], association_species_qualifier => [ qw(id association_id species_id) ], }; $self->{fhs} = { map (("$_.txt" => 0), keys %{$self->{tables}}) }; $self->{pk} = { map (($_ => 0), keys %{$self->{tables}} ) }; } sub apph { my $self = shift; $self->{apph} = shift if @_; return $self->{apph}; } sub _obo_escape { my $s=shift; $s =~ s/\\/\\\\/; $s =~ s/([\{\}])/\\$1/g; $s; } sub safe { my $word = shift; $word =~ s/ /_/g; $word =~ s/\-/_/g; $word =~ s/\'/prime/g; $word =~ tr/a-zA-Z0-9_//cd; $word =~ s/^([0-9])/_$1/; $word; } sub quote { my $word = shift; #$word =~ s/,/\\,/g; ## no longer required $word =~ s/\"/\\\"/g; "\"$word\""; } sub e_prod { my $self = shift; my $prod = shift; my $proddb = $self->up_to('dbset')->get_proddb; # $self->file('gene_product.txt'); done in add_gene_product my $gp_id = $self->add_gene_product($prod, $proddb); my @assocs = $prod->get_assoc; for my $assoc (@assocs) { # first dump the ASSOCIATION table $self->dump_table('association', [ ++$self->{pk}{association}, $self->get_term_id($assoc->get_termacc), $gp_id, stag_get($assoc, IS_NOT), '\N', # role_group current always NULL $assoc->sget_assocdate, $self->get_sourcedb_id($assoc->sget_source_db) ]); # now the qualifiers for my $qual ($assoc->get_qualifier) { $self->dump_table('association_qualifier', [ ++$self->{pk}{association_qualifier}, $self->{pk}{association}, $self->get_term_id($qual, 'association_qualifier'), '\N', # value is currently always NULL ]); } # get species qualifier for dual taxon species for my $species_qual ($assoc->get_species_qualifier) { $self->dump_table('association_species_qualifier', [ ++$self->{pk}{association_species_qualifier}, $self->{pk}{association}, $self->get_taxon_id($species_qual), ]); } # now evidence and evidence dbxref for my $ev ($assoc->get_evidence) { # prioritize PMIDs my ($ref) = grep {$_ =~ /^PMID/} $ev->get_ref(); if (!$ref) { $ref = $ev->sget_ref; } $self->dump_table('evidence', [ ++$self->{pk}{evidence}, $ev->sget_evcode, $self->{pk}{association}, $self->get_dbxref_id($ref), # only the first one here $ev->sget_with || "", # put only the first one here, I dunno why ]); for my $ref ($ev->get_ref) { next; # skip whole loop until we figure this out. $self->dump_table('evidence_dbxref', [ $self->{pk}{evidence}, $self->get_dbxref_id($ref), ]); } for my $with ($ev->get_with) { $self->dump_table('evidence_dbxref', [ $self->{pk}{evidence}, $self->get_dbxref_id($with), ]); } } } } sub add_gene_product { my $self = shift; my $prod = shift; my $proddb = shift; my $acc = $prod->get_prodacc; if ($self->apph->dbxref2gpid_h->{uc($proddb)}->{uc($acc)}) { # check to see if we've already added it # unique key for gene product is actually dbxref_id, but need the gp_id } else { # warn "$proddb, $acc, does not exist, creating"; # if not, write a line to gene_product.txt # new dbxref_id is added by get_dbxref_id. $self->dump_table('gene_product', [ ++$self->{pk}{gene_product}, $prod->sget_prodsymbol, $self->get_dbxref_id($proddb, $acc), $self->get_taxon_id($prod->get_prodtaxa), # '\N', # currently no secondary species ids $self->get_term_id($prod->get_prodtype, 'sequence'), $prod->sget_prodname || "", # that should be full name. ]); $self->apph->dbxref2gpid_h->{uc($proddb)}->{uc($acc)} = $self->{pk}{gene_product}; # add synoyms if necessary for my $syn ($prod->get_prodsyn) { $self->dump_table('gene_product_synonym', [ $self->{pk}{gene_product}, $syn, ]); } } return $self->apph->dbxref2gpid_h->{uc($proddb)}->{uc($acc)}; } sub get_dbxref_id { my $self = shift; my $dbname = shift; my $key = shift; if (!$key) { if ($dbname =~ /^([^:]+):+(\S+)/) { $dbname = $1; $key = $2; } } if (!$dbname || !$key) { warn "Must supply dbname and key: ($dbname),($key) attempting to write $self->{_file}\n"; return 0; } my $ucKey = uc($key); my $ucDb = uc($dbname); # mysql will handle case-insensitivity, but perl keeps seperate return $self->apph->dbxref2id_h->{$ucDb}->{$ucKey} if $self->apph->dbxref2id_h->{$ucDb}->{$ucKey}; # doesn't exist, add it to dbxref file and hash my $oldfile = $self->file; $self->dump_table('dbxref', [ ++$self->{pk}{dbxref}, $dbname, $key, '\N', '\N', ]); $self->file($oldfile); # set filename back $self->apph->dbxref2id_h->{$ucDb}->{$ucKey} = $self->{pk}{dbxref}; # return the id } sub get_term_id { # note this hopeless fails if 2 terms in different CVs have the same name! my $self = shift; my $term = shift; my $termType = shift; my $acc = shift || $term; $term = lc($term) unless $term =~ /^GO:/; # sometimes people use Gene instead of gene return $self->apph->acc2id_h->{$term} if $self->apph->acc2id_h->{$term}; die "No term type specified for $term, and not in hash" if !$termType; # doesn't exist, add it to dbxref file and hash my $oldfile = $self->file; $self->dump_table('term', [ ++$self->{pk}{term}, $term, $termType, $acc, 0, # never is_obsolete 0, # never is_root 0, # never a relationship type ]); $self->file($oldfile); # set file name back; $self->apph->acc2id_h->{$term} = $self->{pk}{term}; # return the id } sub get_sourcedb_id { my $self = shift; my $db = shift; return $self->apph->source2id_h->{uc($db)} if $self->apph->source2id_h->{uc($db)}; # doesn't exist, add it to file and hash my $oldfile = $self->file; $self->dump_table('db', [ ++$self->{pk}{db}, $db, '\N', '\N', '\N', '\N', '\N', '\N', ]); $self->file($oldfile); # set file name back $self->apph->source2id_h->{uc($db)} = $self->{pk}{db}; # return the id } sub get_taxon_id { my $self = shift; my $taxonId = shift || ''; return $self->apph->taxon2id_h->{$taxonId} if $self->apph->taxon2id_h->{$taxonId}; warn "Could not find id in db for taxon $taxonId, adding\n"; my $oldfile = $self->file; $self->dump_table('species', [ ++$self->{pk}{species}, $taxonId, '\N', # name unknown '\N', # lineage unknown '\N', # genuss unknown '\N', # species unknown '\N', # parent_id unknown '\N', # left unknown '\N', # right unknown '\N', # taxonomic rank unknown ]); $self->file($oldfile); # set file name back; $self->apph->taxon2id_h->{$taxonId} = $self->{pk}{species}; # return the id } sub file { # overrides Data::Stag::Writer file # with no arguments, returns current filename # with argument, sets file handle to file handle from {fhs} hash # if file handle not open, opens with safe_fh # returns "new" file name. my $self = shift; my $fh = $self->{fhs}; # hash of filehandles # create the keys if they don't exist, suppresses warnings # first time this is called, might be STDOUT or something $self->{_file} = undef unless $self->{_file}; $self->{_fh} = undef unless $self->{_fh}; if (@_) { $self->{_file} = shift; $self->{_fh} = undef; } if ( !$self->{_file} || !$fh->{$self->{_file}} ) { # print STDERR "opening file $self->{_file}...\n"; $fh->{$self->{_file}} = $self->safe_fh; } $self->{_fh} = $fh->{$self->{_file}} if exists $self->{_file}; return $self->{_file}; } sub close_files { my $self = shift; for my $fh (values %{$self->{fhs}}) { close($fh) if $fh && $fh ; } # close($self->{_fh}) if $self->{_fh}; } sub tables { $_[0]->{tables}; } sub dump_table { my $self = shift; my $tab = shift; my $fieldsRef = shift; die "Don't know anything about $tab" if ( !$self->{tables}->{$tab} || !scalar (@{ $self->{tables}->{$tab} }) ); die "Tried to write wrong number of fields $tab" if scalar(@$fieldsRef) != scalar(@{ $self->{tables}->{$tab} }); $self->file("$tab.txt"); $self->write(join(DELIMITER, @$fieldsRef)); $self->write("\n"); } 1; go-perl-0.15/GO/Handlers/obo_html.pm000644 000765 000024 00000001201 11615622160 017120 0ustar00cjmstaff000000 000000 # $Id: obo_html.pm,v 1.2 2004/09/07 23:51:03 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself =head1 NAME GO::Handlers::obo_html - =head1 SYNOPSIS use GO::Handlers::obo_html =cut =head1 DESCRIPTION =head1 PUBLIC METHODS - =cut # makes objects from parser events package GO::Handlers::obo_html; use base qw(GO::Handlers::xsl_base); use strict; our $d = `dirname $0`; chomp $d; $ENV{XSLT_FILE} = "$d/../xml/xsl/obo_html.xsl"; 1; go-perl-0.15/GO/Handlers/obo_sxpr.pm000644 000765 000024 00000000244 11615622160 017156 0ustar00cjmstaff000000 000000 # stag-handle.pl -p GO::Parsers::GoOntParser -m function/function.ontology package GO::Handlers::obo_sxpr; use base qw(Data::Stag::SxprWriter Exporter); 1; go-perl-0.15/GO/Handlers/obo_text.pm000644 000765 000024 00000025116 11615622160 017153 0ustar00cjmstaff000000 000000 # $Id: obo_text.pm,v 1.16 2008/01/22 23:54:45 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself =head1 NAME GO::Handlers::obo_text - =head1 SYNOPSIS use GO::Handlers::obo_text =cut =head1 DESCRIPTION transforms OBO XML events into OBO Text L =head1 PUBLIC METHODS - =cut # makes objects from parser events package GO::Handlers::obo_text; use Data::Stag qw(:all); use GO::Parsers::ParserEventNames; use base qw(GO::Handlers::base); use strict qw(vars refs); sub s_obo { my $self = shift; #$self->SUPER::s_obo(@_); return; } sub e_header { my $self = shift; my $hdr = shift; my $fmt = stag_get($hdr,'format-version'); $self->tag("format-version"=> (stag_sget($hdr,'format-version') || '1.2')); my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time); $self->tag('date'=>sprintf("%02d:%02d:%04d %02d:%02d", $mday,$mon+1,$year+1900,$hour,$min)); $self->tag('autogenerated-by'=>$0); foreach (stag_tnodes($hdr)) { $self->tag(stag_name($_), _obo_escape($_->data)); } my @sts = stag_get($hdr,'synonymtypedef'); foreach (@sts) { my $scope = stag_sget($_,'scope'); $self->tag(synonymtypedef => sprintf("%s \"%s\" %s", stag_sget($_,ID), stag_sget($_,NAME) || '', ($scope ? uc($scope) : ''))); } my @ssdefs = stag_get($hdr,'subsetdef'); foreach (@ssdefs) { $self->tag(subsetdef => sprintf("%s \"%s\"", stag_sget($_,ID), stag_sget($_,NAME))); } $self->{__emitted_header} = 1; $self->print("\n"); return; } sub e_typedef { my $self = shift; my $t = shift; $self->stanza('Typedef', $t); } sub e_term { my $self = shift; my $t = shift; if (!$self->{__emitted_header}) { $self->e_header(stag_new(HEADER,[])); } $self->stanza('Term', $t); } sub e_annotation { my $self = shift; my $t = shift; if (!$self->{__emitted_header}) { $self->e_header(stag_new(HEADER,[])); } $self->stanza('Annotation', $t); } sub e_instance { my $self = shift; my $t = shift; if (!$self->{__emitted_header}) { $self->e_header(stag_new(HEADER,[])); } $self->stanza('Instance', $t); } sub stanza { my $self = shift; my $stanza = shift; my $t = shift; $self->print("[$stanza]\n"); my @BOOLEAN_TAGS = ( IS_ANONYMOUS, IS_OBSOLETE, IS_CYCLIC, IS_TRANSITIVE, IS_SYMMETRIC, IS_ANTI_SYMMETRIC, IS_REFLEXIVE, IS_METADATA_TAG, ); my @TAGS = (ID, NAME, ALT_ID, NAMESPACE, DEF, COMMENT, SUBSET, IS_A , RELATIONSHIP, UNION_OF, INTERSECTION_OF, SYNONYM, PROPERTY_VALUE, XREF_ANALOG, XREF_UNKNOWN, 'object', @BOOLEAN_TAGS, ); my %IS_BOOLEAN = map { ($_=>1) } @BOOLEAN_TAGS; my @IGNORE = qw(is_root); foreach my $tag (@IGNORE) { stag_unset($t, $tag); } foreach my $tag (@TAGS) { my @vals = stag_get($t, $tag); next unless @vals; if ($tag eq DEF) { my $def = shift @vals; my $defstr = $def->get_defstr; my $qn = stag_sget($t, "$tag/@"); $self->tag(def => _obo_escape($defstr), [$def->get_dbxref], $qn); } elsif ($tag eq RELATIONSHIP) { $self->tag(relationship => sprintf("%s %s", $_->sget_type, $_->sget_to), undef, $_->sget('@')) foreach @vals; } elsif ($tag eq INTERSECTION_OF) { $self->tag(intersection_of => sprintf("%s %s", $_->sget_type, $_->sget_to), undef, $_->sget('@')) foreach @vals; } elsif ($tag eq UNION_OF) { $self->tag(union_of => sprintf("%s %s", $_->sget_type, $_->sget_to), undef, $_->sget('@')) foreach @vals; } elsif ($tag eq SYNONYM) { foreach my $syn (@vals) { my $type = $syn->sget('@/synonym_type'); my $scope = $syn->sget('@/scope'); my @vals = (quote($syn->sget_synonym_text)); push(@vals,uc($scope)) if $scope; push(@vals,$type) if $type; $self->tag($tag, join(' ',@vals), [$syn->get_dbxref]); } } elsif ($tag eq XREF_ANALOG) { $self->tag('xref', dbxref($_),undef,$_->sget('@')) foreach @vals; } elsif ($tag eq PROPERTY_VALUE) { foreach (@vals) { my $dt = $_->sget_datatype; if ($dt) { $self->tag('property_value' => sprintf("%s %s %s", $_->sget_type, quote($_->sget_value), $dt)); } else { $self->tag('property_value' => sprintf("%s %s", $_->sget_type, $_->sget_to)); } } } elsif ($tag eq 'object') { # experimental: obof1.3 $self->tag('object' => $self->obo_id(@vals)); } elsif ($IS_BOOLEAN{$tag}) { $self->tag($tag, $vals[0] ? "true" : "false"); } else { foreach (@vals) { if (ref($_)) { $self->tag($tag, $_->sget('.'),undef,$_->sget('@')) } else { $self->tag($tag, _obo_escape($_)); } } } stag_unset($t, $tag); } my @tnodes = stag_tnodes($t); $self->tag($_->name, _obo_escape($_->data)) foreach @tnodes; my @ntnodes = stag_ntnodes($t); if (@ntnodes) { print STDERR $_->xml foreach @ntnodes; $self->throw( "unknown elements"); } $self->print("\n"); } sub obo_id { my $self = shift; my $v = shift; if (ref($v)) { my $isect = $v->sget_intersection; if ($isect) { my @links = $isect->get_link; my @genus = grep {!$_->get_type} @links; my @diffs = grep {$_->get_type} @links; my $s = join('^', (map {$self->obo_id($_->sget_to)} @genus), (map { sprintf("%s(%s)",$_->sget_type,$self->obo_id($_->sget_to)) } @diffs)); return $s; } else { } } else { return $v; } } sub tag { my $self = shift; my ($t, $v, $xrefsr, $qualsr) = @_; my @xrefs = @{$xrefsr || []}; return unless defined $v; if ($t eq DEF) { $v=quote($v); } my $xrefl = ''; if ($xrefsr) { $xrefl = ' ['.join(', ', map { dbxref($_); } @xrefs).']'; } my $ql = ''; if ($qualsr) { my %qh = stag_pairs($qualsr); $ql = ' {'.join( ', ', map { "$_=".quote($qh{$_}) } keys %qh ).'}'; } $self->printf("%s: %s$xrefl$ql\n", $t, $v); return; } sub _obo_escape { my $s=shift; $s =~ s/\\/\\\\/; $s =~ s/([\{\}])/\\$1/g; $s; } sub dbxref { my $x = shift; if (ref($x)) { my $xref = $x->sget_dbname . ':' . $x->sget_acc; my $name = $x->sget_name; if (defined($name)) { $name =~ s/\"/\\\"/g; $xref." \"$name\""; } else { $xref; } } else { $x; } } sub safe { my $word = shift; $word =~ s/ /_/g; $word =~ s/\-/_/g; $word =~ s/\'/prime/g; $word =~ tr/a-zA-Z0-9_//cd; $word =~ s/^([0-9])/_$1/; $word; } sub quote { my $word = shift; #$word =~ s/,/\\,/g; ## no longer required $word =~ s/\"/\\\"/g; "\"$word\""; } # -- EXPERIMENTAL CODE -- # obo format for gene_assocs # we are hardcoding aspects here; this is OK, only for # gene_assoc file which is GO specific our %ASPECT_IDX = (F => 'has_activity', P => 'involved_in', C => 'localised_to' ); sub e_prod { my $self = shift; my $prod = shift; my $proddb = $self->up_to('dbset')->get_proddb; my $acc = $prod->get_prodacc; my $id = "$proddb:$acc"; my $type = $prod->get_prodtype || 'gene_product'; $self->print("!! ***************************** \n"); $self->print("!! Gene Product: $id \n"); $self->print("!! ***************************** \n"); $self->print("[$type]\n"); $self->tag(id=>$id); $self->tag(dbname=>$proddb); $self->tag(acc=>$acc); $self->tag(symbol=>$prod->sget_prodsymbol); $self->tag(name=>$prod->sget_prodname); $self->tag(synonym=>$_) foreach $prod->sget_prodsyn; $self->tag(has_taxon=>'NCBI:'.$prod->sget_prodtaxa); $self->print("\n"); my @assocs = $prod->get_assoc; foreach my $assoc (@assocs) { my $termacc = $assoc->get_termacc; my $aspect = $assoc->get_aspect; my $ns = $ASPECT_IDX{$aspect}; $self->print("[gene_product_annotation]\n"); $self->tag(involves_gene_product=>$id); $self->tag($ns=>$termacc); $self->tag($_=>'true') foreach $assoc->get_qualifier; $self->tag(date=>$assoc->sget_assocdate); $self->tag(source_db=>$assoc->sget_source_db); my @evs = $assoc->get_evidence; foreach my $ev (@evs) { $self->tag(has_evidence=>$ev->sget_evcode, $ev->get_ref); $self->tag(with=>$_) foreach $ev->get_with; } $self->print("\n"); } $self->print("!! //\n\n"); } sub dbxrefstr { } 1; go-perl-0.15/GO/Handlers/obo_xml.pm000644 000765 000024 00000000242 11615622160 016760 0ustar00cjmstaff000000 000000 # stag-handle.pl -p GO::Parsers::GoOntParser -m function/function.ontology package GO::Handlers::obo_xml; use base qw(Data::Stag::XMLWriter Exporter); 1; go-perl-0.15/GO/Handlers/owl.pm000644 000765 000024 00000010241 11615622160 016122 0ustar00cjmstaff000000 000000 # stag-handle.pl -p GO::Parsers::GoOntParser -m function/function.ontology # $Id: owl.pm,v 1.5 2004/07/08 04:08:42 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself =head1 NAME GO::Handlers::owl - writes OWL =head1 SYNOPSIS use GO::Parser; my $p = GO::Parser->new({handler=>'owl'}); $p->parse("function.ontology"); =head1 DESCRIPTION Consumes an OBO-XML event stream and generates OWL XML See the file go-dev/doc/mapping-obo-to-owl.txt For more details =head1 COMMAND LINE go2fmt.pl -w owl function.obo =cut package GO::Handlers::owl; use base qw(Data::Stag::Writer Exporter); use XML::Writer; use strict; sub is_transform { 0 } sub init { my $self = shift; $self->SUPER::init(@_); my $gen = XML::Writer->new(OUTPUT=>$self->safe_fh); $self->{writer} = $gen; $gen->setDataMode(1); $gen->setDataIndent(4); } sub s_obo { my $self = shift; $self->{writer}->xmlDecl("UTF-8"); # $self->{writer}->doctype("owl:RDF", # '-//Gene Ontology//Custom XML/RDF Version 2.0//EN', # 'http://www.godatabase.org/dtd/go.dtd'); $self->{writer}->startTag('rdf:RDF', 'xmlns:rdf'=>"http://www.w3.org/1999/02/22-rdf-syntax-ns#", 'xmlns:rdfs'=>"http://www.w3.org/2000/01/rdf-schema#", 'xmlns:owl'=>"http://www.w3.org/2002/07/owl#", 'xmlns'=>"http://www.geneontology.org/owl/obo/#", 'xmlns:obo'=>"http://www.geneontology.org/owl/obo/#", 'xml:base'=>"http://www.geneontology.org/owl/obo/", 'xmlns:dc'=>"http://purl.org/dc/elements/1.1/", ); } sub e_obo { my $self = shift; $self->{writer}->endTag('rdf:RDF'); } sub w { shift->{writer} } sub e_term { my ($self, $term) = @_; my $id = $term->get_id || $self->throw($term->sxpr); my $w = $self->w; $id = rdfsafe($id); my $name_h = $self->{name_h}; my $name = $term->get_name; $w->startTag('owl:Class', 'rdf:ID'=>$id); if ($name) { if (!$name_h) { $name_h = {}; $self->{name_h} = $name_h; } $name_h->{$id} = $name; $self->cmt("-- $name --\n"); $w->dataElement('rdfs:label', $name); } my $def = $term->get_definition; if ($def) { $w->dataElement('dc:description', $def->get_definition_text); } my $ont = $term->get_ontology; # if ($ont) { # $self->fact('belongs', [$id, $ont]); # } my @is_as = $term->get_is_a; $w->dataElement('rdfs:subClassOf', '', 'rdf:resource'=>rdfres($_)) foreach @is_as; my @rels = $term->get_relationship; foreach (@rels) { $w->startTag('rdfs:subClassOf'); $w->startTag('owl:Restriction'); $w->dataElement('owl:onProperty', '', 'rdf:resource'=>rdfres($_->get_type)); $w->dataElement('owl:someValuesFrom', '', 'rdf:resource'=>rdfres($_->get_to)); $w->endTag('owl:Restriction'); $w->endTag('rdfs:subClassOf'); } $w->endTag('owl:Class'); return; } sub e_typedef { my ($self, $typedef) = @_; my $id = $typedef->get_id || $self->throw($typedef->sxpr); my $w = $self->w; $id = rdfsafe($id); my $name = $typedef->get_name; $w->startTag('owl:ObjectProperty', 'rdf:ID'=>$id); if ($name) { # $w->dataElement('rdfs:label', $name); } my $def = $typedef->get_definition; if ($def) { $w->dataElement('dc:description', $def->get_definition_text); } my @is_as = $typedef->get_is_a; $w->dataElement('rdfs:subPropertyOf', '', 'rdf:resource'=>rdfres($_)) foreach @is_as; my $domain = $typedef->get_domain; my $range = $typedef->get_range; $w->dataElement('rdfs:domain','','rdf:resource'=>rdfres($domain)) if $domain; $w->dataElement('rdfs:range','','rdf:resource'=>rdfres($range)) if $range; $w->endTag('owl:ObjectProperty'); return; } sub out { my $self = shift; print "@_"; } sub cmt { my $self = shift; my $cmt = shift; # $self->out(" % $cmt") if $cmt; return; } sub rdfres { my $w = rdfsafe(shift); return "#$w"; } sub rdfsafe { my $w = shift; $w =~ s/:/_/g; $w; } 1; go-perl-0.15/GO/Handlers/owl_to_obo_text.pm000644 000765 000024 00000006233 11615622160 020535 0ustar00cjmstaff000000 000000 # $Id: owl_to_obo_text.pm,v 1.2 2004/07/08 04:08:42 cmungall Exp $ # BioPerl module for Bio::Parser::owl_to_obo # # cjm # # POD documentation - main docs before the code =head1 NAME Bio::Parser::owl_to_obo_text =head1 SYNOPSIS Do not use this module directly. =head1 DESCRIPTION =head1 FEEDBACK =head1 AUTHORS - Chris Mungall Email: cjm@fruitfly.org =cut # Let the code begin... package GO::Handlers::owl_to_obo_text; use vars qw(@ISA); use strict; # Object preamble - inherits from Bio::Root::Object use base qw(GO::Handlers::base); our $BASE; sub e_rdf_RDF_xml_base { my ($self, $base) = @_; $BASE = $base->data; return; } sub e_owl_ObjectProperty { my ($self, $prop) = @_; my $id = $prop->sget("owl:ObjectProperty-rdf:ID"); $self->printf("\n[Typedef]\nid:%s\nname:%s\n", $id, $id); $prop->free; return; } sub e_owl_AnnotationProperty { my ($self, $prop) = @_; $prop->free; return; } sub _xml { my $str = shift; my $xml = "$str"; my $struct; eval { $struct = Data::Stag->parsestr($xml); }; if ($@) { print STDERR $@; print STDERR $str,"\n"; $struct = Data::Stag->new(foo=>[]); } $struct; } sub e_owl_Class { my ($self, $owlclass) = @_; print $owlclass->xml; my $id = $owlclass->sget("owl:Class-rdf:ID"); my $name = $owlclass->sget("Preferred_Name") || $id; my @defh = map { my $struct = _xml($_); ($struct->sget("def-definition") => $struct->sget("def-source")); } $owlclass->get("DEFINITION"); my %defh = @defh; my @defrefs = values %defh; my $defref = join(" ", map {"[$_]"} @defrefs) || "[]"; my $def = join(";;\\n", keys %defh); my @subclasses = map { my @R = $_->get("owl:Restriction"); if (@R) { @R; } else { my $sid = $_->sget("rdfs:subClassOf-rdf:resource"); if (!$sid) { die $owlclass->sxpr; $sid = ''; } _get_ID($sid); } } $owlclass->get("rdfs:subClassOf"); my @restrictions = grep {ref($_)} @subclasses; @subclasses = grep {!ref($_)} @subclasses; my @stypes = $owlclass->get("Semantic_Type"); # weird xml-inside-xml my @syns = $owlclass->get("FULL_SYN"); @syns = map { my $struct = _xml($_); $struct->sget("term-name"); } @syns; push(@syns, $owlclass->get("Synonym")); my @lines = (id => $id, name => $name, (map {(is_a => $_ )} @subclasses), (map {(synonym => safeqt($_)." []")} @syns), $def ? (definition => safeqt($def)." $defref") : (), (map { (relationship => sprintf("%s %s", (_get_IDs($_->sfindval("owl:onProperty-rdf:resource")), _get_IDs($_->sfindval("owl:someValuesFrom-rdf:resource")), ))) } @restrictions), ); $self->printf("\n[Term]\n"); while (my ($tag, $val) = splice(@lines, 0, 2)) { $self->print("$tag: $val\n"); } $owlclass->free; return; } sub safeqt { my $str = shift || ''; $str =~ s/\"/\\\"/g; "\"$str\""; } sub _get_ID { my @l = _get_IDs(@_); return shift @l; } sub _get_IDs { my @ids = @_; map { $_ = '' unless $_; s/^\#//; $_; } @ids; } 1; go-perl-0.15/GO/Handlers/pathlist.pm000644 000765 000024 00000000734 11615622160 017157 0ustar00cjmstaff000000 000000 package GO::Handlers::pathlist; use base qw(GO::Handlers::obj); use strict; sub e_obo { my $self = shift; my $g = $self->g; $self->export_graph($g); } sub export_graph { my $self = shift; my $g = shift; $g->iterate(sub { my $n=shift->term; my $paths = $g->paths_to_top($n->acc); foreach my $path (@$paths) { $self->print($n->acc . " "); $self->print($path->to_text('acc')); $self->print("\n"); } }); } 1; go-perl-0.15/GO/Handlers/prolog.pm000644 000765 000024 00000052260 12147577270 016646 0ustar00cjmstaff000000 000000 # stag-handle.pl -p GO::Parsers::GoOntParser -m function/function.ontology package GO::Handlers::prolog; use base qw(GO::Handlers::abstract_prolog_writer Data::Stag::Writer); use strict; sub s_obo { my $self = shift; $self->cmt("-- ********************************************************* --\n"); $self->cmt("-- Autogenerated Prolog factfiles \n"); $self->cmt("-- see http://www.blipkit.org for details \n"); $self->cmt("-- ********************************************************* --\n"); $self->nl; } sub e_header { my ($self, $hdr) = @_; my $idspace = $hdr->sget_idspace; if ($idspace && $idspace =~ /(\S+)\s+(\S+)/) { $self->factq('metadata_db:idspace'=>[$1]); $self->factq('metadata_db:idspace_uri'=>[$1,$2]); } if ($hdr->get_ontology) { $self->factq('ontology'=>[$hdr->sget_ontology]); } foreach ($hdr->get_subsetdef) { my $id = $_->sget_id; my $name = $_->sget_name; $self->factq('metadata_db:partition'=>[$id]); $self->factq('metadata_db:entity_label', [$id, $name]) if $name; } foreach ($hdr->get_synonymtypedef) { my $id = $_->sget_id; my $name = $_->sget_name; my $scope = $_->sget_scope || ''; $self->factq('metadata_db:synonym_type_desc'=>[$id,$scope,$name]); } foreach ($hdr->get_import) { $self->factq('ontol_db:import_directive'=>[$_]); } foreach ($hdr->subnodes) { my $n = $_->name; if ($n =~ /^treat/) { $n =~ s/\-/_/g; my @vals = split(' ',$_->data); $self->factq("ontol_db:$n"=>[@vals]); } } $self->nl; return; } sub e_typedef { my ($self, $typedef) = @_; $self->cmt("-- Property/Slot --\n"); my $ont = $typedef->get_namespace; my $id = $typedef->get_id || $self->throw($typedef->sxpr); my $proptype = 'property'; my $domain = $typedef->get_domain; my $range = $typedef->get_range; if ($range && $range =~ /^xsd:/) { $proptype = 'slot'; } #$self->fact($proptype, [$id, $typedef->sget_name]); $self->factq($proptype, [$id]); my $name = $typedef->sget_name; $self->factq('metadata_db:entity_label', [$id, $name]) if $name; my @is_as = $typedef->get_is_a; foreach my $is_a (@is_as) { if (ref($is_a)) { my $gci_rel = $is_a->sget('@/gci_relation'); if ($gci_rel) { $self->rfactq($_, 'gci_subclass', [$id,$is_a->data, $gci_rel, $is_a->sget('@/gci_filler')]); } else { $self->rfactq($_, 'subclass', [$id, $is_a->data]); } } else { $self->rfactq($_, 'subclass', [$id, $is_a]); } } if ($ont) { $self->factq('metadata_db:entity_resource', [$id, $ont]); } if ($typedef->get_is_obsolete) { $self->factq( 'metadata_db:entity_obsolete', [$id, 'property']); } foreach (qw(is_reflexive is_anti_symmetric is_symmetric is_transitive is_functional is_inverse_functional is_proper is_cyclic is_metadata_tag is_class_level holds_for_all_times is_symmetric_on_instance_level is_transitive_on_instance_level)) { if ($typedef->sget($_)) { $self->rfactq($typedef->sget($_), $_,[$id]); } } foreach (qw(all_some all_only all_some_all_times)) { my $val = $typedef->sget($_); if ($val) { $self->fact('property_relationship',[$id,$_,$val]); } } # if (!$typedef->sget_is_metadata_tag) { # $self->factq( 'all_some',[$id]); # } $self->export_tags($typedef); foreach (qw(domain range)) { my $val = $typedef->sget($_); if ($val) { $self->fact("property_$_",[$id,convert_to_ref($val)]); } } foreach (qw(transitive_over inverse_of class_level_inverse_of inverse_of_on_instance_level transitive_form_of cyclic_form_of cyclic_over complement_of directed_simple_path_over directed_path_over reflexive_over expand_expression_to expand_assertion_to)) { my $val = $typedef->sget($_); if ($val) { $self->factq( $_,[$id,$val]); } } my @relchains = $typedef->get_holds_over_chain; foreach my $relchain (@relchains) { my @rels = $relchain->get_relation; if (@rels) { $self->factq( holds_over_chain=>[$id,\@rels]); } } my @equivchains = $typedef->get_equivalent_to_chain; foreach my $equivchain (@equivchains) { my @rels = $equivchain->get_relation; if (@rels) { $self->factq( equivalent_to_chain=>[$id,\@rels]); } } $self->factq('disjoint_from', [$id, $_]) foreach $typedef->get_disjoint_from; $self->factq('disjoint_over', [$id, $_]) foreach $typedef->get_disjoint_over; my @xpelts = $typedef->get_intersection_of; foreach (@xpelts) { $self->factq( 'property_intersection_element',[$id,$_->get_to]); } @xpelts = $typedef->get_union_of; foreach (@xpelts) { $self->factq( 'property_union_element',[$id,$_->get_to]); } foreach (qw(holds_temporally_between holds_atemporally_between)) { my $holds = $typedef->sget($_); if ($holds) { $self->factq( $_,[$id,$holds->get_subject,$holds->get_object]); } } $self->nl; return; } sub e_term { my ($self, $term) = @_; my $id = $term->get_id || $self->throw($term->sxpr); my $name_h = $self->{name_h}; my $name = $term->get_name; #$name =~ s/_/ /g; # ontologies lack consistency; force use of spc my $ont = $term->get_namespace; if ($name) { # cache the name; useful for use in comment fields later if (!$name_h) { $name_h = {}; $self->{name_h} = $name_h; } $name_h->{$id} = $name; #$self->cmt("-- $name --\n"); $self->factq('metadata_db:entity_label', [$id, $name]) if $name; } if ($ont) { $self->factq('metadata_db:entity_resource', [$id, $ont]); } if ($term->get_is_obsolete) { $self->factq('metadata_db:entity_obsolete', [$id, 'class']); } else { # only declare this to be a class if not obsolete $self->factq('class', [$id]); } #my @is_as = $term->findval_is_a; my @is_as = $term->get_is_a; foreach my $is_a (@is_as) { if (ref($is_a)) { my $gci_rel = $is_a->sget('@/gci_relation'); if ($gci_rel) { $self->rfactq($_, 'gci_subclass', [$id,$is_a->get('.'), $gci_rel, $is_a->sget('@/gci_filler')]); } else { #$self->rfactq($_,'subclass', [$id, ref($is_a) ? $_->get('.') : $_], $name_h->{$_}); $self->rfactq($_, 'subclass', [$id, $is_a->get('.')], $name_h->{$_}); } } else { $self->rfactq($_,'subclass', [$id, $is_a], $name_h->{$is_a}); } } my @equivs = $term->get_equivalent_to; $self->rfactq($_, 'equivalent_class', [$id, ref($_) ? $_->get('.') : $_]) foreach @equivs; my @xp = $term->get_intersection_of; if (scalar(@xp) == 1) { $self->warn("IGNORING single intersection_of tag for $id/$name"); @xp=(); } if (@xp) { my @genus_l = (); @xp = grep { # new style genus-differentia: # we say intersection_of: ID rather than # intersection_of: relation ID if (!$_->get_type || $_->get_type eq 'is_a') { if (@genus_l) { $self->warn(">1 genus for $id/$name"); } push(@genus_l, $_->get_to); 0; } else { 1; } } @xp; $self->factq('genus',[$id, $_]) foreach @genus_l; foreach my $diff (@xp) { my $rel = $diff->get_type; my $min_card = $diff->sget('@/minCardinality'); my $max_card = $diff->sget('@/maxCardinality'); my $card = $diff->sget('@/cardinality'); if ($card) { $min_card = $card; $max_card = $card; } if (defined $min_card && !defined $max_card) { $rel = {card=>[$rel,$min_card || 0]}; } elsif (defined $max_card) { $rel = {card=>[$rel,$min_card || 0,$max_card]}; } else { } $self->factq('differentium', [$id, $rel, $diff->sget_to]) } } # TODO - unify handling of cardinality my @rels = $term->get_relationship; foreach (@rels) { my @args = ($id, $_->get_type, convert_to_ref($_->get_to), map { convert_to_ref($_) } $_->get_additional_argument); my $gci_rel = $_->sget('@/gci_relation'); if ($gci_rel) { $self->rfactq($_, 'gci_restriction', [@args, $gci_rel, $_->sget('@/gci_filler')], $name_h->{$_->get_to}); } else { $self->rfactq($_, 'restriction', [@args], $name_h->{$_->get_to}); } foreach my $cardp (qw(cardinality minCardinality maxCardinality)) { my $card = $_->sget('@/'.$cardp); if ($card) { my @cargs = @args; splice(@cargs,2,0,''); $cargs[2] = $card; my $pred = $cardp; if ($cardp =~ /min/) { $pred = 'min_cardinality'; } elsif ($cardp =~ /max/) { $pred = 'max_cardinality'; } $self->rfact($_, $pred.'_restriction', [@cargs], $name_h->{$_->get_to}); } } } # subject to change: if ($term->get_all_direct_subclasses_disjoint) { $self->factq('all_direct_subclasses_disjoint', [$id]); } $self->factq('disjoint_from', [$id, $_]) foreach $term->get_disjoint_from; $self->factq('class_union_element', [$id, $_->sget_to]) foreach $term->get_union_of; foreach (qw(is_anonymous)) { if ($term->sget($_)) { $self->factq($_,[$id]); } } $self->export_tags($term); $self->nl; # metadata return; } sub _flatten_dbxref { my $x = shift; my $db = $x->sget_dbname; my $acc = $x->sget_acc; if ($db eq "URL" && $acc =~ /http/) { # TODO - check for all URI forms (LSID,...) return $acc; } elsif ($acc eq 'NULL') { return $db; } else { return "$db:$acc"; } } # stuff common to terms and typedefs and insts sub export_tags { my ($self, $entity) = @_; my $def = $entity->get_def; my $id = $entity->sget_id; if ($def) { $self->factq('def',[$id, $def->sget_defstr]); foreach ($def->get_dbxref) { $self->factq('def_xref',[$id, _flatten_dbxref($_)]); } } foreach ($entity->get_alt_id) { $self->factq('metadata_db:entity_alternate_identifier',[$id, $_]); } foreach ($entity->get_consider) { $self->factq('metadata_db:entity_consider',[$id, $_]); } foreach ($entity->get_replaced_by) { $self->factq('metadata_db:entity_replaced_by',[$id, $_]); } foreach ($entity->get_comment) { $self->factq('metadata_db:entity_comment',[$id, $_]); } foreach ($entity->get_example) { $self->factq('metadata_db:entity_example',[$id, $_]); } foreach ($entity->get_subset) { $self->factq('metadata_db:entity_partition',[$id, $_]); } foreach ($entity->get_synonym) { my $syn = $_->sget_synonym_text; my $scope = $_->sget('@/scope'); my $type = $_->sget('@/synonym_type'); $self->factq('metadata_db:entity_synonym',[$id,$syn]); $self->factq('metadata_db:entity_synonym_scope',[$id,$syn,$scope]) if $scope; $self->factq('metadata_db:entity_synonym_type',[$id,$syn,$type]) if $type; $self->factq('metadata_db:entity_synonym_xref',[$id,$syn,_flatten_dbxref($_)]) foreach $_->get_dbxref; } foreach ($entity->get_xref_analog) { my $xref = _flatten_dbxref($_); #$self->factq('class_xref',[$id, sprintf("%s:%s",$_->sget_dbname,$_->sget_acc)]); $self->factq('metadata_db:entity_xref',[$id, $xref]); my $n = $_->sget('name'); if ($n && !$self->{_written_name_for}->{$xref}) { $self->factq('metadata_db:entity_label',[$xref, $n]); $self->{_written_name_for}->{$id} = 1; } } foreach ($entity->get_formula) { $self->factq('logicalformula',[$id,$_->sget_formula_text,$_->sget('@/format')]); } #foreach ($entity->get_subset) { # $self->fact('belongs_subset',$_->findval_scope || '',$_->sget_synonym_text); #} foreach (qw(lexical_category)) { my $val = $entity->sget($_); if ($val) { $self->factq($_,[$id,$val]); } } # property tag-val pairs foreach my $pv ($entity->get_property_value) { my $dt = $pv->sget_datatype; my @args = ($id,$pv->sget_type); my $link_id = $pv->get('@/id'); if ($dt) { $self->factq('inst_sv',[@args,$pv->sget_value,$dt]); } else { $self->factq('inst_rel',[@args,$pv->sget_to]); if ($link_id) { $self->factq('reification', [$link_id,{inst_rel=>[@args,$pv->sget_to]}]); } } } return; } sub nextid_by_prod { my $self = shift; $self->{_nextid_by_prod} = shift if @_; $self->{_nextid_by_prod} = {} unless $self->{_nextid_by_prod}; return $self->{_nextid_by_prod}; } sub e_prod { my ($self, $gp) = @_; my $proddb = $self->up(-1)->sget_proddb; my $prodacc = $gp->sget_prodacc; # all gene products go in seqfeature_db module my $id = "$proddb:$prodacc"; $self->factq('seqfeature_db:feature',[$id]); $self->factq('seqfeature_db:feature_type', [$id,$gp->sget_prodtype]); $self->factq('metadata_db:entity_label', [$id,$gp->sget_prodsymbol]); $self->factq('metadata_db:entity_source', [$id,$gp->sget_proddb]); # duplicate? $self->factq('seqfeature_db:feature_organism', [$id,'NCBITaxon:'.$gp->sget("prodtaxa")]); #$self->factq('taxon_db:entity_taxon', # [$id,'NCBITaxon:'.$gp->sget("prodtaxa")]); $self->factq('seqfeature_db:featureprop', [$id,'description',$gp->sget_prodname]); $self->factq('metadata_db:entity_synonym', [$id,$_]) foreach $gp->get_prodsyn; # associations between gp and term' my @assocs = $gp->get_assoc; my $idh = $self->nextid_by_prod; foreach my $assoc (@assocs) { my $n = $idh->{$id}++; my $term_acc = $assoc->sget_termacc; my $is_not = $assoc->sget_is_not ? 1 : 0; my $aid = "$proddb:association-$id-$term_acc-$is_not"; $self->fact('curation',[$aid]); my $pred = 'curation_statement'; if ($is_not) { $pred = 'negative_'.$pred; } $self->fact($pred, [$aid,$id,'has_role',$term_acc]); my $aspect = $assoc->sget_aspect; if ($aspect) { if (!$self->{_written_aspect}) { $self->{_written_aspect} = {}; } if (!$self->{_written_aspect}->{$term_acc}) { $self->{_written_aspect}->{$term_acc} = 1; my $ont = ''; if ($aspect eq 'F') { $ont = 'molecular_function'; } elsif ($aspect eq 'P') { $ont = 'biological_process'; } elsif ($aspect eq 'C') { $ont = 'cellular_component'; } if ($ont) { $self->fact('metadata_db:entity_resource',[$term_acc,$ont]); } } } my @evs = $assoc->get_evidence; my $ne=0; foreach my $ev (@evs) { my $eid = "$aid-$ne"; $ne++; # eg PMID $self->factq('metadata_db:entity_source', [$aid,$ev->sget_ref]); $self->factq('evidence',[$eid]); $self->factq('curation_evidence', [$aid,$eid]); $self->factq('evidence_type', [$eid,$ev->sget_evcode]); $self->factq('evidence_with', [$eid,$_]) foreach $ev->get_with; } # note: we treat the source DB as the publisher (the source is the provenance) $self->factq('metadata_db:entity_publisher', [$aid,$_]) foreach $assoc->get_source_db; foreach ($assoc->get('properties/link')) { $self->factq('curation_subject_property_value', [$aid,$term_acc,$_->get_type,$_->get_to]) } foreach ($assoc->get_assocdate) { if (length($_) eq 8) { $_ = sprintf("%s-%s-%s", substr($_,0,4), substr($_,4,2), substr($_,6,2)); } $self->factq('metadata_db:entity_created', [$aid,$_]) } my @pvs = $assoc->get_property_value; foreach my $pv (@pvs) { $self->factq('curation_qualifier', [$aid,$pv->sget_type,$pv->sget_to]); } my @quals = $assoc->get_qualifier; foreach my $q (@quals) { next if $q eq 'not'; $self->factq('curation_qualifier', [$aid,$q,"true"]); } } } sub e_annotation { my ($self, $annotation) = @_; my $idh = $self->nextid_by_prod; my $proddb = $annotation->sget_namespace || '_'; my $subj = $annotation->sget_subject; my $rel = $annotation->sget_relation; my $obj = $annotation->sget_object; my $is_not = $annotation->sget_is_not ? 1 : 0; my $aid = "$proddb:$subj-$obj-$is_not"; $self->fact('curation',[$aid]); my $pred = 'curation_statement'; if ($is_not) { $pred = 'negative_'.$pred; } $self->fact($pred, [$aid,$subj,$rel,$obj]); # my @evs = $assoc->get_evidence; # my $ne=0; # foreach my $ev (@evs) { # my $eid = "$aid-$ne"; # $ne++; # # eg PMID # $self->factq('metadata_db:entity_source', # [$aid,$ev->sget_ref]); # $self->factq('evidence',[$eid]); # $self->factq('curation_evidence', # [$aid,$eid]); # $self->factq('evidence_type', # [$eid,$ev->sget_evcode]); # $self->factq('evidence_with', # [$eid,$_]) # foreach $ev->get_with; # } # note: we treat the source DB as the publisher (the source is the provenance) $self->factq('metadata_db:entity_publisher', [$aid,$_]) foreach $annotation->get_provenance; $self->factq('metadata_db:entity_creator', [$aid,$_]) foreach $annotation->get_creator; $self->factq('metadata_db:entity_resource', [$aid,$_]) foreach $annotation->get_namespace; my @pvs = $annotation->get_property_value; foreach my $pv (@pvs) { $self->factq('curation_qualifier', [$aid,$pv->sget_type,$pv->sget_to]); } } sub e_instance { my ($self, $inst) = @_; my $id = $inst->get_id; $self->factq('inst', [$id]); $self->factq('inst_of',[$id,$_]) foreach $inst->get_instance_of; my $name = $inst->sget_name; $self->factq('metadata_db:entity_label', [$id, $name]) if $name; $self->export_tags($inst); foreach my $pv ($inst->get_relationship) { my @args = ($id,$pv->sget_type); my $link_id = $pv->get('@/id'); $self->factq('inst_rel',[@args,$pv->sget_to]); if ($link_id) { $self->factq('reification', [$link_id,{inst_rel=>[@args,$pv->sget_to]}]); } } return; } # todo sub convert_to_ref { my $to = shift; if (ref($to)) { # may be enum return ''; } else { return $to; } } sub rfactq { my $self = shift; my $elt = shift; my $f = shift; my $args = shift; my $cmt = shift; $self->factq($f,$args,$cmt); if (ref($elt)) { my $reif_id = $elt->get('@/id'); if ($reif_id) { $self->factq('reification', [$reif_id,{$f=>$args}]); } } return; } sub rfact { my $self = shift; my $elt = shift; my $f = shift; my $args = shift; my $cmt = shift; $self->fact($f,$args,$cmt); if (ref($elt)) { my $reif_id = $elt->get('@/id'); if ($reif_id) { $self->fact('reification', [$reif_id,{$f=>$args}]); } } return; } 1; go-perl-0.15/GO/Handlers/rdf.pm000644 000765 000024 00000001105 11615622160 016073 0ustar00cjmstaff000000 000000 # makes objects from parser events package GO::Handlers::rdf; use base qw(GO::Handlers::obj); use FileHandle; use GO::IO::XML; use strict; sub _valid_params { qw(w fh strictorder) } #sub init { # my $self = shift; # $self->SUPER::init(@_); # my $fh = FileHandle->new; # my $fh = \*STDOUT; # $self->fh($fh); # return; #} sub e_obo { my $self = shift; my $g = $self->g; my $xml_out = GO::IO::XML->new(-output=>$self->safe_fh); $xml_out->start_document(); $xml_out->draw_node_graph(-graph=>$g); $xml_out->end_document(); return; } 1; go-perl-0.15/GO/Handlers/summary.pm000644 000765 000024 00000003726 11615622160 017030 0ustar00cjmstaff000000 000000 # $Id: summary.pm,v 1.3 2004/11/24 02:28:00 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself =head1 NAME GO::Handlers::summary - =head1 SYNOPSIS =cut =head1 DESCRIPTION =head1 PUBLIC METHODS - =cut package GO::Handlers::summary; use base qw(GO::Handlers::base); sub init { my $self = shift; $self->{i} = 0; $self->{counts} = {}; } sub count { my $self = shift; my $type = shift; if (!$self->{counts}->{$type}) { $self->{counts}->{$type} = 0; } $self->{counts}->{$type}++; } sub start_event { my $self = shift; my $ev = shift; return; } sub end_event { my $self = shift; my $ev = shift; $self->count($ev); if ($ev eq "assocs") { print "TOTAL ASSOCS : $self->{counts}->{assoc}\n"; print "TOTAL PRODUCTS: $self->{counts}->{prod}\n"; print "TOTAL DBSETS : $self->{counts}->{dbset}\n"; } if ($ev eq "obo") { print "TOTAL TERMS : $self->{counts}->{term}\n"; print "TOTAL DEFS : $self->{counts}->{def}\n" if $self->{counts}->{def}; print "TOTAL SYNS : $self->{counts}->{synonym}\n"; print "TOTAL RELS : $self->{counts}->{relationship}\n" if $self->{counts}->{relationship}; print "TOTAL XREFS : $self->{counts}->{xref_analog}\n"; } if ($ev eq "defs") { print "TOTAL DEFS : $self->{counts}->{def}\n"; } if ($ev eq "dbxrefs") { print "TOTAL TERMXREFS : $self->{counts}->{termdbxref}\n"; } #return $self->SUPER::end_event($ev); return; } #sub e_term { # my $self = shift; # my $term = shift; # my $ns = shift; # return; #} sub event { my $self = shift; my $ev = shift; my @args = @_; my $arg = $args[0]; if (!ref($arg)) { } else { $self->start_event($ev); $self->evbody(@args); $self->end_event($ev); } } 1; go-perl-0.15/GO/Handlers/sxpr.pm000644 000765 000024 00000000240 11615622160 016313 0ustar00cjmstaff000000 000000 # stag-handle.pl -p GO::Parsers::GoOntParser -m function/function.ontology package GO::Handlers::sxpr; use base qw(Data::Stag::SxprWriter Exporter); 1; go-perl-0.15/GO/Handlers/tbl.pm000644 000765 000024 00000002515 11615622160 016107 0ustar00cjmstaff000000 000000 # $Id: tbl.pm,v 1.3 2004/11/24 02:28:00 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself =head1 NAME GO::Handlers::tbl - =head1 SYNOPSIS use GO::Handlers::tbl =cut =head1 DESCRIPTION =head1 PUBLIC METHODS - =cut # makes objects from parser events package GO::Handlers::tbl; use base qw(GO::Handlers::base); use strict; sub e_term { my $self = shift; my $t = shift; my $def = $t->get_def; my $defstr = ''; if ($def) { $defstr = $def->get_defstr; } my @syns = $t->get_synonym; my @synstrs = map {$_->get_synonym_text} @syns; my @cols = ($t->get_id, $t->get_name, $defstr, join('; ', @synstrs)); $self->print(join("\t", @cols)); $self->print("\n"); return; } sub e_prod { my $self = shift; my $p = shift; my $proddb = $self->up(1)->sget_proddb; my @cols = ($proddb, $p->get_prodacc, $p->get_prodsymbol, $p->get_prodtype, $p->get_prodtaxa, join('; ', map { ($_->get_is_not ? "NOT:" : "").$_->get_termacc } $p->get_assoc), ); $self->print(join("\t", @cols)); $self->print("\n"); return; } 1; go-perl-0.15/GO/Handlers/text_html.pm000644 000765 000024 00000001156 11615622160 017336 0ustar00cjmstaff000000 000000 # $Id: text_html.pm,v 1.5 2004/07/02 17:46:48 cmungall Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself =head1 NAME GO::Handlers::text_html - =head1 SYNOPSIS use GO::Handlers::text_html =cut =head1 DESCRIPTION =head1 PUBLIC METHODS - =cut # makes objects from parser events package GO::Handlers::text_html; use base qw(GO::Handlers::xsl_base); use strict; $ENV{XSLT_FILE} = "$ENV{GO_ROOT}/xml/xsl/text_html.xsl"; 1; go-perl-0.15/GO/Handlers/xml.pm000644 000765 000024 00000000236 11615622160 016124 0ustar00cjmstaff000000 000000 # stag-handle.pl -p GO::Parsers::GoOntParser -m function/function.ontology package GO::Handlers::xml; use base qw(Data::Stag::XMLWriter Exporter); 1; go-perl-0.15/GO/Handlers/xsl_base.pm000644 000765 000024 00000002025 11615622160 017122 0ustar00cjmstaff000000 000000 # $Id: xsl_base.pm,v 1.1 2004/03/04 23:18:09 bradmars Exp $ # # This GO module is maintained by Chris Mungall # # see also - http://www.geneontology.org # - http://www.godatabase.org/dev # # You may distribute this module under the same terms as perl itself =head1 NAME GO::Handlers::text_html - =head1 SYNOPSIS use GO::Handlers::text_html =cut =head1 DESCRIPTION =head1 PUBLIC METHODS - =cut # makes objects from parser events package GO::Handlers::xsl_base; use base qw(GO::Handlers::base); use XML::LibXML; use XML::LibXSLT; use strict; sub e_obo { my $self = shift; my $obo_stag = shift; my $parser = XML::LibXML->new(); my $source = $parser->parse_string($obo_stag->xml); my $xslt = XML::LibXSLT->new(); my $file_name = $ENV{'XSLT_FILE'}; my $styledoc = $parser->parse_file($file_name); my $stylesheet = $xslt->parse_stylesheet($styledoc); my $results = $stylesheet->transform($source); print $stylesheet->output_string($results); } 1; go-perl-0.15/doc/go-perl-doc.html000644 000765 000024 00000014276 11615622160 016475 0ustar00cjmstaff000000 000000 Using go-perl

Using go-perl

Introduction

The go-perl library provides modules to help parse and navigate GO/OBO style ontologies together with associated gene product annotations.

The go-perl library does not deal with interfacing or querying the GO database; for this you need go-db-perl, part of this distribution. You need go-perl in order for go-db-perl to work

Background

You should already be familiar with the Gene Ontology project:

You should also be familiar with the file formats GO uses:

Documentation on the rest of the go-dev distribution:

GO Database and Developers page:

And you should be familiar with perl, particularly object-oriented perl (unless you just want to run the scripts that are part of go-perl)

Download

You can get the official release from CPAN - http://search.cpan.org/~cmungall/go-perl. You can get the latest bleeding edge version from Sourceforge CVS. In addition, the GO Database daily, weekly, and monthly releases come with the version of the code used to build that release.

Installation

go-perl requires installation of several third-party perl modules. The instructions below should help guide you through this process. If you have never installed perl modules before, and you do not have full write privileges on your machine, you may need the help of a system administrator here.

Full installation instructions are in the file INSTALL.html or INSTALL

Scripts

The go-perl distribution comes with a number of scripts. These should all be executable if you follow the installation instructions.

See go-perl for a full list of scripts.

About

To use the NOTE: if you do not intend to use the go-perl library as a programmer then you don't need to read any further here. Simply follow the installation instructions above, and you will be able to use any of the tools in the scripts directory.

go-perl is a set of perl modules for parsing, manipulating and exporting GO or OBO style ontology files. It includes parsers for the various GO/OBO formats, extendable handlers for dealing with the results of a parse, and an object model.

Unlike packages such as BioPerl, the object model is not strictly necessary for performing a lot of useful tasks. You can actually get by quite well with just using the Parser/Handler framework

Documentation

Most of the relevant documentation is kept in POD format. You can read the HTML version here:

Event Handling Architecture

You can also read about the internal details of the event handling mechanism and how to write your own perl event handlers here: go-perl event handling

Database API

The go-perl module does not have a database API - you need the go-db-perl modules, also part of the go-dev distribution. You also need the go-database - see the GO Database SQL Docs go-dev/sql, or download the latest build from http://www.godatabase.org/dev/database

Mail Lists

  • http://mail.fruitfly.org/mailman/listinfo/go-database -- Announcements and user help with the GO Database downloads and schema
  • http://lists.sourceforge.net/lists/listinfo/gmod-ontol-sw-dev -- go-dev software discussion

    • Chris Mungall
    Last modified: Sat Feb 12 18:00:02 PST 2005 go-perl-0.15/doc/go-perl-event-handling.html000644 000765 000024 00000037626 11615622160 020637 0ustar00cjmstaff000000 000000 Event handling in go-perl

    Event handling in go-perl

    Background

    go-perl general documentation

    Parser/Handler Framework

    Event-based parsing

    go-perl has an event-streaming framework for parsing files. Parsers or Generators read input files and fire XML events. These events are intercepted by Handlers, which do something with the events, such as convert them into another format, or spit out a report.

    This kind of framework has many advantages. It is more efficient, as it is not necessary to parse a whole file into memory before doing something with it.

    Although it is possible to turn the events into objects conforming to the GO object model (below), it is not necessary to learn an object model in order to write your own handlers.

    The framework can easily be used in a mixed programming language environment - for example, the events can be passed as an XML stream to an XSLT processor, or to a java program.

    Nested Event Structure

    The structure of the nested events fired by the parsers correspond to XML. The structure of this XML can be shown as either DTD or stag-schema. See the go-dev/xml/dtd directory for descriptions of the events fired by the various parsers.

    Note that all events generated by any file format corresponding to ontologies are subsets of obo parser events; see obo-parser-events.dtd dtd

    Architecture

    A GO::Parser class reads in a file; it can be in various formats. The parser fires nested events. These are consumed by the handler; the handler may write out these events in an alternate format, or it may transform the events into some different xml. 

    
               [ reads file ]               [ nested events]
    FILE     ---------------->  GO::Parser   -------------> GO::Handler
    ====                        ==========                  ===========

    .obo file                   obo_text_parser             
    .ontology file              go_ont_parser
    .defs file                  go_defs_parser
    xref2go file                go_xrefs_parser
    gene_association file       go_assoc_parser

    Stag XML Events

    The parsers fire off XML events using a limited simplified subset of XML which has no attributes and no mixed elements. I believe this has a number of advantages - the parsing and handling code is more concise, and the events can also be seen as Lisp-style S-Expressions or simple indented text (don't worry if you don't know what an S-Expression is)

    go-perl uses the Data::Stag library for generating and consuming events; you can read more at stag.sourceforge.net

    GO::Parsers

    go-perl comes with the following parsers, all in the GO/Parsers directory.

    GO::Parsers::go_ont_parser
    parses .ontology files into an obo-xml event stream. See go_ont-parser-events.dtd
    GO::Parsers::go_def_parser
    parses .definition files into an obo-xml event stream. See go_def-parser-events.dtd
    GO::Parsers::go_xref_parser
    parses xref2go files into an obo-xml event stream. See go_xref-parser-events.dtd
    GO::Parsers::go_assoc_parser
    parses gene_association files into an obo-xml event stream. See go_assoc-parser-events.dtd
    GO::Parsers::obo_text_parser
    parses .obo files into an obo-xml event stream. See obo-parser-events.dtd
    GO::Parsers::obo_xml_parser
    parses .obo-xml files into an obo-xml event stream. See obo-parser-events.dtd
    GO::Parsers::owl_parser
    EXPERIMENTAL - parses OWL-XML into an obo-xml event stream

    GO::Handlers

    Handlers intercept the stream of events generated by a parser. Typically they will either transform one XML event stream into another (transformation) or they will generate formatted text.

    go-perl comes with the following handlers, all in the GO/Handlers directory

    GO::Handlers::obj
    Intercepts obo-xml events and creates GO::Model:: objects - see the section on the object model, below
    GO::Handlers::obo_text
    Intercepts obo-xml events and generates obo text format output
    GO::Handlers::obo_xml
    Intercepts obo-xml events and generates obo xml output
    GO::Handlers::rdf
    Intercepts obo-xml events and generates GO RDF XML
    GO::Handlers::summary
    Intercepts obo-xml events and generates summary report output
    GO::Handlers::error_report
    Intercepts obo-xml events and generates a report of parse errors or semantic errors in the source input file
    GO::Handlers::prolog
    Intercepts obo-xml events and generates prolog output (mainly for use with the obol project)
    GO::Handlers::sxpr
    Intercepts obo-xml events and generates lisp S-Expressions (aka SXML) using the obo-xml schema. For use with lisp programs.
    GO::Handlers::owl
    Intercepts obo-xml events and generates W3C OWL XML
    GO::Handlers::tbl
    Intercepts obo-xml events and generates simple tabular output summarising the source ontology, one line per term
    GO::Handlers::pathlist
    Intercepts obo-xml events and generates pathlists for every term in the source ontology. A pathlist shows the list of valid paths from a term to the ontology top/root term(s).
    GO::Handlers::obo_html
    Intercepts obo-xml events and generates html-ized obo format output
    GO::Handlers::text_html
    Intercepts obo-xml events and generates html-ized go_ont format output
    GO::Handlers::go_ont
    Intercepts obo-xml events and generates (deprecated) go_ont file format output (ie .ontology files), with parentage indicated by indentation
    GO::Handlers::go_def
    Intercepts obo-xml events and generates (deprecated) go_def style output (ie .definition files)
    GO::Handlers::go_xref
    Intercepts obo-xml events and generates xref2go output, showing mapping between ontology terms and xref_analogs in different dbs
    GO::Handlers::godb_prestore
    Intercepts obo-xml events and transforms the input xml stream into an xml output stream conforming to the schema of the go-database. See go-db-perl for details. This is how the GO database is loaded. The structure of the transformed XML events is described by godb_prestore-events.dtd
    GO::Handlers::chadodb_prestore [EXPERIMENTAL]
    As GO::Handlers::godb_prestore, but maps xml to a chado db schema
    GO::Handlers::owl_to_obo [EXPERIMENTAL]
    Takes an input OWL XML stream and transforms it to obo-xml parse streams

    Most of these handlers come with a corresponding script; for example, you can test the GO::Handlers::pathlist parser by running go2pathlist on any GO or OBO formatted file.

    Writing your own Handler

    Let's say you wish to parse a gene_association file, and produce a formatted report that looks something like this:

    You're going to be intercepting a go-assoc event stream; you can get a rough idea of what this looks like by running the script go2xml on any of the gene_association files in the main GO repository. 

    <assocs>
  <dbset>
    <proddb>RGD</proddb>
    <prod>
      <prodacc>RGD:621326</prodacc>
      <prodsymbol>Arl1</prodsymbol>
      <prodname>ADP-ribosylationfactor-like1</prodname>
      <prodtype>gene</prodtype>
      <prodtaxa>10116</prodtaxa>
      <assoc>
        <assocdate>20040317</assocdate>
        <source_db>RGD</source_db>
        <termacc>GO:0005802</termacc>
        <is_not>0</is_not>
        <aspect>C</aspect>
        <evidence>
          <evcode>IDA</evcode>
          <ref>RGD:724590</ref>
        </evidence>
      </assoc>
    </prod>
    <prod>
      <prodacc>RGD:69327</prodacc>
      <prodsymbol>Arl3</prodsymbol>
      <prodname>ADP-ribosylation-like3</prodname>
      <prodtype>gene</prodtype>
      <prodtaxa>10116</prodtaxa>
      <assoc>
        <assocdate>20040317</assocdate>
        <source_db>RGD</source_db>
        <termacc>GO:0019003</termacc>
        <is_not>0</is_not>
        <aspect>F</aspect>
        <evidence>
          <evcode>IDA</evcode>
          <ref>RGD:68742</ref>
        </evidence>
      </assoc>
      <assoc>
...etc

    Or you can look at the structure of the go-assoc event stream; see go_assoc-parser-events.dtd in the go-dev/xml/dtd directory. The same structure can be shown with the following stag-schema, below: 

      (assocs
   (dbset+
     (proddb "s")
     (prod+
       (prodacc "s")
       (prodsymbol "s")
       (prodtype "s")
       (prodtaxa "i")
       (assoc+
         (assocdate "i")
         (source_db "s")
         (termacc "s")
         (is_not "i")
         (aspect "s")
         (evidence+
           (evcode "s")
           (ref "s"))))))

    We wish to catch <prod> events and write them out 

    package My::Handler;
use base (GO::Handlers::DefHandler);

sub e_prod {
    my ($self, $prod) = @_;
    printf "Gene Product: %s %s\n",
      $prod->get_acc, $prod->get_symbol;
    my @assocs = $prod->get_assoc;
    foreach my $assoc (@assocs) {
        printf "  To Term: %s\n", $assoc->get_termacc;
    }
}
1;

    The get_* methods are automatically provided by the Data::Stag modules. See Data::Stag documentation, on CPAN.

    You can then see the output of your handler using the go2fmt.pl script: 

    go2fmt.pl -w My::Handler gene_associations.sgd

    You can also use your module in code like this: 

    use GO::Parser;

# create a parser object that passes things to an object handler
my $parser = GO::Parser->new({handler=>"My::Handler"});

# the parser will go through the file firing events 
# which will be intercepted by My::Handler
$parser->parse($file);
exit 0;

    Object Model

    Sometimes we find it necessary to do things such as graph traversal on the ontology; this is where the object model comes in handy.

    Before reading on, you should make sure you are reasonably familiar with the slightly abstruse perl object system. You should also be familiar with commands like "perldoc" so you can get more information on any class in the object model.

    Here's a diagram showing the overall structure of the go-perl object model:

    Note that unless you're using the go-db-perl, then you probably don't have any need for many of the classes, such as Association, GeneProduct and Seq

    The 3 core classes are Term, Relationship and Graph. A Term is used to represent a GO or OBO Term/Class, and holds data such as the identifier, the name, definition, synonyms and so forth.

    Perhaps the most useful class in the object model is the GO::Model::Graph class - this holds a collection of Terms and knows the Relationships between them. Note that the Term objects themselves are quite dumb - they have no idea what their context is in the overall DAG/Ontology. You have to use the Graph object to discover this sort of thing.

    The Graph class has various methods for doing graph traversal and querying - see the pod docs for full details

    Using the object model

    use GO::Parser;

# create a parser object that passes things to an object handler
my $parser = GO::Parser->new({handler=>'obj'});

# the parser will go through the file firing events - the
# object handler will catch those events and store them
# in a GO::Model::Graph object
$parser->parse($file);
my $graph = $parser->handler->graph;

    Mail List

    go-database@fruitfly.org

    Chris Mungall
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