Cross-references of external classification systems to GO

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These mappings (or “cross-references”) create a network of information that integrate GO and its annotations with other biological databases and resources.</p> <p>External classification systems mapped to GO terms:</p> <table> <thead> <tr> <th><strong>Database resource</strong></th> <th><strong>Scope</strong></th> <th><strong>Relevant GO aspect(s)</strong></th> <th><strong>Direct access to mapping file(s)</strong></th> </tr> </thead> <tbody> <tr> <td><a href="https://enzyme.expasy.org/" target="blank">Enzyme Commission (EC)</a></td> <td>Catalytic reactions</td> <td>Molecular Function</td> <td><a href="https://geneontology.org/external2go/ec2go">ec2go</a></td> </tr> <tr> <td><a href="http://www.genome.jp/kegg/" target="blank">KEGG: Kyoto Encyclopaedia of Genes and Genomes </a></td> <td>Catalytic reactions</td> <td>Molecular Function</td> <td><a href="https://geneontology.org/external2go/kegg_reaction2go">kegg_reaction2go</a></td> </tr> <tr> <td><a href="http://www.expasy.org/sprot/hamap/" target="blank">HAMAP</a></td> <td>High-Quality Automated and Manual Annotation of Microbial Proteomes</td> <td>All aspects </td> <td> <a href="https://geneontology.org/external2go/hamap2go">hamap2go</a></td> </tr> <tr> <td><a href="http://www.ebi.ac.uk/interpro/" target="blank">InterPro</a></td> <td>Protein families, domains and functional sites. Ecnompasses contributing databases: <a href="https://www.pantherdb.org/">PantherDB</a>, <a href="http://pfam.xfam.org/">PFAM</a>, <a href="https://proteininformationresource.org/pirsf/">PIRSF</a>, [PRINTS], <a href="https://prosite.expasy.org/">PROSITE</a> and <a href="https://smart.embl-heidelberg.de/">SMART</a></td> <td>All aspects</td> <td> <a href="https://geneontology.org/external2go/interpro2go">interpro2go</a></td> </tr> <tr> <td><a href="http://metacyc.org/" target="blank">MetaCyc</a></td> <td>Biological pathways and catalytic reactions</td> <td>Molecular Function & Biological Process</td> <td> <a href="https://geneontology.org/external2go/metacyc2go">metacyc2go</a></td> </tr> <tr> <td><a href="http://www.reactome.org/" target="blank">Reactome</a></td> <td>Events and catalyst activities</td> <td>Molecular Function</td> <td><a href="https://geneontology.org/external2go/reactome2go">reactome2go</a></td> </tr> <tr> <td><a href="http://rfam.xfam.org/" target="blank">Rfam - RNA families</a><br /></td> <td>RNA entities</td> <td>All aspects</td> <td><a href="https://geneontology.org/external2go/rfam2go">rfam2go</a></td> </tr> <tr> <td><a href="https://www.rhea-db.org/" target="blank">Rhea</a></td> <td>Catalytic reactions</td> <td>Molecular Function</td> <td><a href="https://geneontology.org/external2go/rhea2go">rhea2go</a></td> </tr> <tr> <td><a href="http://eawag-bbd.ethz.ch/aboutBBD.html" target="blank">UM-BBD</a></td> <td>Biocatalysis/Biodegradation Database: enzymes, reactions and pathways</td> <td>Molecular Function & Biological Process</td> <td><a href="https://geneontology.org/external2go/um-bbd_enzymeid2go">um-bbd_enzymeid2go</a><br /><a href="https://geneontology.org/external2go/um-bbd_reactionid2go">um-bbd_reactionid2go</a><br /><a href="https://geneontology.org/external2go/um-bbd_pathwayid2go">um-bbd_pathwayid2go</a></td> </tr> <tr> <td><a href="https://www.uniprot.org/keywords/" target="blank">UniProt Keywords</a></td> <td>Mapping of GO terms to UniProt Knowledgebase keywords.</td> <td> All aspects</td> <td><a href="https://geneontology.org/external2go/uniprotkb_kw2go">uniprotkb_kw2go</a></td> </tr> <tr> <td><a href="https://www.uniprot.org/locations/" target="blank">UniProt Subcellular location</a></td> <td>UniProt Subcellular location terms</td> <td>Cellular Component</td> <td><a href="https://geneontology.org/external2go/uniprotkb_sl2go">uniprotkb_sl2go</a></td> </tr> <tr> <td><a href="https://www.uniprot.org/help/unirule" target="blank">UniRules</a></td> <td>UniProt Automatic Annotation pipeline</td> <td>All aspects</td> <td><a href="https://geneontology.org/external2go/unirule2go">unirule2go</a></td> </tr> <tr> <td><a href="https://www.wikipedia.org/" target="blank">Wikipedia</a></td> <td> General</td> <td> All aspects</td> <td><a href="https://current.geneontology.org/ontology/external2go/wikipedia2go">wikipedia2go</a></td> </tr> </tbody> </table> <p>Direct access to the mappings file directory: <a href="https://current.geneontology.org/ontology/external2go/">https://current.geneontology.org/ontology/external2go/</a>.</p> <h2 id="cross-references-files-format">Cross-references files format</h2> <ul> <li> <p>Header describing the date generated and the GO release used, for example:</p> <p><code class="highlighter-rouge">! Generated on 2018-10-05T08:40Z from the ontology 'go' with data version: 'releases/YYYY-MM-DD'</code></p> </li> <li> <p>Each cross-reference is on a different line, in the format:</p> <p><code class="highlighter-rouge">database:term identifier (id/name) > GO:GO term name ; GO:id</code></p> <p>For example: <code class="highlighter-rouge">EC:1.1.1.1 > GO:alcohol dehydrogenase (NAD+) activity ; GO:0004022</code></p> </li> </ul> <h2 id="mapping-types--cardinality">Mapping types & cardinality</h2> <ul> <li>The cardinality of some of cross-references can be many-to-many; others are restricted.</li> <li>Cross-references can be one of 4 types: exact, broad, narrow general database cross references <ul> <li><strong>Exact database cross references</strong>: GO and cross reference object have the same meaning. <ul> <li>Cardinality: 1:1</li> </ul> </li> <li><strong>Narrow database cross references</strong>: The concept represented by the cross-reference represents a <em>narrower</em> or more specific concept than the GO term. <ul> <li>Cardinality: 1 GO:n narrow cross-references</li> </ul> </li> <li><strong>Broad database cross references</strong>: The concept represented by the cross-reference represents a <em>broader</em> or more general concept than the GO term. <ul> <li>Cardinality: n:n</li> </ul> </li> <li><strong>Related database cross references</strong>: The concept represented by the cross-reference is broad in some aspect, narrow in another. <ul> <li>Cardinality: n:n</li> </ul> </li> </ul> </li> <li>Cross references deprecated in the source database should not be included in GO.</li> </ul> <h2 id="using-and-citing-cross-references-and-mappings">Using and citing cross-references and mappings</h2> <p>If you have used a mapping in a publication or presentation, please ensure that you cite both the GO knowledgebase and the source of the mapping. 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Cross-references of external classification systems to GO