https://wiki.geneontology.org/index.php?title=WB_Progress_Report_December_2008&feed=atom&action=historyWB Progress Report December 2008 - Revision history2024-03-29T04:56:39ZRevision history for this page on the wikiMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=WB_Progress_Report_December_2008&diff=21364&oldid=prevMidori at 15:57, 20 August 20092009-08-20T15:57:46Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>We have revised the display of GO data on the gene summary pages of WormBase. Previously, all annotations were grouped by GO aspect and listed alphabetically. We now group annotations within each aspect according to one of three annotation methods: 1) manual annotation, 2) Phenotype2GO mappings, and 3) InterPro2GO mappings. In addition, the annotation details page is being revised to include more information about the supporting evidence (e.g., RNAi phenotype, variation, InterPro domain) for each annotation.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>We have revised the display of GO data on the gene summary pages of WormBase. Previously, all annotations were grouped by GO aspect and listed alphabetically. We now group annotations within each aspect according to one of three annotation methods: 1) manual annotation, 2) Phenotype2GO mappings, and 3) InterPro2GO mappings. In addition, the annotation details page is being revised to include more information about the supporting evidence (e.g., RNAi phenotype, variation, InterPro domain) for each annotation.</div></td></tr>
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</table>Midorihttps://wiki.geneontology.org/index.php?title=WB_Progress_Report_December_2008&diff=16985&oldid=prevVanaukenk: /* '''Staff''' */2008-12-08T20:55:34Z<p><span dir="auto"><span class="autocomment">'''Staff'''</span></span></p>
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<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Ranjana Kishore (funded by GOC <del style="font-weight: bold; text-decoration: none;">NIHGRI </del>grant) – manual annotation, management of GO annotation files (gene_association.wb and WormBase .ace files), Phenotype2GO mapping, GO Newsletter</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Ranjana Kishore (funded by GOC <ins style="font-weight: bold; text-decoration: none;">NHGRI </ins>grant) – manual annotation, management of GO annotation files (gene_association.wb and WormBase .ace files), Phenotype2GO mapping, GO Newsletter</div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Kimberly Van Auken – manual annotation, development of semi-automated curation methods, management of gp2protein file, Phenotype2GO mapping, gohelp desk rotation </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Kimberly Van Auken – manual annotation, development of semi-automated curation methods, management of gp2protein file, Phenotype2GO mapping, gohelp desk rotation </div></td></tr>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=WB_Progress_Report_December_2008&diff=16984&oldid=prevVanaukenk: /* '''Other Highlights''' */2008-12-08T19:08:20Z<p><span dir="auto"><span class="autocomment">'''Other Highlights'''</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">A</del>. Ontology Development Contributions:</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">a</ins>. Ontology Development Contributions:</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>WormBase continues to contribute to ontology development by contributing biological process terms regarding piRNA and 21U-RNA metabolic processes, transdifferentiation, regulation of ovulation, and cell communication processes performed by gap junction proteins.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>WormBase continues to contribute to ontology development by contributing biological process terms regarding piRNA and 21U-RNA metabolic processes, transdifferentiation, regulation of ovulation, and cell communication processes performed by gap junction proteins.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">B</del>. Annotation Outreach and User Advocacy Efforts:</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">b</ins>. Annotation Outreach and User Advocacy Efforts:</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>WormBase has recently performed a pilot experiment for user-solicited ‘first pass’ curation of newly published papers. Users were asked to flag different data types in their papers for more detailed extraction by WormBase curators. We hope that this will help to expedite identification of gene function and expression data for all data types curated by WormBase, including GO annotations. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>WormBase has recently performed a pilot experiment for user-solicited ‘first pass’ curation of newly published papers. Users were asked to flag different data types in their papers for more detailed extraction by WormBase curators. We hope that this will help to expedite identification of gene function and expression data for all data types curated by WormBase, including GO annotations. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">C</del>. Phenote for GO <del style="font-weight: bold; text-decoration: none;">and </del>Other Nematode Genomes:</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">c</ins>. Phenote for GO<ins style="font-weight: bold; text-decoration: none;">, </ins>Other Nematode Genomes<ins style="font-weight: bold; text-decoration: none;">, GO Display in WormBase</ins>:</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>(i) Development of Phenote as a GO Curation Tool:</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>(i) Development of Phenote as a GO Curation Tool:</div></td></tr>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=WB_Progress_Report_December_2008&diff=16983&oldid=prevVanaukenk: /* ''' Methods and Strategies for Annotation''' */2008-12-08T18:59:40Z<p><span dir="auto"><span class="autocomment">''' Methods and Strategies for Annotation'''</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>(ii) Electronic annotation (IEA): This method uses InterPro2GO mappings (the EBI’s assignment of GO terms to conserved protein sequences, http://www.interpro.ebi.ac.uk) provided by the EBI to automatically assign GO terms to gene products via protein domains (Mulder NJ et. al., 2002; Zdobnoy EM, et. al., 2001; Biswas M, et al., 2002).</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>(ii) Electronic annotation (IEA): This method uses InterPro2GO mappings (the EBI’s assignment of GO terms to conserved protein sequences, http://www.interpro.ebi.ac.uk) provided by the EBI to automatically assign GO terms to gene products via protein domains (Mulder NJ et. al., 2002; Zdobnoy EM, et. al., 2001; Biswas M, et al., 2002).</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">(iii) </del> Semi-Automated Cellular Component Curation Using Textpresso: In an effort to improve the efficiency with which we curate cellular component (CC) information from the literature, we have implemented a Textpresso-based semi-automated curation pipeline. On a weekly basis, new papers added to the Caltech literature curation database are automatically searched using C. elegans gene names and three new Textpresso categories developed solely for GO CC curation. Positive sentences returned by the search are then displayed in a curation form that allows curators to easily assign GO annotations based on the returned sentences. </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">c. </ins> Semi-Automated Cellular Component Curation Using Textpresso: In an effort to improve the efficiency with which we curate cellular component (CC) information from the literature, we have implemented a Textpresso-based semi-automated curation pipeline. On a weekly basis, new papers added to the Caltech literature curation database are automatically searched using C. elegans gene names and three new Textpresso categories developed solely for GO CC curation. Positive sentences returned by the search are then displayed in a curation form that allows curators to easily assign GO annotations based on the returned sentences. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The cellular component terms from the sentences and the corresponding GO term chosen for annotation are then recorded in a relationship index so that when a previously curated component term is returned in a new sentence the curation form lists, as suggested annotations, all previous annotations made from that term. The relationship index thus removes the need to repeatedly enter the same GO annotation into the form, thus helping to improve the speed of annotation.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>The cellular component terms from the sentences and the corresponding GO term chosen for annotation are then recorded in a relationship index so that when a previously curated component term is returned in a new sentence the curation form lists, as suggested annotations, all previous annotations made from that term. The relationship index thus removes the need to repeatedly enter the same GO annotation into the form, thus helping to improve the speed of annotation.</div></td></tr>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=WB_Progress_Report_December_2008&diff=16982&oldid=prevVanaukenk: /* ''' Methods and Strategies for Annotation''' */2008-12-08T18:57:26Z<p><span dir="auto"><span class="autocomment">''' Methods and Strategies for Annotation'''</span></span></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>WormBase has two types of computational annotations:</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>WormBase has two types of computational annotations:</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>(i) Phenotype2GO mappings (IMP): This method involves the manual mapping of phenotypes obtained from alleles and RNAi experiments to GO <del style="font-weight: bold; text-decoration: none;">term</del>. The mappings are used during the database build process to automatically assign GO terms to genes based upon a mutant phenotype. For example, a phenotype of ‘egg-laying defective’ (Egl) is automatically mapped to the GO biological process term ‘oviposition’. About 68 distinct phenotypes have been mapped to GO process terms and these mappings were recently updated jointly by WormBase GO and phenotype curators. </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>(i) Phenotype2GO mappings (IMP): This method involves the manual mapping of phenotypes obtained from alleles and RNAi experiments to GO <ins style="font-weight: bold; text-decoration: none;">terms</ins>. The mappings are used during the database build process to automatically assign GO terms to genes based upon a mutant phenotype. For example, a phenotype of ‘egg-laying defective’ (Egl) is automatically mapped to the GO biological process term ‘oviposition’. About 68 distinct phenotypes have been mapped to GO process terms and these mappings were recently updated jointly by WormBase GO and phenotype curators. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>(ii) Electronic annotation (IEA): This method uses InterPro2GO mappings (the EBI’s assignment of GO terms to conserved protein sequences, http://www.interpro.ebi.ac.uk) provided by the EBI to automatically assign GO terms to gene products via protein domains (Mulder NJ et. al., 2002; Zdobnoy EM, et. al., 2001; Biswas M, et al., 2002).</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>(ii) Electronic annotation (IEA): This method uses InterPro2GO mappings (the EBI’s assignment of GO terms to conserved protein sequences, http://www.interpro.ebi.ac.uk) provided by the EBI to automatically assign GO terms to gene products via protein domains (Mulder NJ et. al., 2002; Zdobnoy EM, et. al., 2001; Biswas M, et al., 2002).</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=WB_Progress_Report_December_2008&diff=16981&oldid=prevVanaukenk: /* '''Staff''' */2008-12-08T18:52:10Z<p><span dir="auto"><span class="autocomment">'''Staff'''</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 14:52, 8 December 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l22">Line 22:</td>
<td colspan="2" class="diff-lineno">Line 22:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Igor Antoshechkin – software support for gene_association.wb files</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Igor Antoshechkin – software support for gene_association.wb files</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Juancarlos Chan – software support for gene_association.wb files, .ace files, gp2protein files, curation tool development</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Juancarlos Chan – software support for gene_association.wb files, .ace files, gp2protein files, <ins style="font-weight: bold; text-decoration: none;">Phenote </ins>curation tool development</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Automated annotation based on InterPro2GO and Phenotype2GO mappings: </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Automated annotation based on InterPro2GO and Phenotype2GO mappings: </div></td></tr>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=WB_Progress_Report_December_2008&diff=16965&oldid=prevVanaukenk: /* '''Annotation Progress''' */2008-12-05T19:35:10Z<p><span dir="auto"><span class="autocomment">'''Annotation Progress'''</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:35, 5 December 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l38">Line 38:</td>
<td colspan="2" class="diff-lineno">Line 38:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Total number of genes with Phenotype2GO annotation: 4,679 (+16.98%)</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Total number of genes with Phenotype2GO annotation: 4,679 (+16.98%)</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Total number of genes with InterPro2GO annotation: 12,665 (-31.20%)<del style="font-weight: bold; text-decoration: none;">*</del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Total number of genes with InterPro2GO annotation: 12,665 (-31.20%)</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">*</del>The decrease in number of genes with InterPro2GO (IEA) annotations is due to the fact that we now map these annotations to genes, rather than protein products of which there may be multiple isoforms for a single gene.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The decrease in <ins style="font-weight: bold; text-decoration: none;">the </ins>number of genes with InterPro2GO (IEA) annotations is due to the fact that we now map these annotations to genes, rather than protein products of which there may be multiple isoforms for a single gene.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= ''' Methods and Strategies for Annotation''' =</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= ''' Methods and Strategies for Annotation''' =</div></td></tr>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=WB_Progress_Report_December_2008&diff=16964&oldid=prevVanaukenk: /* '''Annotation Progress''' */2008-12-05T19:34:29Z<p><span dir="auto"><span class="autocomment">'''Annotation Progress'''</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
<col class="diff-marker" />
<col class="diff-content" />
<col class="diff-marker" />
<col class="diff-content" />
<tr class="diff-title" lang="en">
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:34, 5 December 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l38">Line 38:</td>
<td colspan="2" class="diff-lineno">Line 38:</td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Total number of genes with Phenotype2GO annotation: 4,679 (+16.98%)</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Total number of genes with Phenotype2GO annotation: 4,679 (+16.98%)</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Total number of genes with InterPro2GO annotation: 12,665 (-31.<del style="font-weight: bold; text-decoration: none;">5</del>%)*</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Total number of genes with InterPro2GO annotation: 12,665 (-31.<ins style="font-weight: bold; text-decoration: none;">20</ins>%)*</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*The decrease in number of genes with InterPro2GO (IEA) annotations is due to the fact that we now map these annotations to genes, rather than protein products of which there may be multiple isoforms for a single gene.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*The decrease in number of genes with InterPro2GO (IEA) annotations is due to the fact that we now map these annotations to genes, rather than protein products of which there may be multiple isoforms for a single gene.</div></td></tr>
</table>Vanaukenkhttps://wiki.geneontology.org/index.php?title=WB_Progress_Report_December_2008&diff=16963&oldid=prevVanaukenk: New page: GO Progress Report Model Organism Database: WormBase December, 2008 = '''Overview''' = WormBase (www.wormbase.org) is the central repository for genomic and biological data for ...2008-12-05T19:29:53Z<p>New page: GO Progress Report Model Organism Database: WormBase December, 2008 = '''Overview''' = WormBase (www.wormbase.org) is the central repository for genomic and biological data for ...</p>
<p><b>New page</b></p><div>GO Progress Report<br />
<br />
Model Organism Database: WormBase December, 2008 <br />
<br />
<br />
= '''Overview''' =<br />
<br />
WormBase (www.wormbase.org) is the central repository for genomic and biological data for C. elegans and other related nematode species. WormBase actively annotates genes using the Gene Ontology, using both manual and computational strategies. WormBase is an active member of the Reference Genome project striving to provide broad and comprehensive annotation of the C. elegans genome.<br />
<br />
= '''Staff''' =<br />
<br />
GO Curation, Ontology Development, Outreach: <br />
<br />
Ranjana Kishore (funded by GOC NIHGRI grant) – manual annotation, management of GO annotation files (gene_association.wb and WormBase .ace files), Phenotype2GO mapping, GO Newsletter<br />
<br />
Kimberly Van Auken – manual annotation, development of semi-automated curation methods, management of gp2protein file, Phenotype2GO mapping, gohelp desk rotation <br />
<br />
Erich Schwarz – Phenotype2GO mappings <br />
<br />
Software Development and Support: <br />
<br />
Igor Antoshechkin – software support for gene_association.wb files<br />
<br />
Juancarlos Chan – software support for gene_association.wb files, .ace files, gp2protein files, curation tool development<br />
<br />
Automated annotation based on InterPro2GO and Phenotype2GO mappings: <br />
<br />
WormBase groups at Caltech and the Wellcome Trust Sanger Institute, UK.<br />
<br />
= '''Annotation Progress''' =<br />
<br />
WormBase GO Stats as of December 5, 2008:<br />
<br />
Total number of genes with at least one GO annotation: 14,381 (+1.59%) <br />
<br />
Total number of genes with manual annotation: 1,551 (+29.25%)<br />
<br />
Total number of genes with Phenotype2GO annotation: 4,679 (+16.98%)<br />
<br />
Total number of genes with InterPro2GO annotation: 12,665 (-31.5%)*<br />
<br />
*The decrease in number of genes with InterPro2GO (IEA) annotations is due to the fact that we now map these annotations to genes, rather than protein products of which there may be multiple isoforms for a single gene.<br />
<br />
= ''' Methods and Strategies for Annotation''' =<br />
<br />
90% of our effort is concentrated on manual and semi-automated literature-based annotation, with the remaining 10% of our efforts devoted to maintaining automated (IEA) annotations. <br />
<br />
a. Literature curation (All evidence codes except IEA):<br />
<br />
Priority for literature-based curation is as follows:<br />
<br />
1) Reference Genome Project Orthologs<br />
<br />
2) Well-studied C. elegans genes underrepresented with GO annotation<br />
<br />
3) Cellular component annotation as part of our semi-automated Textpresso-based curation pipeline (see below)<br />
<br />
4) Newly published papers with previously unannotated gene function <br />
<br />
5) Orthologs of human disease genes<br />
<br />
b. Computational annotation strategies: <br />
<br />
WormBase has two types of computational annotations:<br />
(i) Phenotype2GO mappings (IMP): This method involves the manual mapping of phenotypes obtained from alleles and RNAi experiments to GO term. The mappings are used during the database build process to automatically assign GO terms to genes based upon a mutant phenotype. For example, a phenotype of ‘egg-laying defective’ (Egl) is automatically mapped to the GO biological process term ‘oviposition’. About 68 distinct phenotypes have been mapped to GO process terms and these mappings were recently updated jointly by WormBase GO and phenotype curators. <br />
(ii) Electronic annotation (IEA): This method uses InterPro2GO mappings (the EBI’s assignment of GO terms to conserved protein sequences, http://www.interpro.ebi.ac.uk) provided by the EBI to automatically assign GO terms to gene products via protein domains (Mulder NJ et. al., 2002; Zdobnoy EM, et. al., 2001; Biswas M, et al., 2002).<br />
<br />
(iii) Semi-Automated Cellular Component Curation Using Textpresso: In an effort to improve the efficiency with which we curate cellular component (CC) information from the literature, we have implemented a Textpresso-based semi-automated curation pipeline. On a weekly basis, new papers added to the Caltech literature curation database are automatically searched using C. elegans gene names and three new Textpresso categories developed solely for GO CC curation. Positive sentences returned by the search are then displayed in a curation form that allows curators to easily assign GO annotations based on the returned sentences. <br />
<br />
The cellular component terms from the sentences and the corresponding GO term chosen for annotation are then recorded in a relationship index so that when a previously curated component term is returned in a new sentence the curation form lists, as suggested annotations, all previous annotations made from that term. The relationship index thus removes the need to repeatedly enter the same GO annotation into the form, thus helping to improve the speed of annotation.<br />
<br />
= '''Presentations and Publications''' =<br />
<br />
a. Papers with substantial GO content: <br />
<br />
Rogers A, et al., (2008) WormBase 2007. NAR Jan; 36 (Database Issue): D612-7.<br />
<br />
Van Auken KM, Jaffery J, Chan J, Mueller HM, Sternberg P (2008) Semi-Automated Curation of Protein Subcellular Localization: A Text Mining-Based Approach to Gene Ontology (GO) Cellular Component Curation. In preparation. <br />
<br />
b. Presentations: No GO-related presentations in 2008.<br />
<br />
<br />
= '''Other Highlights''' =<br />
<br />
A. Ontology Development Contributions:<br />
WormBase continues to contribute to ontology development by contributing biological process terms regarding piRNA and 21U-RNA metabolic processes, transdifferentiation, regulation of ovulation, and cell communication processes performed by gap junction proteins.<br />
<br />
B. Annotation Outreach and User Advocacy Efforts:<br />
WormBase has recently performed a pilot experiment for user-solicited ‘first pass’ curation of newly published papers. Users were asked to flag different data types in their papers for more detailed extraction by WormBase curators. We hope that this will help to expedite identification of gene function and expression data for all data types curated by WormBase, including GO annotations. <br />
<br />
C. Phenote for GO and Other Nematode Genomes:<br />
<br />
(i) Development of Phenote as a GO Curation Tool:<br />
In collaboration with Mark Gibson, WormBase has developed the Phenote annotation tool for use with GO curation. Phenote, a Java-based curation tool originally developed for phenotype and trait annotation using ontologies, has a number of desirable features, such as auto-suggest and bulk annotation, that we felt would be advantageous for GO curation. After several months of development and testing, we have now fully transitioned from our previous web-based GO curation pipeline to Phenote-based curation.<br />
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(ii) Annotation of genes from other nematode species:<br />
In the early part of 2007, WormBase added InterPro2GO annotations for gene products from the related nematode species C. briggsae. As additional nematode genomes are sequenced and incorporated into WormBase, we will add InterPro2GO annotations to both WormBase and the GO Consortium. New species to be added include: C. remanei and P. pacificus.<br />
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D. New GO Display in WormBase<br />
We have revised the display of GO data on the gene summary pages of WormBase. Previously, all annotations were grouped by GO aspect and listed alphabetically. We now group annotations within each aspect according to one of three annotation methods: 1) manual annotation, 2) Phenotype2GO mappings, and 3) InterPro2GO mappings. In addition, the annotation details page is being revised to include more information about the supporting evidence (e.g., RNAi phenotype, variation, InterPro domain) for each annotation.</div>Vanaukenk