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2024-03-28T15:45:05Z
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https://wiki.geneontology.org/index.php?title=Projects_update_meeting_2024-03-27&diff=86789&oldid=86780
Projects update meeting 2024-03-27
2024-03-27T15:18:57Z
<p><span dir="auto"><span class="autocomment"> Pipeline</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 11:18, 27 March 2024</td>
</tr><tr><td colspan="4" class="diff-multi" lang="en">(3 intermediate revisions by the same user not shown)</td></tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l14">Line 14:</td>
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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"></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>==Update on projects==</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>==Update on projects==</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>===<del style="font-weight: bold; text-decoration: none;">Pipeline</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>===<ins style="font-weight: bold; text-decoration: none;">[https://github.com/geneontology/project-management/issues/88 Pipeline]</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>* New system with snapshot being promoted to a release being put in place</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>* New system with snapshot being promoted to a release being put in place</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>* Pascale checked diff: long lag, many differences</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>* Pascale checked diff: long lag, many differences</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>* QUESTION: Should we release TreeGrafter annotations? considering quite a few errors, I think because IBD are not picked up and therefore not filtered by the P2GO pipeline</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>* QUESTION: Should we release TreeGrafter annotations? considering quite a few errors, I think because IBD are not picked up and therefore not filtered by the P2GO pipeline</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>* Request is for GOA to filter the 143 Panther species; Alex was reluctant to do that, but it seems we're adding a lot of undesired 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>* Request is for GOA to filter the 143 Panther species; Alex was reluctant to do that, but it seems we're adding a lot of undesired 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> </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;">* AI Pascale create gorule </ins></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;"><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>[[Category: GO Managers Meetings]]</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>[[Category: GO Managers Meetings]]</div></td></tr>
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Pascale
https://wiki.geneontology.org/index.php?title=Ontology_meeting_2024-04-08&diff=86785&oldid=86769
Ontology meeting 2024-04-08
2024-03-27T07:22:52Z
<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 03:22, 27 March 2024</td>
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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>=Discussion points= </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>=Discussion points= </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>Ontobot action to add a term to the 'do not annotate' subset does not create the comment we used to have (something like, "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.") (questing indirectly coming from https://github.com/geneontology/go-ontology/issues/27194) </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;">==Ontobot actions==</ins></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><del style="font-weight: bold; text-decoration: none;">*</del>* Should Ontobot also do that? </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;">===Triggering multiple actions???=== </ins></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><del style="font-weight: bold; text-decoration: none;">*</del>* Can we/should we add a check that all 'do not annotate' terms have a comment? </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>Ontobot action to add a term to the 'do not annotate' subset does not create the comment we used to have (something like, "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.") (questing indirectly coming from https://github.com/geneontology/go-ontology/issues/27194) </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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>* Should Ontobot also do that? </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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>* Can we/should we add a check that all 'do not annotate' terms have a comment? </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 colspan="2" class="diff-side-deleted"></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;">===Proposals for new ontobot actions===</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">====Removing a term from a subset====</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">====Obsoletion====</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">* Edits needed to obsolete a term: </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">** term label (=append obsolete)</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">** term definition (=append OBSOLETE.)</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">** insert obsoletion comment (note that this clashes when there is another existing comment; is this restriction useful?)</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">** insert 'replace by' or 'consider'</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">** remove obsolete cross-references (can be done as an automated post-processing step? ie create a check that removes any obsolete/deprecated cross reference from obsolete terms)</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 colspan="2" class="diff-side-deleted"></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;">====Obsoletion & 'consider' terms in the logical definition====</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">* This would be useful to bulk obsolete pre-composed terms</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 colspan="2" class="diff-side-deleted"></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;">====Bulk update specific keywords====</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">* Workflow 1: replacement of a ChEBI term in the logical definitions of x terms (or asserted superclasses) </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">(see PR here: https://github.com/geneontology/go-ontology/commit/fb12048ab6385e6890621d2971e9aed6862692ec; this is just 3-4 ChEBI terms, and some terms are not fully updated yet)</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">(For example for the ChEBI 7.3 work: we want to replace 'tyrosine' by 'L-tyrosine' in all the terms that use L-tyrosine in the LD): </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">** step 1: replace all instances of chebi:tyrosine to chebi:L-tyrosine (this would be manual or at least a separate PR to ensure that this replacement doesn't go on unintended terms) </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">** automatic steps</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">*** replace chebi:tyrosine to chebi:L-tyrosine in ***term label*** (note that we also need to insert the old term label as a broad synonym or we will get a Travis error; maybe this can be relaxed)</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">*** replace chebi:tyrosine to chebi:L-tyrosine in ***term definition***</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">*** replace chebi:tyrosine to chebi:L-tyrosine in ***term synonyms***</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">==New subsets yaml==</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">* 2 points are not checked off here: https://github.com/geneontology/go-ontology/pull/27414#event-12256156352</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">** add checks to github actions (@balhoff @kltm we are using latest-ish version of odk? in which case linkml is included)</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">** make an OBO PURL that resolves to this</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">do they need to be done? </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">* should we make sure we use the 'main label' for each field, and not aliases (ie 'type' versus 'role'). In other words, how are users interacting with this file? Are we sure that they will be able to use field with various/varied labels ? (it's not more work for us to be consistent)</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>[[Category:Meetings]]</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>[[Category:Meetings]]</div></td></tr>
</table>
Pascale
https://wiki.geneontology.org/index.php?title=Talk:Annotation_Conf._Call_2024-03-26&diff=86784&oldid=86783
Talk:Annotation Conf. Call 2024-03-26
2024-03-26T19:14:23Z
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Suzialeksander
https://wiki.geneontology.org/index.php?title=Talk:Annotation_Conf._Call_2024-03-26&diff=86783&oldid=0
Talk:Annotation Conf. Call 2024-03-26
2024-03-26T19:13:32Z
<p>Created page with "GO Annotation Call Today at 09:00 wpk Notes Generated by Wudpecker Like what you see? Try Wudpecker. For free. Try Wudpecker 00:00 /53:49 Kimberly Van Auken 00:17 Susie, did you just set up the recording? Suzi Aleksander 00:23 I did not set it up. I thought I think Stasha set it up on all of SGDs. I don't didn't she didn't say she applied it to this. Okay. Kimberly Van Auken 00:32 Bye. I'm just wondering. Suzi Aleksander 00:34 Yeah. It's like an AI thing that takes not..."</p>
<p><b>New page</b></p><div>GO Annotation Call<br />
<br />
Today at 09:00<br />
wpk<br />
Notes Generated by Wudpecker<br />
<br />
Like what you see? Try Wudpecker. For free.<br />
Try Wudpecker<br />
00:00<br />
/53:49<br />
Kimberly Van Auken<br />
00:17<br />
Susie, did you just set up the recording?<br />
Suzi Aleksander<br />
00:23<br />
I did not set it up. I thought I think Stasha set it up on all of SGDs. I don't didn't she didn't say she applied it to this. Okay.<br />
Kimberly Van Auken<br />
00:32<br />
Bye. I'm just wondering.<br />
Suzi Aleksander<br />
00:34<br />
Yeah. It's like an AI thing that takes notes for you somehow.<br />
Malcolm Fisher<br />
00:38<br />
Okay. Is is it Wudpecker?<br />
Kimberly Van Auken<br />
00:41<br />
Yes. Yes.<br />
Malcolm Fisher<br />
00:43<br />
Yeah. We we try that. It's not great. It's not terrible. Okay.<br />
Kimberly Van Auken<br />
00:52<br />
Yeah. Just wanted to make sure I understood what was going on. And also, I mean, recording these calls is not something we routinely do. I know people would find that helpful. We could certainly consider that.<br />
Suzi Aleksander<br />
01:14<br />
Yeah. Let's give it a shot and then I'll review the the notes that it takes and see if they're<br />
Kimberly Van Auken<br />
01:20<br />
Yeah. No. That'd be all informative. I mean, it might be helpful, yeah, for them taking that. And, putting, putting things back on the wiki. Yeah.<br />
Suzi Aleksander<br />
01:31<br />
Yeah. We'll see.<br />
Malcolm Fisher<br />
01:33<br />
Okay. I I'd say I think it kind of is useful to have the the the automated transcript. It's just it it's a shame. It's not a little bit better at actually understanding what people are saying. Okay. But it's a technical we use a lot of technical language. It's not super surprising that it has trouble parsing that sort of thing in it.<br />
Kimberly Van Auken<br />
01:51<br />
Okay. Alright. Well, let's try it.<br />
Suzi Aleksander<br />
02:01<br />
Okay.<br />
Kimberly Van Auken<br />
02:08<br />
So I'll try to speak very clearly then. Okay. So, thanks everybody for coming. Today's, announcement. So we will have our, next March, not to an outage this coming Thursday from about, 4 to 6 PM, Pacific daylight time. And the link to the ticket where, we go through all of our regular outage tasks. And if there's anything special for this outage, it will be there as well. So just make sure at the end of the day, on Thursday, if you've been working on KnockTuit, check the landing page and make sure all of your work is saved. Isn't usually a problem, but I just, like people to double check. Next week, the week of April first, is a no go calls week. It is the week after Easter. So I think some people, are gonna be away anyway for easter holidays. I know Pascal and I are both out, that week. But, just so everybody knows on the Nicole calls week, we cancel most of our regularly scheduled go meetings just to give people a little bit more time, to do other work. Our, again, our next in person consortium meeting is, in May hosted by Jim Balhoff, in Chapel Hill. North Carolina. So the plan right now is to have a user's meeting that Monday, with some local, go users and attendees. And then our actual consortium meeting dates will be Tuesday, Wednesday, and Thursday. If you are planning, to attend, please register. I think Susie is either both in person and virtual, right, just so we know. Sorry. I had forgotten from when I, registered.<br />
Suzi Aleksander<br />
04:14<br />
Yeah. There's in person and there's, there will be a normal virtual option. And if you're sharing a connection with somebody, go ahead and register each person just so we know how many people are are attending.<br />
Kimberly Van Auken<br />
04:28<br />
Yep. Okay. Great. And some I know Jim has put some additional, logistics up, more recently about, travel. So, we talked about airports. There's some more specific information here about the Raleigh Durham, airport. And then also he has blocked rooms at 2 hotels that are within walking distance. And so 1 of those boxes open until the nineteenth, 1 of them is only open, until, into next week. So if you are going to, attend in person, make sure you get, if you wanna stay at 1 of these hotels, make sure you get your reservation done. And then, we continue to sort of work on the agenda, But I think if there are things in particular that, people would like to talk about or hear about, please let us know or put a comment here on the agenda, so that we can start, shoring this up soon. Alright. Onto the go release pipeline. So, We're almost towards the end of March, so I think it looks like some other issues have cropped up, with trying to get a snapshot released. Out. I hear so.<br />
Seth Carbon<br />
06:06<br />
Well, snap shot may have cleared. So I think that's yeah. I know. I think we've figured a bunch of stuff out, and I think we actually have a good forward. So it looks like a snapshot may have cleared. That will be checked.<br />
Pascale Gaudet<br />
06:17<br />
There is a snapshot. Right? Like, it's there. Yeah.<br />
Seth Carbon<br />
06:22<br />
Yeah. Yeah. I just wanna make sure it looks okay to<br />
Pascale Gaudet<br />
06:24<br />
Yeah. Yeah. Right. But we never just check it. Yeah. Yeah. I know.<br />
Seth Carbon<br />
06:28<br />
So, yeah, this is just a single 1 time quality control ask if you pass<br />
Pascale Gaudet<br />
06:32<br />
out just to make No. No. No. I understand, but just, you know, so people may maybe know what we're gonna do moving forward. But, you know, this is, like, in the old days, we would say the snapshot part.<br />
Kimberly Van Auken<br />
06:45<br />
Yeah. So It's there. Yeah.<br />
Seth Carbon<br />
06:47<br />
Yeah. There's a snapshot there. It is the it is the most, updated thing we're we're taking a look at just to make sure the changes we made have any effects that we don't understand. But I believe that using this method will now have a very assuming this this worked out okay within the next day or so it will by 1 method or another, we'll be starting the release process. So we're we're actually feeling pretty good about that right now. But yeah, so things are probably gonna be taking over again and are likely Again, if this thing we did work, we're likely to be taking over into the future as well. This will be a a fairly good fix for the issues we've been having.<br />
Kimberly Van Auken<br />
07:28<br />
Okay. Fantastic.<br />
Pascale Gaudet<br />
07:29<br />
That is<br />
Kimberly Van Auken<br />
07:30<br />
great to hear. 1 thing I did wanna follow-up from last week is because I was looking last night for more information about this. So we had talked about sort of independently producing, you know, up to date ontology files. Or, able to slurp up into their tools. And I was trying to look because I thought I had seen a ticket come by about more information about these. And I couldn't find it again last night. So is there an update here that I can add?<br />
Pascale Gaudet<br />
08:03<br />
So this is now happening. Protein to go is now loading it. So normally people annotating and protein to go, they would have, like, every day, the new version of the ontology. Okay. And if you go on the Wiki, I put a link to this. If you go on the Wiki main page, and then if she resource for contributing group, I put rosling build up the oncology. So when we talked about this last week, I called it daily and said corrected me in design with that. It's multiple daily, and it may be that some days if really something is broken that something will not happen. So it's rolling in a sense that it's, like, pretty much I don't wanna say continuous, but, you know Well, I mean, it actually is. Yeah.<br />
Seth Carbon<br />
08:51<br />
I know it absolutely it it is actually again, these are these are super, like, I'm I'm being very specific about the words for Yeah. Maybe a very good reasons. But But it's but it is essentially this is an extension of our ontology QC process. So if it's passing the extended QC process, it automatically gets elevated. And this is attempted 3 times a day on the ontology. So<br />
Pascale Gaudet<br />
09:13<br />
So the g c process is all automated just to<br />
Seth Carbon<br />
09:16<br />
Yes. Yes. This is a fully automated extended QZ process on the apology.<br />
Pascale Gaudet<br />
09:20<br />
So I'd like the pipeline where I check a few things. This is Yeah.<br />
Seth Carbon<br />
09:23<br />
Yeah. Yeah. This is fully automated.<br />
Kimberly Van Auken<br />
09:26<br />
Right. Right.<br />
Seth Carbon<br />
09:27<br />
But basically, it's it's because there are not, like, some QC checks can't run inside of GitHub. And so we're running them on a larger machine essentially. And if it's passing that extended set, the the the larger set of QC, it automatically gets promoted to this. Location. And so that's what you're that's what we're working with here. So it is m usually, it's gonna be multiple times a day. It's going to be the it's checking out from GitHub and just building it and putting it out. It's not, you know, it's not dated and archived like the other stuff. It really is just sort of a rolling release, the current ontology as it is right now. Okay.<br />
Kimberly Van Auken<br />
10:08<br />
And so It says here is producing, and Seth, you said attempting. So I just wanted to yeah. Yeah. What's the what's really the expectation. Yeah.<br />
Seth Carbon<br />
10:27<br />
We'll see the expectation essentially. And and I think the people who work on the ontology, you know, sometimes, you know, something breaks. Some either data has gotten into the oboe file and it's no longer able to build or there's some upstream build issue. And essentially, that is the this is an extension of that. So it's basically that plus additional check. So if there are issues in the ontology, This may not be built for days. Right? Right. So, however, to formulate this, that this is essentially 3 time, just 1 moment. It's it's attempted 3 times a day, and, it's, basically gonna go on the same kind of, a schedule as yeah. I'm sorry. I lost my train of thought there.<br />
Kimberly Van Auken<br />
11:21<br />
Yeah. But I mean, I guess<br />
Pascale Gaudet<br />
11:23<br />
the question was, how to formulate it? Yeah. I'm doing the<br />
Kimberly Van Auken<br />
11:27<br />
So it sounds like, go. We'll attempt to produce it 3 times a day, but There's a possibility if something happens with, say, an ontology pull request or a QC check.<br />
Pascale Gaudet<br />
11:38<br />
Yeah.<br />
Kimberly Van Auken<br />
11:39<br />
It may not. Be 3 times a day.<br />
Pascale Gaudet<br />
11:41<br />
So so maybe I can It is attempted.<br />
Seth Carbon<br />
11:43<br />
Yeah. Yeah.<br />
Kimberly Van Auken<br />
11:45<br />
Okay. Because I think we<br />
Pascale Gaudet<br />
11:47<br />
we should keep while in this thermostat. In theory, especially this is not very big. You know, so maybe I just add, like, that if there are problems, it may be that this is not being built, you know.<br />
Kimberly Van Auken<br />
12:06<br />
Right.<br />
Seth Carbon<br />
12:06<br />
Yeah. I mean, that that's really what it is.<br />
Kimberly Van Auken<br />
12:16<br />
The frequency maybe less or something like that. Okay.<br />
Pascale Gaudet<br />
12:29<br />
Yeah.<br />
Kimberly Van Auken<br />
12:32<br />
Just wanna make sure.<br />
Pascale Gaudet<br />
12:33<br />
Yeah. Yeah. Yeah. The the the yeah.<br />
Kimberly Van Auken<br />
12:36<br />
Is there something else that I yeah. I just wanna make sure it's the expectation is clear. Mhmm. But this is great, though. I mean, I think it allow us to have much better So I'm just gonna put the link here.<br />
Pascale Gaudet<br />
12:58<br />
So that's why I wrote please look at the file to see, but this is this is, I'm just gonna add this.<br />
Kimberly Van Auken<br />
13:05<br />
Okay.<br />
Pascale Gaudet<br />
13:05<br />
To the other point. And so, yeah, just reformulating this, you can it can reload, but you can give feedback. I mean, we can always right edit this, but it was just put some documentation. Yep. And I I this was also sent to, Bumbays and Thair. I don't know if other groups wanna have access to this directly for their annotation tool. Yeah, but But, yeah, this is this is where we're at. It's very good. Like, Yeah. To be able to have a more up to date version of the internet.<br />
Kimberly Van Auken<br />
13:52<br />
Okay. Great. Thanks. So that was generally all that we had you're formally on the agenda. The 1 thing I also just wanted to mention is, the status of the noctua standard annotation tool. So I I was doing some testing this morning. There are a few more things I wanna work out with Jermaine before, unleashing it on the rest<br />
Pascale Gaudet<br />
14:15<br />
of the<br />
Kimberly Van Auken<br />
14:15<br />
curators. But my hope is that, you know, when we get back from the the early April breaks, that this can go out to some curators for some some feedback. Our aim is to have, something ready to go by the May consortium meeting, but I definitely want, curator feedback before then. It is on not to a dev. If anybody wants to take a look, but I will, issue a fair warning that it is still a work in progress. So there are definitely things that we know we still have to do, but I just wanna keep everybody up to date on what going on with that. Thanks, Leonor. And then, unless there's anything else that people would like to, ask about or discuss, then, as we often do, I was just going to propose that we use the remainder of the time. For people, to work together on annotation reviews. So if you have any questions, we can all, be here, to help with that.<br />
Suzi Aleksander<br />
15:43<br />
Alright.<br />
Kimberly Van Auken<br />
15:49<br />
Then, I will just go on mute and if people want to stay to work on reviews, that's great. If not, you have another extra 40 minutes in your day. Hey, Pascal. I have a question for you. Mhmm. Because I'm just looking over some of the annotation reviews that, Wormace recently got flagged for.<br />
Pascale Gaudet<br />
25:57<br />
Okay. And,<br />
Kimberly Van Auken<br />
26:00<br />
I had actually already done them. Right?<br />
Pascale Gaudet<br />
26:03<br />
Oh, that's okay.<br />
Kimberly Van Auken<br />
26:05<br />
Yeah. And I done them in protein to go. But it looks like they haven't percolated to<br />
Pascale Gaudet<br />
26:12<br />
No. That wasn't a release. Yeah. That's why it's super confusing when we don't get it at least forever. I don't wanna go ahead and do anything. Yeah. We all waste a lot of time with this. I'm sorry.<br />
Kimberly Van Auken<br />
26:25<br />
And Yeah. It's it's okay. Right? It's say, but I guess what I'm wondering is that, So these were I mean, since these were done in protein to go and edited in pro team to go. Yeah. If so I guess 1 is the the the source that ontology editors always use for this is amigo. Is that right? Or do you use quick go to<br />
Pascale Gaudet<br />
27:02<br />
Oh, no. No. Yeah. I normally use, yeah, I normally use quick go Amigo because we also we have these little, like, actions, you know, where we can easily get everything.<br />
Kimberly Van Auken<br />
27:14<br />
But Yeah.<br />
Pascale Gaudet<br />
27:15<br />
I mean, this is 1 big, issue with not having frequent releases because then we all, you know, waste time. Like, I go and like, this is not fixed. And I guess I should have thought check-in protein to go. And, you know, sometimes I open it like 3 months ago, so I just wanna know where standing now.<br />
Kimberly Van Auken<br />
27:38<br />
Right. Right.<br />
Pascale Gaudet<br />
27:38<br />
And then it's always, you know. Because between the quick release, and our release, we can be 3, 4 months out of date.<br />
Kimberly Van Auken<br />
27:48<br />
Yeah. And then add the worm base release. So I belong to that. It could be<br />
Pascale Gaudet<br />
27:53<br />
Sure. Produce. And so, you know, this is, like, I find this is where we it's like, where we waste a lot of time and energy. Yeah. You know, like, because I look at this. I'm like, okay, I think I know what I have to do. Oh, oops. There's many people who need to change their annotation. I'm not gonna pull the carpet under them. Yeah. Yeah. Right. And so then I try not to do that. Then I send another notification, then you go, you waste your time.<br />
Kimberly Van Auken<br />
28:25<br />
So Yeah. Yeah. No. But I had the same thing. I'm like, darn. I thought I did this.<br />
Pascale Gaudet<br />
28:32<br />
Well, I just wonder if maybe I could also, It sounds like it sounds like we need to get this at the source.<br />
Kimberly Van Auken<br />
28:42<br />
Yes. We would need<br />
Pascale Gaudet<br />
28:43<br />
to get this in, like, to, and in, you know, protein to go, not even a quick go.<br />
Kimberly Van Auken<br />
28:49<br />
Exactly. Exactly. Yeah. Yeah. Yep. Okay. Yeah. Just just double checking.<br />
Pascale Gaudet<br />
28:57<br />
Yeah. Yeah. But it's like it's super Like, it's a massive waste of it of energy and of like, you know, task switching. This is like, yeah.<br />
Kimberly Van Auken<br />
29:11<br />
Yep. Okay. Very costly. Yeah. Yeah. Yeah.<br />
Pascale Gaudet<br />
29:18<br />
Okay. Anyways, let's keep in mind. But, you know, I don't like to have an immediate solution. Right.<br />
Malcolm Fisher<br />
29:24<br />
Right.<br />
Pascale Gaudet<br />
29:25<br />
But honestly, Yeah. Honestly, I think this is a high priority. I guess this is why I'm just trying to see can I Let me come up with something clever?<br />
Kimberly Van Auken<br />
29:38<br />
Yeah. I mean, I think right. The the short answer is we need immediate access to the curation databases.<br />
Pascale Gaudet<br />
29:49<br />
Exactly. Yeah.<br />
Kimberly Van Auken<br />
29:52<br />
Yep. Okay. Mhmm.<br />
Pascale Gaudet<br />
29:56<br />
Yep.<br />
Siegele, Deborah A<br />
40:42<br />
Kimberly. This is Debbie.<br />
Kimberly Van Auken<br />
40:46<br />
Hey, Debbie.<br />
Siegele, Deborah A<br />
40:47<br />
Hey. Is there a way in protein to go to, look for the annotations that, cacao made or any particular group made<br />
Kimberly Van Auken<br />
41:03<br />
I believe you can do that with their reports.<br />
Siegele, Deborah A<br />
41:07<br />
Oh, okay.<br />
Pascale Gaudet<br />
41:10<br />
Let<br />
Kimberly Van Auken<br />
41:13<br />
me share my screen. Okay. Yeah. So we go to reports. Think that. Oh, 0, okay. I can do this.<br />
Siegele, Deborah A<br />
41:37<br />
Okay. Oh, great. Because I was trying to fix some things in protein to go. And I thought it would be easier if I could just pull up all of the cacao ones instead of, like, searching by protein. Mhmm.<br />
Pascale Gaudet<br />
41:57<br />
And here yeah. You should also, be able to see, like, air reports, you know, like, give me everything.<br />
Siegele, Deborah A<br />
42:07<br />
Oh, okay.<br />
Pascale Gaudet<br />
42:08<br />
Like, the sanity checks, they call it. Yeah. Oh, I think that's selling. So, you know,<br />
Siegele, Deborah A<br />
42:13<br />
the Oh, yes. Yes. Yeah.<br />
Pascale Gaudet<br />
42:15<br />
Not quite the same as, the tickets to create. But, yeah, if you have any heirs?<br />
Siegele, Deborah A<br />
42:24<br />
Yeah. This this is this is helpful.<br />
Kimberly Van Auken<br />
42:27<br />
Yep. This is a time saver for sure. Yes.<br />
Siegele, Deborah A<br />
42:31<br />
Okay. Thank you. Sure. Bye bye.<br />
Pascale Gaudet<br />
53:31<br />
Okay. I'm gonna disconnect because I need to change rooms for the next Paul. Okay.<br />
Kimberly Van Auken<br />
53:36<br />
Alright. Sounds good. I wanna call then. Thanks, everybody, for coming. And,<br />
Pascale Gaudet<br />
53:43<br />
see you in a minute.<br />
Kimberly Van Auken<br />
53:44<br />
Talk in 2 weeks.<br />
Pascale Gaudet<br />
53:45<br />
Okay. Yeah. Bye.</div>
Suzialeksander
https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2024-03-26&diff=86782&oldid=86779
Annotation Conf. Call 2024-03-26
2024-03-26T19:09:27Z
<p><span dir="auto"><span class="autocomment">AI summary</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:09, 26 March 2024</td>
</tr><tr><td colspan="4" class="diff-multi" lang="en">(One intermediate revision by the same user not shown)</td></tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l36">Line 36:</td>
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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>== Ontology ==</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>== Ontology ==</div></td></tr>
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<tr><td colspan="2" class="diff-side-deleted"></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;">= AI summary=</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">Wudpecker (https://app.wudpecker.io/shared/cb3b5920-a970-4fd7-ac9e-38a77aa47f19)</ins></div></td></tr>
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<tr><td colspan="2" class="diff-side-deleted"></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;">Key Decisions</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"> Agreement to consider recording calls for future use and review the notes it takes.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"> Approval of an upcoming outage on Thursday from 4 to 6 PM PDT, with a link provided for regular outage tasks.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"> Decision to hold the next in-person consortium meeting in May in Chapel Hill, North Carolina, with both in-person and virtual options available.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">Recording Calls</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"> Kimberly Van Auken suggests considering recording calls for future use.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"> Suzi Aleksander agrees to try it and review the notes it takes.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"> Malcolm Fisher comments on the usefulness of automated transcripts but acknowledges their limitations with technical language.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">Upcoming Outage and Meetings</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"> An outage is announced for Thursday from 4 to 6 PM PDT.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"> The next in-person consortium meeting will be held in May, hosted by Jim Balhoff in Chapel Hill, North Carolina.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"> There will be both in-person and virtual options for attending the meeting.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">Go Release Pipeline Update</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"> Seth Carbon provides an update on the go release pipeline, mentioning that a snapshot may have cleared and they are feeling good about starting the release process soon.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"> Pascale Gaudet confirms the existence of a snapshot and mentions ongoing work to ensure its quality.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"> Kimberly Van Auken expresses satisfaction with the progress and asks about independently producing up-to-date ontology files.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">Ontology Building Process</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"> Pascale Gaudet explains that Protein2GO is now loading the ontology daily and provides a link to the Wiki page with more information.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"> Seth Carbon elaborates on the automated extended QC process for the ontology and how it is used to produce the rolling release of the ontology multiple times a day.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"> Kimberly Van Auken seeks clarification on the frequency and expectations of the rolling release.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">Annotation Reviews</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"> Issues with annotation reviews not being updated in a timely manner were discussed.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"> The source used for annotation reviews is AmiGO, but there can be delays between releases.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"> Importance of immediate access to curation databases to avoid wasting time and energy was highlighted.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"></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;"><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>
Suzialeksander
https://wiki.geneontology.org/index.php?title=Projects_update_meeting_2024-03-27&diff=86780&oldid=0
Projects update meeting 2024-03-27
2024-03-26T15:54:58Z
<p>Created page with "= Attendees = * Members: Kimberly, Pascale, Seth, Suzi, Jim, Huaiyu, Paul, Chris, Cynthia * Present: * Regrets: = Discussion topics = ==GO meeting== * Registration form by March 15th * Agenda by May 1st * Which days do we need on either side? * Draft agenda: https://docs.google.com/document/d/1FwGxa4jx8rJFjWBcbn4Q7ZzOHCY6-oF0azOrtK3quyk/edit#heading=h.2jptrbvdxk9r * GO Users meeting: https://docs.google.com/document/d/1sIamECzTS5IMOy4GeldzWXdawnmOLvT9s5vClMAs3Bo/edit..."</p>
<p><b>New page</b></p><div>= Attendees =<br />
* Members: Kimberly, Pascale, Seth, Suzi, Jim, Huaiyu, Paul, Chris, Cynthia<br />
* Present:<br />
* Regrets:<br />
<br />
= Discussion topics =<br />
<br />
==GO meeting==<br />
* Registration form by March 15th<br />
* Agenda by May 1st<br />
* Which days do we need on either side?<br />
* Draft agenda: https://docs.google.com/document/d/1FwGxa4jx8rJFjWBcbn4Q7ZzOHCY6-oF0azOrtK3quyk/edit#heading=h.2jptrbvdxk9r<br />
* GO Users meeting: https://docs.google.com/document/d/1sIamECzTS5IMOy4GeldzWXdawnmOLvT9s5vClMAs3Bo/edit<br />
<br />
==Update on projects==<br />
===Pipeline===<br />
* New system with snapshot being promoted to a release being put in place<br />
* Pascale checked diff: long lag, many differences<br />
* QUESTION: Should we release TreeGrafter annotations? considering quite a few errors, I think because IBD are not picked up and therefore not filtered by the P2GO pipeline<br />
* Request is for GOA to filter the 143 Panther species; Alex was reluctant to do that, but it seems we're adding a lot of undesired annotations <br />
<br />
<br />
<br />
[[Category: GO Managers Meetings]]</div>
Pascale
https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2024-03-26&diff=86779&oldid=86775
Annotation Conf. Call 2024-03-26
2024-03-26T15:17:03Z
<p><span dir="auto"><span class="autocomment">Attendees</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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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 11:17, 26 March 2024</td>
</tr><tr><td colspan="4" class="diff-multi" lang="en">(One intermediate revision by the same user not shown)</td></tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l23">Line 23:</td>
<td colspan="2" class="diff-lineno">Line 23:</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>** Up-to-date ontology files are now being produced independently, though</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>** Up-to-date ontology files are now being produced independently, though</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>** Pascale will provide more information on how to access these for your curation tools/pipelines</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>** Pascale will provide more information on how to access these for your curation tools/pipelines</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">** https://wiki.geneontology.org/Rolling_build_of_the_Gene_Ontology</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>* #release-pipeline Slack channel for updates</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>* #release-pipeline Slack channel for updates</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 colspan="2" class="diff-lineno" id="mw-diff-left-l38">Line 38:</td>
<td colspan="2" class="diff-lineno">Line 39:</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>== Attendees ==</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>== Attendees ==</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>*On call: Debby, Dmitry, Dustin, Edith, Kimberly, Leonore, Li, Malcolm, Mary, Pascal, Pascale, Patrick, Raymond, Rossana, Seth, Sridhar, Steven, Suzi</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>*On call: Debby, Dmitry, Dustin, Edith, Kimberly, Leonore, Li, Malcolm, Mary, Pascal, Pascale, Patrick, Raymond, Rossana, Seth, Sridhar, Steven, Suzi<ins style="font-weight: bold; text-decoration: none;">, Val</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>[[Category:Annotation Working Group]]</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>[[Category:Annotation Working Group]]</div></td></tr>
</table>
Vanaukenk
https://wiki.geneontology.org/index.php?title=Rolling_build_of_the_Gene_Ontology&diff=86778&oldid=86776
Rolling build of the Gene Ontology
2024-03-26T15:14:40Z
<p></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 11:14, 26 March 2024</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l2">Line 2:</td>
<td colspan="2" class="diff-lineno">Line 2:</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>As of March 18, 2024, GO will attempt to produce the latest version of the ontology 3 times a day. '''This version is not checked or versioned or archived, therefore not citable. If there are problems with the ontology build, the frequency may be less.'''</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>As of March 18, 2024, GO will attempt to produce the latest version of the ontology 3 times a day. '''This version is not checked or versioned or archived, therefore not citable. If there are problems with the ontology build, the frequency may be less.'''</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>The latest build of the ontology can be found here: https://ontology-build.geneontology.org/</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;">* </ins>The latest build of the ontology can be found here: https://ontology-build.geneontology.org/</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>Please look in the file header to see when the file was generated.</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;">* Note that if there is a failure of the ontology build, the ontology production will be automatically halted until the issue is resolved. </ins>Please look in the file header to see when the file was generated.</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>==Who should use this file==</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>==Who should use this file==</div></td></tr>
</table>
Pascale
https://wiki.geneontology.org/index.php?title=Rolling_build_of_the_Gene_Ontology&diff=86776&oldid=86752
Rolling build of the Gene Ontology
2024-03-26T15:13:57Z
<p><span dir="auto"><span class="autocomment">Purpose of the rolling build of GO</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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<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 11:13, 26 March 2024</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</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>=Purpose of the rolling build of GO=</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>=Purpose of the rolling build of GO=</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>As of March 18, 2024, GO <del style="font-weight: bold; text-decoration: none;">is producing </del>the ontology 3 times a day. '''This version is not checked or versioned or archived, therefore not citable. '''</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>As of March 18, 2024, GO <ins style="font-weight: bold; text-decoration: none;">will attempt to produce the latest version of </ins>the ontology 3 times a day. '''This version is not checked or versioned or archived, therefore not citable. <ins style="font-weight: bold; text-decoration: none;">If there are problems with the ontology build, the frequency may be less.</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 latest build of the ontology can be found here: https://ontology-build.geneontology.org/</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 latest build of the ontology can be found here: https://ontology-build.geneontology.org/</div></td></tr>
</table>
Vanaukenk
https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2024-03-26&diff=86775&oldid=86765
Annotation Conf. Call 2024-03-26
2024-03-26T15:08:54Z
<p><span dir="auto"><span class="autocomment">GO Release Pipeline</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<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 11:08, 26 March 2024</td>
</tr><tr><td colspan="4" class="diff-multi" lang="en">(5 intermediate revisions by the same user not shown)</td></tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l20">Line 20:</td>
<td colspan="2" class="diff-lineno">Line 20:</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>== GO Release Pipeline ==</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>== GO Release Pipeline ==</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>* March release.....</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>* March release.....</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>** <del style="font-weight: bold; text-decoration: none;">Still trying to get a </del>snapshot release out <del style="font-weight: bold; text-decoration: none;">- waiting on some new hardware, but other issues have cropped up</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>** <ins style="font-weight: bold; text-decoration: none;">A </ins>snapshot release <ins style="font-weight: bold; text-decoration: none;">is </ins>out<ins style="font-weight: bold; text-decoration: none;">; Seth is going to do a little checking</ins></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>** <del style="font-weight: bold; text-decoration: none;">Uo</del>-to-date ontology files are now being produced independently, though</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;">Up</ins>-to-date ontology files are now being produced independently, though</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>** Pascale will provide more information on how to access these for your curation tools/pipelines</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>** Pascale will provide more information on how to access these for your curation tools/pipelines</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>* #release-pipeline Slack channel for updates</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>* #release-pipeline Slack channel for updates</div></td></tr>
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<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;"><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>== Attendees ==</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>== Attendees ==</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>*On call: </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>*On call: <ins style="font-weight: bold; text-decoration: none;">Debby, Dmitry, Dustin, Edith, Kimberly, Leonore, Li, Malcolm, Mary, Pascal, Pascale, Patrick, Raymond, Rossana, Seth, Sridhar, Steven, Suzi</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>[[Category:Annotation Working Group]]</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>[[Category:Annotation Working Group]]</div></td></tr>
</table>
Vanaukenk
https://wiki.geneontology.org/index.php?title=Ontology_meeting_2024-04-08&diff=86769&oldid=86768
Ontology meeting 2024-04-08
2024-03-26T10:24:43Z
<p><span dir="auto"><span class="autocomment">Discussion points</span></span></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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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 06:24, 26 March 2024</td>
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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"></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>=Discussion points= </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>=Discussion points= </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>* Ontobot action to add a term to the 'do not annotate' subset does not create the comment we used to have (something like, "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.") </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> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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>* Ontobot action to add a term to the 'do not annotate' subset does not create the comment we used to have (something like, "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term."<ins style="font-weight: bold; text-decoration: none;">) (questing indirectly coming from https://github.com/geneontology/go-ontology/issues/27194</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>** Should Ontobot also do that? </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>** Should Ontobot also do that? </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>** Can we/should we add a check that all 'do not annotate' terms have a comment? </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>** Can we/should we add a check that all 'do not annotate' terms have a comment? </div></td></tr>
</table>
Pascale
https://wiki.geneontology.org/index.php?title=Ontology_meeting_2024-04-08&diff=86768&oldid=0
Ontology meeting 2024-04-08
2024-03-26T10:24:16Z
<p>Created page with "* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul * '''Present: ''' =Discussion points= * Ontobot action to add a term to the 'do not annotate' subset does not create the comment we used to have (something like, "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.") ** Should Ontobot also do that? ** Can we/should we add a check t..."</p>
<p><b>New page</b></p><div>* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul<br />
* '''Present: '''<br />
<br />
<br />
=Discussion points= <br />
* Ontobot action to add a term to the 'do not annotate' subset does not create the comment we used to have (something like, "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.") <br />
** Should Ontobot also do that? <br />
** Can we/should we add a check that all 'do not annotate' terms have a comment? <br />
<br />
<br />
<br />
<br />
[[Category:Meetings]]</div>
Pascale
https://wiki.geneontology.org/index.php?title=Ontology_meeting_2024-03-25&diff=86767&oldid=86759
Ontology meeting 2024-03-25
2024-03-26T10:21:33Z
<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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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 06:21, 26 March 2024</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td>
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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>* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul</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>* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul</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>* '''Present: ''' Raymond, Kimberly, Li, Peter, Pascale, Steven, Edith, Val, Tanya </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>* '''Present: ''' Raymond, Kimberly, Li, Peter, Pascale, Steven, Edith, Val, Tanya </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>* '''Regrets: ''' Jim, Chris</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>* '''Regrets: ''' Jim, Chris<ins style="font-weight: bold; text-decoration: none;">, Paul</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;"><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>
Pascale
https://wiki.geneontology.org/index.php?title=Ontology_editors%27_conference_call_minutes_2024&diff=86766&oldid=86753
Ontology editors' conference call minutes 2024
2024-03-26T10:21:16Z
<p></p>
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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 06:21, 26 March 2024</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l10">Line 10:</td>
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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>* [[Ontology meeting 2024-03-18|Mar 18]]</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>* [[Ontology meeting 2024-03-18|Mar 18]]</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>* [[Ontology meeting 2024-03-25|Mar 25]]</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>* [[Ontology meeting 2024-03-25|Mar 25]]</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">* [[Ontology meeting 2024-04-08|Apr 8]]</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;"><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>[[Category:Meetings]]</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>[[Category:Meetings]]</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>[[Category:Ontology]]</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>[[Category:Ontology]]</div></td></tr>
</table>
Pascale
https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2024-03-26&diff=86765&oldid=86761
Annotation Conf. Call 2024-03-26
2024-03-26T00:44:26Z
<p><span dir="auto"><span class="autocomment">Agenda and Minutes</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:44, 25 March 2024</td>
</tr><tr><td colspan="4" class="diff-multi" lang="en">(3 intermediate revisions by the same user not shown)</td></tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l7">Line 7:</td>
<td colspan="2" class="diff-lineno">Line 7:</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>** Thursday, March 28th, 4-6pm PDT</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>** Thursday, March 28th, 4-6pm PDT</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>*** [https://github.com/geneontology/noctua/issues/869 Outage tasks]</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>*** [https://github.com/geneontology/noctua/issues/869 Outage tasks]</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">=== No GO Calls Week ===</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">* Next week (week of April 1st) is a no GO calls week</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>=== Next In-Person Consortium Meeting ===</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>=== Next In-Person Consortium Meeting ===</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l23">Line 23:</td>
<td colspan="2" class="diff-lineno">Line 26:</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>== AmiGO ==</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>== AmiGO ==</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><del style="font-weight: bold; text-decoration: none;">* Not showing taxon constraints anymore, since it was only showing 'only in taxon' and not 'never in taxon'. We will restore once the indexing issue is resolved. </del></div></td><td colspan="2" class="diff-side-added"></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>== 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>== Annotation ==</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;">gocheck_do_not_annotate ===</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>=== <ins style="font-weight: bold; text-decoration: none;">Work on Annotation Reviews </ins>===</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><del style="font-weight: bold; text-decoration: none;">* Remove filtering of ‘do_not_annotate’ terms in QuickGO</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>* <ins style="font-weight: bold; text-decoration: none;">We </ins>will <ins style="font-weight: bold; text-decoration: none;">use </ins>the <ins style="font-weight: bold; text-decoration: none;">remainder </ins>of the <ins style="font-weight: bold; text-decoration: none;">call </ins>to work <ins style="font-weight: bold; text-decoration: none;">together </ins>on <ins style="font-weight: bold; text-decoration: none;">annotation reviews</ins>.</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><del style="font-weight: bold; text-decoration: none;">* Are we all good with this one?</del></div></td><td colspan="2" class="diff-side-added"></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> </div></td><td colspan="2" class="diff-side-added"></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;">=== 'Unfolding annotation extensions in Protein2GO </del>===</div></td><td colspan="2" class="diff-side-added"></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;">Annotations of "Gene X 'involved in' BP ‘part_of’ BP y" </del>will <del style="font-weight: bold; text-decoration: none;">be unfolded to also create the annotation "Gene X 'involved in' BP y". </del></div></td><td colspan="2" class="diff-side-added"></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;">* This is correct because of </del>the <del style="font-weight: bold; text-decoration: none;">transitivity </del>of the <del style="font-weight: bold; text-decoration: none;">'part of' relation.</del></div></td><td colspan="2" class="diff-side-added"></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;">* Alex needs </del>to <del style="font-weight: bold; text-decoration: none;">do some </del>work <del style="font-weight: bold; text-decoration: none;">to implement this, but we want to confirm that curators are </del>on <del style="font-weight: bold; text-decoration: none;">board with this. </del></div></td><td colspan="2" class="diff-side-added"></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;">* This unfolding will create 13k new annotations</del>.</div></td><td colspan="2" class="diff-side-added"></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>== GO-CAM and Noctua ==</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>== GO-CAM and Noctua ==</div></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l43">Line 43:</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;"><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>== Attendees ==</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>== Attendees ==</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>*On call: <del style="font-weight: bold; text-decoration: none;">Antonia, Chris, Debby, Dmitry, Dustin, Edith, Giulia, Helen, Karen, Kimberly, Leonore, Li, Malcolm, Mary, Pascal, Pascale, Raymond, Rob, Rossana, Seth, Sridhar, Steve, Suzi, Val</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>*On call: </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>[[Category:Annotation Working Group]]</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>[[Category:Annotation Working Group]]</div></td></tr>
</table>
Vanaukenk
https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2024-03-26&diff=86761&oldid=0
Annotation Conf. Call 2024-03-26
2024-03-26T00:30:48Z
<p>Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, March 28th, 4-6pm PDT *** [https://github.com/geneontology/noctua/issues/869 Outage tasks] === Next In-Person Consortium Meeting === * Week of May 20th - actual meeting dates: Tuesday, May 21 - Thursday, May 23 * Users Meeting, Monday, May 20th * Hosted by Jim Balhoff in Chapel Hill, NC * Start thinking about [https://docs.google.com/document/d..."</p>
<p><b>New page</b></p><div>= Agenda and Minutes =<br />
<br />
== Meetings and Announcements ==<br />
<br />
=== Noctua ===<br />
* Next regularly scheduled Noctua outage:<br />
** Thursday, March 28th, 4-6pm PDT<br />
*** [https://github.com/geneontology/noctua/issues/869 Outage tasks]<br />
<br />
=== Next In-Person Consortium Meeting ===<br />
* Week of May 20th - actual meeting dates: Tuesday, May 21 - Thursday, May 23<br />
* Users Meeting, Monday, May 20th<br />
* Hosted by Jim Balhoff in Chapel Hill, NC<br />
* Start thinking about [https://docs.google.com/document/d/1FwGxa4jx8rJFjWBcbn4Q7ZzOHCY6-oF0azOrtK3quyk/edit#heading=h.faqtkfatd45w agenda items, special topics, breakout groups]<br />
* [https://www.ticketleap.events/tickets/geneontology/spring2024goc Registration] - Deadline: April 12th<br />
<br />
== GO Release Pipeline ==<br />
* March release.....<br />
** Still trying to get a snapshot release out - waiting on some new hardware, but other issues have cropped up<br />
** Uo-to-date ontology files are now being produced independently, though<br />
** Pascale will provide more information on how to access these for your curation tools/pipelines<br />
* #release-pipeline Slack channel for updates<br />
<br />
== AmiGO ==<br />
* Not showing taxon constraints anymore, since it was only showing 'only in taxon' and not 'never in taxon'. We will restore once the indexing issue is resolved. <br />
<br />
== Annotation ==<br />
<br />
=== gocheck_do_not_annotate ===<br />
* Remove filtering of ‘do_not_annotate’ terms in QuickGO<br />
* Are we all good with this one?<br />
<br />
=== 'Unfolding annotation extensions in Protein2GO ===<br />
* Annotations of "Gene X 'involved in' BP ‘part_of’ BP y" will be unfolded to also create the annotation "Gene X 'involved in' BP y". <br />
* This is correct because of the transitivity of the 'part of' relation.<br />
* Alex needs to do some work to implement this, but we want to confirm that curators are on board with this. <br />
* This unfolding will create 13k new annotations.<br />
<br />
== GO-CAM and Noctua ==<br />
<br />
== Ontology ==<br />
<br />
<br />
== Attendees ==<br />
*On call: Antonia, Chris, Debby, Dmitry, Dustin, Edith, Giulia, Helen, Karen, Kimberly, Leonore, Li, Malcolm, Mary, Pascal, Pascale, Raymond, Rob, Rossana, Seth, Sridhar, Steve, Suzi, Val<br />
<br />
[[Category:Annotation Working Group]]</div>
Vanaukenk
https://wiki.geneontology.org/index.php?title=Annotation_Call_2024_Agenda_and_Minutes&diff=86760&oldid=86736
Annotation Call 2024 Agenda and Minutes
2024-03-26T00:29:11Z
<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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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 20:29, 25 March 2024</td>
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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>* [[Annotation Conf. Call 2024-03-12]]</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>* [[Annotation Conf. Call 2024-03-12]]</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>* [[Annotation Conf. Call 2024-03-19]]</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>* [[Annotation Conf. Call 2024-03-19]]</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">* [[Annotation Conf. Call 2024-03-26]]</ins></div></td></tr>
</table>
Vanaukenk
https://wiki.geneontology.org/index.php?title=Ontology_meeting_2024-03-25&diff=86759&oldid=86754
Ontology meeting 2024-03-25
2024-03-25T16:12:25Z
<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:12, 25 March 2024</td>
</tr><tr><td colspan="4" class="diff-multi" lang="en">(4 intermediate revisions by the same user not shown)</td></tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td>
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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>* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul</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>* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul</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>* '''Present: ''' </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>* '''Present: ''' <ins style="font-weight: bold; text-decoration: none;">Raymond, Kimberly, Li, Peter, Pascale, Steven, Edith, Val, Tanya </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">* '''Regrets: ''' Jim, Chris</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;"><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>=Discussion points= </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>=Discussion points= </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">* Pascale made a new ticket for obsolete ECs: https://github.com/geneontology/go-ontology/issues/27410</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></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;">* Pascale to check with Elisabeth Coudert of RHEA to answer Steven's question here: https://github.com/geneontology/go-ontology/issues/27278#issuecomment-2009066470</ins></div></td></tr>
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Pascale
https://wiki.geneontology.org/index.php?title=Ontology_meeting_2024-03-25&diff=86754&oldid=0
Ontology meeting 2024-03-25
2024-03-25T08:38:04Z
<p>Created page with "* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul * '''Present: ''' =Discussion points= <a href="/Category:Meetings" title="Category:Meetings">Category:Meetings</a>"</p>
<p><b>New page</b></p><div>* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul<br />
* '''Present: ''' <br />
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=Discussion points= <br />
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[[Category:Meetings]]</div>
Pascale
https://wiki.geneontology.org/index.php?title=Ontology_editors%27_conference_call_minutes_2024&diff=86753&oldid=86675
Ontology editors' conference call minutes 2024
2024-03-25T08:37:12Z
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 04:37, 25 March 2024</td>
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Pascale