https://wiki.geneontology.org/index.php?title=Ontology_meeting_2019-09-23&feed=atom&action=history
Ontology meeting 2019-09-23 - Revision history
2024-03-28T19:38:29Z
Revision history for this page on the wiki
MediaWiki 1.40.0
https://wiki.geneontology.org/index.php?title=Ontology_meeting_2019-09-23&diff=76231&oldid=prev
David: /* GOC Meeting */
2019-09-23T15:40:21Z
<p><span dir="auto"><span class="autocomment">GOC Meeting</span></span></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 11:40, 23 September 2019</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>** [[2019 Berkeley GOC Meeting Agenda]]</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>** [[2019 Berkeley GOC Meeting Agenda]]</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>* We need to decide who is presenting what at <del style="font-weight: bold; text-decoration: none;">each of </del>the meeting.</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>* We need to decide who is presenting what at the meeting.</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>===PRs from 'non-editors'===</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>===PRs from 'non-editors'===</div></td></tr>
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David
https://wiki.geneontology.org/index.php?title=Ontology_meeting_2019-09-23&diff=76230&oldid=prev
David: /* CC relations: overlaps/adjacent_to */
2019-09-23T13:31:25Z
<p><span dir="auto"><span class="autocomment">CC relations: overlaps/adjacent_to</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 09:31, 23 September 2019</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>Should we restrict pull requests to the ontology to only GO ontology editors?</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 we restrict pull requests to the ontology to only GO ontology editors?</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>==CC relations: overlaps/adjacent_to==</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>==CC relations: overlaps/adjacent_to<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;"><div>* Draft documentation: </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>* Draft documentation: </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://docs.google.com/document/d/1OsE19zh8KE_2wT3-8oJysqEGqy-fahnhcjthO34IWP4/edit#</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://docs.google.com/document/d/1OsE19zh8KE_2wT3-8oJysqEGqy-fahnhcjthO34IWP4/edit#</div></td></tr>
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David
https://wiki.geneontology.org/index.php?title=Ontology_meeting_2019-09-23&diff=76229&oldid=prev
David: /* Discussion topics */
2019-09-23T13:31:03Z
<p><span dir="auto"><span class="autocomment">Discussion topics</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 09:31, 23 September 2019</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>* We need to decide who is presenting what at each of the 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>* We need to decide who is presenting what at each of the meeting.</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;">===PRs from 'non-editors'===</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 restrict pull requests to the ontology to only GO ontology editors?</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>==CC relations: overlaps/adjacent_to==</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>==CC relations: overlaps/adjacent_to==</div></td></tr>
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David
https://wiki.geneontology.org/index.php?title=Ontology_meeting_2019-09-23&diff=76228&oldid=prev
David: Created page with "= Conference Line = See calendar for details = Agenda = ==Discussion topics== ===GOC Meeting=== * 2019 Oct GOC meeting - Berkeley, CA: October 7-10, 2019 (User Meeting Oc..."
2019-09-23T13:15:32Z
<p>Created page with "= Conference Line = See calendar for details = Agenda = ==Discussion topics== ===GOC Meeting=== * 2019 Oct GOC meeting - Berkeley, CA: October 7-10, 2019 (User Meeting Oc..."</p>
<p><b>New page</b></p><div>= Conference Line =<br />
See calendar for details<br />
= Agenda =<br />
<br />
<br />
==Discussion topics==<br />
<br />
<br />
===GOC Meeting===<br />
<br />
* 2019 Oct GOC meeting - Berkeley, CA: October 7-10, 2019 (User Meeting Oct 7, GOC meeting Oct 8-10, SAB meeting Oct 11)<br />
** [[2019 Berkeley GOC Meeting Agenda]]<br />
<br />
* We need to decide who is presenting what at each of the meeting.<br />
<br />
==CC relations: overlaps/adjacent_to==<br />
* Draft documentation: <br />
https://docs.google.com/document/d/1OsE19zh8KE_2wT3-8oJysqEGqy-fahnhcjthO34IWP4/edit#<br />
<br />
* Annotations to 'adjacent_to': https://docs.google.com/spreadsheets/d/1WiiynQPDqwcEYruLhR5UCEAwaCNCw-_hlnhmGGqGMm8/edit#gid=0<br />
<br />
* No annotations to 'overlaps' in the download from June 2019<br />
<br />
* How can we make rules for these two relations? <br />
** Do we need to define in the ontology, components that are adjacent to cells, and components that overlap? <br />
** Should we make a distinction (ie use a different relation) for intracellular adjacency vs. extracellular ? <br />
** 'Overlaps': Current usage in the ontology: <br />
<br />
'''In LD: '''<br />
*'neuromuscular junction' <http://purl.obolibrary.org/obo/GO_0031594><br />
*'neuromuscular junction of myotube' <http://purl.obolibrary.org/obo/GO_0098523><br />
*'neuromuscular junction of somatic muscle' <http://purl.obolibrary.org/obo/GO_0098527><br />
*'excitatory neuromuscular junction' <http://purl.obolibrary.org/obo/GO_0098520><br />
*'inhibitory neuromuscular junction' <http://purl.obolibrary.org/obo/GO_0098521><br />
*'neuromuscular junction of somatic muscle myotube' <http://purl.obolibrary.org/obo/GO_0098524><br />
*'nucleus-vacuole junction' <http://purl.obolibrary.org/obo/GO_0071561><br />
*'trans-synaptic protein complex' <http://purl.obolibrary.org/obo/GO_0098820><br />
*'neuromuscular junction of skeletal muscle fiber' <http://purl.obolibrary.org/obo/GO_0098522><br />
*'hemidesmosome associated protein complex' <http://purl.obolibrary.org/obo/GO_0098733><br />
*'excitatory neuromuscular junction of somatic myotube' <http://purl.obolibrary.org/obo/GO_0098525><br />
*'inhibitory neuromuscular junction of somatic myotube' <http://purl.obolibrary.org/obo/GO_0098526><br />
*'vacuole-mitochondrion membrane contact site' <http://purl.obolibrary.org/obo/GO_1990816><br />
*'olfactory tract linking bulb to ipsilateral ventral telencephalon' <http://purl.obolibrary.org/obo/UBERON_2000238><br />
*'endoplasmic reticulum-plasma membrane contact site' <http://purl.obolibrary.org/obo/GO_0140268><br />
*'endoplasmic reticulum-vacuole membrane contact site' <http://purl.obolibrary.org/obo/GO_0098853><br />
*'endoplasmic reticulum-endosome membrane contact site' <http://purl.obolibrary.org/obo/GO_0140284><br />
*'mitochondria-associated endoplasmic reticulum membrane' <http://purl.obolibrary.org/obo/GO_0044233><br />
<br />
'''In Subclasses: '''<br />
*'slit diaphragm' <http://purl.obolibrary.org/obo/GO_0036057><br />
*'arciform density' <http://purl.obolibrary.org/obo/GO_0098682><br />
*'collagen type XVII trimer' <http://purl.obolibrary.org/obo/GO_0030937><br />
*'photoreceptor ribbon synapse' <http://purl.obolibrary.org/obo/GO_0098684><br />
*'Schaffer collateral - CA1 synapse' <http://purl.obolibrary.org/obo/GO_0098685><br />
*'cochlear hair cell ribbon synapse' <http://purl.obolibrary.org/obo/GO_0098683><br />
*'collagen type VII anchoring fibril' <http://purl.obolibrary.org/obo/GO_0098652><br />
*'parallel fiber to Purkinje cell synapse' <http://purl.obolibrary.org/obo/GO_0098688><br />
*'synapse-associated extracellular matrix' <http://purl.obolibrary.org/obo/GO_0099535><br />
*'cerebellar Golgi cell to granule cell synapse' <http://purl.obolibrary.org/obo/GO_0099192><br />
*'cerebellar granule cell to Purkinje cell synapse' <http://purl.obolibrary.org/obo/GO_0150048><br />
*'cerebellar climbing fiber to Purkinje cell synapse' <http://purl.obolibrary.org/obo/GO_0150053><br />
*'olfactory tract linking bulb to ipsilateral ventral telencephalon' <http://purl.obolibrary.org/obo/UBERON_2000238><br />
<br />
===Update on the roles project===<br />
<br />
<br />
===Other Business===<br />
https://github.com/geneontology/go-ontology/projects/1<br />
<br />
====Minutes should be recorded on individual tickets and in individual projects====<br />
<br />
<br />
[[Category:Meetings]]<br />
[[Category:Ontology]]</div>
David