Ontology meeting 2019-09-23: Difference between revisions
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(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...") |
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** [[2019 Berkeley GOC Meeting Agenda]] | ** [[2019 Berkeley GOC Meeting Agenda]] | ||
* We need to decide who is presenting what at | * We need to decide who is presenting what at the meeting. | ||
==CC relations: overlaps/adjacent_to== | ===PRs from 'non-editors'=== | ||
Should we restrict pull requests to the ontology to only GO ontology editors? | |||
===CC relations: overlaps/adjacent_to=== | |||
* Draft documentation: | * Draft documentation: | ||
https://docs.google.com/document/d/1OsE19zh8KE_2wT3-8oJysqEGqy-fahnhcjthO34IWP4/edit# | https://docs.google.com/document/d/1OsE19zh8KE_2wT3-8oJysqEGqy-fahnhcjthO34IWP4/edit# |
Latest revision as of 11:40, 23 September 2019
Conference Line
See calendar for details
Agenda
Discussion topics
GOC Meeting
- 2019 Oct GOC meeting - Berkeley, CA: October 7-10, 2019 (User Meeting Oct 7, GOC meeting Oct 8-10, SAB meeting Oct 11)
- We need to decide who is presenting what at the meeting.
PRs from 'non-editors'
Should we restrict pull requests to the ontology to only GO ontology editors?
CC relations: overlaps/adjacent_to
- Draft documentation:
https://docs.google.com/document/d/1OsE19zh8KE_2wT3-8oJysqEGqy-fahnhcjthO34IWP4/edit#
- Annotations to 'adjacent_to': https://docs.google.com/spreadsheets/d/1WiiynQPDqwcEYruLhR5UCEAwaCNCw-_hlnhmGGqGMm8/edit#gid=0
- No annotations to 'overlaps' in the download from June 2019
- How can we make rules for these two relations?
- Do we need to define in the ontology, components that are adjacent to cells, and components that overlap?
- Should we make a distinction (ie use a different relation) for intracellular adjacency vs. extracellular ?
- 'Overlaps': Current usage in the ontology:
In LD:
- 'neuromuscular junction' <http://purl.obolibrary.org/obo/GO_0031594>
- 'neuromuscular junction of myotube' <http://purl.obolibrary.org/obo/GO_0098523>
- 'neuromuscular junction of somatic muscle' <http://purl.obolibrary.org/obo/GO_0098527>
- 'excitatory neuromuscular junction' <http://purl.obolibrary.org/obo/GO_0098520>
- 'inhibitory neuromuscular junction' <http://purl.obolibrary.org/obo/GO_0098521>
- 'neuromuscular junction of somatic muscle myotube' <http://purl.obolibrary.org/obo/GO_0098524>
- 'nucleus-vacuole junction' <http://purl.obolibrary.org/obo/GO_0071561>
- 'trans-synaptic protein complex' <http://purl.obolibrary.org/obo/GO_0098820>
- 'neuromuscular junction of skeletal muscle fiber' <http://purl.obolibrary.org/obo/GO_0098522>
- 'hemidesmosome associated protein complex' <http://purl.obolibrary.org/obo/GO_0098733>
- 'excitatory neuromuscular junction of somatic myotube' <http://purl.obolibrary.org/obo/GO_0098525>
- 'inhibitory neuromuscular junction of somatic myotube' <http://purl.obolibrary.org/obo/GO_0098526>
- 'vacuole-mitochondrion membrane contact site' <http://purl.obolibrary.org/obo/GO_1990816>
- 'olfactory tract linking bulb to ipsilateral ventral telencephalon' <http://purl.obolibrary.org/obo/UBERON_2000238>
- 'endoplasmic reticulum-plasma membrane contact site' <http://purl.obolibrary.org/obo/GO_0140268>
- 'endoplasmic reticulum-vacuole membrane contact site' <http://purl.obolibrary.org/obo/GO_0098853>
- 'endoplasmic reticulum-endosome membrane contact site' <http://purl.obolibrary.org/obo/GO_0140284>
- 'mitochondria-associated endoplasmic reticulum membrane' <http://purl.obolibrary.org/obo/GO_0044233>
In Subclasses:
- 'slit diaphragm' <http://purl.obolibrary.org/obo/GO_0036057>
- 'arciform density' <http://purl.obolibrary.org/obo/GO_0098682>
- 'collagen type XVII trimer' <http://purl.obolibrary.org/obo/GO_0030937>
- 'photoreceptor ribbon synapse' <http://purl.obolibrary.org/obo/GO_0098684>
- 'Schaffer collateral - CA1 synapse' <http://purl.obolibrary.org/obo/GO_0098685>
- 'cochlear hair cell ribbon synapse' <http://purl.obolibrary.org/obo/GO_0098683>
- 'collagen type VII anchoring fibril' <http://purl.obolibrary.org/obo/GO_0098652>
- 'parallel fiber to Purkinje cell synapse' <http://purl.obolibrary.org/obo/GO_0098688>
- 'synapse-associated extracellular matrix' <http://purl.obolibrary.org/obo/GO_0099535>
- 'cerebellar Golgi cell to granule cell synapse' <http://purl.obolibrary.org/obo/GO_0099192>
- 'cerebellar granule cell to Purkinje cell synapse' <http://purl.obolibrary.org/obo/GO_0150048>
- 'cerebellar climbing fiber to Purkinje cell synapse' <http://purl.obolibrary.org/obo/GO_0150053>
- 'olfactory tract linking bulb to ipsilateral ventral telencephalon' <http://purl.obolibrary.org/obo/UBERON_2000238>
Update on the roles project
Other Business
https://github.com/geneontology/go-ontology/projects/1