Ontology meeting 2019-09-23

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)
  • 2019 Berkeley GOC Meeting Agenda

• 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>

Other Business

https://github.com/geneontology/go-ontology/projects/1