Ontology meeting 2022-09-26
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- Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
- Present: Pascale, Karen, Harold, Raymond, Peter, Kimberly, David
- Regrets: Jim, Tanya, Chris, Paul
Announcements
Editors discussion items
Continue discussion on relations
Pascale
- Started to implement the proposal we presented last week - [ticket] / pull request
- Some questions:
- We had proposed to change the label of 'directly provides input for' to 'provides input for' ; however I would like to confirm that we really want to do this, as this would result in:
- 'causally upstream of or within, positive effect'
- 'transitively provides input for'
- provides input for
- 'transitively provides input for'
- Doesn't 'provides input for' sound more general than 'transitively' and 'directly'?
- Decision: 'directly' is clearer to curators; will not change the label
- 'causally upstream of or within, positive effect'
- We had proposed to create 'directly positively regulates' and 'directly negatively regulates'; however RO already has 'directly activates' and 'directly inhibits', with synonyms 'directly positively regulates' and 'directly negatively regulates'; should I swap term labels and synonyms? or do we really want to create these new terms?
- Decision: Create a RO ticket for activates/inhibits + check which ontologies use it (see https://ontobee.org/ontology/RO?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002406)
- 'regulates' has definition source =GO'(but as far I as can tell, no other terms.) Is this useful? should this be added to more terms?
- A few relations (regulates & children) link to https://github.com/oborel/obo-relations/wiki/causal-relations; this seems very general; should it move 'up' to 'causally related to'? does it need to be linked in all subclasses?
- We had proposed to change the label of 'directly provides input for' to 'provides input for' ; however I would like to confirm that we really want to do this, as this would result in:
Stem cell taxonomic range
https://github.com/geneontology/go-ontology/issues/23764
'Nested' regulation
https://github.com/geneontology/go-ontology/issues/12976 I think we are obsoleting these terms? "regulation of X by regulation of Y" We still have 'regulation of x by regulation of release of sequestered calcium ions' (maybe others)
Hindgut contraction
https://github.com/geneontology/go-ontology/issues/11758 Maybe we only need 'smooth muscle contraction' and the we can use 'occurs in' the appropriate anatomical structure?
Follow up on previous discussion topics
Regulation of a process in another organism
- AI (Pascale) should create a new triad of relations for linking the modulation of a process in another organism- for eg, modulates process in another organism (something along these lines)
- AI (Pascale) Open a RO ticket to make in_taxon over regulates transitive
Next jamboree
Date & topic
For a future call/project
- https://wiki.geneontology.org/Ontology_meeting_2022-07-18#Glycosylation_ontology
- Ordering of subset/ribbon terms: make a tsv file - we just need to know who needs this; would Alliance, UniProt use it?
- COB: Jim and Chris could give an overview of COB + biological phase superclass https://github.com/OBOFoundry/COB/issues/51