Ontology meeting 2022-09-26: Difference between revisions

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*# 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?  
*# 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?  
*# '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?  
*# '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?  
*# 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?
*# 'removes input for' has 2 definitions in our doc; which is right,
*#* the first: "removes input for q iff p is immediately causally upstream of q, there exists some c such that p has_input c and q has_input c, and the availability of c is rate limiting for execution of q."
*#* or the second: "p removes input for q iff p is causally upstream of q, there exists some c such that p has_input c and q has_input c, p reduces the levels of c, and c is rate limiting for execution of q. "


==Stem cell taxonomic range==
==Stem cell taxonomic range==

Revision as of 04:50, 26 September 2022

  • Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
  • Present:
  • Regrets:

Announcements

Editors discussion items

Continue discussion on relations

Pascale

  • Started to implement the proposal we presented last week
  • Some questions:
    1. 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
      • Doesn't 'provides input for' sound more general than 'transitively' and 'directly'?
    2. 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?
    3. '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?
    4. 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?

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