Ontology meeting 2021-03-01

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Attendees

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



Agenda

Announcements

No call next week - No GO Calls Week

Discussion

Follow up: Cellular Component, ShEx, and GO-CAMs -- BLOCKING FOR GO-CAM

  • The ShEx specifications state that MFs can occur in an Anatomical Entity and that GPs or Protein-Containing Complexes can be located in an Anatomical Entity.
  • Most non-protein-containing complex GO CC terms are a child of Cellular Anatomical Entity which is a subclass of Anatomical Entity.
  • However, annotations to root Cellular Component result in ShEx violations because root Cellular Component is NOT a subclass of Anatomical Entity.

Discussion

  • Chris: suggests keeping the current practice and use root Cellular Component and ND.
  • Action would be to change the ShEX to allow a direct annotation to occurs_is/is active in root Cellular Component

Is this still OK?

  • Need to look at ShEx with Jim



'process has causal agent' relation

Raymond proposed to use in LD: https://github.com/geneontology/go-ontology/issues/13307#issuecomment-786985814

extrasynaptic signalling via GABA 'cell-cell signaling' and ('process has causal agent' some 'gamma-aminobutyric acid zwitterion') and ('occurs in' some 'perisynaptic space')

  • See proposal in ticket

New relationships after using equivalent Rhea reaction

https://github.com/geneontology/go-ontology/issues/20839

Jim generated a ttl file.

*Discussion:

  • Created Logical definition
  • Plan: going forward, creating new terms:
    • add Rhea description in textual definition
    • bring EC mapping from Rhea
    • pull EC name automatically
    • retrospectively  ??''
  • Next step:
    • check if those logical definitions cause problems in inferences
    • Jim to check if some subsumptions are missing

id ranges file

https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/go-idranges.txt

  • do we need "The Original Set (OS) of GO terms"
  • do we need both the text and owl files?

merge GO:0019539 siderophore biosynthetic process from hydroxamic acid

https://github.com/geneontology/go-ontology/issues/20975

see the number of siderophores here: https://pdfs.semanticscholar.org/7946/e6339f9fbb60b054747ee4d706e53958b980.pdf?_ga=2.67985041.1432405903.1614609213-563084161.1614609213



xref types

Other Business

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


Minutes should be recorded on individual tickets and in individual projects