Ontology meeting 2021-03-01
- Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul, Eric
- Regrets: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
No call next week - No GO Calls Week
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.
- 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
- Is this the relation use want to use for x-mediated processes? See for example 'GO:0002443 | leukocyte mediated immunity' in https://github.com/geneontology/go-ontology/issues/17613
- (RO question): should 'process has causal agent' be a child of 'causal relation between material entity and a process' or 'causal agent in process'? Now it's a direct descendant of 'causally related to', see https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002410&viewMode=All&siblings=false
New relationships after using equivalent Rhea reaction
Jim generated a ttl file.
- 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
- 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
see the number of siderophores here: https://pdfs.semanticscholar.org/7946/e6339f9fbb60b054747ee4d706e53958b980.pdf?_ga=2.67985041.1432405903.1614609213-563084161.1614609213
- Documentation: Guidelines_for_'database_cross_references'_and_'definition_database_cross_references'#Adding_cross-reference_types