Ontology meeting 2023-03-20

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

GOC consortium

• April 27th-29th, Padua, Italy
• Any suggestions for working group sessions?

New Protege version

• New Instruction page Protege5_6_setup_for_GO_Eds in progress
• Did everyone have a chance to test?

OntoBot change agent demo

• Chris to demo [5-10 mins]

Editors discussion items

Pharynx terms in GO

• Pharynx terms used for C. elegans annotations get flagged if the GO term uses the UBERON pharynx (or child) term in the logical definition
• We might be stalled here by UBERON work: https://github.com/obophenotype/uberon/issues/2728

Phagocytosis versus endocytsosis

• phagocytosis versus endocytsosis

Asserted classes versus logical definitions

Example: mRNA phosphatase activity is_a pyrophosphatase, not a phosphatase

not sure this is the easiest example Cjm (talk) 22:07, 19 March 2023 (EDT)

 Logical definitions should do most of the work for us

Procedure to mark terms to be obsoleted

• This would give curators and editors of ontologies using GO a way to know which terms are scheduled for obsoletion
• There is a property that we can use

Test new process to when obsoleting terms with taxon constraints

• Use GH actions ? Pascale to test

https://github.com/geneontology/go-ontology/issues/24489 https://github.com/geneontology/go-ontology/issues/24490

CARO vs UBERON

• https://github.com/oborel/obo-relations/issues/695
• Implications for ontology development and ShEx

GO, RHEA, EC aligment

• Created a project in the go-ontology repo
• Will update guidelines
  • https://wiki.geneontology.org/Database_cross_references
  • https://wiki.geneontology.org/Enzymes_and_EC_mappings
• Question: Do we need to keep comments about obsolete/transferred ECs, such as GO:0047091 , has comment "Note that EC:1.13.12.10 was merged into this term."