Ontology meeting 2023-03-13

• 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
• Jim testing ontology build: [1] 
• Today: Will get everyone started

Script to download annotations

• Moved the script in the go-annotation repo - status
• Instructions >>> https://wiki.geneontology.org/Obsoleting_an_Existing_Ontology_Term#2._Create_an_Annotation_Review_Request_ticket_and_add_the_link_in_the_GitHub_ticket.

Editors discussion items

Obsolete versus merge

Are there situations where we can merge? see

• x involved in y: https://github.com/geneontology/go-ontology/issues/24990
• more specific substrates: https://github.com/geneontology/go-ontology/issues/24738

Phagocytosis versus endocytsosis

• phagocytosis versus endocytsosis

Asserted classes versus logical definitions

Example: mRNA phosphatase activity is_a pyrophosphatase, not a phosphatase

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

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."