Ontology meeting 2023-05-08

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

Next GOC consortium meeting

• October 17th-19th, 2023, Virtual

Action points

Chris to send the dictionary for the script that generates annotation reports

GOC meeting recap

• For reference: slides for the ontology status presentation at the GOC meeting
• Stats for annotation review, see example here: https://docs.google.com/presentation/d/13toZ2e0EhN0brIcN6LGkzBE0b-iGyyN82qiFkzQfLrQ/edit#slide=id.g23b5a2846ac_0_5
• Decision to create a new type of annotation, 'annotations can be replaced by', which means that annotations can be automatically be transferred to a certain term even though that term does not have the exact same meaning as the term being obsoleted. Hopefully that should make annotation review/obsoletion easier.
• Discussion of 'Signaling cassettes' - ie intracellular signaling pathways such as MAPK, JAK, NFKB. Proposal to work on this with Helen, Guilia and Ruth, now that non-coding RNA work is finished

Change Language

Proposal by Chris and Mark Musen https://incatools.github.io/kgcl/

Ontology priorities

• BP refactoring:
  • Obsolete single step processes
  • Obsolete "Regulation of molecular function" processes terms
  • Homeostasis + other areas in BP for the BP refactoring
• RNA processing
• Multi-species processes: ongoing: alignment with PathGO ontology
• GO-EC-RHEA xref maintenance
• Transcription (including chromatin remodeling processes and regulation of transcription by regulators non-coding RNAs)
• Aging

Other

• Quick question on obsolete IDs in slims: https://github.com/geneontology/go-ontology/issues/14677

Editors discussion items from previous calls

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."

Pending Action items

GOCHE documentation

From 2023-03-13 call

• AI: Review GOCHE documentation (confusion about ChEBI roles and GOCHE roles)
• AI: Check with terms use GOCHE terms
• AI: Close open PRs