Ontology meeting 2023-05-15
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- Group members: Pascale, Raymond, Val, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul
- Present: Pascale, Raymond, Val, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul
- Regrets:
Action points from last call
Chris to send the dictionary for the script that generates annotation reports: see https://incatools.github.io/ontology-access-kit/datamodels/association/AssociationChange.html
New QC check
- Obsolete IDs in slims will now cause a Travis error; ontology editors need to remove subsets when obsoleting terms
Annotation review scripts
- Now also include mappings, see https://github.com/geneontology/go-annotation/issues/4568
- there is a first pass at the data dictionary for the association diffs here: https://w3id.org/oak/association/AssociationChange.html
- Create a new Annotation review template for annotation review including regulation children, see https://github.com/geneontology/go-annotation/issues/templates/edit
- The templates add the labels, ie automatically create the review report.
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 & enzyme tickets (76)
- Transcription (including chromatin remodeling processes and regulation of transcription by regulators non-coding RNAs)
- Aging
- New term requests (70)
Editors discussion items from previous calls
Asserted classes versus logical definitions
Example: mRNA phosphatase activity is_a pyrophosphatase, not a phosphatase
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
- 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."
Tickets by ontology editors
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