Ontology meeting 2023-03-13: Difference between revisions
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* New Instruction page [[Protege5_6_setup_for_GO_Eds]] in progress | * New Instruction page [[Protege5_6_setup_for_GO_Eds]] in progress | ||
* Jim testing ontology build: [https://github.com/geneontology/go-ontology/issues/25019#issuecomment-1444987133] | * Jim testing ontology build: [https://github.com/geneontology/go-ontology/issues/25019#issuecomment-1444987133] | ||
* Noting issue with ID ranges : Jim renamed our ID range file because this feature is broken | * Noting issue with ID ranges : Jim renamed our ID range file because this feature is broken. ID ranges will keep on working the same way they were before | ||
* Today: Will get everyone started | * Today: Will get everyone started | ||
* Review unmerged pull requests - will need to have conflicts resolved or redone after new Protege save | * Review unmerged pull requests - will need to have conflicts resolved or redone after new Protege save | ||
Revision as of 12:10, 13 March 2023
- 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]
- Noting issue with ID ranges : Jim renamed our ID range file because this feature is broken. ID ranges will keep on working the same way they were before
- Today: Will get everyone started
- Review unmerged pull requests - will need to have conflicts resolved or redone after new Protege save
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
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."