Ontology meeting 2023-03-13: Difference between revisions
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(Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * '''Present:''' * '''Regrets:''' =Announcements= ==GOC consortium== * April 27th-29th, Padua, Italy * Draft agenda: https://docs.google.com/document/d/1eTKwfGT4o4w85HM2OYOekgmIJ5Hpm9LYBNWvg0udsRQ/edit# =Discussion points= * [https://github.com/geneontology/project-management/issues/42 Discuss and create roadmap for integrating remaining resource upstream files] D...") |
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* '''Group members:''' Pascale, Raymond, Val, Edith, Peter, Jim, Tanya, Kimberly, David, Chris, Paul | |||
* | * '''Present:''' Pascale, Raymond, Val, Edith, Peter, Jim, Tanya, Kimberly, David, Chris, Paul | ||
* '''Present:''' | |||
* '''Regrets:''' | * '''Regrets:''' | ||
==GOC consortium== | ==GOC consortium== | ||
* April 27th-29th, Padua, Italy | * 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: [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. 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 | |||
==Reviewing pending PRs== | |||
* '''AI: Review GOCHE documentation''' (confusion about ChEBI roles and GOCHE roles) | |||
* '''AI: Check with terms use GOCHE terms''' | |||
* '''AI: Close open PRs''' | |||
=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== | |||
* [https://github.com/geneontology/go-ontology/issues/24907#issuecomment-1433358637 phagocytosis versus endocytsosis] | |||
= | ==Asserted classes versus logical definitions== | ||
Example: mRNA phosphatase activity | |||
is_a pyrophosphatase, not a phosphatase | |||
[[Guidelines_for_logical_definitions | 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 | 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 [https://github.com/geneontology/go-ontology/projects/37 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." | |||
=Tickets by ontology editors= | |||
[[Category: | [[Category:Meetings]] | ||
[[Category:Ontology]] |
Latest revision as of 04:32, 20 March 2023
- Group members: Pascale, Raymond, Val, Edith, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
- Present: Pascale, Raymond, Val, Edith, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
- 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
Reviewing pending PRs
- AI: Review GOCHE documentation (confusion about ChEBI roles and GOCHE roles)
- AI: Check with terms use GOCHE terms
- AI: Close open PRs
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."