Ontology meeting 2023-03-13: Difference between revisions
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* '''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: [https://github.com/geneontology/go-ontology/issues/25019#issuecomment-1444987133] | |||
* 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= | |||
==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 | |||
== 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 [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:Meetings]] | |||
[[Category:Ontology]] |
Revision as of 05:39, 6 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]
- 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
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
- 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."