Ontology meeting 2023-03-20: Difference between revisions

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* '''Group members:''' Pascale, Raymond, Val, Edith, Peter, Jim, Tanya, Karen, Kimberly, David, Chris, Paul
* '''Group members:''' Pascale, Raymond, Val, Edith, Jim, Tanya, Kimberly, David, Chris, Paul
* '''Present:'''  
* '''Present:''' Pascale, Raymond, Edith,  Jim, Tanya, Kimberly, David, Chris, Paul
* '''Regrets:'''
* '''Regrets:''' Val, Peter
 
=Announcements=


==GOC consortium==
==GOC consortium==
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* Any suggestions for working group sessions?  
* Any suggestions for working group sessions?  


=New Protege version=
=No call next week=
Alliance all hands meeting, some people will be traveling; Pascale out next week
 
=Editors discussion items=
==New Protege version==
* 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] 
* Did everyone have a chance to test?
* 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


=OntoBot change agent demo=
==OntoBot change agent demo==
* Chris to demo [5-10 mins]
* Chris to demo [5-10 mins]
 
* AI mention at GOC meeting
=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


== Pharynx terms in GO ==
== Pharynx terms in GO ==
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=Tickets by ontology editors=
=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'''


[[Category:Meetings]]
[[Category:Meetings]]
[[Category:Ontology]]
[[Category:Ontology]]

Latest revision as of 12:05, 22 March 2023

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

Announcements

GOC consortium

  • April 27th-29th, Padua, Italy
  • Any suggestions for working group sessions?

No call next week

Alliance all hands meeting, some people will be traveling; Pascale out next week

Editors discussion items

New Protege version

OntoBot change agent demo

  • Chris to demo [5-10 mins]
  • AI mention at GOC meeting

Pharynx terms in GO

Phagocytosis versus endocytsosis

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

GO, RHEA, EC aligment

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