Ontology meeting 2023-03-13: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
(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...")
 
mNo edit summary
 
(11 intermediate revisions by 3 users not shown)
Line 1: Line 1:
= Attendees =
* '''Group members:''' Pascale, Raymond, Val, Edith, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
* Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia
* '''Present:''' Pascale, Raymond, Val, Edith, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
* Present:
* '''Present:'''  
* '''Regrets:'''
* '''Regrets:'''
=Announcements=


==GOC consortium==
==GOC consortium==
* April 27th-29th, Padua, Italy
* April 27th-29th, Padua, Italy
* Draft agenda: https://docs.google.com/document/d/1eTKwfGT4o4w85HM2OYOekgmIJ5Hpm9LYBNWvg0udsRQ/edit#
* 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]


=Discussion points=
==Asserted classes versus logical definitions==
* [https://github.com/geneontology/project-management/issues/42 Discuss and create roadmap for integrating remaining resource upstream files]
Example: mRNA phosphatase activity
David
is_a pyrophosphatase, not a phosphatase


=Projects reviews=
[[Guidelines_for_logical_definitions | Logical definitions]] should do most of the work for us
https://github.com/orgs/geneontology/projects/108/views/3


== 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


'''Project management kaban'''
https://github.com/geneontology/go-ontology/issues/24489
https://github.com/orgs/geneontology/projects/108/views/1
https://github.com/geneontology/go-ontology/issues/24490


'''Proposed priorities for the next 6 months'''
==CARO vs UBERON==
* [https://docs.google.com/document/d/17ikwodMNC_xwEGZhBre_tilw4Fd8NI1IWZ8KxefSPBU/edit Main tasks Oct 22-March 23]
*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: GO Managers Meetings]]
[[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

Editors discussion items

Obsolete versus merge

Are there situations where we can merge? see

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

GO, RHEA, EC aligment

Tickets by ontology editors