Difference between revisions of "Ontology meeting 2022-01-24"

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* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
* '''Present: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul '''
* '''Present: ''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul  
* '''Regrets: '''   
* '''Regrets: '''   


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Did not discuss today:  
==Did not discuss today: ==
===Protein-complex organization/assembly/disassembly===
===Protein-complex organization/assembly/disassembly===
Problem with relations used in logical definition
Problem with relations used in logical definition

Revision as of 03:39, 25 January 2022

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

Announcements

Agenda

Following up on previous items

ChEBI update

https://github.com/geneontology/go-ontology/pull/22092 Jan 1 release was supposed to remove the links of fumaric acid, succinic acid, and malonic acid to lipid; can we start the import again?

HJD: One still remained but I contacted CHEBI
see 
https://github.com/geneontology/go-ontology/pull/22657
and reponse to chebi ticket
https://github.com/ebi-chebi/ChEBI/issues/4176#issuecomment-1017574603
So this will be gone in the next release but should we hold up the import?

ACTIONS

  1.  Jim to load the latest 'good' version of CheBI; if that seems fine we'll skip the current version (that still contains succinyl CoA as a lipid)
  2.  Chris, Paul: Make a list of requests for ChEBI - including

Design patterns

Implemented in ontology see for example GO:2001077

Question: do we need to remove the 'conforms to dp' when we obsolete terms? Are these automatically calculated at each GO release?

  • Yes, lets remove those. This field should be populated automatically (frequency TBD)

ACTIONS

  1. Pascale: document how to deal with 'conforms to dp' during term obsoletion and merge
  2. Jim: create automatic process to regenerating 'conforms to dp' info in the ontology

Making localization and metabolic process disjoint

OK to merge? https://github.com/geneontology/go-ontology/pull/22648

  • Yes, let's merge (DONE)

Changing the relation for transport and transporter activity from 'transports or maintains localization of' to 'has input'

https://github.com/geneontology/go-ontology/pull/22642

  • Decision is to use 'has direct input' -> ACTIONS Pascale - close PR and redo

Property range violations

https://github.com/geneontology/go-ontology/issues/16524

Progress:

  • Looks like an issue in GO, where 'cavity development' may be redundant with the equivalent 'tube' terms, or the 'tube terms are missing'?

ACTIONS: Review 'cavity terms


Did not discuss today:

Protein-complex organization/assembly/disassembly

Problem with relations used in logical definition https://github.com/geneontology/go-ontology/issues/22488

RO has been changed, so that the logical issue is fixed; however do we want to use 'results in assembly of' or 'has output' for protein-containing complex assembly? This decision impacts the relations used in GO-CAM and extensions, since we aim to align them.


Other Business

https://github.com/geneontology/go-ontology/projects/1