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

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https://github.com/geneontology/go-ontology/pull/22092
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?
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
HJD: One still remained but I contacted CHEBI
  see  
  see  
  https://github.com/geneontology/go-ontology/pull/22657
  https://github.com/geneontology/go-ontology/pull/22657

Revision as of 12:54, 24 January 2022

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

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?


Making localization and metabolic process disjoint

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

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

Property range violations

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

Progress:

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