Ontology meeting 2022-01-24

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



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

and reponse to chebi ticket
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'


Property range violations



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