Ontology meeting 2022-01-24

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  • 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:



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?


  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 requesting 'developer' versions of ChEBI so we can test it ahead of releases

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)


  1. DONE 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: https://github.com/geneontology/go-ontology/issues/22723

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'


Property range violations



  • 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 subarachnoid space development | subarachnoid space tube lumen cavitation | tube lumen neural rod cavitation | neural tube lumen pronephric sinus development | pronephric sinus

Sinus terms: Not sure why only 'pronephric sinus development' is causing problems others do have LDs:

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