Ontology meeting 2022-01-31

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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:


Aging miniproject

(Proposed by Val) This became a higher priority last week because there will be a NSF workshop in Florida this week about microbial annotation, and one possible outcome is the increase in automatic/text-mining-based annotation, and phenotypes are often misannoatated by these tools. Val mentions function prediction people working with fission yeast researchers making predictions to ageing. All they are probably doing really is extrapolating phenotypes like this: https://pubmed.ncbi.nlm.nih.gov/33878922/ (an ageing phenotype, already has 415 annotation) and inferences from other species to the GO term "ageing". (which as far as we know is just 'cells survive longer under starvation before they die) it's just knockouts which increase viability (mainly those that attenuate growth like genes involved in TOR signalling and translation or carbohydrate utilization.

It is difficult for to say these predictions are invalid if GO has such terms.


Next Priorities for Ontology group

  • Ongoing:
    • Multi-org
    • transcription
    • roles
    • aging
  • Content meetings?

Following up on previous items

  • ChEBI: 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

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

New taxon constraints

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

Sinus terms: Not sure why only 'pronephric sinus development' is causing problems others do have LDs: Chris: only 'pronephric sinus development' describes a sinus; other describe valves, venosus

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