Difference between revisions of "Ontology meeting 2022-01-31"

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==[https://github.com/orgs/geneontology/projects/82 Aging miniproject]==
==[https://github.com/orgs/geneontology/projects/82 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.  
(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.


=Agenda=
=Agenda=

Revision as of 08:58, 27 January 2022

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

Announcements

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.

Agenda

Next Priorities for Ontology group

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'

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:

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