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

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(Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present: ''' * '''Regrets: ''' =Announcements= ==[https://git...")
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Revision as of 03:07, 26 January 2022

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


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