Ontology meeting 2021-11-15

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


Agenda

New goslim_generic BP now in the ontology

https://github.com/geneontology/go-ontology/issues/22294

  • present at the next annotation call?
  • next: update the MF goslim-generic

Metabolic/biosynthetic process DP and term creation guidelines

Excretion

https://github.com/geneontology/go-ontology/issues/22368

How to find terms used in other ontologies

Chris will send link to the tool by email


ATP-dependent activity

Brought up by Raymond Issues are :

  • people don't see the relation in ontology browsers
  • annotations are not instantiated; should be
  • also other issue is that some part_of relation are missing from GO basic

https://github.com/geneontology/go-ontology/issues/19954

Design patterns

Jim has been working on new DP, not on the repo yet

utilization

There are 4 terms, 'x utilization', directly under BP: GO:0009758 carbohydrate utilization GO:0015976 carbon utilization  GO:0006794 phosphorus utilization GO:0006791 sulfur utilization   What does 'utilization' means in this context? Is it different from 'x-containing catabolic process', for example 'carbohydrate-compound containing catabolic process'? Maybe they could merge into their catabolic equivalent? PD comment - but consider uptake of something used for further biosyntheses - so maybe this is an argument that 'utilization' means 'x-containing metabolic process'?

Or could they be moved under

  • GO:0031670 cellular response to nutrient, maybe related to other children there?
    • GO:0045990 carbon catabolite regulation of transcription
    • GO:0061984 catabolite repression

Primary input/output versus input and output in the ontology versus in annotations

Follow up on decision to keep using has input, this means the same as what we currently use as 'has primary input', use 'has participant' for other reaction participants

Proposals http://wiki.geneontology.org/index.php?title=Ontology_meeting_2021-11-01&action=edit&section=2

Signaling issues encountered in subset workshop

https://github.com/geneontology/go-ontology/issues/22273


Follow up on ChEBI representation of lipids

https://github.com/geneontology/go-ontology/pull/22092

  • AI from last week: Harold and Pascale to write to Alan, Anne
  • See PR - Harold will write to CHeBI and request the 8 categories mentioned by Alan


Is the ribosome a complex or a CC

Or could it be both? This violates current ShEx rules https://github.com/geneontology/go-ontology/issues/21143

Other Business

https://github.com/geneontology/go-ontology/projects/1