Ontology meeting 2021-11-15: Difference between revisions
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GO:0006791 sulfur 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? | 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 | Or could they be moved under | ||
Revision as of 13:06, 12 November 2021
- Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, Sierra, David, Chris, Paul
- Present:
- Regrets:
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
Excretion
https://github.com/geneontology/go-ontology/issues/22368
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
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, Anneticket
- 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