Ontology meeting 2021-11-15
- 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
- Marc F requested 2 terms (https://github.com/geneontology/go-ontology/issues/22374, https://github.com/geneontology/go-ontology/issues/22373); would like to create 10's more
- These are unlikely to be much annotated, as some secondary metabolites are specific to specific species
- The entire pathway is often known
- Other 'metabolic' term requested: mycofactocin-coupled metabolic process; is this a valid GO term?
- May not fit proposed DP, 'has primary input or output' some x
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§ion=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