Ontology meeting 2022-01-31
- Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
- Present: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
(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.
Next Priorities for Ontology group
- Finish Boomer tickets
- strategy to create new GO terms
- New taxon constraints
- Review single step BPs + BP refactoring
- Jamboree to close tickets?
- Design patterns: implement new design patterns and enforce usage in the ontology
- Content meetings?
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'
- ACTIONS Decision is to use 'has primary input' -> https://github.com/geneontology/go-ontology/issues/22721
- See ticket for outline of steps needed to implement.
- 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: https://github.com/geneontology/go-ontology/issues/22784
- neural rod cavitation | neural tube lumen: https://github.com/geneontology/go-ontology/issues/22784
- pronephric sinus development | pronephric sinus: see https://github.com/obophenotype/uberon/issues/2274
- 'neural rod cavitation' <http://purl.obolibrary.org/obo/GO_0014024>
- 'tube lumen cavitation' <http://purl.obolibrary.org/obo/GO_0060605>
- 'salivary gland cavitation' <http://purl.obolibrary.org/obo/GO_0060662> (no LD, so not causing problems in Jim's PR, but still needs reviewing)
- 'mammary gland duct cavitation' <http://purl.obolibrary.org/obo/GO_0060604> (no LD, so not causing problems in Jim's PR, but still needs reviewing)
- 'regulation of tube lumen cavitation' <http://purl.obolibrary.org/obo/GO_1903132>
- 'secondary neural tube rod cavitation' <http://purl.obolibrary.org/obo/GO_0014027>
- 'negative regulation of tube lumen cavitation' <http://purl.obolibrary.org/obo/GO_1903133>
- 'apoptotic process involved in tube lumen cavitation' <http://purl.obolibrary.org/obo/GO_0060609>
- 'apoptotic process involved in salivary gland cavitation' <http://purl.obolibrary.org/obo/GO_0060663>
Sinus terms: Not sure why only 'pronephric sinus development' is causing problems others do have LDs: Chris: only 'pronephric sinus development' describes a sinus; other describe valves, venosus
- 'sinus venosus development' <http://purl.obolibrary.org/obo/GO_0003235>
- 'sinus venosus formation' <http://purl.obolibrary.org/obo/GO_0003237>
- 'sinus venosus morphogenesis' <http://purl.obolibrary.org/obo/GO_0003236>
- 'coronary sinus valve development' <http://purl.obolibrary.org/obo/GO_0003178>
- 'coronary sinus valve formation' <http://purl.obolibrary.org/obo/GO_0003191>
- 'coronary sinus valve morphogenesis' <http://purl.obolibrary.org/obo/GO_0003182>
- 'pronephric sinus development' <http://purl.obolibrary.org/obo/GO_0039012>
- 'left horn of sinus venosus development' <http://purl.obolibrary.org/obo/GO_0061079>
- 'right horn of sinus venosus development' <http://purl.obolibrary.org/obo/GO_0061080>
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.