Ontology meeting 2022-03-28
- Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
- Regrets: Peter, Kimberly
See details here: https://github.com/geneontology/go-site/issues/1813
Please move the files you own:
Missing inferences from external ontologies
see Missing part-of relation for: GO:0060658 nipple morphogenesis; should we request changes from upstream ontologies?
- To rediscuss next week when Jim is here
Transport or maintains localization relation
- Pascale changed relations in the ontology
- Next: Add property chains for 'has primary input' and 'has primary output' that mirror existing chain for 'has input'? ?
Schedule a jamboree
Pascale away during the no GO calls week; can we do this next week?
- BP refactor
Obsolete RHEA xrefs errors
- Obsolete Rhea ID used in xref: RHEA:16681 (RHEA:16681 has been replaced by RHEA:30595); GO:0052881 already assigned RHEA:30595 using FADH; GO:0018660 assigned to RHEA 16681 with NAD vs FAD; 3 IEA; suggest obsoletion of GO:0018660
- Obsolete Rhea ID used in xref: RHEA:24124 Not enough experimental evidence to support reaction.)
- Obsolete Rhea ID used in xref: RHEA:21784 (Not enough experimental evidence to support reaction.)
- Obsolete Rhea ID used in xref: RHEA:14897 (This reaction has turned out to be incorrect.)
- Obsolete Rhea ID used in xref: RHEA:21872 (RHEA:21872 has been replaced by RHEA:48100 already assigned)
- Obsolete Rhea ID used in xref: RHEA:14577 (The activity has now been shown to be due to RHEA:28526 and RHEA:28338)
- Obsolete Rhea ID used in xref: RHEA:23740 (RHEA:23740 has been replaced by RHEA:50732 not used yet)
- Obsolete Rhea ID used in xref: RHEA:13533 (The reaction has been deleted as it is the result of the activity of two separate enzymes: vestitone reductase (EC 22.214.171.1248) and medicarpin synthase (EC 126.96.36.199).)
Valid def xrefs
- UniProt KW?
- Viral Zone?
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
- 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>
With Paul in Geneva, making a plan as to how to refactor, see project
- Pascale/Paul presented. Overall positive reaction
- 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
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.