Ontology meeting 2022-01-24: Difference between revisions
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'''ACTIONS''' | '''ACTIONS''' | ||
# Pascale: document how to deal with 'conforms to dp' during term obsoletion and merge | # '''DONE''' Pascale: document how to deal with 'conforms to dp' during term obsoletion and merge | ||
# Jim: create automatic process to regenerating 'conforms to dp' info in the ontology | # Jim: create automatic process to regenerating 'conforms to dp' info in the ontology | ||
Revision as of 04:31, 25 January 2022
- 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
- Regrets:
Announcements
Agenda
Following up on previous items
ChEBI update
https://github.com/geneontology/go-ontology/pull/22092 Jan 1 release was supposed to remove the links of fumaric acid, succinic acid, and malonic acid to lipid; can we start the import again?
HJD: One still remained but I contacted CHEBI see https://github.com/geneontology/go-ontology/pull/22657 and reponse to chebi ticket https://github.com/ebi-chebi/ChEBI/issues/4176#issuecomment-1017574603 So this will be gone in the next release but should we hold up the import?
ACTIONS
- Jim to load the latest 'good' version of CheBI; if that seems fine we'll skip the current version (that still contains succinyl CoA as a lipid)
- Chris, Paul: Make a list of requests for ChEBI - including
Design patterns
Implemented in ontology see for example GO:2001077
Question: do we need to remove the 'conforms to dp' when we obsolete terms? Are these automatically calculated at each GO release?
- Yes, lets remove those. This field should be populated automatically (frequency TBD)
ACTIONS
- DONE Pascale: document how to deal with 'conforms to dp' during term obsoletion and merge
- Jim: create automatic process to regenerating 'conforms to dp' info in the ontology
Making localization and metabolic process disjoint
OK to merge? https://github.com/geneontology/go-ontology/pull/22648
- Yes, let's merge (DONE)
Changing the relation for transport and transporter activity from 'transports or maintains localization of' to 'has input'
https://github.com/geneontology/go-ontology/pull/22642
- Decision is to use 'has direct input' -> ACTIONS Pascale - close PR and redo: https://github.com/geneontology/go-ontology/issues/22721
Property range violations
https://github.com/geneontology/go-ontology/issues/16524
Progress:
- New relation(s): (positively|negatively) regulates characteristic
- Remaining blocker: https://github.com/obophenotype/uberon/issues/2218
- 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 neural rod cavitation | neural tube lumen pronephric sinus development | pronephric sinus
- '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:
- '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>
Did not discuss today:
Protein-complex organization/assembly/disassembly
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.