Ontology meeting 2022-01-24: Difference between revisions
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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? | 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? | ||
One still remained but I contacted CHEBI | HJD: One still remained but I contacted CHEBI | ||
see | see | ||
https://github.com/geneontology/go-ontology/pull/22657 | https://github.com/geneontology/go-ontology/pull/22657 | ||
and reponse to chebi ticket | and reponse to chebi ticket | ||
https://github.com/ebi-chebi/ChEBI/issues/4176#issuecomment-1017574603 | 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? | So this will be gone in the next release but should we hold up the import? | ||
===Design patterns=== | ===Design patterns=== | ||
Revision as of 12:54, 24 January 2022
- Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
- Present:
- 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?
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?
Making localization and metabolic process disjoint
OK to merge? https://github.com/geneontology/go-ontology/pull/22648
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
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
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.