Ontology meeting 2022-01-24: Difference between revisions
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* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul | * '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul | ||
* '''Present: ''' | * '''Present: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul ''' | ||
* '''Regrets: ''' | * '''Regrets: ''' | ||
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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? | ||
'''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=== | ===Design patterns=== | ||
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Question: do we need to remove the 'conforms to dp' when we obsolete terms? Are these automatically calculated at each GO release? | 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''' | |||
# 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=== | ===Making localization and metabolic process disjoint=== | ||
OK to merge? | OK to merge? | ||
https://github.com/geneontology/go-ontology/pull/22648 | 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'=== | ===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 | https://github.com/geneontology/go-ontology/pull/22642 | ||
* Decision is to use 'has direct input' -> '''ACTIONS''' Pascale - close PR and redo | |||
===Property range violations=== | ===Property range violations=== | ||
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* Remaining blocker: https://github.com/obophenotype/uberon/issues/2218 | * 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 | |||
Did not discuss today: | |||
===Protein-complex organization/assembly/disassembly=== | ===Protein-complex organization/assembly/disassembly=== | ||
Problem with relations used in logical definition | Problem with relations used in logical definition |
Revision as of 03:38, 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
- 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
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
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.