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/geneontology/go-ontology/pull/22092 | 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? | 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 requesting 'developer' versions of ChEBI so we can test it ahead of releases | |||
===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''' | |||
# '''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: https://github.com/geneontology/go-ontology/issues/22723 | |||
===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: https://github.com/geneontology/go-ontology/issues/22721 | |||
===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 | |||
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=== | ===Protein-complex organization/assembly/disassembly=== | ||
Problem with relations used in logical definition | Problem with relations used in logical definition |
Latest revision as of 04:35, 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 requesting 'developer' versions of ChEBI so we can test it ahead of releases
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: https://github.com/geneontology/go-ontology/issues/22723
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.