Ontology meeting 2022-03-28: 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, Jim, David, | ||
* '''Regrets: ''' Peter, Kimberly | * '''Regrets: ''' Peter, Kimberly | ||
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See details here: https://github.com/geneontology/go-site/issues/1813 | See details here: https://github.com/geneontology/go-site/issues/1813 | ||
Please move the files you own | Please move the files you own | ||
===Missing inferences from external ontologies=== | ===Missing inferences from external ontologies=== | ||
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https://github.com/geneontology/go-ontology/issues/22721 | https://github.com/geneontology/go-ontology/issues/22721 | ||
* Pascale changed relations in the ontology | * Pascale changed relations in the ontology | ||
* | * OK Checked - Property chains for 'has primary input' and 'has primary output' mirror existing ones for 'has input' | ||
==Schedule a jamboree== | ==Schedule a jamboree== | ||
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==Obsolete RHEA xrefs errors== | ==Obsolete RHEA xrefs errors== | ||
Travis reports: | Travis reports: | ||
* Obsolete Rhea ID used in xref: RHEA:16681 (RHEA:16681 has been replaced by RHEA:30595) | * Obsolete Rhea ID used in xref: RHEA:16681 (RHEA:16681 has been replaced by RHEA:30595); GO:0052881 already assigned RHEA:30595 using FADH; GO:0018660 assigned to RHEA 16681 with NAD vs FAD; 3 IEA; suggest obsoletion of GO:0018660 | ||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: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: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: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* Obsolete Rhea ID used in xref: RHEA:21872 (RHEA:21872 has been replaced by RHEA:48100) | * Obsolete Rhea ID used in xref: RHEA:21872 (RHEA:21872 has been replaced by RHEA:48100 already assigned) | ||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: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) | * 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 1.1.1.348) and medicarpin synthase (EC 4.2.1.139).) | * 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 1.1.1.348) and medicarpin synthase (EC 4.2.1.139).) | ||
etc | etc | ||
* [https://github.com/geneontology/go-ontology/issues/23098 Obsolete RHEA mappings ticket] | |||
==Valid def xrefs== | ==Valid def xrefs== | ||
* UniProt KW? | * UniProt KW? | ||
* Viral Zone? | * Viral Zone? -> no, spoke to Patrick Masson, these are just links to SPKW | ||
* | * | ||
===[https://github.com/geneontology/go-ontology/issues/16524 Property range violations]=== | |||
Now all gone :) | |||
==Following up on previous items== | ==Following up on previous items== | ||
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===[https://github.com/orgs/geneontology/projects/71 New taxon constraints]=== | ===[https://github.com/orgs/geneontology/projects/71 New taxon constraints]=== | ||
===[https://github.com/orgs/geneontology/projects/5 BP refactor]=== | ===[https://github.com/orgs/geneontology/projects/5 BP refactor]=== | ||
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** [https://github.com/orgs/geneontology/projects/73 Finish Boomer tickets] | ** [https://github.com/orgs/geneontology/projects/73 Finish Boomer tickets] | ||
** strategy to create new GO terms | ** strategy to create new GO terms | ||
* [https://github.com/orgs/geneontology/projects/81 Review single step BPs] + [https://github.com/orgs/geneontology/projects/5 BP refactoring] | * [https://github.com/orgs/geneontology/projects/81 Review single step BPs] + [https://github.com/orgs/geneontology/projects/5 BP refactoring] | ||
* Jamboree to close tickets? | * Jamboree to close tickets? |
Latest revision as of 01:48, 1 April 2022
- Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
- Present: Pascale, Karen, Harold, Raymond, Jim, David,
- Regrets: Peter, Kimberly
Discussion points
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
https://github.com/geneontology/go-ontology/issues/22721
- Pascale changed relations in the ontology
- OK Checked - Property chains for 'has primary input' and 'has primary output' mirror existing ones for 'has input'
Schedule a jamboree
Pascale away during the no GO calls week; can we do this next week?
- BP refactor
- Roles
Obsolete RHEA xrefs errors
Travis reports:
- 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 1.1.1.348) and medicarpin synthase (EC 4.2.1.139).)
etc
Valid def xrefs
- UniProt KW?
- Viral Zone? -> no, spoke to Patrick Masson, these are just links to SPKW
Property range violations
Now all gone :)
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
New taxon constraints
BP refactor
With Paul in Geneva, making a plan as to how to refactor, see project
- Pascale/Paul presented. Overall positive reaction
- GO-RHEA:
- Finish Boomer tickets
- strategy to create new GO terms
- Review single step BPs + BP refactoring
- Jamboree to close tickets?
- Design patterns: implement new design patterns and enforce usage in the ontology
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.