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
* Next: Add property chains for 'has primary input' and 'has primary output' that mirror existing chain for 'has input'? ?
* 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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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/geneontology/go-ontology/issues/16524 Property range violations]===
* 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: https://github.com/geneontology/go-ontology/issues/22784
* neural rod cavitation | neural tube lumen: https://github.com/geneontology/go-ontology/issues/22784
* pronephric sinus development | pronephric sinus: see https://github.com/obophenotype/uberon/issues/2274
----
* '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:
Chris: only  'pronephric sinus development' describes a sinus; other describe valves, venosus
* '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>


===[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/71 New taxon constraints]
* [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

Moving the Google drive to a 'Shared' drive

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

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.

Other Business

https://github.com/geneontology/go-ontology/projects/1

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