Difference between revisions of "Ontology meeting 2022-03-28"

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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* Obsolete Rhea ID used in xref: RHEA:16681  (RHEA:16681 has been replaced by RHEA:30595)
* Obsolete Rhea ID used in xref: RHEA:16681  (RHEA:16681 has been replaced by RHEA:30595); GO:0052881 already assigned RHEA:30595 using FADH; GO:0018660 assigned to RHEA 16681 with NAD vs FAD; 3 IEA; suggest obsoletion of GO:0018660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* Obsolete Rhea ID used in xref: RHEA:21872 (RHEA:21872 has been replaced by RHEA:48100)
* Obsolete Rhea ID used in xref: RHEA:21872 (RHEA:21872 has been replaced by RHEA:48100 already assigned)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* Obsolete Rhea ID used in xref: RHEA:23740 (RHEA:23740 has been replaced by RHEA:50732)
* Obsolete Rhea ID used in xref: RHEA:23740 (RHEA:23740 has been replaced by RHEA:50732 not used yet)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).)



Revision as of 10:50, 28 March 2022

  • Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul
  • Present:
  • 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
  • Next: Add property chains for 'has primary input' and 'has primary output' that mirror existing chain 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?

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

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



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

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