Difference between revisions of "Ontology meeting 2021-03-15"

From GO Wiki
Jump to navigation Jump to search
m
 
(5 intermediate revisions by 2 users not shown)
Line 11: Line 11:


==Announcements==
==Announcements==
* New Rheas: we propose NOT to wait for the Rhea to be public to add it to a GO term. Too much waiting and going back. We need to close tickets.
* New Rheas: Pascale & Harold propose NOT to wait for the Rhea to be public to add it to a GO term. Too much waiting and going back. We need to close tickets.
* Obsoletions: For terms with no annotations, no mappings, no xrefs, not in subsets: announce + obsolete immediately. We can always restore the term in the unlikely event that there is an objection
* Obsoletions: For terms that are clearly wrong & with no annotations, no mappings, no xrefs, not in subsets: announce + obsolete immediately. We can always restore the term in the unlikely event that there is an objection
 
* New helpdesk ticket from Paul Pavlidis about releases: https://github.com/geneontology/helpdesk/issues/302


==Slack demo==
==Slack demo==
Chris  
Chris  
<hr>
=== Follow up: Cellular Component, ShEx, and GO-CAMs  -- BLOCKING FOR GO-CAM ===
Pascale spoke to Patrick Masson
Proposal is to have 3 branches:
* cellular anatomical entity
** move 'other organism part' here (if we don't obsolete that term)
* virion compoment (merge of 'virion' and 'virion part' (no annotations))
* protein-containing complex
* On a related note, 'host cell' and 'host cell part' can probably merge into 'host cellular component' - see https://github.com/geneontology/go-ontology/issues/19800
Thoughts?


<hr>
<hr>
Line 45: Line 60:


<hr>
<hr>
==merge GO:0019539 siderophore biosynthetic process from hydroxamic acid==
https://github.com/geneontology/go-ontology/issues/20975
see the number of siderophores here: https://pdfs.semanticscholar.org/7946/e6339f9fbb60b054747ee4d706e53958b980.pdf?_ga=2.67985041.1432405903.1614609213-563084161.1614609213





Latest revision as of 12:13, 15 March 2021

Attendees

  • Group members: Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul, Eric
  • Present:
  • Regrets:



Agenda

Announcements

  • New Rheas: Pascale & Harold propose NOT to wait for the Rhea to be public to add it to a GO term. Too much waiting and going back. We need to close tickets.
  • Obsoletions: For terms that are clearly wrong & with no annotations, no mappings, no xrefs, not in subsets: announce + obsolete immediately. We can always restore the term in the unlikely event that there is an objection
  • New helpdesk ticket from Paul Pavlidis about releases: https://github.com/geneontology/helpdesk/issues/302

Slack demo

Chris


Follow up: Cellular Component, ShEx, and GO-CAMs -- BLOCKING FOR GO-CAM

Pascale spoke to Patrick Masson Proposal is to have 3 branches:

  • cellular anatomical entity
    • move 'other organism part' here (if we don't obsolete that term)
  • virion compoment (merge of 'virion' and 'virion part' (no annotations))
  • protein-containing complex


Thoughts?


New relationships after using equivalent Rhea reaction

https://github.com/geneontology/go-ontology/issues/20839

Jim generated a ttl file.

*Discussion:

  • Created Logical definition
  • Plan: going forward, creating new terms:
    • add Rhea description in textual definition
    • bring EC mapping from Rhea
    • pull EC name automatically
    • retrospectively  ??''
  • Next step:
    • check if those logical definitions cause problems in inferences
    • Jim to check if some subsumptions are missing

id ranges file

https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/go-idranges.txt

  • do we need "The Original Set (OS) of GO terms"
  • do we need both the text and owl files?



xref types

Other Business

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


Minutes should be recorded on individual tickets and in individual projects