Ontology meeting 2021-03-01: Difference between revisions

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




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Is this still OK?
Is this still OK?
* ''Need to look at ShEx with Jim ''




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extrasynaptic signalling via GABA  
extrasynaptic signalling via GABA  
'cell-cell signaling' and ('process has causal agent' some 'gamma-aminobutyric acid zwitterion') and ('occurs in' some 'perisynaptic space')
'cell-cell signaling' and ('process has causal agent' some 'gamma-aminobutyric acid zwitterion') and ('occurs in' some 'perisynaptic space')
* ''See proposal in ticket''


* Is this the relation use want to use for x-mediated processes? See for example 'GO:0002443 | leukocyte mediated immunity' in https://github.com/geneontology/go-ontology/issues/17613
* Is this the relation use want to use for x-mediated processes? See for example 'GO:0002443 | leukocyte mediated immunity' in https://github.com/geneontology/go-ontology/issues/17613
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<hr>
<hr>
==New relationships after using equivalent Rhea reaction==
==New relationships after using equivalent Rhea reaction==
https://github.com/geneontology/go-ontology/issues/20839
https://github.com/geneontology/go-ontology/issues/20839
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Jim generated a ttl file.
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''


<hr>
<hr>
==id ranges file==
==id ranges file==
https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/go-idranges.txt
https://raw.githubusercontent.com/geneontology/go-ontology/master/src/ontology/go-idranges.txt
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<hr>
<hr>
===merge GO:0019539 siderophore biosynthetic process from hydroxamic acid===
==merge GO:0019539 siderophore biosynthetic process from hydroxamic acid==
https://github.com/geneontology/go-ontology/issues/20975
https://github.com/geneontology/go-ontology/issues/20975



Latest revision as of 15:46, 1 March 2021

Attendees

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



Agenda

Announcements

No call next week - No GO Calls Week

Discussion

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

  • The ShEx specifications state that MFs can occur in an Anatomical Entity and that GPs or Protein-Containing Complexes can be located in an Anatomical Entity.
  • Most non-protein-containing complex GO CC terms are a child of Cellular Anatomical Entity which is a subclass of Anatomical Entity.
  • However, annotations to root Cellular Component result in ShEx violations because root Cellular Component is NOT a subclass of Anatomical Entity.

Discussion

  • Chris: suggests keeping the current practice and use root Cellular Component and ND.
  • Action would be to change the ShEX to allow a direct annotation to occurs_is/is active in root Cellular Component

Is this still OK?

  • Need to look at ShEx with Jim



'process has causal agent' relation

Raymond proposed to use in LD: https://github.com/geneontology/go-ontology/issues/13307#issuecomment-786985814

extrasynaptic signalling via GABA 'cell-cell signaling' and ('process has causal agent' some 'gamma-aminobutyric acid zwitterion') and ('occurs in' some 'perisynaptic space')

  • See proposal in ticket

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?

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



xref types

Other Business

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


Minutes should be recorded on individual tickets and in individual projects