Difference between revisions of "Ontology meeting 2022-01-24"

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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, Peter, Jim, Tanya, Kimberly, David, Chris, Paul '''  
* '''Regrets: '''   
* '''Regrets: '''   


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  https://github.com/ebi-chebi/ChEBI/issues/4176#issuecomment-1017574603
  https://github.com/ebi-chebi/ChEBI/issues/4176#issuecomment-1017574603
  So this will be gone in the next release but should we hold up the import?
  So this will be gone in the next release but should we hold up the import?
'''ACTIONS'''
# Jim to load the latest 'good' version of CheBI; if that seems fine we'll skip the current version (that still contains succinyl CoA as a lipid)
# Chris, Paul: Make a list of requests for ChEBI - including


===Design patterns===
===Design patterns===
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Question: do we need to remove the 'conforms to dp' when we obsolete terms? Are these automatically calculated at each GO release?  
Question: do we need to remove the 'conforms to dp' when we obsolete terms? Are these automatically calculated at each GO release?  
* Yes, lets remove those. This field should be populated automatically (frequency TBD)


'''ACTIONS'''
# Pascale: document how to deal with 'conforms to dp' during term obsoletion and merge
# Jim: create automatic process to regenerating 'conforms to dp' info in the ontology


===Making localization and metabolic process disjoint===
===Making localization and metabolic process disjoint===
OK to merge?  
OK to merge?  
https://github.com/geneontology/go-ontology/pull/22648
https://github.com/geneontology/go-ontology/pull/22648
* Yes, let's merge (DONE)


===Changing the relation for transport and transporter activity from 'transports or maintains localization of' to 'has input'===
===Changing the relation for transport and transporter activity from 'transports or maintains localization of' to 'has input'===


https://github.com/geneontology/go-ontology/pull/22642
https://github.com/geneontology/go-ontology/pull/22642
* Decision is to use 'has direct input' -> '''ACTIONS''' Pascale - close PR and redo


===Property range violations===
===Property range violations===
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* Remaining blocker: https://github.com/obophenotype/uberon/issues/2218
* Remaining blocker: https://github.com/obophenotype/uberon/issues/2218


* 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
Did not discuss today:
===Protein-complex organization/assembly/disassembly===
===Protein-complex organization/assembly/disassembly===
Problem with relations used in logical definition
Problem with relations used in logical definition

Revision as of 03:38, 25 January 2022

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

Announcements

Agenda

Following up on previous items

ChEBI update

https://github.com/geneontology/go-ontology/pull/22092 Jan 1 release was supposed to remove the links of fumaric acid, succinic acid, and malonic acid to lipid; can we start the import again?

HJD: One still remained but I contacted CHEBI
see 
https://github.com/geneontology/go-ontology/pull/22657
and reponse to chebi ticket
https://github.com/ebi-chebi/ChEBI/issues/4176#issuecomment-1017574603
So this will be gone in the next release but should we hold up the import?

ACTIONS

  1.  Jim to load the latest 'good' version of CheBI; if that seems fine we'll skip the current version (that still contains succinyl CoA as a lipid)
  2.  Chris, Paul: Make a list of requests for ChEBI - including

Design patterns

Implemented in ontology see for example GO:2001077

Question: do we need to remove the 'conforms to dp' when we obsolete terms? Are these automatically calculated at each GO release?

  • Yes, lets remove those. This field should be populated automatically (frequency TBD)

ACTIONS

  1. Pascale: document how to deal with 'conforms to dp' during term obsoletion and merge
  2. Jim: create automatic process to regenerating 'conforms to dp' info in the ontology

Making localization and metabolic process disjoint

OK to merge? https://github.com/geneontology/go-ontology/pull/22648

  • Yes, let's merge (DONE)

Changing the relation for transport and transporter activity from 'transports or maintains localization of' to 'has input'

https://github.com/geneontology/go-ontology/pull/22642

  • Decision is to use 'has direct input' -> ACTIONS Pascale - close PR and redo

Property range violations

https://github.com/geneontology/go-ontology/issues/16524

Progress:

  • 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


Did not discuss today:

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