Ontology meeting 2022-01-24: 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, 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 requesting 'developer' versions of ChEBI so we can test it ahead of releases


===Design patterns===
===Design patterns===
Line 23: Line 27:


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'''
# '''DONE''' 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: https://github.com/geneontology/go-ontology/issues/22723


===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: https://github.com/geneontology/go-ontology/issues/22721


===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
subarachnoid space development | subarachnoid space
tube lumen cavitation | tube lumen
neural rod cavitation | neural tube lumen
pronephric sinus development | pronephric sinus
* '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:
* '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>
==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

Latest revision as of 04:35, 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 requesting 'developer' versions of ChEBI so we can test it ahead of releases

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. DONE 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: https://github.com/geneontology/go-ontology/issues/22723

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

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 subarachnoid space development | subarachnoid space tube lumen cavitation | tube lumen neural rod cavitation | neural tube lumen pronephric sinus development | pronephric sinus


Sinus terms: Not sure why only 'pronephric sinus development' is causing problems others do have LDs:

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