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

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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
* 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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* Looks like an issue in GO, where 'cavity development' may be redundant with the equivalent 'tube' terms, or the 'tube terms are missing'?  
* 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  
'''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: ==
==Did not discuss today: ==

Revision as of 03:53, 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

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