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
===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.


===Property range violations===
===Property range violations===
Line 41: Line 35:
* New relation(s): (positively|negatively) regulates characteristic
* New relation(s): (positively|negatively) regulates characteristic
* Remaining blocker: https://github.com/obophenotype/uberon/issues/2218
* Remaining blocker: https://github.com/obophenotype/uberon/issues/2218
===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 ==
== Other Business ==

Revision as of 01:25, 24 January 2022

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

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?


Making localization and metabolic process disjoint

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

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:

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