Ontology meeting 2022-10-24
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- Group members: Pascale, Harold, Raymond, Val, Peter, Jim, Tanya, Karen, Kimberly, David, Chris, Paul
- Present: Pascale, Harold, Raymond, Val, Peter, Jim, Tanya, Karen, Kimberly, David, Paul
- Regrets: Chris
Announcements
- Pascale, Paul: Oct 17th - Nov 4th
- First aim of the BP refactoring is to separate 'cellular processes' and 'organism-level processes' - for example walking behavior and cell motility should not be under a common 'locomotion' parent, as these processes dont use the same molecular mechanisms.
- 'behavior' was moved under 'multicellular organism process' back in March
- GO:0044267 cellular protein metabolic process was merged into GO:0019538 protein metabolic process, likewise for the children
- Past couple of weeks:
- biomineralization
- homeostatic process
Editors discussion items
Follow up on MF to MF Relations
- This has been merged; is there anything this group would like to discuss/review?
- I added the new RO relations to the ShEx, but until they are released by RO and then incorporated into go-lego-reacto, the pull request will continue to fail (Kimberly).
Are the ShEx rules the "source of truth" for the ontology as well as annotation?
- Need to define the scope of ShEX - some of us understood that the rules for the ontology were to be derived from ShEx; is this right ?
- If that's the case, how are we going to capture rules for relations that are specific to the ontology?
- Can we make use of comments or RO subsets in the ShEx to capture usage? This has also been discussed in the context of which annotation extension relations to add to the Noctua form and pathway editors.
- -> Jim: it would be complicated to make the ontology rules. Our GO-CAM ShEx are designed to define instances
- -> The design patterns would be where these rules would be encoded
GO practice for obsoletion versus merges
- Chris prefers we obsolete terms and use REPLACED BY rather than merging terms, which seems to confuse users.
- Are there objections in the group?
- We can email go-consortium to as whether other people have issues with that; any other group we should notify? obo mailing list?
inhibition of ectopic tissue mineralization
For the BP refactoring:
- biomineralization: split into cellular level, ie created magnetosome assembly, proposed to obsolete the 'biomineralization' superclass, so that the top level term will be 'GO:0031214 biomineral tissue development'
Current:
- GO:0110148 biomineralization
- GO:0048513 animal organ development
- GO:0009888 tissue development
- GO:0031214 biomineral tissue development
- GO:0031214 biomineral tissue development
- GO:0030282 bone mineralization
- GO:0036340 chitin-based cuticle sclerotization by biomineralization
- GO:0045299 otolith mineralization
- GO:0031215 shell calcification
- GO:0034505 tooth mineralization
- GO:0031214 biomineral tissue development
- GO:0031214 biomineral tissue development
Proposed:
- GO:0048513 animal organ development
- GO:0009888 tissue development
- GO:0031214 biomineral tissue development
- GO:0030282 bone mineralization
- GO:0036340 chitin-based cuticle sclerotization by biomineralization
- GO:0045299 otolith mineralization
- GO:0031215 shell calcification
- GO:0034505 tooth mineralization
- GO:0031214 biomineral tissue development
https://github.com/geneontology/go-ontology/issues/24228
See also discussion in the annotation review ticket: https://github.com/geneontology/go-annotation/issues/4338
- Discussion: 'ectopic' sounds abnormal. AI Pascale: remove 'ectopic' from term label and term definition. See GH ticket
Suggestions for editors workflow improvements
(Raymond)
- Automatization of obsoletion - are close is this functionality from being deployed?
- Pascale: sometimes closes several tickets at once (especially for 'simple' obsoletions), to avoid having to close and re-open Protégé, which for easy tickets, takes the largest % time relative to the actual work.
- command line query for taxon constraints - Protégé is very slow
Tickets by ontology editors
Other tickets
Tanya: endodermis: https://github.com/geneontology/go-ontology/issues/24248