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

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).

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

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?

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:

Proposed:

Discussion: 'ectopic' sounds abnormal. AI Pascale: remove 'ectopic' from term label and term definition. See GH ticket

(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