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oborel / obo-relations

RO is an ontology of relations for use with biological ontologies
http://oborel.github.io/
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add process to domain to range of concretizes #650

Closed wdduncan closed 2 months ago

wdduncan commented 1 year ago

In BFO-2020 the domain of concretizes at some time is process or 'specifically dependent continuant'. The domain of RO's concretizes should be updated to include process for sake of consistency.

cmungall commented 1 year ago

I have no objection but this should be taken to the main stakeholders of this relation, which would include OBI. I am not sure who else uses these abstract relations.

bpeters42 commented 1 year ago

Discussed in OBI call 1/9/2023. Relaxing the domain from 'specifically dependent continuant' only to add 'process' should be okay from OBI's point of view.

wdduncan commented 1 year ago

@anitacaron @matentzn I opened a new branch for this issue (branch issue-650). After I made my changes, it reverted the license annotation back to http://purl.org/dc/elements/1.1/license: 

-    <!-- http://purl.org/dc/terms/license -->
+    <!-- http://purl.org/dc/elements/1.1/license -->

-    <owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/license"/>
+    <owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/license"/>

Any ideas why?

anitacaron commented 1 year ago

I commented in the PR.

cmungall commented 2 months ago

Summarizing from RO call today.

I'm going to rewrite the original ask more precisely: the goal is to relax the domain to change it from SDC to a union SDC or biological process, to be consistent with BFO (http://purl.obolibrary.org/obo/BFO_0000059 -- simply "concretizes" in http://purl.obolibrary.org/obo/bfo/2020/bfo-core.owl)

If we do this, then we should:

  1. Change the text definition to be consistent. Currently it is "A relationship between a specifically dependent continuant and..."
  2. Add an example of usage. We currently have two examples of usages, and both have SDCs (IAs). We need an example of process.
  3. There were various references in the call to a talk, and also to a previous discussion in an OBI call but we should have links here so we can all examine the case

As an aside, we also noticed that we are manually duplicating annotations for inverses. This is not good practice, it violates DRY. @cmungall will look for documentation on existing practice and what we should do here (refer vs automatically propagate in release file).