Open cmungall opened 2 years ago
Hi @cmungall, What will oio:Subset be used for? Could you please give more details?
Her is an example of a term that has many subsets:
http://www.ontobee.org/ontology/GO?iri=http://purl.obolibrary.org/obo/GO_0038023
The general idea is to group terms together in a way that cannot be done in a logical way: for example, a user group may care about certain terms in an ontology but not others (aka the flybase subset). Or in a disease ontology, you could say: this disease belongs to the "Harrison" subset, i.e. is mentioned by the textbook by Dr. Harrison (while, lets say, its sub and superclasses are not).
From @mellybelly (https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1989)
We are getting closer than ever to having the OBO library ontologies work really well together and as we aim for orthogonality, we also need to aim to be able to generate slices of multiple ontologies for different applications. The creation of a common set of subset tags and registry for such artifacts might help with the proliferation of overlapping ontologies and promote reuse and alignment.
@mellybelly - can you expand a bit more on use cases for a common set of subset tags and how we might maintain them?
This issue is about putting the oio:inSubset and oio:Subset into OMO. Having a shared ontology for the subsets themselves is a good idea but should be a separate issue.
The case for including these two are clear, they are used in dozens of ontologies, is there any objection to adding these in OMO?
I don't think there is any big objection now! We can go ahead, see #123 on how to do it
Proposal is to formally include
in OMO
Note the way @dosumis and I chose to model subsets is a little odd, see
https://owlcollab.github.io/oboformat/doc/obo-syntax.html#5.0.3
This avoids introducing individuals into the ontology
Subsets are particularly important for ontologies including but not limited to
Subsets provide a variety of purposes
We need a standard way of annotating a subset with its purpose. Tools can then use this to determine the correct behavior
Alternative to using inSubset should be considered:
After these alternatives are considered, subsets are still necessary
We also need to standardize how different tools work with different slims.
[incomplete list, I will update later]
Advanced applications can use metadata associated with subsets intelligently, e.g.
A part-of some B part-of some C, transitive: part-of
,extract(A,C)
=>A part-of some C
I think this issue replaces
6
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