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Phyloreferencing Ontology and OWL DL reasoning with phyloreferences
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An object property for referencing taxonomic units from specifiers #6

Closed gaurav closed 5 years ago

gaurav commented 6 years ago

Proposed term: cdao:represents_TU (object property) Definition: A taxonomic unit referenced by an entity that can be identified to a taxon. This entity might reference multiple taxonomic units, any of which can be matched. Domain: Specifier (#5) or Node (CDAO_0000140) Range: TU (obo:CDAO_0000138 or #10) See also: scratch ontology, PHYX context

Competency questions:

hlapp commented 6 years ago

See comment on #8 re: supporting competency question(s). Isn't there references_TU already in CDAO, so that we could simply import that term?

gaurav commented 6 years ago

I've added a competency question -- let me know what you think! We could use cdao:represents_TU instead, but that term has an explicit domain of cdao:Node -- so using it would imply that a Specifier is also a Node, which doesn't make sense to me. Could we somehow include it without including that implication?

hlapp commented 6 years ago

I've added a competency question -- let me know what you think!

Good start, but it doesn't necessarily show (yet?) why we need this property. For example, wouldn't we be able to get the answer by simply querying which objects of type cdao:TU are linked to the specifier subject, regardless of property?

We could use cdao:represents_TU instead, but that term has an explicit domain of cdao:Node -- so using it would imply that a Specifier is also a Node, which doesn't make sense to me.

Right. I think that's an issue to be reported to the CDAO tracker.

Are you saying that if that were fixed in CDAO, there would be no hindrance to reusing the CDAO property?

Could we somehow include it without including that implication?

Yes, at least temporarily. I think it may not be viable anyway to import CDAO as a whole as it's now (because it drives up the required expressivity profile), so we'll probably at least in the interim end up extracting a subset of axioms from CDAO.

gaurav commented 6 years ago

Good start, but it doesn't necessarily show (yet?) why we need this property. For example, wouldn't we be able to get the answer by simply querying which objects of type cdao:TU are linked to the specifier subject, regardless of property?

I'm not sure I understand what you mean. If this isn't the property used to link Specifiers to cdao:TU, then what is? Or do you mean that my competency question should be more specific? I've added two new competency questions to the issue that might help with this -- let me know what you think!

We could use cdao:represents_TU instead, but that term has an explicit domain of cdao:Node -- so using it would imply that a Specifier is also a Node, which doesn't make sense to me. Right. I think that's an issue to be reported to the CDAO tracker.

Are you saying that if that were fixed in CDAO, there would be no hindrance to reusing the CDAO property?

Actually, yes. I think node identification and specifier identification are similar enough that we could refer to them in the same way.

Could we somehow include it without including that implication? Yes, at least temporarily. I think it may not be viable anyway to import CDAO as a whole as it's now (because it drives up the required expressivity profile), so we'll probably at least in the interim end up extracting a subset of axioms from CDAO.

Sounds good! I've modified this issue to incorporate cdao:represents_TU rather than creating our own term. If we do this and it works successfully, we could open an issue with them to broaden the range of cdao:represents_TU.

hlapp commented 5 years ago

In light of the conclusion from recent discussions that at least for purposes of phylogenetic clade definitions there is no discernible difference between a specifier and a referent to a taxon concept, I would argue the concern about the domain constraint of cdao:represents_TU is no longer pertinent, since there is no good reason not to link directly from a node to the cdao:TU that it represents. Therefore this should be closed.

gaurav commented 5 years ago

Agreed! Closing.