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phyloref / phyloref-ontology

Phyloreferencing Ontology and OWL DL reasoning with phyloreferences
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An object property for indicating taxonomic units involved in a Taxonomic Unit match #11

Closed gaurav closed 3 years ago

gaurav commented 6 years ago

Proposed term: matches_taxonomic_unit (class) Definition: Indicates a taxonomic unit that is involved in a Taxonomic Unit match Domain: A taxonomic unit match (#9) Range: A taxonomic unit (#10) See also: scratch ontology, PHYX context

Competency questions:

hlapp commented 6 years ago

It seems like a TUMatch instance would link two TU instances with the semantics that there is some kind of match between them, and properties further qualifying the nature of the match.

Given that, having matches semantics expressly in the property linking the TUMatch instance to TU instances seems wholly redundant.

More generally, we really need much stronger competency questions, in that they need not only demonstrate that the link they create is worth navigating, but that a more generic property will not do. So for example, the competency question does not answer why cdao:references_TU will not do. The default has to be to not create a new property (or class) and reuse what's already there.

gaurav commented 6 years ago

I see what you mean! We can't use cdao:represents_TU (#6) as currently defined, since it is defined to only relate nodes to TUs, but we could broaden the definition. However, given that it specifically refers to entities representing TUs, I don't think we should use it for TUMatches, as they don't "represent" TUs.

Instead, I think it would be better to say that the TUs are part_of a TUMatch, i.e. to say that TUMatches are composed of TUs. The competency question would then be, "Which taxonomic units compose a particular taxonomic unit match?". Would that make sense?

hlapp commented 6 years ago

Instead, I think it would be better to say that the TUs are part_of a TUMatch, i.e. to say that TUMatches are composed of TUs.

But wouldn't that make it difficult to say how these parts of the TUMatch are unequal? I.e., this would perhaps work fine if we can assume that we don't need to qualify the strength, confidence etc of each (or some) TU being part of the match. I thought that therefore each TUMatch would reference only a single TU.

hlapp commented 3 years ago

So there's a matches_TU property in the Phyloref ontology now (albeit without label or definition yet). It's asserted as a superproperty of cdao:represents_TU. There's no domain constraint (nor do I think there should or needs to be one). @gaurav would that address this issue?

gaurav commented 3 years ago

Yes, I think that would work! Especially since the definitions for includes_TU and excludes_TU already includes property chains that should allow the reasoner to use a matched TU in place of the represented TU. I've opened an issue in Phyx.js at https://github.com/phyloref/phyx.js/issues/97 to try this out.

hlapp commented 3 years ago

As of today we decided to close this issue due to lack of a supporting use-case. Once a use-case does surface, we'll reopen it.