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phyloref / phyloref-ontology

Phyloreferencing Ontology and OWL DL reasoning with phyloreferences
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A class for a PHYX study #14

Closed gaurav closed 5 years ago

gaurav commented 6 years ago

Proposed term: PHYXStudy (class) Subclass of: document Definition: A study consists of a set of phyloreferences as well as a set of phylogenies that can be used to test those phyloreferences. A PHYX file consists of a single PHYX study and are usually derived from a single publication or a small number of publications (e.g. if the phyloreferences are published in one paper based on phylogenies published in another).

Competency questions:

Currently referred to as a PhyloreferenceTestCase, but I think "PHYX Study" is a better term.

hlapp commented 6 years ago

Is this different from an attribute connecting a phyloreference instance to a phylogeny?

gaurav commented 6 years ago

I see this as a representation of the PHYX study itself in RDF, though perhaps it's not necessary to define it in OWL. Instances of this class would assert that a group of phylogenies and a group of phyloreferences were grouped together by an author, and would have annotations reflecting authorship, publication status, and so on. In which case, a better competency question might be, "Which phylogenies and phyloreferences are included in a particular study?". This isn't very useful for the Ontology of Phyloreferences, though, so in retrospect it probably isn't worth including in the Phyloref Ontology either.

We do need a term for asserting that a curator expects a Phyloreference to resolve to a particular Node (#26). If we had such a term, then the Tree within which that Node is located must be a reference phylogeny for the phyloreference, and so would act as an attribute connecting a phyloreference instance to a phylogeny. I think that would be useful to include in the Ontology of Phyloreferences.

hlapp commented 6 years ago

You are using Ontology of Phyloreferences in two places above, but we have obsoleted this term because it is confusing. Case in point, I think in the first instance you mean Clade Ontology, but it seems in the second instance you may actually mean Phyloreferencing Ontology?

hlapp commented 6 years ago

And why can't we simply use IAO:document? I think to justify being defined as a subclass of that, the definition will have to follow the genus-differentia pattern. I.e., An instance of PHYXStudy is an IAO:document that ..., followed by qualifying how PHYXStudy documents can be distinguished from all other IAO:document instances. Then this still needs to be followed by an argument as to how that differentia is valuable to and matters for our goals.

hlapp commented 5 years ago

I'm unclear what the open issue here is. It seems that the relationship between a phyloreference and a study from which it was curated is one of provenance (such as prov:wasDerivedFrom) (see #16), and that between a phyloreference and a reference phylogeny is one of supporting evidence (see #15).

gaurav commented 5 years ago

The original idea here was to model the PHYX file itself -- as a collection of related phyloreferences and phylogenies -- but linking phyloreferences to the document they were published in with prov:wasDerivedFrom and to their reference phylogenies with has evidence should provide all the information we need. Closing this issue.