Closed gaurav closed 5 years ago
Is this different from an attribute connecting a phyloreference instance to a phylogeny?
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.
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?
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.
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).
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.
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.