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Implement citations for phyloreferences in the Clade Ontology #64

@gaurav

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@gaurav

Every phyloreference in the Clade Ontology can have three kinds of citations:

  • pre-existing citation: the citation for the scientific name, i.e. its dwc:namePublishedIn.
  • definitional citation: where the clade definition was published. For most Phylonym definitions, this will be Phylonym itself, but it's possible that some of the clades have been published elsewhere first.
  • reference phylogeny citation: a citation to the phylogeny that should be used as a reference phylogeny. One of these will be the primary reference phylogeny, but there might be secondary citations as well.

The first two should be fairly straightforward to model:

  • pre-existing citations can be recorded using dwc:namePublishedIn, e.g. :phyloref1 dwc:namePublishedIn { bibo:doi "10.1010/...." ... }.
  • definitional citation can be recorded using IAO:definition source, e.g. :phyloref1 "IAO:definition source" { bibo:doi "10.1010/..." ... }

For the last one, note that we don't currently mandate that the phylogenies in a Phyx file are explicitly marked as the primary phylogeny. phyloref/klados#133 covers updating the Curation Tool so that we can set that. Once that's working, we can use something like prov:wasQuotedFrom or prov:hadPrimarySource to link the phylogeny to its primary source.

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