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phyloref / phyloref-ontology

Phyloreferencing Ontology and OWL DL reasoning with phyloreferences
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Clarify the definition of Taxonomic Units #10

Closed gaurav closed 5 years ago

gaurav commented 6 years ago

In CDAO, obo:CDAO_0000138 (taxonomic units or TUs) are defined as:

A unit of analysis that may be tied to a node in a tree and to a row in a character matrix. It subsumes the traditional concepts of 'OTU' and 'HTU'.

I propose we modify this definition to:

A subset of a dwc:Taxon. TUs may be as broad as a entire taxon or as specific as a single organism (obo:OBI_0100026).

A competency question for this interpretation of this term is "what taxon or subset of a taxon does a particular node on a phylogeny represent?"

I propose we import this term into the Phyloref Ontology and give it another definition to make it clear how we plan to use this term in our ontology. This issue is for tracking this import. We could also propose this change to CDAO or just import it unchanged and make our interpretation of this term clear in the Phyloreferencing Specification.

hlapp commented 6 years ago

I really don't see the need to or benefit from tying the concept that strongly to dwc:Taxon (which has lots of issues, not the least of which it's exceedingly squishy definition).

If we are going to use the class in certain ways it's easy to annotate that through comments (or more specific IAO attributes).

The only counterargument would be if we were to use the concept in a way that's evidently in conflict with its definition. But I don't see that.

hlapp commented 5 years ago

The TCAN ontology formalizes the alignment between classes in different ontologies and vocabularies that represent a taxon concept. This includes dwc:Taxon, tc:TaxonConcept, and openbiodiv:TaxonomicConcept. See #28.

This alignment may need future amendment, but I think this issue can be closed once #28 is merged.