Thanks for the elaboration Chris - as usual better expressed than when I tried :)
One minor clarification: On Jul 16, 2007, at 11:24 PM, Chris Mungall wrote:
I read "broad classes of proteins" as being more inclusive than the class denoted by OPSD_HUMAN in my interpretation, but also including for example all human opsin proteins, all vertebrate opsins, ...
To clarify, no, I didn't mean this. I meant that the definition of Uniprot records are already broad in the sense that sometimes multiple splice variants are included in a single record, as are population and disease-causing variants, according to Eric. Basically I don't know what set of proteins people currently intend to denote when they use a uniprot id as a protein, and I'm not entirely certain what the curators intend. So step one would be an english description of how to figure out what the curator's intent is, and we could go on from there to define OWL definitions based on that. I suspect that people currently using Uniprot ids may be using them in both broader and narrow ways, but we could leave the discovery of such cases to a reasoner once we had the basics in place.
Best, Alan
