Another question: why don't you have links to UniProt URIs ? Is this because it is not clear what they represent ? (which I would completely understand).

I'm not sure what you mean here, about not having links. We have cross-references to UniProtKB. I have in mind a better system of linking, but we've been constrained by the requirements of the OBO Foundry. These requirements are starting to loosen up, though, so I might be able to do more in the near future. Anyway, I just want to make sure I understand what you mean.

I mean "purl.uniprot.org" URIs. But I know OBO a little bit, and understand that if you only cross-reference UniProtKB (instead of using specific relationships), then I understand why you don't use our URIs. (by the way, I'd be relunctant to use them as well, since it is very unclear what they exactly identify).

Aaaargh! Upon translating to OWL, those "UniProtKB:" prefixes should be converted to a URI. The URI is even specified in the OBO file. That being said, I now notice that the URI we're specifying is 'www.uniprot.org' instead of 'purl.uniprot.org'. I'll fix that now. Getting the URIs properly put in might be fixed in the updated converter, but if not I can add a post-processing step to do it.