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Re: BioRDF Telcon

From: Marc-Alexandre Nolin <lotus@ieee.org>
Date: Tue, 19 Jun 2007 21:29:41 -0400
Message-ID: <d6a9bb0d0706191829r40403131yd9c51f6d785e8b29@mail.gmail.com>
To: public-semweb-lifesci@w3.org

It's true, both are just web pages, but I was also refering about
DBpedia wich is the RDF version of wikipedia
http://dbpedia.org/data/Hexokinase. What I wanted to point out with
this is people work with concept. P19367 is the identificator to
access the information about the Hexokinase concept in the Uniprot
database. P19367 doesn't have a sense in itself, it is only a string
of number with a letter in prefix. P19367 only have a meaning in the
context of the Uniprot Database. DBpedia or something else could
provide a hub for the concept that link to ressource that define this
hub, because there might be many ressources from differents places.

I'm ready to admit that uniprot:P19367 is Hexokinase for the homo
sapiens and not all Hexokinase, but so is hgnc:4922 from the hugo
database, geneid:3098 from Entrez Gene, ensembl:ensg00000156515 from
Ensembl or ec:2.7.1.1 for Expasy EC. All of those describe Hexokinase
for the homo sapiens. By concept, I mean that when I search for a
concept, I want the information for this concept from wherever the
database, Uniprot included. Disclaimer: I'm more a computer scientist
than a biologist, I may have made error in the id I choose above.

It could be something like this:

/concept/homo_sapiens/protein/Hexokinase
isDefined by uniprot:P19367
isDefined by ensembl:ensg00000156515
isDefined by ec:2.7.1.1
isDefined by geneid:3098
isDefined by hgnc:4922

Later, if I want to filter the protein search to only bring back the
information from Uniprot, I can.

Maybe this is far fetch for the current discussion about URI, and I'm
driving away from the subject with this.

Marc-Alexandre

>
> Note that uniprot:P19367 doesn't represent "Hexokinase", but "Hexokinase in
> Homo sapiens". Here are all the hexokinases: http://tinyurl.com/2l83au.
>
> Other than that, how is http://en.wikipedia.org/wiki/Hexokinase more of a
> concept than http://beta.uniprot.org/uniprot/P19367 (could argue that both
> are just Web pages) or urn:lsid:uniprot.org:uniprot:P19367?
>
>
>
Received on Wednesday, 20 June 2007 01:29:45 GMT

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