W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > May 2007

Re: UniProt RDF via HTTP

From: Eric Jain <Eric.Jain@isb-sib.ch>
Date: Sat, 12 May 2007 12:49:35 +0200
Message-ID: <46459BBF.4020000@isb-sib.ch>
To: Alan Ruttenberg <alanruttenberg@gmail.com>
CC: public-semweb-lifesci <public-semweb-lifesci@w3.org>

Alan Ruttenberg wrote:
> Would it be possible to add a service so that I can get from the lsid 
> directly to rdf and xml versions at least? Would it be correct to assume 
> that all lsids in uniprot have such versions?

The only common format in UniProt is RDF (e.g. there is no XML 
representation of the taxonomy data).

<http://beta.uniprot.org/uniprot/P12345> could return different formats 
based on the "Accept" header, however this would complicate caching...

Another option (which would also allow you to link to rather than retrieve 
a specific representation) would be an optional "format" parameter.

> Are the LSIDs supposed to be able to be resolved by an lsid resolver? If 
> so is there one that ebi runs that I could play with?

None that I'm aware of, and I'm afraid setting up a "correct" resolver that 
behaves as required by the specs would be difficult, if not impossible :-(

The question is, what is worse crime against humanity: Misusing an existing 
scheme, or inventing your own :-)

> I might suggest the following:
> http://beta.uniprot.org/uniprot/what/urn:lsid:uniprot.org:uniprot:P12345
> return some rdf that lists the specific formats that resource is 
> available in, and urls where they can be fetched from?
> Or if you have some simple rules for forming the URLs, could you share 
> those?

The simple rule is to append .ext to the URL of the resource, where "ext" 
is rdf|xml|fasta|txt|...

> Do you assign LSIDs to those resources too? If so is there a way to 
> figure out which are "yours" and which are "theirs"?

One of the main reasons for using LSIDs was that I need proper URIs for all 
the resources we reference, and most resources have two meter long, 
frequently changing cgi-bin URLs (OK, I'm exaggerating, but not much).

Moreover, what is "ours" and what is "theirs" isn't always clear (again, 
consider the taxonomy data, which is basically the NCBI taxonomy), though 
in general if it resolves to one of our servers, then it's probably ours.
Received on Saturday, 12 May 2007 10:50:09 UTC

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