Re: UniProt RDF via HTTP

Alan Ruttenberg wrote:
> Is there http access given a lsid.
> 
> I have already figured out that I can get the html for 
> urn:lsid:uniprot.org:uniprot:P00750  with:
> 
> http://beta.uniprot.org/?dataset=uniprot&query=urn:lsid:uniprot.org:uniprot:P00750&sort=score&lucky=no&random=no 

Looks like you discovered a (mostly) undocumented feature :-)

<http://beta.uniprot.org/?query=urn:lsid:uniprot.org:uniprot:P12345>


> What url could I use to get the rdf,xml, and fasta versions respectively?

The LSID is always resolved to a Web page; I'm afraid that's the greatest 
common denominator among all the resources for which we assign LSIDs...

I assume you already saw

<http://beta.uniprot.org/uniprot/P12345.rdf>
<http://beta.uniprot.org/uniprot/P12345.xml>
<http://beta.uniprot.org/uniprot/P12345.fasta>
...

So I guess the question is how do you discover what formats are available?

The RDF representation is referenced from the Web page like so:

<link rel="alternate" type="application/rdf+xml" href="..."/>

Amazingly some tools can make use of this (e.g. PiggyBank).

Note that this applies only to our own resources, other databases may not 
have an RDF version -- some don't have anything machine readable at all!

Ideally there would be some standard way to get a list of formats for a 
resource (maybe using HTTP OPTIONS), but I'm not aware of anything?


> What do you consider to be the data and the metadata for the LSID?

I'm honestly not sure where the metadata ends and the data starts...


> Also, will you be using LSID versions, and, if so, how?

To properly support version numbers, I assume you'd need to be able to 
retrieve old versions of a resource? I can only do this for part of our 
data (UniProtKB), and even there, only in text and fasta format...

In any case I'll fix the "resolver" so:

<http://beta.uniprot.org/?query=urn:lsid:uniprot.org:uniprot:P12345:2>

Takes you to:

<http://beta.uniprot.org/uniprot/P12345?version=2>

Received on Friday, 11 May 2007 20:51:42 UTC