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Re: UniProt RDF via HTTP

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Fri, 11 May 2007 15:08:51 -0600
Message-Id: <53E19C68-A308-4E8D-A732-549E3428E374@gmail.com>
Cc: public-semweb-lifesci <public-semweb-lifesci@w3.org>
To: Eric Jain <Eric.Jain@isb-sib.ch>


On May 11, 2007, at 2:49 PM, Eric Jain wrote:

> Alan Ruttenberg wrote:
>> 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>
> ...

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?

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?

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

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 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!

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

-Alan

>
> 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 21:07:05 UTC

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