[Owl-devel] Uniprot in a relational db

[Henning Stehr]

I know that they have a local Uniprot installation here in the
institute but I don't know in which format. If you find a solution to
parse it into relational form, I would also be interested.
So far I was using the Uniprot Java API
(http://www.ebi.ac.uk/uniprot/remotingAPI/) and my UniprotConnection
is just a customized interface to this. This may be an alternative to
a local installation with the obvious drawback that it relies on the
internet connection and server availibility.

Cheers,
Henning

On Wed, Mar 17, 2010 at 2:48 PM, Jose M. Duarte <jose.m.duarte at gmail.com> wrote:
> Ok adding something to that I just found that they provide the data in RDF
> format:
>
> http://dev.isb-sib.ch/projects/uniprot-rdf/
> ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/
>
> Now, I don't know much about RDF but that seems to be almost the solution.
> There must be standard tools out there to go from RDF to relational, aren't
> there?
>
> Jose
>
>
>
> On 17 March 2010 14:37, Jose M. Duarte <jose.m.duarte at gmail.com> wrote:
>>
>> Not exactly belonging to this list, but I thought it was an easy way to
>> reach all of you together :-)
>>
>> I am after having a local copy of the Uniprot Knowledge Base in relational
>> db format. I remember that Dan had something like this running locally
>> before.
>>
>> The data seems to be available here:
>>
>> http://www.uniprot.org/downloads
>>
>> in a nice XML format, plus the schema is also available. So really
>> converting it into a database should be pretty straight forward.
>>
>> Somebody knows of tools to do this?
>>
>> Cheers
>>
>> Jose
>
>
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