[Owl-devel] Uniprot in a relational db

Dan Bolser dan.bolser at gmail.com
Wed Mar 17 13:10:47 EDT 2010

Hi all,

Seems UniProt has an underlying object model that all the parsers
(Perl, Java or whatever) plug into (and that the RDF will
re-capitulate) ... hopefully.

However, an object to relation mapping is not necessarily trivial
(especially if you want a 'usable' database in the end).

My UniProt RDB had an emphasis on being simple and usable, and was
based on the SwissKnife Perl parser.

I can put that somewhere if you would like to develop it.

You could try loading the RDF into a triple store like Sesamy.

Then you just need to learn SPARQL and you are all set... If you learn
SPARQL I'll make you my friend ;-) (Because I need to learn it too).

All the best,

On 17 March 2010 14:31, Henning Stehr <stehr at molgen.mpg.de> wrote:
> 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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