[Owl-devel] Uniprot in a relational db

[Jose M. Duarte]

Cheers Dan

Yes I didn't realise that, mapping to a relational schema from the object
model is not necessarily easy.

Anyway that SwissKnife parser sounds more or less like the solution. I'll
look into it when I get some time. Will get back to you on that.

Jose



On 17 March 2010 18:10, Dan Bolser <dan.bolser at gmail.com> wrote:

> 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,
> Dan.
>
> 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
> >>
> >>
> >> _______________________________________________
> >> Owl-devel mailing list
> >> Owl-devel at bioinformatics.org
> >> http://www.bioinformatics.org/mailman/listinfo/owl-devel
> >>
> >>
> >
> > _______________________________________________
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> > http://www.bioinformatics.org/mailman/listinfo/owl-devel
> >
>
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