Cheers Dan<br><br>Yes I didn't realise that, mapping to a relational schema from the object model is not necessarily easy. <br><br>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.<br>
<br>Jose<br><br><br><br><div class="gmail_quote">On 17 March 2010 18:10, Dan Bolser <span dir="ltr"><<a href="mailto:dan.bolser@gmail.com">dan.bolser@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi all,<br>
<br>
Seems UniProt has an underlying object model that all the parsers<br>
(Perl, Java or whatever) plug into (and that the RDF will<br>
re-capitulate) ... hopefully.<br>
<br>
However, an object to relation mapping is not necessarily trivial<br>
(especially if you want a 'usable' database in the end).<br>
<br>
My UniProt RDB had an emphasis on being simple and usable, and was<br>
based on the SwissKnife Perl parser.<br>
<br>
I can put that somewhere if you would like to develop it.<br>
<br>
<br>
You could try loading the RDF into a triple store like Sesamy.<br>
<br>
Then you just need to learn SPARQL and you are all set... If you learn<br>
SPARQL I'll make you my friend ;-) (Because I need to learn it too).<br>
<br>
<br>
<br>
All the best,<br>
<font color="#888888">Dan.<br>
</font><div><div></div><div class="h5"><br>
On 17 March 2010 14:31, Henning Stehr <<a href="mailto:stehr@molgen.mpg.de">stehr@molgen.mpg.de</a>> wrote:<br>
> I know that they have a local Uniprot installation here in the<br>
> institute but I don't know in which format. If you find a solution to<br>
> parse it into relational form, I would also be interested.<br>
> So far I was using the Uniprot Java API<br>
> (<a href="http://www.ebi.ac.uk/uniprot/remotingAPI/" target="_blank">http://www.ebi.ac.uk/uniprot/remotingAPI/</a>) and my UniprotConnection<br>
> is just a customized interface to this. This may be an alternative to<br>
> a local installation with the obvious drawback that it relies on the<br>
> internet connection and server availibility.<br>
><br>
> Cheers,<br>
> Henning<br>
><br>
> On Wed, Mar 17, 2010 at 2:48 PM, Jose M. Duarte <<a href="mailto:jose.m.duarte@gmail.com">jose.m.duarte@gmail.com</a>> wrote:<br>
>> Ok adding something to that I just found that they provide the data in RDF<br>
>> format:<br>
>><br>
>> <a href="http://dev.isb-sib.ch/projects/uniprot-rdf/" target="_blank">http://dev.isb-sib.ch/projects/uniprot-rdf/</a><br>
>> <a href="ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/" target="_blank">ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/</a><br>
>><br>
>> Now, I don't know much about RDF but that seems to be almost the solution.<br>
>> There must be standard tools out there to go from RDF to relational, aren't<br>
>> there?<br>
>><br>
>> Jose<br>
>><br>
>><br>
>><br>
>> On 17 March 2010 14:37, Jose M. Duarte <<a href="mailto:jose.m.duarte@gmail.com">jose.m.duarte@gmail.com</a>> wrote:<br>
>>><br>
>>> Not exactly belonging to this list, but I thought it was an easy way to<br>
>>> reach all of you together :-)<br>
>>><br>
>>> I am after having a local copy of the Uniprot Knowledge Base in relational<br>
>>> db format. I remember that Dan had something like this running locally<br>
>>> before.<br>
>>><br>
>>> The data seems to be available here:<br>
>>><br>
>>> <a href="http://www.uniprot.org/downloads" target="_blank">http://www.uniprot.org/downloads</a><br>
>>><br>
>>> in a nice XML format, plus the schema is also available. So really<br>
>>> converting it into a database should be pretty straight forward.<br>
>>><br>
>>> Somebody knows of tools to do this?<br>
>>><br>
>>> Cheers<br>
>>><br>
>>> Jose<br>
>><br>
>><br>
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>><br>
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</div></div></blockquote></div><br>