On 14/02/10 10:44 PM, "Peter Ansell" <[email protected]> wrote:
> On 15 February 2010 11:56, Arek Kasprzyk <[email protected]> wrote:
>> On 14/02/10 5:58 PM, "Peter Ansell" <[email protected]> wrote:
>>
>>> Hi all,
>>>
>>> I am interested in creating an RDF output format to BioMart but I am a
>>> little lost looking through the source code about where to start. To
>>> start off with I would like to add functionality to support URI's for
>>> columns to match RDF predicates, and add URI support for identifiers
>>> in the database so that they can be identified as items in the RDF. I
>>> know it will require some changes to the XML definitions, and an
>>> output class to suit, but I am not sure what needs to be done other
>>> than that, or how much I have to rely on the current code for doing
>>> that.
>>>
>>> Thanks,
>>>
>>> Peter
>>
>> Hi Peter,
>> We are in the middle of re-writing the configuration system so we can easily
>> extend it contain the predicate information. I was thinking about your
>> problem recently and thought that rather dumping marts to RDF would probably
>> be better to think about either SPARQL end point or some other web services
>> based equivalent to make mart look semantic web compliant. For instance we
>> could extend the existing web service to return RDF triples. Would that
>> help?
>
> After the configuration has support for predicates and mapping item
> identifiers to URI's, the SPARQL endpoint would be the next logical
> step, because from that level you can generate RDF documents as you
> like anyway. Let me know if you want any comments on the new
> configuration code.
>
> The Filters mechanism in Biomart seems to map conceptually onto SPARQL
> Filters so the query performance of the SPARQL endpoint could be
> similar to current filtered queries.
>
> Given the number of bioinformatics databases that host their data
> using Biomart it would be a very useful from my point of view to have
> SPARQL/RDF support.
>
Hi Peter,
Yes definitely. We are now finishing the new configuration system so should
have something to present to you soon. It would be great to have your
comments on that
a.
> Cheers,
>
> Peter
