On 19 February 2010 12:34, Arek Kasprzyk <[email protected]> wrote: > 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
Did a SPARQL interface (and the configuration to map Biomarts to RDF and URIs) make it into the 0.8 release candidates? Cheers, Peter _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
