Very cool. On Thu, May 12, 2011 at 3:26 PM, Joachim Baran <[email protected]> wrote: > Hello! > We have implemented rudimentary semantic-web support in BioMart > and set-up a test-server under http://central.biomart.org. > The test-server provides a single point of access to 34 biological > databases distributed around the world. The system is still under > development, but we would like to hear your feedback on our current > implementation. > SEMANTIC WEB FEATURES > --------------------- > The following simple features are supported in BioMart 0.8rc6: > - automatic OWL-ontology generation on a per-access-point basis > - SPARQL SELECT-queries over the automatically generated ontologies > Each access point of BioMart comes with its own OWL-ontology that is > accessible via the URL: > http://central.biomart.org/martsemantics/*accesspointname*/ontology. > Access-point names coincide with the "config" parameters listed under > http://central.biomart.org/martservice/marts; we are working on a solution > to represent this information as an OWL-ontology too. > SPARQL SELECT-queries can be made on access points that have an ontology > defined for them, where we only support basic graph patterns in queries > for now. This permits querying attributes via `?mart > attribute:*attributename* ?values` and setting filters via `?mart > attribute:*attributename* "*value*"`. The only supported solution sequence > modifier is "LIMIT". > More details can be found in the current BioMart 0.8rc6 documentation > in Section 11.5, http://www.biomart.org/rc6_documentation.pdf. > EXAMPLES > -------- > Run-through of a semantic query workflow: > 1. Opening an OWL-ontology in Protégé > - get Protégé from http://protege.stanford.edu/ > - open Protégé and select "Open OWL ontology from URI" > - as URI use: > http://central.biomart.org/martsemantics/cosmic_gene_config/ontology > - see Protégé's "Classes" and "Data Properties" tab > 2. Generating a SPARQL-query within BioMart's web-interface > - open the following URL in your browser: http://central.biomart.org > - click on "Cancer Genes" in the "Gene retrieval"-tab of the "Tools" box > - restrict the search as appropriate, then click "Go" > - click on "SPARQL" on top of the results table to get an equivalent > SPARQL SELECT-query > 3. Querying an access point with SPARQL > - encode your SPARQL SELECT-query from example 2 for use with HTTP GET > (e.g. using http://meyerweb.com/eric/tools/dencoder/) > - submit your query as HTTP GET via the command: > curl -H "Accept: application/sparql-results+xml" -v \\ > > http://central.biomart.org/martsemantics/cosmic_gene_config/SPARQLXML/get/?query=*encodedquery* > - the result will be formatted according to > http://www.w3.org/TR/rdf-sparql-XMLres/ > We are focusing on implementing support for custom ontologies in the > future. It would be great to hear some opinions whether you prefer if we > supported to import ontologies from tools such as Protégé, or if you would > rather see us build in ontology support into MartConfigurator. > Best Wishes, > Joachim Baran on behalf of the BioMart team >
-- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading, RG6 6BX, United Kingdom Tel: +44 (0) 118 378 7535 http://rutgervos.blogspot.com _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
