Re: [BioMart Users] New SPARQL-Query and OWL-Ontology Support in BioMart
On Thu, May 12, 2011 at 3:26 PM, Joachim Baran <[hidden email]> wrote:
> 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
> 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:
> 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.
> 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