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
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