[BioMart Users] New SPARQL-Query and OWL-Ontology Support in BioMart

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[BioMart Users] New SPARQL-Query and OWL-Ontology Support in BioMart

Joachim Baran-2
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:
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:
    - 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
    - submit your query as HTTP GET via the command:
      curl -H "Accept: application/sparql-results+xml" -v \\
    - the result will be formatted according to

  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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Re: [BioMart Users] New SPARQL-Query and OWL-Ontology Support in BioMart

Rutger Vos
Very cool.

On Thu, May 12, 2011 at 3:26 PM, Joachim Baran <[hidden email]> 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
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