Hi Nina,

thanks a lot. This should be sufficient for my problem right now.

Best regards,
Tobias

On 02/07/2011 09:41 AM, Nina Jeliazkova wrote:
> Hi Tobias, All,
>
> I am currently preparing "how to" document on this topic, but here is 
> a quick answer with the available options:
>
> 1) Run the query directly on the dataset service
>
> (all datasets with numeric entries and
> http://apps.ideaconsult.net:8080/ambit2/dataset?feature_name=IC50&feature_type=NUMERIC 
> <http://apps.ideaconsult.net:8080/ambit2/dataset?feature_name=IC50&feature_type=NUMERIC>
>
> (all datasets with features same as an entry, defined by echa ontology)
> http://apps.ideaconsult.net:8080/ambit2/dataset?feature_sameas=http%3A%2F%2Fwww.opentox.org%2FechaEndpoints.owl%23Receptor-binding_specify_receptor 
> <http://apps.ideaconsult.net:8080/ambit2/dataset?feature_sameas=http%3A%2F%2Fwww.opentox.org%2FechaEndpoints.owl%23Receptor-binding_specify_receptor>
>
>
> (all datasets with features having hasSource TUM CDK descriptor 
> algorithms)
> http://apps.ideaconsult.net:8080/ambit2/dataset?feature_hassource=http%3A%2F%2Fopentox.informatik.tu-muenchen.de%3A8080%2FOpenTox-dev%2Falgorithm%2FCDKPhysChem%2FALOGPDescriptor
>
> (we have to discuss/agree whether such search parameters need to be 
> specified in the API)
>
> 2) Retrieve features into local RDF model (on the client) and do the 
> SPARQL  querying there
>
> 3) Register features/dataset metadata on ontology server and do the 
> SPARQL querying there, or query only what is currently registered.
>
> The SPARQL query might be similar to the one below
>
> PREFIX ot:<http://www.opentox.org/api/1.1#>
> PREFIX ota:<http://www.opentox.org/algorithms.owl#>
> PREFIX owl:<http://www.w3.org/2002/07/owl#>
> PREFIX dc:<http://purl.org/dc/elements/1.1/>
> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
> PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
> PREFIX otee:<http://www.opentox.org/echaEndpoints.owl#>
>     select *
>     where {
>     ?Feature rdf:type ot:Feature.
>         ?Feature dc:title ?title.
>         ?Feature ot:hasSource ?src.  //look for datasets here
>         ?Feature owl:sameAs  ?sameas.
> //replace sameas with the relevant ontology entry , e.g. from 
> http://opentox.org/echaEndpoints.owl 
> <http://opentox.org/echaEndpoints.owl>.
> //Of course the features have to be properly annotated.
>     }
>
> Best regards,
> Nina
>
> On 3 February 2011 15:21, Tobias Girschick <tobias.girschick at in.tum.de 
> <mailto:tobias.girschick at in.tum.de>> wrote:
>
>     Hey Nina,
>
>     is there a tutorial/how to/documentation how to query the ontology
>     behind AMBIT?
>     What I want to do, is to find out all datasets that have a
>     numerical IC50 or pIC50 endpoint. Is something like that possible?
>
>     best regards,
>     Tobias
>     -- 
>
>     Dipl.-Bioinf. Tobias Girschick
>
>     Technische Universität München
>     Institut für Informatik
>     Lehrstuhl I12 - Bioinformatik
>     Bolzmannstr. 3
>     85748 Garching b. München, Germany
>
>     Room: MI 01.09.042
>     Phone: +49 (89) 289-18002
>     Email: tobias.girschick at in.tum.de <mailto:tobias.girschick at in.tum.de>
>     Web: http://wwwkramer.in.tum.de/girschick
>
>

-- 

Dipl.-Bioinf. Tobias Girschick

Technische Universität München
Institut für Informatik
Lehrstuhl I12 - Bioinformatik
Bolzmannstr. 3
85748 Garching b. München, Germany

Room: MI 01.09.042
Phone: +49 (89) 289-18002
Email: tobias.girschick at in.tum.de <mailto:tobias.girschick at in.tum.de>
Web: http://wwwkramer.in.tum.de/girschick