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

(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
.
//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>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
> Web: http://wwwkramer.in.tum.de/girschick
>