Hi Nina,
this is them code generating the curl output for model

            OntModel jenaModel = createJenaRDFModel();
            OT.OTClass.Model.createOntClass(jenaModel);

            Individual model =
jenaModel.createIndividual(MaxtoxApplicationSettings.getServerRootPath() +
"/model/" + model_number, OT.OTClass.Model.getOntClass(jenaModel));
            model.addLiteral(DC.title, jenaModel.createTypedLiteral("Model
Number : " + model_number, XSDDatatype.XSDstring));
            model.addLiteral(DC.description,
jenaModel.createTypedLiteral(modelDetails.get("description"),
XSDDatatype.XSDstring));
            model.addLiteral(DC.identifier,
jenaModel.createTypedLiteral(MaxtoxApplicationSettings.getServerRootPath() +
"/model/" + model_number, XSDDatatype.XSDanyURI));
            model.addProperty(OT.isA, "
http://www.opentox.org/modelTypes.owl#MCSSBasedToxicityPredictor");

            Individual dictionaryProducingDataset =
jenaModel.createIndividual(OT.OTClass.Dataset.getOntClass(jenaModel));
            dictionaryProducingDataset.addLiteral(DC.title,
jenaModel.createTypedLiteral("dictionaryProducingDataset",
XSDDatatype.XSDstring));
            dictionaryProducingDataset.addLiteral(DC.description,
jenaModel.createTypedLiteral("The dataset which was used to get the
fragments in the dictionary for this model", XSDDatatype.XSDstring));
            dictionaryProducingDataset.addLiteral(DC.identifier,
jenaModel.createTypedLiteral(modelDetails.get("dataset_uri"),
XSDDatatype.XSDanyURI));
            model.addProperty(OT.trainingDataset,
dictionaryProducingDataset);

            Individual fragmentDataset =
jenaModel.createIndividual(OT.OTClass.Dataset.getOntClass(jenaModel));
            fragmentDataset.addLiteral(DC.title,
jenaModel.createTypedLiteral("fragmentDataset", XSDDatatype.XSDstring));
            fragmentDataset.addLiteral(DC.description,
jenaModel.createTypedLiteral("The dataset which shows all the fragments in
the dictionary", XSDDatatype.XSDstring));
            fragmentDataset.addLiteral(DC.identifier,
jenaModel.createTypedLiteral(modelDetails.get("fragmentset_uri"),
XSDDatatype.XSDanyURI));
            model.addProperty(OT.trainingDataset, fragmentDataset);

            Individual endpoint =
jenaModel.createIndividual(OT.OTClass.Parameter.getOntClass(jenaModel));
            endpoint.addLiteral(DC.title,
jenaModel.createTypedLiteral("ToxicityEndpoint", XSDDatatype.XSDstring));
            endpoint.addLiteral(DC.description,
jenaModel.createTypedLiteral(modelDetails.get("endpoint"),
XSDDatatype.XSDstring));
            //endpoint.addLiteral(DC.identifier,
jenaModel.createTypedLiteral(MaxtoxApplicationSettings.getServerRootPath() +
"/parameter/moleculeSizeCutoffParameter", XSDDatatype.XSDanyURI));
            model.addProperty(OT.parameters, endpoint);

            Individual compound_uri =
jenaModel.createIndividual(OT.OTClass.Parameter.getOntClass(jenaModel));
            compound_uri.addLiteral(DC.title,
jenaModel.createTypedLiteral("compound_uri", XSDDatatype.XSDstring));
            compound_uri.addLiteral(DC.description,
jenaModel.createTypedLiteral("URI of compound whose toxicity needs to be
predicted.", XSDDatatype.XSDstring));
            compound_uri.addLiteral(DC.identifier,
jenaModel.createTypedLiteral(MaxtoxApplicationSettings.getServerRootPath() +
"/parameter/compound_uri", XSDDatatype.XSDanyURI));
            compound_uri.addLiteral(OT.paramValue,
jenaModel.createTypedLiteral("Any URI", XSDDatatype.XSDstring));
            compound_uri.addLiteral(OT.paramScope,
jenaModel.createTypedLiteral("mandatory", XSDDatatype.XSDstring));
            model.addProperty(OT.parameters, compound_uri);


Could you tell me how to do it correctly ?

Cheers
Surajit

On Thu, Mar 18, 2010 at 9:28 PM, Nina Jeliazkova <nina at acad.bg> wrote:

> Hello Surajit,
>
> >>
> >
> > curl http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/model<
> http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/rest/model>
> >
> >
> > should return what you want .... just remove the rest word in the middle
> > ....
> >
> Having a look at RDF output of the model
> http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/model  , I
> have the following comments :
>
>
>    <rdf:RDF
>        xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>        xmlns:ot="http://www.opentox.org/api/1.1#"
>        xmlns:owl="http://www.w3.org/2002/07/owl#"
>        xmlns:dc="http://purl.org/dc/elements/1.1/"
>        xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
>        xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
>      <owl:Class rdf:about="http://www.opentox.org/api/1.1#Model"/>
>    // this is fine
>      <ot:Model
>    rdf:about="
> http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/model/1">
>    //ot:parameters are meant to hold parameters specific for model
>    calculations, e.g. max number of decision tree nodes , not clear how
>    dc:description and dc:title here are related to parameters
>        <ot:parameters rdf:parseType="Resource">
>          <dc:description
>    rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>          >mutagenic activity in Salmonella typhimurium
>    TA100</dc:description>
>          <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>          >ToxicityEndpoint</dc:title>
>        </ot:parameters>
>
> /*The dataset should be defined as ot:Dataset object and the
> trainingDataset property should look like
> <ot:trainingDataset>      <ot:Dataset
> rdf:about="http://ambit.uni-plovdiv.bg:8080/ambit2/dataset/194"/>
> </ot:trainingDataset>
>
> otherwise, as it is written currently, it will not be recognized as a
> dataset (and owl validation might fail )
> */
>
>
>        <ot:trainingDataset rdf:parseType="Resource">
>          <dc:identifier
>    rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI"
>
>    >
> http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/dataset/FT_1
> </dc:identifier>
>          <dc:description
>    rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>          >The dataset which shows all the fragments in the
>    dictionary</dc:description>
>          <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>          >fragmentDataset</dc:title>
>        </ot:trainingDataset>
>        <ot:trainingDataset rdf:parseType="Resource">
>          <dc:identifier
>    rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI"
>
>    >
> http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/dataset/MT_1
> </dc:identifier>
>          <dc:description
>    rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>          >The dataset which was used to get the fragments in the
>    dictionary for this model</dc:description>
>          <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>          >dictionaryProducingDataset</dc:title>
>        </ot:trainingDataset>
>
> /*
> There is  no modelTypes.owl defined - could you consider extending
> AlgorithmTypes.owl or BlueObelisk descriptors.owl instead , and change
> the reference.
> */
>
>
>    <ot:isA>
> http://www.opentox.org/modelTypes.owl#MCSSBasedToxicityPredictor</ot:isA>
>        <dc:identifier
>    rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI"
>
>    >http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/model/1
> </dc:identifier>
>        <dc:description
>    rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>        >Model and dictionary built from 55 active and 55 inactive
>    compounds</dc:description>
>        <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>        >Model Number : 1</dc:title>
>
> /*
> This representation does not contain ot:independentVariables,
> ot:dependentVariables nor ot:predictedVariables.  While
> ot:independentVariables can be skipped, if you are generating
> descriptors on the fly, it is important to include the rest two,
> otherwise the clients will not be able to find out where the results are
> stored.  Please consult the existing services of other partners for
> examples.
> */
>
>      </ot:Model>
>    </rdf:RDF>
>
>
>
> Best regards,
> Nina
> > cheers
> > Surajit
> >
> >
> >
> >>
> http://ambit.uni-plovdiv.bg:8080/ambit2/ontology/test?search=+http%3A%2F%2Fopentox2.informatik.uni-freiburg.de%3A8080%2FMaxtoxTest%2Frest%2Fmodel
> >>
> >> In particular, when you fix the problem, a reference to model 1 should
> >> appear in the "Model [http://www.opentox.org/api/1.1#Model]"  section
> >> at the bottom of the ontology playground page.
> >>
> >> According to opentox.owl, the RDF represnetation of a model should
> >> include a statement that the model is of type
> >> <http://www.opentox.org/api/1.1#Model> (or if abbreviated - ot:Model)
> >> , e.g. there should be a triple like
> >>
> >> <http://opentox2.informatik.uni-freiburg.de:8080/MaxtoxTest/model/1>
> >> rdf:type ot:Model .
> >>
> >> Kind regards,
> >> Vedrin
> >>
> >> PS: You might want to check the output of the following two queries as
> >> an example of RDF representations of list of models and specific
> >> model:
> >>
> >> curl -H "Accept:application/rdf+xml"
> >> http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/model
> >> curl -H "Accept:application/rdf+xml"
> >>
> >>
> http://opentox.informatik.tu-muenchen.de:8080/OpenTox-dev/model/TUMOpenToxModel_kNN_6
> >> _______________________________________________
> >> Development mailing list
> >> Development at opentox.org
> >> http://www.opentox.org/mailman/listinfo/development
> >>
> >>
> >
> >
> >
> >
>
>
> _______________________________________________
> Development mailing list
> Development at opentox.org
> http://www.opentox.org/mailman/listinfo/development
>
>


-- 
Surajit Ray
Partner
www.rareindianart.com