Hi Surajit,

The main issue is the code has some deviation in representing objects
and properties, compared to those defined in
http://opentox.org/api/1.1/opentox.owl .

IMHO, the most convenient way to familiarize oneself with objects and
relationships is to open opentox.owl with Protege and explore OWLClasses
tab with properties view. 

The list of properties , defined for ot:Model object are in the middle
panel.





surajit ray wrote:
> 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));

links to other ontologies are to be established between ot:Algorithm,
not ot:Model , so a statement below is not relevant for ot:Model
>             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);
>
Endpoints are assigned via ot:Feature, not as parameters of ot:Model
>             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);
>
URI of the compound used for prediction is not  parameter of the model
>             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);
>
and finally ot:algorithm, ot:independentVariables,
ot:dependentVariables, ot:predictedVariables properties are missing.
>
> Could you tell me how to do it correctly ?
Please have a look at

https://ambit.svn.sourceforge.net/svnroot/ambit/branches/opentox/opentox-client/src/main/java/org/opentox/rdf/representation/ModelRepresentation.java

The code at
https://ambit.svn.sourceforge.net/svnroot/ambit/branches/opentox/opentox-client
depends only on Jena and Restlet and can be directly used in others
projects.

Best regards,
Nina
>
> Cheers
> Surajit
>
> On Thu, Mar 18, 2010 at 9:28 PM, Nina Jeliazkova <nina at acad.bg
> <mailto: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 <mailto:Development at opentox.org>
>     >> http://www.opentox.org/mailman/listinfo/development
>     >>
>     >>
>     >
>     >
>     >
>     >
>
>
>     _______________________________________________
>     Development mailing list
>     Development at opentox.org <mailto:Development at opentox.org>
>     http://www.opentox.org/mailman/listinfo/development
>
>
>
>
> -- 
> Surajit Ray
> Partner
> www.rareindianart.com <http://www.rareindianart.com>