Jena code snippets
Short examples how to use jena.sourceforge.net
JENA
An introduction to RDF and the Jena RDF API
Examples for using OWL reasoners and SPARQL
OpenTox classes and properties
package org.opentox.owl;
import com.hp.hpl.jena.ontology.OntClass;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.Resource;
public class OT {
public enum OTClass {
Compound,
Conformer,
Dataset,
DataEntry,
Feature,
FeatureValue,
Algorithm,
Model,
Validation,
ValidationInfo;
public String getNS() {
return String.format(_NS, toString());
}
public OntClass getOntClass(OntModel model) {
return model.getOntClass(getNS());
}
public OntClass createOntClass(OntModel model) {
return model.createClass(getNS());
}
public Property createProperty(OntModel model) {
return model.createProperty(getNS());
}
};
/** <p>The RDF model that holds the vocabulary terms</p> */
private static Model m_model = ModelFactory.createDefaultModel();
/** <p>The namespace of the vocabalary as a string ({@value})</p> */
protected static final String _NS = "http://www.opentox.org/api/1.1#%s";
public static final String NS = String.format(_NS,"");
public static String getURI() {return NS;}
/** <p>The namespace of the vocabalary as a resource</p> */
public static final Resource NAMESPACE = m_model.createResource( NS );
/**
* Object properties
*/
public static final Property dataEntry = m_model.createProperty(String.format(_NS, "dataEntry"));
public static final Property compound = m_model.createProperty(String.format(_NS, "compound"));
public static final Property feature = m_model.createProperty(String.format(_NS, "feature"));
public static final Property values = m_model.createProperty(String.format(_NS, "values"));
public static final Property hasSource = m_model.createProperty(String.format(_NS, "hasSource"));
public static final Property conformer = m_model.createProperty(String.format(_NS, "conformer"));
public static final Property isA = m_model.createProperty(String.format(_NS, "isA"));
public static final Property model = m_model.createProperty(String.format(_NS, "model"));
public static final Property report = m_model.createProperty(String.format(_NS, "report"));
public static final Property algorithm = m_model.createProperty(String.format(_NS, "algorithm"));
public static final Property dependentVariables = m_model.createProperty(String.format(_NS, "dependentVariables"));
public static final Property independentVariables = m_model.createProperty(String.format(_NS, "independentVariables"));
public static final Property predictedVariables = m_model.createProperty(String.format(_NS, "predictedVariables"));
public static final Property trainingDataset = m_model.createProperty(String.format(_NS, "trainingDataset"));
public static final Property validationReport = m_model.createProperty(String.format(_NS, "validationReport"));
public static final Property validation = m_model.createProperty(String.format(_NS, "validation"));
public static final Property hasValidationInfo = m_model.createProperty(String.format(_NS, "hasValidationInfo"));
public static final Property validationModel = m_model.createProperty(String.format(_NS, "validationModel"));
public static final Property validationPredictionDataset = m_model.createProperty(String.format(_NS, "validationPredictionDataset"));
public static final Property validationTestDataset = m_model.createProperty(String.format(_NS, "validationTestDataset"));
/**
* Data properties
*/
public static final Property value = m_model.createProperty(String.format(_NS, "value"));
public static final Property units = m_model.createProperty(String.format(_NS, "units"));
public static final Property has3Dstructure = m_model.createProperty(String.format(_NS, "has3Dstructure"));
public static final Property hasStatus = m_model.createProperty(String.format(_NS, "hasStatus"));
public static final Property paramScope = m_model.createProperty(String.format(_NS, "paramScope"));
public static final Property paramValue = m_model.createProperty(String.format(_NS, "paramValue"));
public static final Property statisticsSupported = m_model.createProperty(String.format(_NS, "statisticsSupported"));
}
Create Jena Model with support for OWL
Create an empty model
OntModel jenaModel = createModel();
..
public OntModel createModel() throws Exception {
OntModel jenaModel = ModelFactory.createOntologyModel( OntModelSpec.OWL_DL_MEM,null);
jenaModel.setNsPrefix( "ot", OT.NS );
jenaModel.setNsPrefix( "owl", OWL.NS );
jenaModel.setNsPrefix( "dc", DC.NS );
return jenaModel;
}
Add an empy Dataset
Individual dataset = jenaModel.createIndividual("Dataset URI",
jenaModel.getOntClass(OT.OTClass.Dataset.getNS()));
OT.OTClass.Dataset.createOntClass(jenaModel);
OT.OTClass.DataEntry.createOntClass(jenaModel);
OT.OTClass.Feature.createOntClass(jenaModel);
OT.OTClass.FeatureValue.createOntClass(jenaModel);
OT.OTClass.Compound.createOntClass(jenaModel);
Add an empty Data Entry to the dataset
Individual dataEntry = jenaModel.createIndividual(OT.OTClass.DataEntry.getOntClass(jenaModel)); dataset.addProperty(OT.dataEntry,dataEntry);
Set Compound to the data entry
Individual compound = jenaModel.createIndividual("compoundURI",OT.OTClass.Compound.getOntClass(jenaModel));
dataEntry.addProperty(OT.compound, compound);
Add feature values
//First value
Individual feature1 = jenaModel.createIndividual("featureURI1",OT.OTClass.Feature.getOntClass(jenaModel));
Individual featureValu1e = jenaModel.createIndividual(OT.OTClass.FeatureValue.getOntClass(jenaModel));
featureValue1.addProperty(OT.feature,feature1);
featureValue1.addLiteral(OT.value,jenaModel.createTypedLiteral("formaldehyde",XSDDatatype.XSDstring));
//Second value
Individual feature2 = jenaModel.createIndividual("featureURI2",OT.OTClass.Feature.getOntClass(jenaModel));
Individual featureValue2 = jenaModel.createIndividual(OT.OTClass.FeatureValue.getOntClass(jenaModel));
featureValue2.addProperty(OT.feature,feature2);
featureValue2.addLiteral(OT.value,jenaModel.createTypedLiteral(3.14, XSDDatatype.XSDdouble));
//and finally add values to the data entry
dataEntry.addProperty(OT.values,featureValue1);
dataEntry.addProperty(OT.values,featureValue2);
Write output
import org.restlet.data.MediaType;
public void write(OutputStream output) {
if (mediaType.equals(MediaType.APPLICATION_RDF_XML))
//jenaModel.write(output,"RDF/XML"); //this is faster
jenaModel.write(output,"RDF/XML-ABBREV"); //this is more readable
else if (mediaType.equals(MediaType.APPLICATION_RDF_TURTLE))
jenaModel.write(output,"TURTLE");
else if (mediaType.equals(MediaType.TEXT_RDF_N3))
jenaModel.write(output,"N3");
else if (mediaType.equals(MediaType.TEXT_RDF_NTRIPLES))
jenaModel.write(output,"N-TRIPLE");
else
jenaModel.write(output,"RDF/XML-ABBREV");
};
The result
RDF/XML-ABBREV
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:ot="http://www.opentox.org/api/1.1#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:dc="http://purl.org/dc/elements/1.1/">
<owl:Class rdf:about="http://www.opentox.org/api/1.1#FeatureValue"/>
<owl:Class rdf:about="http://www.opentox.org/api/1.1#Dataset"/>
<owl:Class rdf:about="http://www.opentox.org/api/1.1#Compound"/>
<owl:Class rdf:about="http://www.opentox.org/api/1.1#Feature"/>
<owl:Class rdf:about="http://www.opentox.org/api/1.1#DataEntry"/>
<rdf:Description rdf:about="Dataset URI">
<ot:dataEntry>
<ot:DataEntry>
<ot:values>
<ot:FeatureValue>
<ot:value xml:lang="http://www.w3.org/2001/XMLSchema"
>3.14</ot:value>
<ot:feature>
<ot:Feature rdf:about="featureURI2"/>
</ot:feature>
</ot:FeatureValue>
</ot:values>
<ot:values>
<ot:FeatureValue>
<ot:value xml:lang="http://www.w3.org/2001/XMLSchema"
>formaldehyde</ot:value>
<ot:feature>
<ot:Feature rdf:about="featureURI1"/>
</ot:feature>
</ot:FeatureValue>
</ot:values>
<ot:compound>
<ot:Compound rdf:about="compoundURI"/>
</ot:compound>
</ot:DataEntry>
</ot:dataEntry>
</rdf:Description>
</rdf:RDF>
TURTLE
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix ot: <http://www.opentox.org/api/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 owl: <http://www.w3.org/2002/07/owl#> .
<http://localhost:8080/ambit2-www/feature_definition/1>
a ot:Feature .
ot:FeatureValue
a owl:Class .
ot:Dataset
a owl:Class .
<featureURI2>
a ot:Feature .
<Dataset URI>
ot:dataEntry
[ a ot:DataEntry ;
ot:compound <compoundURI> ;
ot:values
[ a ot:FeatureValue ;
ot:feature <featureURI2> ;
ot:value "3.14"^^xsd:float
] ;
ot:values
[ a ot:FeatureValue ;
ot:feature <featureURI1> ;
ot:value "formaldehyde"^^xsd:string
]
] .
ot:Compound
a owl:Class .
<compoundURI>
a ot:Compound .
ot:Feature
a owl:Class .
ot:DataEntry
a owl:Class .
More about Features
Create
An example how to create Feature with name, units and links to another ontology
Individual feature = jenaModel.createIndividual("featureURI",
OT.OTClass.Feature.getOntClass(jenaModel));
feature.addProperty(DC.title, "featureName");
feature.addProperty(DC.identifier,"featureURI");
feature.addProperty(OT.units,"mmol");
feature.addProperty(OWL.sameAs,"Reference to an individual from another ontology");
feature.addProperty(OT.isA,"Reference to an individual from another ontology");
feature.addProperty(OT.hasSource, "URI of dataste, algorithm or model");
Read
An example how to read Features from RDF input stream:
InputStream in;
...
OntModel jenaModel = OT.createModel();
jenaModel.read(in, null);
OntClass featureClass = OT.OTClass.Feature.getOntClass(jenaModel);
//get all instances of Feature class
ExtendedIterator<? extends OntResource> features = featureClass.listInstances();
while (features.hasNext()) {
OntResource feature = features.next();
System.out.println(feature);
System.out.println(feature.getProperty(DC.title));
System.out.println(feature.getProperty(DC.identifier));
System.out.println(feature.getProperty(OT.units));
System.out.println(feature.getProperty(OT.hasSource));
System.out.println(feature.getProperty(OWL.sameAs));
}
Possible output:
http://localhost:8181/feature/1 [http://localhost:8181/feature/1, http://purl.org/dc/elements/1.1/title, "Property 1"] [http://localhost:8181/feature/1, http://purl.org/dc/elements/1.1/identifier, "http://localhost:8181/feature/1"] [http://localhost:8181/feature/1, http://www.opentox.org/api/1.1#units, ""] [http://localhost:8181/feature/1, http://www.opentox.org/api/1.1#hasSource, "somereference"] [http://localhost:8181/feature/1, http://www.w3.org/2002/07/owl#sameAs, "PropertyFromAnotherOntology"]
OpenTox Model
Create
An example how to create Model
Individual model = jenaModel.createIndividual("modelURI",OT.OTClass.Model.getOntClass(jenaModel));
model.addProperty(DC.title, "Model name");
model.addProperty(DC.identifier,"modelURI");
model.addProperty(DC.creator,"N/A");
model.addProperty(DC.date,"N/A");
model.addProperty(DC.format,"N/A");
//the algorithm
Individual algorithm = jenaModel.createIndividual("algorithm URI",OT.OTClass.Algorithm.getOntClass(jenaModel));
model.addProperty(OT.algorithm, algorithm);
//assign training dataset (same as above)
Individual dataset = jenaModel.createIndividual("dataset",OT.OTClass.Dataset.getOntClass(jenaModel));
model.addProperty(OT.trainingDataset,dataset);
//independent variables
Individual feature_independent1 = jenaModel.createIndividual("featureURI1",OT.OTClass.Feature.getOntClass(jenaModel));
model.addProperty(OT.independentVariables, feature_independent1);
Individual feature_independent2 = jenaModel.createIndividual("featureURI2",OT.OTClass.Feature.getOntClass(jenaModel));
model.addProperty(OT.independentVariables, feature_independent2);
//dependent variables
Individual feature_dependent1 = jenaModel.createIndividual("featureURI3",OT.OTClass.Feature.getOntClass(jenaModel));
model.addProperty(OT.dependentVariables, feature_dependent1);
//predicted (where the result will be written)
Individual feature_result = jenaModel.createIndividual("featureURI4",OT.OTClass.Feature.getOntClass(jenaModel));
Read
An example how to read a Model
InputStream in;
...
OntModel jenaModel = OT.createModel();
jenaModel.read(in, null);
OntClass modelClass = OT.OTClass.Model.getOntClass(jenaModel);
ExtendedIterator<? extends OntResource> models = modelClass.listInstances();
if (models!=null)
while (models.hasNext()) {
OntResource model = models.next();
System.out.println(model);
System.out.println(model.getProperty(DC.title));
System.out.println(model.getProperty(DC.identifier));
System.out.println(model.getProperty(DC.creator));
System.out.println(model.getProperty(DC.date));
System.out.println(model.getProperty(OT.algorithm));
System.out.println(model.getProperty(OT.independentVariables));
System.out.println(model.getProperty(OT.dependentVariables));
System.out.println(model.getProperty(OT.predictedVariables));
System.out.println(model.getProperty(OT.trainingDataset));
}
Possible output:
http://localhost:8181/model/1 [http://localhost:8181/model/1, http://purl.org/dc/elements/1.1/title, "Toxtree: Cramer rules"] [http://localhost:8181/model/1, http://purl.org/dc/elements/1.1/identifier, "http://localhost:8181/model/1"] [http://localhost:8181/model/1, http://purl.org/dc/elements/1.1/creator, "N/A"] [http://localhost:8181/model/1, http://purl.org/dc/elements/1.1/date, "N/A"] [http://localhost:8181/model/1, http://www.opentox.org/api/1.1#algorithm, http://localhost:8181/alg
OpenTox Algorithm
Create
An example how to create Algorithm
OntModel jenaModel = OT.createModel();
// defines Algorithm and Parameter classes
OT.OTClass.Algorithm.createOntClass(jenaModel);
OT.OTClass.Parameter.createOntClass(jenaModel);
Individual algorithm = jenaModel.createIndividual("alg_uri",OT.OTClass.Algorithm.getOntClass(jenaModel));
algorithm.addLiteral(DC.title,jenaModel.createTypedLiteral("title",XSDDatatype.XSDstring));
algorithm.addLiteral(DC.identifier,jenaModel.createTypedLiteral("http://myservice/algorithm/1",XSDDatatype.XSDanyURI));
...
algorithm.addProperty(OT.isA, "http://www.opentox.org/algorithmTypes.owl#RegressionEagerSingleTarget");
algorithm.addLiteral(OT.statisticsSupported,jenaModel.createTypedLiteral("statistics-1",XSDDatatype.XSDstring));
Individual iparam = jenaModel.createIndividual(OT.OTClass.Parameter.getOntClass(jenaModel));
iparam.addLiteral(OT.paramValue,jenaModel.createTypedLiteral(10,XSDDatatype.XSDinteger));
iparam.addLiteral(OT.paramScope,jenaModel.createTypedLiteral("mandatory",XSDDatatype.XSDstring));
algorithm.addProperty(OT.parameters, iparam);
Individual iparam1 = jenaModel.createIndividual(OT.OTClass.Parameter.getOntClass(jenaModel));
iparam1.addLiteral(OT.paramValue,jenaModel.createTypedLiteral("newparam",XSDDatatype.XSDString));
iparam1.addLiteral(OT.paramScope,jenaModel.createTypedLiteral("optional",XSDDatatype.XSDstring));
algorithm.addProperty(OT.parameters, iparam1);
Read
An example how to read an Algorithm
InputStream in;
...
OntModel jenaModel = createModel();
jenaModel.read(in, null);
OntClass algClass = OT.OTClass.Algorithm.getOntClass(jenaModel);
ExtendedIterator<? extends OntResource> algorithms = algClass.listInstances();
if (algorithms!=null)
while (algorithms.hasNext()) {
OntResource algorithm= algorithms.next();
System.out.println(algorithm);
System.out.println(algorithm.getProperty(DC.title));
System.out.println(algorithm.getProperty(DC.identifier));
System.out.println(algorithm.getProperty(OT.parameters));
System.out.println(algorithm.getProperty(OT.statisticsSupported));
System.out.println(algorithm.getProperty(OT.isA));
...
}
OpenTox Dataset
Retrieve all datasets:
OntClass aClass = OT.OTClass.Dataset.getOntClass(jenaModel);
if (aClass != null) {
ExtendedIterator<? extends OntResource> a = aClass.listInstances();
if (a!=null)
while (a.hasNext()) {
parseDataset(jenaModel, out,a.next());
}
}
Parse RDF representation of a Dataset:
protected void parseDataset(OntModel jenaModel, OutputStreamWriter out, OntResource dataset) throws IOException {
out.write(String.format("<h3>%s %s</h3>","Dataset", dataset==null?"":dataset));
StmtIterator iter = jenaModel.listStatements(new SimpleSelector(dataset,OT.dataEntry,(RDFNode)null));
while (iter.hasNext()) {
Statement st = iter.next();
if (!st.getObject().isResource()) continue;
Resource dataEntry = (Resource) st.getObject();
out.write(String.format("<h4>DataEntry %s</h4>",dataEntry));
parseDataEntry(jenaModel, out, dataEntry);
}
}
Parse RDF representation of a DataEntry
protected void parseDataEntry(OntModel jenaModel, OutputStreamWriter out, Resource dataEntry) throws IOException {
//get the compound
StmtIterator compound = jenaModel.listStatements(new SimpleSelector(dataEntry,OT.compound,(RDFNode)null));
while (compound.hasNext()) {
Statement st = compound.next();
out.write(String.format("<h5>%s %s</h5>","Compound", st.getObject()));
}
//get feature values
parseFeatureValues(jenaModel, out, dataEntry);
}
Parse RDF representation of FeatureValues
protected void parseFeatureValues(OntModel jenaModel, OutputStreamWriter out, Resource dataEntry) throws IOException {
StmtIterator values = jenaModel.listStatements(new SimpleSelector(dataEntry,OT.values,(RDFNode)null));
out.write(String.format("<h5>%s</h5>","Values"));
while (values.hasNext()) {
Statement st = values.next();
if (st.getObject().isResource()) {
Resource fv = (Resource)st.getObject();
RDFNode value = fv.getProperty(OT.value).getObject();
out.write(String.format("%s = %s<br>",
//Feature
fv.getProperty(OT.feature).getObject().toString(),
//Value
value
));
}
}
}
Possible output:
-555a6061:12575437b71:-7ffa Compound http://ambit.uni-plovdiv.bg:8080/ambit2/compound/1 http://ambit.uni-plovdiv.bg:8080/ambit2/feature/2 = formaldehyde http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11 = C=O http://ambit.uni-plovdiv.bg:8080/ambit2/feature/13 = InChI=1/CH2O/c1-2/h1H2 http://ambit.uni-plovdiv.bg:8080/ambit2/feature/7 = formaldehyde http://ambit.uni-plovdiv.bg:8080/ambit2/feature/8 = 30.026 http://ambit.uni-plovdiv.bg:8080/ambit2/feature/9 = formaldehyde http://ambit.uni-plovdiv.bg:8080/ambit2/feature/3 = VeryHigh http://ambit.uni-plovdiv.bg:8080/ambit2/feature/5 = 200-001-8 http://ambit.uni-plovdiv.bg:8080/ambit2/feature/4 = CH2O http://ambit.uni-plovdiv.bg:8080/ambit2/feature/1 = CH2O http://ambit.uni-plovdiv.bg:8080/ambit2/feature/10 = DSL,TSCA http://ambit.uni-plovdiv.bg:8080/ambit2/feature/6 = 50-00-0 http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12 = 1.0 -555a6061:12575437b71:-7ffb Compound http://ambit.uni-plovdiv.bg:8080/ambit2/compound/2 http://ambit.uni-plovdiv.bg:8080/ambit2/feature/6 = 50-01-1 http://ambit.uni-plovdiv.bg:8080/ambit2/feature/5 = 200-002-3 http://ambit.uni-plovdiv.bg:8080/ambit2/feature/3 = Low http://ambit.uni-plovdiv.bg:8080/ambit2/feature/13 = InChI=1/CH5N3.ClH/c2-1(3)4;/h(H5,2,3,4);1H http://ambit.uni-plovdiv.bg:8080/ambit2/feature/7 = guanidinium chloride http://ambit.uni-plovdiv.bg:8080/ambit2/feature/11 = [Cl-].NC(=N)[NH3+] http://ambit.uni-plovdiv.bg:8080/ambit2/feature/2 = guanidinium chloride http://ambit.uni-plovdiv.bg:8080/ambit2/feature/9 = amino(imino)methanaminium chloride http://ambit.uni-plovdiv.bg:8080/ambit2/feature/10 = DSL,TSCA http://ambit.uni-plovdiv.bg:8080/ambit2/feature/12 = 2.0 http://ambit.uni-plovdiv.bg:8080/ambit2/feature/1 = CH5N3.ClH http://ambit.uni-plovdiv.bg:8080/ambit2/feature/8 = 95.5314 (35.4535+60.0779) http://ambit.uni-plovdiv.bg:8080/ambit2/feature/4 = CH6ClN3
