- Author:
- Matthias K?nig <matthias.koenig@charite.de>
- Date:
- 2013-04-18 21:52:42+02:00
- Desc:
- Wolf Heinrich Example implemented and working !
- Permanent Source URI:
- https://models.cellml.org/w/matthiaskoenig/MetabolicComponentLibrary/rawfile/b9be078f1e2152d7c1b817af12a7ddcb8db3c0df/CellML-source/CellMLTools/src/annotate/AnnotationTest.java
package annotate;
import pjm.XPCOMDerived;
import cellml_api.CellMLComponent;
import cellml_api.Model;
import cellml_api.RDFRepresentation;
import rdf_api.TripleEnumerator;
import rdf_api.TripleSet;
import rdf_api.Triple;
import rdf_api.RDFAPIRepresentation;
import rdf_api.DataSource;
import rdf_api.Node;
import rdf_api.URIReference;
import tools.CellMLWriter;
/*
* Model annotations should be generated as RDF bags in the following format:
SBML annotation:
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#metaid_0000003">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/obo.go/GO:0005737"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#metaid_0000004">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/obo.chebi/CHEBI:17234"/>
<rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00293"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
CellML annotation:
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#id_00001">
<is xmlns="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="http://identifiers.org/obo.go/GO:0005829"/>
</is>
</rdf:Description>
</rdf:RDF>
*/
public class AnnotationTest {
public static void getTripletsFromModel(Model model){
// Retrieve the RDF representation for the model
RDFRepresentation rdfrep = model.getRDFRepresentation("http://www.cellml.org/RDF/API");
RDFAPIRepresentation rar = pjm2pcm.rdf_api.RDFAPIRepresentation.queryInterface(
(XPCOMDerived) model.getRDFRepresentation( "http://www.cellml.org/RDF/API" ) );
DataSource ds = rar.getSource();
TripleSet tripleSet = ds.getAllTriples();
TripleEnumerator tripleEnumerator = tripleSet.enumerateTriples();
System.out.println("RDF Triplets in current model:");
while (true) {
Triple triple = tripleEnumerator.getNextTriple();
if (triple == null)
break;
System.out.println("--------------------");
// TODO: better RDF output
Node nObject = triple.getObject();
System.out.println(nObject.toString());
Node pObject = triple.getPredicate();
System.out.println(pObject.toString());
Node sObject = triple.getSubject();
System.out.println(sObject.toString());
}
// TODO: make changes and write the source back
rar.setSource(ds);
}
/* Generate the following RDF annotation
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="../../#0001">
<title xmlns="http://purl.org/dc/elements/1.1/" rdf:datatype="http://purl.org/dc/elements/1.1/title">test title
</title>
</rdf:Description>
</rdf:RDF>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<rdf:Description rdf:about="#id_00001">
<is xmlns="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="http://identifiers.org/obo.go/GO:0005829"/>
</is>
</rdf:Description>
</rdf:RDF>
*/
private static void setComponentRdfInModel(CellMLComponent c, Model model){
// get/set the metaID for the component so one can refer in the RDF to it
String metaID = c.getCmetaId();
if (metaID == null || metaID.length()==0){
//TODO: what is standard way to create metaIDs?
metaID = c.getName() + "_0001";
c.setCmetaId(metaID);
}
System.out.println("metaID: "+metaID);
rdf_api.RDFAPIRepresentation rar =
pjm2pcm.rdf_api.RDFAPIRepresentation.queryInterface( (XPCOMDerived) model.getRDFRepresentation( "http://www.cellml.org/RDF/API" ) );
DataSource ds = rar.getSource( );
rar.setSource( ds );
// Get the link reference
URIReference compResource = ds.getURIReference( "#" + metaID );
String titleURI = "http://purl.org/dc/elements/1.1/title";
String title = "test title";
URIReference uriRef = ds.getURIReference( titleURI );
compResource.createTripleOutOf( uriRef, ds.getTypedLiteral(title, titleURI ) );
rar.setSource( ds );
//String s = model.getSerialisedText( );
//String formattedS = new XMLFormatter( ).format( s );
//System.out.println( formattedS );
}
public void createTriplett(String pSubject, String pBioQualifier, String pResource, String pId){
//When setting RDF annotations, you can use the rdf_api methods (see the documentation for details), e.g.
// To refer to a component from RDF, you need to give the component a unique
// cmeta:id (if it doesn't already have one)...
// mycomponent.setCmetaId("someuniqueidentifier");
// URIReference compResource = ds.getURIReference("#" + mycomponent.getCmetaId());
// compResource.createTripleOutOf(ds.getURIReference("http://example.org/mypredicate"), ds.getPlainLiteral("my plain English value", "en"));
/*
new CellmlFileRdfTriple(this, rdfTriple);
CellmlFileRdfTriple
mType = pType;
mModelQualifier = pModelQualifier;
mBioQualifier = pBioQualifier;
mResource = pResource;
mId = pId;
// needs the file reference for init
CellmlFileRdfTriple
CellmlFileRdfTripletElement
*/
//Node mSubject = new CellmlFileRdfTripleElement()
/*
CellmlFileRdfTriple::CellmlFileRdfTriple(CellmlFile *pCellmlFile,
const QString pSubject,
const BioQualifier &pBioQualifier,
const QString &pResource,
const QString &pId){
// Construct ourselves
constructor(pCellmlFile, 0, BioModelsDotNetQualifier,
ModelUnknown, pBioQualifier, pResource, pId);
// Create our RDF triple elements
mSubject = new CellmlFileRdfTripleElement(pSubject);
mPredicate = new CellmlFileRdfTripleElement(QString("http://biomodels.net/biology-qualifiers/%1").arg(bioQualifierAsString(pBioQualifier).remove(QRegularExpression("^bio:"))));
mObject = new CellmlFileRdfTripleElement(QString("http://identifiers.org/%1/%2").arg(pResource, pId));
}
*/
}
public static void main(String[] args){
//String url = "http://www.cellml.org/models/hodgkin_huxley_1952_version07/download";
String url = "./models/TestModel.cellml";
AnnotateVariable avtest = new AnnotateVariable(url);
//avtest.iterateModelElements();
Model model = avtest.getModel();
getTripletsFromModel(model);
// set RDF for the first component
CellMLComponent c = model.getAllComponents().getComponent("component1");
setComponentRdfInModel(c, model);
CellMLWriter.writeToFile(model, "./models/TestModelRDF.cellml");
}
}
