public static void main(String[] args) { System.loadLibrary("sbmlj"); if (args.length != 2) { System.out.println(" usage: addingEvidenceCodes_2 <input-filename> <output-filename>"); System.out.println(" Adds controlled vocabulary term to a species"); System.out.println(); System.exit(2); } SBMLDocument d = libsbml.readSBML(args[0]); long errors = d.getNumErrors(); if (errors > 0) { System.out.println("Read Error(s):"); d.printErrors(); System.out.println("Correct the above and re-run."); } else { long n = d.getModel().getNumSpecies(); if (n <= 0) { System.out.println("Model has no species.\n Cannot add CV terms\n"); } else { Species s = d.getModel().getSpecies(0); /* * check that the species has a metaid no CVTerms will be added * if there is no metaid to reference */ if (!s.isSetMetaId()) s.setMetaId("metaid_0000052"); CVTerm cv1 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER); cv1.setBiologicalQualifierType(libsbml.BQB_OCCURS_IN); cv1.addResource("urn:miriam:obo.go:GO%3A0005764"); s.addCVTerm(cv1); // now create the additional annotation // <rdf:Statement> // <rdf:subject rdf:resource="#metaid_0000052"/> // <rdf:predicate // rdf:resource="http://biomodels.net/biology-qualifiers/occursIn"/> // <rdf:object rdf:resource="urn:miriam:obo.go:GO%3A0005764"/> // <bqbiol:isDescribedBy> // <rdf:Bag> // <rdf:li rdf:resource="urn:miriam:obo.eco:ECO%3A0000004"/> // <rdf:li rdf:resource="urn:miriam:pubmed:7017716"/> // </rdf:Bag> // </bqbiol:isDescribedBy> // </rdf:Statement> /* attributes */ XMLAttributes blank_att = new XMLAttributes(); XMLAttributes resource_att = new XMLAttributes(); /* create the outer statement node */ XMLTriple statement_triple = new XMLTriple("Statement", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf"); XMLToken statement_token = new XMLToken(statement_triple, blank_att); XMLNode statement = new XMLNode(statement_token); /* create the subject node */ XMLTriple subject_triple = new XMLTriple("subject", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf"); resource_att.clear(); resource_att.add("rdf:resource", "#" + s.getMetaId()); XMLToken subject_token = new XMLToken(subject_triple, resource_att); XMLNode subject = new XMLNode(subject_token); /* create the predicate node */ XMLTriple predicate_triple = new XMLTriple("predicate", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf"); resource_att.clear(); resource_att.add("rdf:resource", "http://biomodels.net/biology-qualifiers/occursIn"); XMLToken predicate_token = new XMLToken(predicate_triple, resource_att); XMLNode predicate = new XMLNode(predicate_token); /* create the object node */ XMLTriple object_triple = new XMLTriple("object", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf"); resource_att.clear(); resource_att.add("rdf:resource", "urn:miriam:obo.go:GO%3A0005764"); XMLToken object_token = new XMLToken(object_triple, resource_att); XMLNode object_ = new XMLNode(object_token); /* create the bqbiol node */ XMLTriple bqbiol_triple = new XMLTriple("isDescribedBy", "http://biomodels.net/biology-qualifiers/", "bqbiol"); XMLToken bqbiol_token = new XMLToken(bqbiol_triple, blank_att); XMLNode bqbiol = new XMLNode(bqbiol_token); /* create the bag node */ XMLTriple bag_triple = new XMLTriple("Bag", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf"); XMLToken bag_token = new XMLToken(bag_triple, blank_att); XMLNode bag = new XMLNode(bag_token); /* create each li node and add to the bag */ XMLTriple li_triple = new XMLTriple("li", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf"); resource_att.clear(); resource_att.add("rdf:resource", "urn:miriam:obo.eco:ECO%3A0000004"); XMLToken li_token = new XMLToken(li_triple, resource_att); li_token.setEnd(); XMLNode li = new XMLNode(li_token); bag.addChild(li); resource_att.clear(); resource_att.add("rdf:resource", "urn:miriam:pubmed:7017716"); li_token = new XMLToken(li_triple, resource_att); li_token.setEnd(); li = new XMLNode(li_token); bag.addChild(li); /* add the bag to bqbiol */ bqbiol.addChild(bag); /* add subject, predicate, object and bqbiol to statement */ statement.addChild(subject); statement.addChild(predicate); statement.addChild(object_); statement.addChild(bqbiol); /* * create a top-level RDF element this will ensure correct * merging */ XMLNamespaces xmlns = new XMLNamespaces(); xmlns.add("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf"); xmlns.add("http://purl.org/dc/elements/1.1/", "dc"); xmlns.add("http://purl.org/dc/terms/", "dcterms"); xmlns.add("http://www.w3.org/2001/vcard-rdf/3.0#", "vCard"); xmlns.add("http://biomodels.net/biology-qualifiers/", "bqbiol"); xmlns.add("http://biomodels.net/model-qualifiers/", "bqmodel"); XMLTriple RDF_triple = new XMLTriple("RDF", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf"); XMLToken RDF_token = new XMLToken(RDF_triple, blank_att, xmlns); XMLNode annotation = new XMLNode(RDF_token); /* add the staement node to the RDF node */ annotation.addChild(statement); s.appendAnnotation(annotation); libsbml.writeSBML(d, args[1]); } } System.exit((int) errors); }