public void GenerateRDFExamples() throws Exception {
String soNameSpace = "http://purl.org/obo/owl/SO#";
rdfHelper = new RDFHelper(sbolNameSpace);
rdfHelper.AddNameSpace(soNameSpace, "so");
Resource promoter = rdfHelper.CreateResource("http://fakeuri.org/part/prom1");
CreateDnaComponent(
promoter, soNameSpace + "SO_0000167", "prom1", "Promoter 1", "An example promoter", "aaa");
Resource doublePromoter = rdfHelper.CreateResource("http://fakeuri.org/part/doubleprom1");
Resource annotation1 =
CreateSequenceAnnotation(
"http://fakeuri.org/part/doubleprom1_1_3", "1", "3", "+", promoter);
Resource annotation2 =
CreateSequenceAnnotation(
"http://fakeuri.org/part/doubleprom1_4_6", "4", "6", "+", promoter);
rdfHelper.AddProperty(doublePromoter, "annotation", annotation1);
rdfHelper.AddProperty(doublePromoter, "annotation", annotation2);
CreateDnaComponent(
doublePromoter,
soNameSpace + "SO_0000167",
"doubleprom1",
"Double Promoter 1",
"A double promoter example",
"aaaaaa");
Resource dnaComponentResource = rdfHelper.CreateResource("http://sbols.org/v1#DnaComponent");
Resource dnaSequenceResource = rdfHelper.CreateResource("http://sbols.org/v1#DnaSequence");
Resource[] topLevelResources = new Resource[] {dnaComponentResource, dnaSequenceResource};
// rdfHelper.Write(rdfHelper,RDFFormat.RDFXML_ABBREV,topLevelResources,"RDFExamples",true);
rdfHelper.Write(rdfHelper, "RDF/XML-ABBREV", topLevelResources, "RDFExamples/pretty.xml", true);
rdfHelper.Write(rdfHelper, "RDF/XML", topLevelResources, "RDFExamples/plain.xml", true);
rdfHelper.Write(rdfHelper, "Turtle", topLevelResources, "RDFExamples/turtle.xml", true);
rdfHelper.Write(rdfHelper, RDFFormat.TRIG_BLOCKS, "RDFExamples/turtleblocks.xml", true);
// SBOLDocument sbolDocument= SBOLHelper.Read("RDFExamples/pretty.xml");
/*Write (rdfHelper, RDFFormat.RDFXML_ABBREV,true);
Write (rdfHelper, RDFFormat.RDFXML_PLAIN,true);
Write (rdfHelper, RDFFormat.TRIG_BLOCKS,true);*/
}
private Resource CreateSequenceAnnotation(
String uri, String start, String end, String strand, Resource subComponent) {
Resource resource = rdfHelper.CreateResource(uri);
rdfHelper.AddProperty(resource, "subComponent", subComponent);
rdfHelper.AddProperty(resource, "strand", strand);
rdfHelper.AddProperty(resource, "bioEnd", end);
rdfHelper.AddProperty(resource, "bioStart", start);
rdfHelper.AddProperty(resource, RDF.type, sbolNameSpace + "SequenceAnnotation");
return resource;
}
private Resource CreateDnaComponent(
Resource resource,
String type,
String displayId,
String name,
String description,
String nucleotideSequence) {
Resource resourceNA = rdfHelper.CreateResource(resource.getURI() + "/NA");
rdfHelper.AddProperty(resourceNA, RDF.type, sbolNameSpace + "DnaSequence");
rdfHelper.AddProperty(resourceNA, "nucleotides", nucleotideSequence);
rdfHelper.AddProperty(resource, "dnaSequence", resourceNA);
rdfHelper.AddProperty(resource, "description", description);
rdfHelper.AddProperty(resource, "name", name);
rdfHelper.AddProperty(resource, "displayId", displayId);
rdfHelper.AddProperty(resource, RDF.type, type);
rdfHelper.AddProperty(resource, RDF.type, sbolNameSpace + "DnaComponent");
return resource;
}
