Hi I'm trying to convert a GenBank file into a rdf file. The gene of interest can be found a t : http://www.ncbi.nlm.nih.gov/protein/284794945
With the below code I can read the GenBank file and I manage to retrieve information and convert them in a rdf format. However I don't succeed in retrieving some information such as Title, protein or product. According to this page (http://www.biojava.org/wiki/BioJava:BioJavaXDocs#GenBan)it is possible to do so. Please help me find what I do wrong or what should be done to achieve my goal. //read the GeneBank File public static RichSequenceIterator readFile(String input, RichSequenceBuilderFactory seqFactory, Namespace ns) throws IOException, NoSuchElementException, BioException { ns = null; InputStream stream = new FileInputStream(input); BufferedReader rdfFile = new BufferedReader(new InputStreamReader(stream)); RichSequenceIterator seqs = RichSequence.IOTools.readGenbankDNA(rdfFile,ns); return seqs; } //Retrieve information and convert them in rdf format public void writeToRDFFile(RichSequenceIterator rsi, String output) throws IOException, NoSuchElementException, BioException { //create model for the ontology OntModel model = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM, null); OntClass parents; String URI = "http://pbr.wur.nl/#";; while(rsi.hasNext()) { RichSequence seq = rsi.nextRichSequence(); String id = seq.getName(); parents = model.createClass(URI + id); Set author = seq.getRankedDocRefs();//code to clean up Set&convert toString String definition = seq.getDescription(); //code to clean up String //Add to model parents.addProperty(DC.description, definition); parents.addProperty(DC.publisher, authors); parents.addComment(taxonomy, "EN"); parents.addProperty(DC.type, organism); //print in rdf format model.write(out, "RDF/XML"); out.close(); } } Thanks, Jean-Charles Ferrières Une messagerie gratuite, garantie à vie et des services en plus, ça vous tente ? Je crée ma boîte mail www.laposte.net _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
