I tried once again with the new version of BioJava but without succeding. Any idea or suggestion?
Thanks in advance Regards, Jean-Charles Ferrières > Message du 22/10/10 10:11 > De : "jc.lucky" > A : [email protected] > Copie à : > Objet : [Biojava-l] Retrieve Information from GenBank file > > > 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 _____________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > 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
