[Biojava-l] Tr: Retrieve Information from GenBank file

[jc.lucky]

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 : biojava-l at lists.open-bio.org
> 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
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