How to parse an Ontology (OBO) file

BioJava now contains a parser for .OBO files. The BioJava parser is re-using parts of the parser contained in the OBO-Edit software package,but does not require to have the obo-edit library and user interface installed in order to parse the files. Thanks to the OBO-Edit developers for giving permission to re-use part of their source code.

This code will be released with the next biojava release. To use it at the moment you will require a recent build from SVN.

```java @since 1.7 public static void main (String[] args) {

       String fileName = args[0];

   OboParser parser = new OboParser();
   InputStream inStream =  new FileInputStream(fileName);
       
   BufferedReader oboFile = new BufferedReader ( new InputStreamReader ( inStream ) );
       try {
           Ontology ontology = parser.parseOBO(oboFile, "my Ontology name", "description of ontology");
                       
           Set keys = ontology.getTerms();
           Iterator iter = keys.iterator();
           while (iter.hasNext()){
               Term term = (Term) iter.next();
               System.out.println("TERM: " + term.getName() + " " + term.getDescription());
               System.out.println(term.getAnnotation());
               Object[] synonyms =  term.getSynonyms();
               for ( Object syn : synonyms ) {
                   System.out.println(syn);
               }                   
           }           
       } catch (Exception e){
           e.printStackTrace();
       }

} ```