From BioJava

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.

@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();
		}
}