Input / Output

OntoLib provides support for loading OBO files into objects implementing the Ontology interface. Currently, there is no generic parsing of OBO files (yet), so you just select one of the supported ontologies (GO, HPO, MPO, or ZPO) and use the specialized parser. For example, for the Gene Ontology:

final GoOboParser parser = new GoOboParser(inputFile);
final GoOntology go;
try {
  hpo = parser.parse();
} catch (IOException e) {
  // handle error
}

Similarly, for the Human Phenotype Ontology:

final HpoOboParser parser = new HpoOboParser(inputFile);
final GoOntology go;
try {
  hpo = parser.parse();
} catch (IOException e) {
  // handle error
}