+ /**
+ * Reads, parses and stores the OBO file data
+ *
+ * @param is
+ * @throws ParseException
+ * @throws IOException
+ */
+ protected void loadOboFile(InputStream is) throws ParseException,
+ IOException
+ {
+ BufferedReader oboFile = new BufferedReader(new InputStreamReader(is));
+ OboParser parser = new OboParser();
+ ontology = parser.parseOBO(oboFile, "SO", "the SO ontology");
+ isA = ontology.getTerm("is_a");
+ storeTermNames();
+ }
+
+ /**
+ * Store a lookup table of terms by their description. Note that description
+ * is not guaranteed unique - currently reporting 8 duplicates.
+ */