How to visualize an Ontology (OBO) file as a directed acyclic graph

With the help of GraphViz an ontology can be visualized as a directed acyclic graph. The example code shown below demonstrates how to generate a GraphViz file from an ontology that draws the desired sub-graph rooted on a given internal node (this can also be the top-level element).

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 /**

* @author Andreas Dräger, Universität Tübingen.
* @since 1.8
*/

public class OBO2GraphViz {

   Ontology ontology;
   List` arcs;` `   Set`` nodes;`

   public OBO2GraphViz(String oboFileName, String ontoName,
           String ontoDescription, String root) throws ParseException,
           FileNotFoundException, IOException {
       OboParser parser = new OboParser();
       ontology = parser.parseOBO(new BufferedReader(new FileReader(
               oboFileName)), ontoName, ontoDescription);
       arcs = new Vector`();` `       nodes = new HashSet``();` `       traverse(ontology.getTerm(root));` `       System.out.print("digraph ");` `       System.out.print(ontology.getName());` `       System.out.println(" {");` `       for (Term t : nodes) {` `           System.out.print("  ");` `           System.out.print(t.getName().replace(":", ""));` `           System.out.println(" [label=\""` `                   + lineBreaks(t.getDescription(), 18) + "\"];");` `       }` `       for (String arc : arcs) {` `           System.out.print("  ");` `           System.out.println(arc);` `       }` `       System.out.println('}');` `   }`

   /**
    * Inserts line breaks within the given string.
    * 
    * @param orig
    * @param length
    * @return
    */
   private String lineBreaks(String orig, int length) {
       StringBuffer out = new StringBuffer();
       // Symol \u00e4 is a German umlaut a, a letter that will
       // normally not occur in our original Strings.
       String tmp = orig.replace("\\,", ",").replace(" ", " \u00e4");
       tmp = tmp.replace("-", "-\u00e4");
       String parts[] = tmp.contains("\u00e4") ? tmp.split("\u00e4")
               : new String[] { orig };
       for (int i = 0, curr = 0; i < parts.length; i++) {
           String part = parts[i];
           if ((part.length() + curr >= length)
                   || (i < parts.length - 1 && part.length()
                           + parts[i + 1].length() + curr >= length)) {
               out.append(part.trim());
               out.append("\\n");
               curr = 0;
           } else {
               out.append(part);
               curr += part.length();
           }
       }
       return out.toString();
   }

   private void traverse(Term subject) {
       Set` triples = ontology.getTriples(null, subject, null);` `       String arc;` `       for (Triple triple : triples) {` `           nodes.add(triple.getSubject());` `           nodes.add(triple.getObject());` `           arc = triple.toString().replace(triple.getPredicate().getName(),` `                   "->").replace(":", "");` `           if (!arcs.contains(arc))` `               arcs.add(arc);` `           traverse(triple.getSubject());` `       }` `   }`

   /**
    * @param args
    */
   public static void main(String[] args) {
       try {
           new OBO2GraphViz(args[0], args[1], args[2], args[3]);
       } catch (ParseException e) {
           e.printStackTrace();
       } catch (FileNotFoundException e) {
           e.printStackTrace();
       } catch (IOException e) {
           e.printStackTrace();
       }
   }

} ```