From BioJava

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.

/**
 * @author Andreas Dräger, Universität Tübingen.
 * @since 1.8
 */
public class OBO2GraphViz {
 
	Ontology ontology;
	List<String> arcs;
	Set<Term> 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<String>();
		nodes = new HashSet<Term>();
		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<Triple> 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();
		}
	}
 
}