Showing posts with label Java OBO parser. Show all posts
Showing posts with label Java OBO parser. Show all posts

Thursday, September 24, 2009

Java OBO Parser

I've been task with importing a large OBO file into a database. However, I had trouble finding a parser pre-bundled as a set of JAR files. There is one Java OBO parser that exists but it lives within a much larger application found here:

http://www.geneontology.org/GO.java.obo.parser.shtml

He goes into some details about the writing some code, but isn't clear about which JAR files from the SVN source that are needed to get it working. Here I will provide the list of 3 JARs needed for a Java OBO parser:

For some sample code see below:


DefaultOBOParser parser = new DefaultOBOParser();
OBOParseEngine engine = new OBOParseEngine(parser);

String path = "C:/MPheno_OBO.ontology";
Collection paths = new LinkedList();
paths.add(path);
engine.setPaths(paths);

engine.parse();
To import the OBO file, I plan writing my own implementation of OBOParser for better memory usage.

Cheers,
Phil