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Gene Ontology Parsing

Michael Moorhouse m.moorhouse at
Mon Apr 17 04:00:58 PDT 2006

We - well, one of my colleagues / ex- Intern students - have been using 
the API of GQ Zhang, see: .
I've seen the sub graphs it has created and I can find classes 
(methods?) called things like buildSubGraph, getPath2Root, getPath2Node 
in the Java documentation I recognise from my Perl go-perl API 
experiences building parts of our prototype.
Personally all my experience is with Perl & go-perl API though.
Michael M.

> Hi,
> My name is George Papachristoudis, I am a student at Electrical and 
> Computer Engineering Department of Aristotle University, Thessaloniki, 
> Greece.
> I have a problem concerning the parsing of Gene Ontology which is a 
> part of my undergraduate research.
> I am looking for a Java API Package (and its  accompanying help 
> documentation) in order to parse and edit Gene Ontology .obo or flat 
> files via Java commands.
> In other words, I would like to find all the paths of a GO term up to 
> the root (one of the three ontologies) as shown in the interfaces DAG- 
> and OBO-Editor. However, the problem is that I have to do this job via 
> Java commands (not manually as is done to both editors).
> So, I have to find a corresponding Java API Package.
> Is there anyone who can shed a light upon my problem?
> Thank you in advance,
> George Papachristoudis

Dr. Michael J Moorhouse
Department of Virology,
Office Ee 17.14
Dr. Molewaterplein 50,
Erasmus MC
The Netherlands
Tel: +31 10 408 71 02
Email: m.moorhouse at

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