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Gene Ontology Parsing

George Fou gio.fou at gmail.com
Mon Apr 17 02:25:10 PDT 2006


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
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