Check out the Bioconductor case studies book (By Florian Hahne, Wolfgang Huber, Robert Gentleman, Seth Falcon). There's a whole chapter about this. The code is also available online. It will save you lots of time...

In reply to Re^3: BioPerl: Best Gene Ontology API by lima1
in thread BioPerl: Best Gene Ontology API by BioLion

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