TO BINGO, GOrilla or CLUEGO???

[Marko Radulovic]

Dear All,

I noticed a funny thing with GO tools, every one of them gives a bit of a different result, but seemingly not due to different algorithms and settings, but
because the pool of available GO terms seems to be different. BINGO simply does not recognize quite a few GO ID's.

Quite amazing as I imagined that they all use the official GO database from the GENEONTOLOGY.ORG

I would be grateful if anyone could explain the discrepancies between GO tools and recommend one, whether Cytoscape-based or not.

cheers
marko

[Scooter Morris]

Hi Marko,
     Well, my suggestion would be to go to the App Store (apps.cytoscape.org) and see how the various tools were rated.  Each has advantages and disadvantages and, as you point out, each one has pulled their ontology at potentially different times, leading to some discrepancies.  Most of the tools do provide the option for you to pull a copy of GO yourself and use that copy.  Maybe that will help?

-- scooter

[Marko Radulovic]

Many thanks Scooter, I can now feel a resolution of the GO mystery, but did not get exactly what you meant by PULL A COPY OF GO YOURSELF, did you think of the GO database which can be extracted and searched manually?
cheers
marko

[Scooter Morris]

On 05/08/2014 08:53 AM, Marko Radulovic wrote:

Many thanks Scooter, I can now feel a resolution of the GO mystery, but did not get exactly what you meant by PULL A COPY OF GO YOURSELF, did you think of the GO database which can be extracted and searched manually?

Sure, go to www.geneontology.org and there are several ontologies that can be downloaded (look under Downloads).  In BiNGO, for example, if you look at the "Select ontology file" and "Select organism/annotation" both of these have a "Custom..." option than can be used to import a downloaded ontology and/or annotation file from GO.

-- scooter

cheers
marko

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