BiNGO not working with updated ontology files

[pporra...@gmail.com]

Hi,

I am trying to use BiNGO with both legacy and up to date ontology and annotation files obtained from the Gene Ontology website (see http://geneontology.org/ontology/go-basic.obo and http://geneontology.org/gene-associations/goa_human.gaf.gz for the up-to-date files) and I cannot get it to run the analysis.  I tried different versions of the files and it only seems to work with a legacy version of the annotation and ontology files I got on February. I cannot really put my finger on whatever is wrong with the ontology or annotation files, but I think it is important to fix this so users can use updated files.

Would it be possible to contact with whoever is currently maintaining BiNGO to try to solve these issues?

Thanks and cheers,

Pablo.

[Tim Hull]

When you downloaded the .obo file, was a .txt extension added? You need to remove that if so - the file will only work properly with BiNGO with a .obo extension. You may have to use the command line to do this on Mac - it seems to be particularly fussy about adding a .txt extension to ontology files.

Also, did you unzip the goa_human.gaf.gz file? 

If you did all those and it still doesn't work, can you send a copy of the versions that do? The ontology should work fine as long as it has a .obo extension, though I am having issues with the goa_human annotation - other annotations work fine, so I'm wondering if something has changed since the old version that breaks BiNGO...

Tim

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[Pablo Porras Millán]

Hi Tim,

I am travelling at the mometn, will get back to you with the files on Monday.

Thanks for your help,

Pablo.

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[Pablo Porras Millán]

Hi,

I managed to make it work by adding the .obo extension and by changing the name of the association file to gene_association.goa_ref_human. Why the name of the file should matter at all, I have no idea.

Anyway, thanks for pointing me in the right direction!

Cheers,

Pablo.

[Pablo Porras Millán]

By the way, it would bencie to know if there is a way to eliminate this dependency of BiNGO to the file name, it seems like a bug to me.

Cheers,

Pablo.