Filtering Go Terms By Evidence Code And Apply A Semantic Similarity Measure

Question

[jfertaj]

Hello,

I have a list of different pathways and I would like to filter this pathways based on the semantic similarity (Resnik distance, e.g) of the GO terms associated to each gene. However, I would like to consider only the GO terms with evidence codes related to experimental support. Could you tell me any approach, mainly in R/Bioconductor. I have tested GOsemsim but I am not able to filter firs the evidence codes.

Thanks a lot

[Alastair Kerr]

GO evidence codes are certainly in Biomart as I use custom tables from ensembl biomart for this (or via the Perl API). Regarding R, BiomaRt would be a good place to check but I do not use it: http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html

[jfertaj]

Ok, I'll try also with Biomart, but I just realised that GOsemsim has an option to drop the evidence codes that you are not interested in