[BioC] Genes2GO and suggestions to make it faster

Sean Davis sdavis2 at mail.nih.gov
Mon Aug 18 18:34:44 CEST 2014

On Mon, Aug 18, 2014 at 8:52 AM, Konika Chawla <chawla at ntnu.no> wrote:

> Hi,
> I have created this webapp (http://norstore-trd-bio0.hpc.
> ntnu.no:8080/Genes2GO/clearpage.do) to makes a binary matrix between user
> specified genes and user selected GO term to represent the gene annotations
> by either 1 or 0. Users can also specify just some query terms and the
> program will find the related GO terms.
> Its small and useful tool for biologists.
> The tools uses annotation data from biomaRt and GO.DB to find GO terms.
> 1) The tool is bit slow sometimes.  Any suggestion to make it faster would
> be helpful.
> A small part of code is
> "ensembl = useMart("ensembl", dataset = organism)
> godata<-getBM(attributes = c(list_type,"go_id","name_1006"), filters =
> list_type, values = genelist[,1], mart = ensembl)
> godata<-trim(as.matrix(godata))"

I'd suggest eliminating the biomaRt call in the webapp.  Simply use biomaRt
to get all results for all genes and then do the filtering in R.  The call
to biomaRt will almost certainly be the most time-consuming process.

> 2) Is it possible to show a progress bar on the webpage which could
> represent how much time is remaining to finish the process. That is if we
> can know how much time the process is going to take.

As written above, that probably will not be possible.  In general, to make
a progress bar, you'll need to be able to measure progress somehow and that
really isn't possible with biomaRt.


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