[BioC] Help using biomaRt

john seers (IFR) john.seers at bbsrc.ac.uk
Thu Jan 29 10:26:30 CET 2009

Hi Steffen

Thank you very much for the reply.

I am now pretty much sorted out for the queries I needed. Thanks for the

I used the various commands successfully to list the categories and
groups but what is a puzzle is this did not really help to understand
which pages they belonged to or how to build the query. In my example I
use "rank" and "ensembl_exon_id" which are both from "EXON: Structures"
but they do not apparently work together, at least in this query. I
guess I am missing something. Perhaps there are not hard edges to these

>This is a bit easier to interpret on the web browser based BioMart
>interface (try one on http://www.biomart.org).

Yes, exactly what I did but using www.ensembl.org. Once I had been round
the houses a few times that was very helpful.

>The dev version of biomaRt now checks at the R side if all attributes
>from the same page and will provide a warning before sending out the
>to the BioMart web service.  Note also that in the dev version we use
>term page instead of category in order to be more compatible with the
>BioMart nomenclature.

These sound very good enhancements. I suggest that there might still be
a need for some help in understanding what will work with what, so trial
and error is not the only approach. The examples in the pdf are very
good and very helpful to get started. Perhaps more working examples
would be an idea - perhaps a repository of biomart queries?  



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