Hi Andreas,
I wonder if you see the same response time when you connect to the
website directly or using webservice API. Just trying to isolate the
R-specific and biomart-specific response time. I am assuming that your
institutional internet speed is good enough. I suggest the above because
if the response time could be improved, it can save you a lot of time
and hassle of managing these database locally.
Best,
Syed
On 12/04/2012 15:27, andreas H wrote:
Hi Syed,
thanks for your reply,
speed, bandwidth are the reasons.
e.g. **unless I am doing something wrong**
right now using R and biomaRt (with factory settings) :
require(biomaRt)
a_mart=useMart(biomart="ensembl",dataset='hsapiens_gene_ensembl')
system.time({getBM(attributes=c('go_id'),filters='hgnc_symbol',values=c("KRAS"),
mart=a_mart) })
# user system elapsed
# 0.007 0.001 23.218
which is too slow. Admittedly, the second time this runs *within the
same R session*, it drops down to 3 seconds, but this is not a likely
scenario.
Thanks,
Andreas
On 12/04/2012 14:59, Syed Haider wrote:
Hi Andreas,
Before getting into the details of database updates, i wonder why would
you prefer to have databases downloaded locally as opposed to using it
whereever its hosted. BioMart is a system that enables data integration
by means of federation. Hence, it kind of defeats the purpose if one
downloads everything locally. Moreover, if you have data locally, you
enter into a rather bigger probem of updates for each of the sources you
downloaded as all of them have their own major/minor release cycles etc.
I might be missing something important w.r.t your requirements, hence i
ask :)
Best,
Syed
On 12/04/2012 14:10, andreas H wrote:
Hello there,
After days of searching around I can't find a simple step-by-step guide
on how to install biomart locally including databases. Could you point
me to such a document if what I want to do is possible at all?
I have also read the biomart 0.8 install manual, I have managed to set
up a webserver, I can make it read data from local source but I can't
find how to automatically download and install these sources locally.
If you can contribute more, then preferably:
1) I would like to know how to select a database and transfer it locally
to my own, local mysql server, without having to go to each vendor's
website download their files and install it to my local db. I mean is
there a click-and-install feature in *mart-configurator* or something? I
visualise this as I give my local mysql password and the databses are
install automatically there.
2) I would like to install only a small subset of databases locally -
the ones that i use a lot.
3) Ideally, I would like with a few clicks to update the biomart
databases which are installed locally, every few weeks/months.
My aim right now is to convert between ensembl, uniprot, hugo protein
IDs and get GO terms for each protein.
Thanking you in advance,
andreas
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