On 7 Dec 2007, at 09:38, Michael Wicks wrote:
Dear Biomart,
I have been investigating the use of Biomart with our database
(http://www.eurepxress.org), following on from a recently departed
colleague (Chuang-Kee Ong, who some of you may have dealt with
recently). and I have a couple of questions:
1. Once a Mart has been created, how do you refresh the contents of the
Mart if the database on which it is based changes?
Our database grows daily with new data, and without some procedures or
processes, preferably non-manual, put in place, the Mart will almost
immediately become inconsistent with our base data. I can see how to
do
this with the tools supplied but only manually. Also I don't really
want to start building something myself, as it occurred to me that this
must have been an issue before with other Marts, and that there might
be
a pre-existing solution to refreshing Marts already.
Have you come across this issue before, and if so, can you suggest a
solution please?
Hi Michael,
so far we have been relying on re-building a mart from scratch with a
new update
in the source database. These builds tend to be very quick in comparison
with the usual release schedule so it has not been an issue so far.
Having said
that we are now thinking of providing more support for proper 'updates'
of mart
triggered by data updates in the source db but this is still a future
plan without a solid deadline.
2. Documentation. I can't find anywhere in the documentation any
explanation of how to go about implementing Importables and Exportable
fields. Our data has a number of potential linking fields and we would
like to implement these links when we put our Mart live.
the exporables and importables simply expose atts and filters
and in turn columns in your tables which you intend to you use for
linking.
you may find helpful looking at the existing xml configs available from
martdb.ensembl.org -P3316 -uanonymous
Also if you have any specific questions about it please fire off your
queries
to this list and someone will help you. This will also help us to
improve the docs
Do you have a document that explains this in more detail please (I have
been looking at a document called "Biomart 0.6 Documentation" so far)?
(A minor documentation issue: when configuring a Mart, the Perl script
configure.pl has to be run. I'm still not sure of the difference
between the "Y" and "N" options that I'm presented with when this
script
runs, even after looking at the documentation. So I run the script
twice! Can you explain what is going on here please?)
do you mean:
Do you want to install in API only mode [y/n] [n]:
this simply asks you if you are installing the software as a webserver
(which i believe you do) so the expected answer to this question
is 'N' (default). If you say 'y' you will have the installation with
less
dependencies which are only required to run it in API mode
hope that helps,
a.
Many thanks for your time.
Yours
Mike Wicks
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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