[Bioperl-l] Getting started with bioperl-db

Lutz Gehlen lrg_ml at gmx.net
Tue Jul 12 00:33:30 UTC 2011

Hello everybody,
I have a local BioSQL database and would like to extract data using 
the bioperl-db distribution. However, I am new to BioPerl and am 
really struggling with it. I hope that someone can point me to the 
right documentation, because it seems pretty hard to find.

My first question is about the installation of bioperl-db. The docu 
says that you need to install the BioSQL package first. What ist the 
BioSQL package? Is it a Perl module? The docu refers to biosql.org, 
but the only thing it seems to offer for download is the BioSQL 
schema. Is this what is meant with the BioSQL package? The 
http://bioperl.org/wiki/Bioperl-db page refers to http://obda.open-
bio.org/ for the "BioSQL package", but this page also only refers to 
the BioSQL schema at biosql.org. Plus, this page has not been 
updated since 2002. So I'm a bit lost here. If I call Build.PL of 
bioperl-db and just claim that I have the BioSQL package, test suite 
and installation seem to work without errors, but am I really set up 

The next problems come when using bioperl-db. As I said, I already 
have a BioSQL database. My questions are of the type like "Is there 
a gene that overlaps with the region 15000-17000 on chromosome XY?" 
or "What are the coordinates of gene ABC123?" I haven't found any 
documentation on bioperl-db that would help me do that. From my 
search I rather got the impression that I have to understand a 
substantial part of BioPerl first before I can get going. However, 
it is very difficult to identify which parts of the HUGE BioPerl 
project I have to work through. Plus I haven't found any 
comprehensive documentation of BioPerl at all.

I would be very thankful if someone could give me some hints on 
where to start.

Thank you very much for your help

More information about the Bioperl-l mailing list