[Bioperl-l] Getting started with bioperl-db

Lutz Gehlen lrg_ml at gmx.net
Wed Jul 13 05:50:51 UTC 2011

Hello Chris,
thank you for your reply.

On Tuesday, July 12, 2011 14:04:30 Chris Fields wrote:
> On Jul 11, 2011, at 7:33 PM, Lutz Gehlen wrote:
> > 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.
> It does involve some overhead.
> > Plus I haven't found any
> > comprehensive documentation of BioPerl at all.
> I find that a bit hard to believe (the 'at all' part).  Yes, some
> parts are less-than-optimally documented, but the wiki has quite
> a bit.  See here:
> http://www.bioperl.org/wiki/Main_Page

I would like to apologize for that criticism. It was inaccurate and 
likely to offend which was not my intention at all. You are right, 
there is a lot of documentation (not for bioperl-db, though, as far 
as I know), for the inexperienced user, it is just very hard to get 
an overview.

Please don't get me wrong. It might sound that I just came here to 
complain. This is not the case. I appreciate the massive work that 
has been done and I am well aware that the developers have no 
obligation at all to make it easier for other people to get into 

However, in my case, I have abandoned the attempt for now. For the 
simple scenarios that I have the cost-benefit ratio is just too bad. 
I will rather query the BioSQL database directly.

Thanks again for your help

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