[Bioperl-l] Getting started with bioperl-db

[Hilmar Lapp]

Hi Lutz,

Yes, indeed there is significantly less documentation for BioPerl-db, though there is quite a bit in the perldoc of the modules. The best starting points are probably Bio::DB::BioDB, Bio::DB::BioSQL::DBAdaptor, and Bio::DB::BioSQL::BasePersistenceAdaptor. Also there is the 2003 slideshow linked that explains the basic overview.

Thanks for pointing out the errors on the wiki page, I've fixed them now.

And finally, querying BioSQL directly is a perfectly fine solution. I've done that many times.

-hilmar

Sent with a tap.

On Jul 13, 2011, at 1:50 AM, Lutz Gehlen <lrg_ml at gmx.net> wrote:

> 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 
> BioPerl.
> 
> 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
> Lutz
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