[Bioperl-l] Getting started with bioperl-db

[Chris Fields]

On Jul 11, 2011, at 7:33 PM, Lutz Gehlen wrote:

> 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?

No, it is the BioSQL schema.

> 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?

Yes.

> 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.

That's correct (both the BioSQL website and the ODBA page.  It should probably be redirected to point to the biosql.org wiki.

> 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 
> correctly?

BioSQL is distributed separately, mainly b/c it is supposed to be Bio*-agnostic.  The BioSQL distribution itself comes with some basic documentation to help; I think the biosql.org site also has information.  If you want the latest (developer) version of BioSQL it is now available on github (there are some small updates I think):

https://github.com/biosql/biosql

Installation instructions are here:

https://github.com/biosql/biosql/blob/master/INSTALL

> 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

under 'Documentation'.  The various HOWTO's are a good place to start.  Also, in general all modules come with some synopsis code.

BioPerl is not simple, but neither are the types of data that are represented.  In some cases it's probably over-engineered, but most users find it works for them.

> I would be very thankful if someone could give me some hints on 
> where to start.
> 
> Thank you very much for your help
> Lutz

The best place to start is the HOWTO's, and this mail list (the archives on Gmane are searchable and typically have many answers to questions).

chris