[Bioperl-l] OBDA Bioperl Documentation

[Lincoln Stein]

OBDA-REGISTRY.txt is old and should be removed.  I thought I'd done that, but 
I guess not.  I've just removed it.

FLAT-DATABASES-HOWTO.txt exists, but wasn't committed to the repository.  I 
just fixed that.

BIOSQL-HOWTO.txt or its equivalent probably lives in the BioSQL distribution, 
but should be mirrored in BioPerl, even if all it does is to tell people how 
to obtain BioSQL.  Hilmar can help with that.

Lincoln


On Tuesday 25 February 2003 08:03 pm, Peter Schattner wrote:
> I’m a little confused regarding the documentation for the Bioperl interface
> to OBDA.  I thought that there was supposed to be one "HOWTO" for setting
> up the registry (to be written by Lincoln) and one "HOWTO" describing the
> syntax for accessing records once the registry had been setup (that I was
> supposed to write.)
>
> However, when I look in the HOWTO section of Bioperl CVS,  I already find
> two documents: BIODATABASE_ACCESS.txt and OBDA-REGISTRY.txt. 
> OBDA-REGISTRY.txt is indeed a description of how to set up the registry.
> BIODATABASE_ACCESS.txt includes all the text of OBDA-REGISTRY.txt plus a
> description of how to access sequences from the registry. In addition
> BIODATABASE_ACCESS.txt refers to  two more "HOWTOs":
> FLAT-DATABASES-HOWTO.txt and BIOSQL-HOWTO.txt.  I can’t tell whether these
> latter two documents have not yet been written or whether they exist but I
> am unable to locate them.
>
> Anyway, I would suggest that:
> 1) The redundant text from OBDA-REGISTRY.txt be removed  from
> BIODATABASE_ACCESS.txt.
> 2) With a little bit of editing (which I am willing to do), the remainder
> of BIODATABASE_ACCESS.txt can be the "HOWTO" describing the syntax for
> accessing records under OBDA
> 3) BIODATABASE_ACCESS.txt be edited to indicate where to find
> FLAT-DATABASES-HOWTO.txt and BIOSQL-HOWTO.txt or to state that they are
> still under development (Heikki can you help me with this?)
> 4) I will add a few lines to the bptutorial to point people to these
> HOWTOs.
>
> Lincoln, Heikki does this work  for you? If so, I’ll make the changes
> described.
>
> Peter
>
>
>
>
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-- 
Lincoln Stein
lstein at cshl.org
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)