[Bioperl-l] OBDA Bioperl Documentation

[Peter Schattner]

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