Path: utzoo!utgpu!watserv1!watmath!uunet!wuarchive!bcm!bionet!vax.oxford.ac.uk!JREES
From: JREES@vax.oxford.ac.uk
Newsgroups: bionet.molbio.genbank
Subject: Re: A question for FTP users
Message-ID: <9101241737.AA27782@genbank.bio.net>
Date: 24 Jan 91 12:41:00 GMT
Sender: daemon@genbank.bio.net
Lines: 56


	Time I guess to say my piece also...

	It shouldn't even need questioning that reformatting the databases
form one format to another is inappropriate, and I won't reiterate the
arguements made before here as to, that has been done already.

	But I am going to add my voice to those who would see ALL the software
packages accept the format distributed by the databases as the one to use for
access to the databases in straight ascii format. Will Gilbert articulated
this whole area very clearly on INFO-GCG last August, and perhaps he can be
persuaded to repost to this discussion, but in essence it is very simple for
everyone using the flat format files to interface to them in "native" format
and to provide utilities to index the access in a fashion which facilitates
access for their own package. Some programmers seem willing to do this (Rodger
Staden for one has stated a willingness to use whatever format is chosen by
PIR, and has no objection to using "native" format if they do), others seem
very determined to go their own way in the face of opposition (perhaps rather
silent oppostion until now) from those are actually on the receiving end of
the effect of this dogma.

	Since there can be no programming advantage that I can see for the
reformatting the question is why is noone willing to standardise? It is clear
that the standard HAS to be that created by the database in question, and that
software can be written to meet whatever format it is presented with, and that
all the packages COULD use whatever format the database was presented to them
in (EMBL, Genbank, PIR, Codata, whatever) by setting the appropriate parameter
to the package at the start.

	Perhaps if this were done then there would be less time and effort
wasted making multiple copies for everyday use. The problems the Genbank/IG
have with disk space probably apply to most of use - my own operations running
software and databases in Oxford and at MIT run 700MB on each machine,
reformatting databases generally means finding 150 MB of spare space at a
minimum, more if the active version is not deleted first, and this is getting
worse as the databases get larger each year.

	Clearly the change we could have all hoped for in the construction of
the relational format Genbank and Embl has not yet gained the active interest
of the programming community as an option, it is my hope that this will be the
way forward in the long term, and that those in a position to advance this
will do so on this forum.

	Finally to avoid the point being missed, I am fully in support of the
use for total reformattting where it achieves a significant change in the
response to the user, the preprocessing required to run BLAST or GCG's Quick
software is an investment well worth making - even when the overall cost in
resource has been higher, but the problem under discussion here does NOT
achieve that end.

	Jasper Rees

	Jrees@Vax.Oxford.ac.uk   (%nsfnet-relay.ac.uk)
	Seqtest@Wccf.MIT.edu

	"One World, One database format ?"