Path: utzoo!attcan!uunet!snorkelwacker!bionet!CU.NIH.GOV!CZJ
From: CZJ@CU.NIH.GOV
Newsgroups: bionet.molbio.genbank
Subject: GenBank software
Message-ID: <9008081410.AA02507@alw.nih.gov>
Date: 8 Aug 90 14:12:16 GMT
Sender: daemon@genbank.BIO.NET
Lines: 53

As one of the Project Officers of the GenBank Contract, I thought it
would be appropriate to respond to some of the issues raised by Dan
Davison in his "I must have been out of the room" messages.

The history of the new features table goes back several years.  I
remember the first GenBank Advisors's meeting I attended in October
1985.  The subject that came up then, and at every advisors' meeting
hence, was the difficulty in translating an entry from EMBL to GenBank
format and vice versa.  This difficulty had an obvious impact in
delaying the incorporation of EMBL data into GenBank.  The major
impediments to automatically translating an EMBL entry into a GenBank
were incompatibilities in the features table formats.  Neither GenBank
nor EMBL staffs felt that they represented features adequately.
Therefore, a series of meetings, which began with a workshop involving
members of the scientific community, was held to design a features
table format that could better represent the complexities of
biological features.  The result is the new features table effective
with release 64.  I would point out that there was plenty of advance
warning.  This warning included several example entries.

I am sure that David Benton can comment better on the advantages of
the new format.  Rather I would like to discuss briefly Dan's wish to
have GenBank personnel write code that parses the new features table
and distribute it free.  First I would begin by reminding the
community that the purpose of GenBank has been to collect and
distribute data.  The development of sofware was left to the
community.  The success of this policy can be seen by the development
of several excellent packages both by commercial firms and the public.
If you are privy to the problems of the Cambridge Small Molecule
Crystallographic database, you know the problems of linking software
development to database distribution.  Thus it is consciously beyond
the scope of the GenBank contract to develop software to parse the
features table.

Despite this position, it is obvious that some software, i.e. Jim
Fickett's program to translate GenBank is in use by GenBank and will
have to be modified to parse the new features table.  Although it is
perfectly feasible to distribute this program, the problem for GenBank
is one of support.  That is some one has to answer the many questions
about installation, why the program will not work on a specific
machine, modifications,etc.  There is also the question of
updates--that is code used internally is often modified to meet
specific purposes often associated with new releases.  The bottom line
is that the responsible distribution of "free" software can be an
expensive proposition.  Right now the only way for the GenBank to meet
this obligation would be to cut down on services elsewhere.

I hope these comments have been helpful.  One of the gratifying things
to me has been the community spirit among GenBank users and the
willingness to distribute software that takes advantage of the GenBank
resource.  I trust this will continue in the future.

Jim Cassatt