From: michael@TEMIN.LANL.GOV (Michael J. Cinkosky)
Newsgroups: bionet.molbio.genbank
Subject: notes from GenBank at LANL
Date: 11 Sep 92 16:04:07 GMT
Distribution: bionet


Here are a few unrelated notes on recent (or at least never
before announced) developments from the GenBank project at
Los Alamos.


DOCUMENTATION AVAILABLE

Over the past year or so we have produced a manual largely
for in-house training and reference, but which might be of
some interest to a broader audience.  This manual is now
available for anonymous ftp from genome.lanl.gov.

Some of the chapters explain internal procedures that will
be of little interest to people outside of LANL, but others
explain the use of the software that we have produced for
our use that might be of interest to others.  (Two of the
largest sections are reference manual for our Annotator's
WorkBench (AWB) and the new, soon-to-be released Open Look
AWB.)  In addition, the complete schema for the LANL relational
database is included.

The manual can be found (compressed) in: pub/doc/genbank_manual/*.Z



RELATIONAL TABLE DUMPS AVAILABLE 

We have for some time had relational table dumps available
for anonymous ftp for use by our satellite sites, but we
have never made this known to our users at large.  The files
are in Sybase's bcp format (and compressed), which is essentially
tab-delimited fields in newline-delimited records.

These dumps are updated only occassionally, but we expect to
move soon to a system in which they are updated at least monthly.

The table dumps can be found in: pub/install/*.bcp.Z



DATABASE CLEANUP

Many of you have been extremely helpful in regularly reporting
problems in the database such as innaccurate or vague annotation.
We find this sort of input invaluable in our efforts to maintain
as complete and accurate a collection of data as possible.  In an
effort to further encourage this sort of feedback, I thought it
would be useful to give you some idea of the impact on the database
over the past 12 months.  During this time, largely with the aid
of input from our users, we have:

	fixed approximately 20,000 CDS features that did not
	translate properly as annotated;

	converted approximately 5,000 misc_signals to polya_signals and
	poly_sites;

	converted approximately 2,000 misc_features to CAAT_signals,
	TATA_signals, C_regions, D_regions, J_regions, V_regions, LTRs
	repeat_regions and stem_loops;

	removed almost 6,000 "aa at ##"'s from the feature /note and
	put the information into the /codon_start qualifier;

	moved the "exon ##" information from over 19,000 features
	to the /number qualifier.

We are by no means done, though.  There remain many problems (even
a number in the above categories that were harder to identify and/or
correct).  But it is important for everyone using the database to know
that their feedback really does make a difference in the quality of
the data.

(Of course, we have, in addition to cleaning up existing problems, put
considerable effort into creating the software checks that prevent (or
at least discourage) the entering of similar bad or sloppy data in
the future.  Over the past year, these checks have greatly reduced the
number of errors in new entries that we have had to correct after the
original release of the data.  Design and creation of this type of
software will continue to be one of our highest priorities in the
future.)

The bottom line here is that we want to continue to hear about problems
(both systematic as well as individual) in the database.  This helps
us both in our clean-up efforts and in our system/software design,
which results in a higher quality database for everyone.


Michael Cinkosky
GenBank / Los Alamos