From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Subject: Re: Beyond GenBank.  
Organization: Frederick Cancer Research and Development Center
Distribution: bionet.molbio.bio-matrix
Date: Wed, 16 Dec 1992 02:28:21 GMT

In article <BRIANF.92Dec14175130@dna.uvm.edu> brianf@dna.uvm.edu
(Brain Foley) writes:

>	Thus there is a wealth of information about DNA sequences that
>is not getting into GenBank.

YES!  This is why I have the middle name I do.  This huge loss of data is going
to catch up with us sooner or later (I'd say within 5 years) and people will
not be able to track down all the data.  It's just about impossible NOW!  Can
Sankar Adhya - world renouned expert on CRP - give me a current list of all
known sites (ie experimentally proven - none of this garbage prediction
stuff)?  NO!  What about IHF, FIS, splice junctions, etc?  The data is being
lost into our huge literature at a horrible rate.  (Tell me, are you willing to
slog through 6000, yes SIX THOUSAND splice junctions for humans to remove all
the 2000 YES TWO THOUSAND ESTIMATED ERRORS in GenBank?  If so, I have a nice
job for you to do - collaboratively.  The results will be important but getting
there is tough with the current mess.  Oh yes, by the time you are done in a
year and a half, there will be an equivalent amount of NEW mess ready to be
done!)

The reason that GenBank was formed was to prevent people all over the world
from duplicating their efforts at getting sequences in the computer.  Now we
have EXACTLY THE ANALOGOUS SITUATION with the so-called features.

But NCBI refuses to acknowledge and deal STRONGLY with this growing disaster,
and until more people recognize the problem (as you did, congratulations!) it
will only become worse.  ("Strong" means to have a policy in effect which
will lead to the assured capture of all experimentally supported data
on sequence features.  Guesses should not be in the database.)

>Most of this information does not even
>truly belong in GenBank, but rather in a secondary database devoted to
>the topic at hand.

Here I disagree.  The information should be integrated directly into
the same database.  There is no reason for a separation, and doing
so would cause delays, taking up researcher's time.

Also, your proposal will fail.  The trouble is that cross reference indexes are
all wrecked or poor.

LOCUS name changes at the whim of the moment, and is no longer meaningful
for any long term storage.  It really should be eliminated.

ACCESSION number keeps being updated and altered.  At least the old one is
there, but there are not ABSOLUTE names in sequences to which one can refer.
So the locations of mutations are FORCED by this (excuse me) stupid system to
be numbers.  That means that when the sequence numbering changes (eg, merge of
sequences - which HAS to be done!!! or error correction) the pointers in the
secondary database will be blown away.  There is no assured mechanism to give
coordinates RELATIVE to standard marks in the sequence.  (The folks who
followed last years row on this subject will see that the ideas never change.
The database doesn't improve.  Only the date changes and the time to disaster
shortens.)

There isn't anything else to hang references on.  NCBI is unwilling to face
these tough issues.  It's that time of year folks.  Have we made much progress
since last year?

Dear David Lipman, I'm sorry to say: no.

Let's discuss this on the net David, where everybody can "listen".

  Tom "Cassandra" Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov