GenBank errors

Foteos Macrides MACRIDES at WFEB2.BITNET
Mon Oct 21 18:46:00 EST 1991


On 16-OCT-1991 toms at fcs260c2.ncifcrf.gov wrote:
>GenBank is:
>  INCONSISTENT
>  REDUNDANT
>  FULL OF ERRORS
and added the cheap shot (for which he subsequently apologized):
>No wonder they lost the contract.

On 16-OCT-1991 kristoff at genbank.bio.net commented:
>I have been an advocate at several NIH meetings of having a dedicated
>newsgroup for every NIH project like GenBank to help ensure public
>accountability.

On 18-OCT-1991 CZJ at CU.NIH.GOV reviewed the history of the GenBank contracts
and explained the planned move of Genbank to NCBI, including the comment:
>I think the folks at NCBI will have their hands full matching the excellent
>record for customer service rendered by the current contractor,
>Intelligenetics.

On 19-OCT-1991 Peter.Rice at EMBL-HEIDELBERG.DE commented:
>The discussion appears to be an all-american flame war against GenBank.  The
>data in GenBank is actually entered and maintained by three collaborating
>international database groups. The data is transferred between these groups to
>save enormously on the effort and manpower required. At least two of the
>entries referred to were originally entered by EMBL. Other entries may come
>from the DNA Data Bank of Japan.

On 19-OCT-91 marr at cshl.org commented:
>I think a letter should be sent to the Director of NIH by the GenBank staff
>describing this recent exchange, showing her a good example of WHAT HAPPENS
>WHEN THE PEER REVIEW PROCESS IS CIRCUMVENTED.
(emphasis mine)

On 21-OCT-1991 kumar at cshl.org commented:
I think the debate over genbank errors is good, but is moving in the *WRONG*
>direction.  Rather than argue over who said what about whom,  I think there
>should be some discussion about software methods for detecting and correcting
>errors as well as the proper way of annotating these errors in the database
>entries.

        The passions associated with this discussion thread have been moving
it in several interrelated directions, none of which are "wrong" (IMHO).  The
most informative and coherent discussion has been about the nature of the
database(s?):  Is the objective to maintain it(them?) as an essentially
"historical" record of research output, updated and distributed at rapidly as
possible, or as a body of "knowledge" and if the latter, who will decide what
the "truth" is and how?   This goes far beyond the issue of how to correct
unambiguous errors, or where they should be reported, or how they might be
prevented in the first place.  In this connection, why is it that phrases like
"three collaborating international database groups" have not been present in
the messages from any level of the GenBank hierarchy (honest, I'm not just
trying to perpetuate an "all-american flame war")?  What about the protein
databases?

        Another "direction" relates to the issue of "accountability" and has
been pursued in a much less coherent manner.  In this connection, wouldn't it
be wonderful if the kind of effort which the "current contractor" has put into
the development of bionet/BIOSCI persisted under circumstances in which
there's no need to worry about criticisms inadvertantly becoming public pink
sheets?  Is that possible?  Has it been thought about explicitly in
conjunction with the planned move of GenBank to NCBI?

                                Fote

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 Foteos Macrides           Worcester Foundation for Experimental Biology
 MACRIDES at WFEB2.BITNET     222 Maple Avenue, Shrewsbury, MA 01545
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