GenBank errors

Foteos Macrides MACRIDES at WFEB2.BITNET
Wed Oct 23 12:12:00 EST 1991


>>        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,
>
>        I'm not quite clear on what you are suggesting above.  Perhaps
>you could restate it?!
>
>                                Sincerely,
>
>                                Dave Kristofferson
>                                GenBank Manager
>
>                                kristoff at genbank.bio.net

        I'm not clear myself.  Perhaps I can figure it out by trying to
restate it.

        I feel that the ability of scientists (among others) to communicate
rapidly, directly, and INFORMALLY with each other in public electronic forums
from virtually anywhere in the world is the most exciting thing that's
happened since the invention of the printing press.  The development and
refinement of this ability, e.g., via the bionet/BIOSCI news groups, is as
important, in my view even more important, than the development and refinement
of the database(s) being discussed.  I also suspect that the majority of
biologists do want the bionet/BIOSCI forums to be managed in an manner which
maintains a high signal to noise ratio and is devoid of personal criticisms
(even if on a private level some of us might prefer Plato and Socrates to
Aristotle).

        It is not yet clear to me to what extent bionet and GenBank are tied
together administatively and/or financially.  My impression is that you have
been the prime advocate of bionet as a set of public forums maintained in
conjunction with the GenBank contract.  I have no doubt that electronic means
of communicating with NCBI for distribution of information, clarifications,
and "feedback" about the database efforts and related services will persist
with the move of GenBank to "in house" facilities, but I wonder if an
equivalent dedication to "international public forums" per se will persist.
Is the latter an explicit component of the the NLM and/or NCBI mission(s)?

        I am unsure whether the co-management of bionet and the GenBank
database activities is a good or bad arrangement.  On October 16
bionet.general/BIONEWS became a "high volume" news group for almost a full
week.  If one looks past the vitriolic parts of the postings to the
substantive issues being raised, clearly some kind of cork had been pulled out
of the bottle.  I can't quite put it together rationally yet, but my intuition
tells me that this has something to do, unfairly and insensitively, with the
current GenBank DATABASE management becoming lame ducks, and something to do
with real or imagined aspects of peer review mechanisms or their actual or
imagined absence in the GenBank project.  So I can't help but wonder whether
that cork will go back into the bottle (not intentionally) in September 1992.
Though the majority of your own postings may be expressions of purely personal
opinions, they all carry the title "GenBank Manager" in the signature.  It's
unfortunate, but to some extent understandable, that some might react to them
as expressions of dogma from the "thought police."  In a previous "passionate"
discussion thread I contributed to "passionately," the point was raised that
GenBank program officers read this international forum, which on the face of
it is good, but in that context came across as something to worry out.
There's also persistent, unintended ambiguity about the "internationality" of
the databasing efforts, Irene's recent posting not withstanding.  It is
understandable that postings from the GenBank/LANL staff regularly include
suggestions that one or another aspect the bionet.general/BIONEWS discussion
be moved to the genbank bboard, but in many of those instances the issue was
germaine to all of the databases and the "internationalization" effort.  There
is in fact very little posted to either the GENBANKB or EMBL-DB bboards, and
very little of that is specific to the GenBank versus EMBL versions.  On the
heels of this week's "general" discussion, one of the postings to EMBL-DB
(from a consistently polite and constructive contributor) included the caveat:

>Of course, the vectorial sequences originate from the submitters and this
>problem is NOT restricted to EMBL-databases. In my last posting i mentioned
>only EMBL-entries because this is the database i usually query first.

        The pros and cons of a truly "free press" have been debated since its
invention.  There are pros and cons to "free international electronic forums"
-- there are both technical and political hurdles, as well as cultural
differences to overcome.  I guess what I was trying to say is that it would be
nice, if possible, to have a "general" forum in which all aspects of all the
database efforts and any plans concerning them can be discussed in detail,
under circumstances in which EVERY contributor and reader -- users, database
development staff, persons high in the funding and decision making heirarchy
-- are ALL unambiguously writing and reading merely as "peers" in an
international scientific effort.  Is that possible?

        Sorry, but this is the best I can do to explain myself at the moment.

                                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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