Release of GenBank sequences

scarr at kean.ucs.mun.ca scarr at kean.ucs.mun.ca
Thu Nov 18 11:39:17 EST 1993


      The following is a slightly edited [to remove personal
identifications] version of a letter I sent to the Editor of
JME concerning my (perceived) difficulty with the GenBank
database. Has anyone else experienced similar difficulties? Is
 generic solution, with the onus on the journal and/or
GenBank, necessary or desirable?

Steve

[BTW, the sequences turned up in GenBank later that day.]

************************************************************
Steven M. Carr
Dept. of Biology
Memorial University of Newfoundland
St. John's NF A1B 3X9
ANADA

(709) 737-4776 office / -4713 lab / -4000 FAX
scarr at kean.ucs.mun.ca
************************************************************


08 November 1993

Editor
Journal of Molecular Evolution

      Dear [Sir]

      May I recommend a new item of editorial policy for JME?

      The [current] number of JME contains a paper ... that
references several GenBank DNA sequence accession numbers
without giving the actual sequences so referenced. An
immediate gopher search of both GenBank and the updated
GenBank turned up nothing associated with those numbers. A
call to Los Alamos referred me to EMBL, the prefix of the
GenBank numbers indicating submission there. An EMBL search
for new citations/listings ... came up dry. EMBL responded to
my e-mail for help with a request for a complete citation in
order to release the sequences....  The sequence information
is urgently needed for an MS in press.

       All of this is of course quite tedious. EMBL (and
NIH/DOE or whoever these days) apparently have no mechanism
for automatic release of 'held' sequences once they are
actually published: they rely on a note from the author or the
appearance of the paper in SCI. Thus sequence data in a paper
may be available only weeks (or perhaps months) after
publication ....        

     May I suggest that JME take it upon itself to notify the
various databases, simultaneously with publication of each new
number of the journal, that any GenBank accession numbers
referenced therein can be released? This is especially
important when (as in this case) the data are not included in
the original paper. In principal, this could be done as a
formal AUTHORIN update, giving the actual title, volume, and
page numbers; in practice, a simple listing would apparently
suffice. The molecular journals in general should perhaps
adopt this as routine practice: perhaps a matter for the
Council of Biology Editors? May I add that, in general, and
space considerations aside, I would prefer to have the
complete printed data available in the printed article as well
as the electronically accessible forms.

      Thank you for your consideration.



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