sequence not available

Paul Gilna pgil at TEMIN.LANL.GOV
Thu Apr 1 11:33:30 EST 1993

Keith Robison makes the point:

> 	This is clearly not a complete solution to the problem.  There
> is a related problem of released entries whose JOURNAL fields are stuck
> at "in press" -- it makes tracking down citations a real nuisance.
> I think that all entries marked "in press" or being held should be
> periodically reviewed (perhaps after 3 months).  This, plus the journal
> scanning by NCBI, should greatly reduce the number of entries which are
> marooned in one fashion or another.
and Renee Lippens suggests

> 	The suggestion is good but 3 months is really too long,
>   I feel that screening every month will be necessary.
>   But why not ask to the Journals or Publishers to notify the databanks when
>   a publication containing an Accession Number is issued.

Keith makes a good point regarding the lack of progression from "in
press" to published. However the solutions proposed all suggest that
the databases devote some effort to scanning the publication medium to
address the problem AFTER it`s occurred.

Let me ask the following (rhetorical please!) question: does someone
continually remind you to renew your driving permit or auto tax once
they have expired?  More to the point, does someone do it for you? Not
in this country, it is assumed that ownership of a vehicle or
possession of driving permit bring with it the responsibility for
keeping either current, you're lucky if you get a reminder at all.

When you submit your data to GenBank, you are explicitly asked
(extracted from GenBank submission acknowlegement text):

> We list the citation associated with your sequence data as follows:
>         rDNA sequences of Encephalitozoon hellem and Encephalitizoon 
>         cuniculi: species identification and phylogenetic construction
>         J. Eukaryot. Microbiol. (1993) In Press
> Please inform us of changes in the citation or corrections to sequence data
> by sending electronic mail to
> 	update at ncbi.nlm.nih.gov 

In other words, we have conferred upon the submitting author, the
responsibility for updating and maintaining his or her data.

Michael Cinkosky mentioned:

> During the
> time between submission and publication, we repeatedly contact the original
> submitters requesting information on the status of the publication and
> asking for permission to release the data.  In this way, many of the
> submissions that are originally confidential are still released prior to
> publication (with the authors permission).

We believe that we can provide a better and more effective service to
our submitting customer (and in turn the community) if we can help them
exercise that responsibility rather then have us do it for them.

At the moment, we are doing this relatively manually, but expect to
have automated a lot of this step within the next few months so that
"reminder" messages go out automatically on a periodic basis.  While we
hadn't specifically considered it before this, Keith's observation
suggests that extending this to other publication statuses (manuscript
in prep, submitted to "journal", unpublished, etc.,) would be a
worthwhile move.

The primary gain from this approach (in addition to reinforcing the
notion that responsibility for data maintenance lies with the owner of the
data) is that one increases one's chances of updating the data BEFORE
they go wrong.

Today, for each new sequence that we release to the nets, we release at
least another updated sequence, where the update was provided to us by
the submitting author. This suggests that along with the exponential
increase in volume of new data, the changes to those data are keeping
the same pace. Not long ago, I was fond of quoting the fact that
updates from authors represented a third of our output--I think this
vision thing is catching on!

Finally, I should mention that our contract with NCBI calls for us to
develop a data importing capability for their ASN.1 feed, which should
give us an automated method for flagging changes in publication status
for submissions which have been published; this should give us a
partial failsafe for those authors who have yet to catch on (even
there, however, I expect we would pass something back to the author)!



Paul Gilna
co-PI, GenBank/LANL

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