database input requested

Jim Croft jrc at ANBG.GOV.AU
Sat Nov 13 10:32:27 CST 1993

Hi Judy

>    This posting is to elicite some feedback from potential users
> of SST.

ok - some feedback from a stochastic, reticulate, randomized,
non-sequential type of person in an organization preoccupied with whole,
for the most part photosynthetic, organizms...

> Would you use such a resource?

Possibly, but not for the sequence stuff at this stage, although it may
become useful for our phylogenetic reconstruction projects later.

> Would you submit data to this database?  How important would
> simultaneous submission to other databases such as Genbank be?

Yes - we would make our taxonomic and bibliographic information
available if you are interested in plants.

Simultaneous submission to multiple databases may be a problem -
it raises all manner of horrible questions relating to updates, version
control and maintenance and often confusion as to where the latest and
'official' version resides.  Having said that, simultaneous submission,
if you can keep it under control, might be a good idea, at least until
the nirvana of a transparently distributed databases across different
platforms arrives.

> What kinds of information would be relevant to your research area if
> you searched this database?

To start with, we would be interested in seeing what taxa were being
covered and how the names associated with these were handled and the
types of information associated with each taxon.  As a museum-type
institution we are not particularly interested in the sequence
information per se, but rather as a tool to sort out problems of
systematics; to be of any use we will need comparable information from
each member of the particular group we are interested in at the time -
we may have a very long wait...

> What platforms (Mac, PC, UNIX) are available to you?

All of the above.  However, I would strongly recommend that you consider
also making the information through established internet protocols such
as Gopher and World Wide Web for which simple and free clients exist for
all the major hardware and operating system platforms - most users will
want to read and extract the data rather than edit it.

>    SST will be implemented in Sybase and linked to our gene expression
> and function database, EGAD (Expressed Gene Anatomy Database). EGAD
> will also be publicly accessible late in 1994.  We would like to see
> SST become part a community-wide federation of databases, and will
> make the design, semantics, and data themselves available to the
> community and to other databases in the federation.

The choice of database software is not a major issue.  What is important
is use of a sound design of your information system and the use of
standard, or at least widely understood, conventions on how the data is
stored, what does it mean, and agreed protocols for delivering and
exchanging data.  A 'community-wide federation' of sequence databases is
the way to go, but make sure it includes the federation of taxonomic
databases and the federation specimen databases and the federation of...
(May the Force be with you as you boldly go...)

>   While a taxon designation will be assigned to each sequence based on
> the voucher identification, taxonomic relationships will be referenced
> to or directly linked to other specialized databases, as will the
> finer details of vouchering and collection management.  Our primary
> concern is that sequences and their associated information be linked
> to voucher specimens and locality data.  We welcome discussion with
> collection managers, taxonomic specialists and others as to how we all
> can make the most of the power of electronic information systems.

Yes! The need for properly prepared and curated voucher specimens for this
type of enterprise can not be over emphasised.  The only reliable way to
sort out the taxonomy of much published information is to inspect the
voucher specimens - all else is supposition.   Adopt the working slogan:
'No voucher, no data!'.

> Pease send comments and suggestions!
> Judith A. Blake, Ph.D.
> The Institute for Genomic Research            Telephone: 301-216-9592
> 932 Clopper Road                              FAX:       301-869-9423
> Gaithersbury, MD  20878                       email:     blake at

Jim Croft           [Herbarium CBG]               internet: jrc at
Australian National Botanic Gardens                  voice:  +61-6-2509 490
GPO Box 1777, Canberra, ACT 2601, AUSTRALIA            fax:  +61-6-2509 599
______Biodiversity Directorate, Australian Nature Conservation Agency______

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