database input requested

Judith Blake blake at TIGR.ORG
Fri Nov 12 16:52:31 CST 1993



Integration of Molecular Sequences with Specimen, Collection and
Taxonomic Data in a Publicly-accessible Relational Database

   Several colleagues and I here at The Institute for Genomic Research
are developing a relational database called "Sequences, Sources, Taxa
(SST)" that will support links between DNA and protein sequence data,
alignments, citations, taxonomic, collection, and specimen data. This
database is intended to answer queries such as:

"Return a list of all taxa collected in Panama between 1988 and 1993
for which sequence data are available, together with names of the
genes sequenced and voucher specimen locations."

SST will facilitate the use of molecular tools in species
identification, systematics, and diversity studies, and the use of
documented collections in molecular evolution and molecular genetics.
We have contacted a number of collections managers and taxonomists,
and support for an effort along these lines appears to be quite high.

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

Would you use such a resource?

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

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

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

   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. One component of
the SST effort will be the development of direct submission interfaces
(first email, then client). In addition, we are currently working with
colleaques at other database sites to implement joint submission of
sequences to several linked databases simultaneously.

  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.

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

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