GenBank/museum connection

Gordon Jarrell fnghj at UAF.EDU
Tue Nov 19 10:25:20 CET 2002

   The University of Alaska Museum (UAM) is linking its online specimen
data to GenBank, and GenBank has reciprocated by linking sequence
accessions to UAM specimen records. With a click, users of either
resource can jump from a record in one database to the associated record
in the other. This enhances scientific reproducibility and begins to
realize the potential of independent, yet coordinated, online databases
as analytic tools.

NCBI's GenBank, with its collaborators in Japan (DNA DataBank of Japan,
DDBJ) and in Europe (European Molecular Biology Laboratory, EMBL), is
the world's largest, most important biological database, and sequences
come from any lifeform, whether cultivated, cultured, or sampled from
nature. Submitting sequences to GenBank is a requirement for publication
of most sequence-based research, but the supporting data associated with
sequences from wild organisms is variable and often renders them
unreproducible . For the best of sequence records, additional DNA or
tissue samples are archived and source descriptions include institution
names and catalog numbers that would permit another investigator to find
more information or more material.

For UAM, the GenBank connection is a benefit of operating an online
database based on the relational model of UC Berkeley's Museum of
Vertebrate Zoology (MVZ). That model can contain most of the information
a museum associates with its specimens, including "other identifiers,"
of which a cataloged item can have any number. GenBank numbers are
included as a searchable type of "other identifier." In UAM's individual
specimen records, GenBank numbers are hyperlinks to GenBank. Thus, when
you find a specimen with a GenBank number, you can click on it and look
at the sequence. From GenBank's sequence pages you would click on
"LinkOut" then the UAM catalog number to look at the specimen data.

We are committed to gather and report the data on which our systems are
now linked. GenBank can be more than an appendix to published
literature. By complementing sequences with documentation of their
sources and with documentation of subsequent taxonomic and analytic
treatments, we build a composite resource that will be a powerful tool
for increasingly fine-grained analyses of genetic variation in nature.

Gordon Jarrell, UAM
Scott Federhen, NCBI

A demonstration/tutorial:

Database development at UAM has been supported by grants from NSF
(DEB-9981915, DBI-0108161, DBI-9876837) and the Alaska Coastal Marine
Institute (U. S. Minerals Managent Service).

Gordon H. Jarrell, Ph.D
Coordinator Alaska Frozen Tissue Collection
Acting Curator of Mammals
University of Alaska Museum
Fairbanks, Alaska USA 99775-6960
office: (907) 474-6946
fax: (907)474-5469

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