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: http://arctos.museum.uaf.edu:8080/demo/demo_frameset.html
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