November 2002 - tdwg - lists.tdwg.org

GenBank/museum connection
by Gordon Jarrell 19 Nov '02

19 Nov '02

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

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Request for distribution
by Walter Berendsohn 11 Nov '02

11 Nov '02

Request for Distribution Dear Colleagues, most probably, you have received the RfC below several times already. However, there may be many more people interested apart from those reached by the mailing lists given below. So please, do re-distribute the request in your country to user communities that may not have it yet, and in your institute to colleages who may not be reached otherwise. Please remember to put Biological Collection Data Standard - Request for Comment in the subject line, so that people are able to identify duplicates. Thank you very much Walter - Please excuse crossposting of this message - Request for Comment Dear Colleague, The Access to Biological Collections Data (ABCD) Task Group is developing an XML Schema as a data interchange standard for unit-level data. A unit may be a specimen, culture, living organism, or observation of an organism. The standard, intended for use in distributed query systems for unit-level databases, has reached a degree of development where the Group welcomes comments and suggestions from the wider community. The current draft of the schema, labelled CTB version 1.39, can be found at the Content Subgroup's Web-site at http://www.bgbm.org/TDWG/CODATA/Schema/ along with further information about the project and the group itself. The profile is available as a .xsd file or as a very large HTML file with diagrams to show the structure. I may also be viewed through a special browser-based schema viewer. The Schema is intended to provide a comprehensive basic structure and is consequently quite large and highly structured. It will be used as the standard format in which the results of a distributed query will be returned. The Group seeks comments on the adequacy of the element set and the definition of the element's semantics ("documentation"). We would particularly value comments on where the element count may be reduced, rather than enlarged, without impairing its function. Please would you take a look at the current draft, and send comments and suggestions to abcd(a)bgbm.org by the December 3, 2002. For the ABCD Standard Editors Group J. Croft, N. Thomson, and W. Berendsohn (Please note: this message has already been posted to Taxacom, TDWG, NHColl- L, BioCASE, ENHSIN, CETAF, BiolSyst, and VegBank lists)

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Four different Vinca flowers
by shinde 31 Oct '02

31 Oct '02

I have come across 4 varieties of Vinca rosea (Apocynaceae). 1. Pink flower with dark pink center 2. Pink flower with white center 3. white flower with pink center 4. pure white flower. What could be the possible explaination. Can some one help? Is it genetic variation Transposons etc. or hybrid breeding? all four were at one place. Rajendra Shinde

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