- tdwg - lists.tdwg.org

OSIS platform update
by Guillaume Rousse 25 Feb '03

25 Feb '03

I just updated the web site of OSIS, a software framework developped in my laboratory. This project aims to create a shared code base to build systematics application from a common trunk instead of reinventing the wheel constantly, as molecular biology community already do with biojava, bioperl, and similar projects. The only implementation available currently is in Perl, and the only use case is related to database management, but the project scope is wider. It is of course a free software project, so all comments, critics or contributions are welcomed. The web site is located at http://lis.snv.jussieu.fr/~rousse/recherche -- Any cool program always requires more memory than you have. -- Murphy's Computer Laws n°2

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TDWG Meeting in 2004 Costa Rica
by Jim Beach 03 Feb '03

03 Feb '03

Stan Blum and I have been discussing the possiblity of holding a TDWG meeting, likely in Oct-Nov 2004 in Costa Rica at the OTS LA Selva field station. La Selva is a rain forest site and now has nice meeting rooms Internet connectivity and of course spectacular scenery. Housing is field station quality with some private an some double or quad bunk bed rooms. Food and logistics are excellent at the site. I would be grateful for any feedback on whether you would be able to travel to Costa Rica that time of year in 2004 for the TDWG annual meeting. Many thanks, Jim Beach

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Data Entry Query
by Fran Kern 09 Jan '03

09 Jan '03

Hello. I'm currently working on a project to identify and quantify time/cost bottlenecks in data-basing natural history collections. Would anyone know of similar projects happening elsewhere? Or be able to point me in the direction of relevant articles, journals, or meetings? I am casting my net wide by posting this message on several lists - apologies for repetition if you subscribe to the others. Thank you for your help, Fran ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Francisca Kern Rapid Data Entry Assessment Project, Department of Botany The Natural History Museum, Cromwell Road, London SW7 5BD

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Announcement: Mansfeld Symposium 2001 Proceedings
by Dr. Helmut Knuepffer 05 Dec '02

05 Dec '02

Dear colleagues, members of the TDWG Mailing List, we would like to inform you that we are in the final phase of preparing the proceedings volume of the Symposium "Rudolf Mansfeld and Plant Genetic Resources" (held in October 2001 in Gatersleben, Germany) for publication. Attached please find brief information (including the table of contents) about this publication, which is expected to appear in February/March 2003. The Proceedings will contain, among others, some contributions about the Mansfeld Database and other taxonomic databases. In addition, several papers deal with questions of the taxonomy of cultivated plants. Therefore, we consider that some members of the TDWG mailing list might be interested in this information. If you are interested in buying these proceedings (at a price of 10 Euro, including shipment), please inform us as soon as possible, not later than December 20, 2002. We will calculate the number of copies to be printed, based on the expressions of interest received. Please, also inform your colleagues and scientific libraries about this possibility. P.S. We apologise for the possibility of sending multiple copies of this announcement to the same address, due to membership in different mailing lists. With best regards, yours, Helmut Knüpffer and Jörg Ochsmann Editors of the Proceedings Dr. Helmut Knuepffer, Genebank Department Dr. Jörg Ochsmann, Taxonomy Department Institute of Plant Genetics and Crop Plant Research (IPK) Corrensstr. 3 D-06466 Gatersleben, Germany phone: +49-39482-5283 (HK) fax: +49-39482-5155 knupffer(a)ipk-gatersleben.de, ochsmann(a)ipk-gatersleben.de IPK: http://www.ipk-gatersleben.de Genebank Database: http://fox-serv.ipk-gatersleben.de EU Barley Evaluation Project: http://barley.ipk-gatersleben.de/ Mansfeld Database of Cultivated Plants: http://mansfeld.ipk-gatersleben.de

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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 12 Nov '02

12 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 01 Nov '02

01 Nov '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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Bioinformatics positions IPK Gatersleben
by Dr. Helmut Knuepffer 28 Oct '02

28 Oct '02

Dear colleagues, I would like to inform you about a bioinformatics position (research group leader) at IPK Gatersleben. Please distribute them also to colleagues who might be interested to apply. See also: http://bic-gh.ipk-gatersleben.de/jobs.php Helmut Knuepffer Dr. Helmut Knuepffer Abt. Genbank, Institut fuer Pflanzengenetik und Kulturpflanzenforschung (IPK) Genebank Department, Institute of Plant Genetics and Crop Plant Research (IPK) Corrensstr. 3 D-06466 Gatersleben, Germany phone: +49-39482-5283 fax: +49-39482-5155 knupffer(a)ipk-gatersleben.de, HKnuepffer(a)web.de IPK: http://www.ipk-gatersleben.de Genebank Database: http://fox-serv.ipk-gatersleben.de Mansfeld Database of Cultivated Plants: http://mansfeld.ipk-gatersleben.de

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Re: Multinational and Special Characters in Data - Call for papers
by Adrian Rissone 19 Sep '02

19 Sep '02

This message is to confirm that the workshop ("International and Special Characters") will take place. The exact date/time has not yet been scheduled. We would welcome additional short presentations. Please send the title and abstract to me at A.Rissone(a)nhm.ac.uk so as to arrive by latest 17:00 on 25 September 2002 (UK time). It would help planning if you could respond before that deadline! Regards, Adrian Rissone Natural History Museum London SW7 5BD

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Multinational and Special Characters in Data
by Adrian Rissone 13 Sep '02

13 Sep '02

If you are interested in attending a workshop on "Multinational and Special Characters in Data" during the TDWG meeting in Brazil in October, please reply by email to A.Rissone(a)nhm.ac.uk The idea is to have a few short presentations followed by discussion. It would be helpful if you can indicate the database(s) you are using and their current methods of handling non-ASCII characters. See you in Brazil!

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