May 2008 - tdwg-content - lists.tdwg.org

[tdwg-lit] plos one taxonomic publication
by Donat Agosti 29 May '08

29 May '08

Below some comments to a press release from PLOS-one regarding yesterday's online publication of new ant species (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001787) complemented by semantically enhanced XML versions. This means, that the taxonomic domain specific XML mark up schema (TaxonX) has been used to mark up the content of the publication. Enhanced in the context that elements such as taxonomic names or materials citations have been amended with additional information. For names, that means LSIDs from either Zoobank and or the Hymenoptera Name Server have been added, for materials citation, if available, each record has been amended with a collection code form the supporting information available through the publication, and if available with the BenBank accession number, when the specimen has been used for barcoding. This file is in appendix S2. A further file, including an experimental mark up containing PLoS One schema complemented with Taxonx is available here (http://hdl.handle.net/10199/15447 : see pone.0001787_enhanced.xml). The value of this step is, that the XML can be read by machine and imported into other projects. Our implementation on plazi.org is here http://plazi.org:8080/GgSRS/search?214588052.ModsDocID=21401 <http://plazi.org:8080/GgSRS/search?214588052.ModsDocID=21401&indexId=0&subI n> &indexId=0&subIn . The content of this publication has been imported into SRS on plazi, where it resides on a dedicated database that allows exporting it in various versions. In the above link, an html version of each of the treatments is available, that includes links to the Name Servers (HNS, Zoobank), the specimens (CAS in this case, which provides for each specimen a dedicated Webpage), parts of specimens that has been used for DNA analysis, allowing to monitor the whereabout of material used for genetic analysis (in this case linked to CAS), plus the GenBank reocord (GB) Plazi can be harvested using for example a dedicated TAPIR service. Once GBIF harvests this particular data, it will be available on their database as well (http://data.gbif.org/datasets/provider/241 ) from where hopefully soon links will be set up to get back to the original record. Availability of the names: Deposition of CD-Rom and printed material In accordance with section 8.6 of the ICZN's International Code of Zoological Nomenclature, printed copies, and a pdf version of the article have been sent to be deposited at the following six publicly accessible libraries: Natural History Museum, London, UK; American Museum of Natural History, New York, USA; Smithsonian National Museum of Natural History, Washington DC, USA; Museum National d'Histoire Naturelle, Paris, France; Russian Academy of Sciences, Moscow, Russia; Academia Sinica, Taipei, Taiwan. Furthermore, which is not relevant for Art. 8.6, but an option to be considered for the purpose of providing a permanent scientific record (Art. 8(a.1) a digital copy has been deposited at the Public Archive at PubMed Central. Additionally, XML versions of the publication are also available at plazi.org (http://hdl.handle.net/10199/15447) The value of this experimental publication is, that the content, especially descriptions, are immediately open access and, could potentially harvested by machines, like Zoobank, that would automatically add the original descriptions. A similar publication has been posted on Zootaxa (http://www.mapress.com/zootaxa/2008/f/zt01671p031.pdf and http://plazi.org:8080/dspace/handle/10199/15417 . There are many issues involved in implementing such systems, not least sustainable business models. But it seems to be the only way forward so that this information is shared and distributed the widest possible. Adoption of XML based production workflow will become most efficient, if we begin to used editing tools to create our publications from begin with as XML (or similar kind of) documents. The mark up has been a collaboration between PloS-One and Plazi. Any comments are welcome, especially on the publications Web Site at PloS-one to improvie this process (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0001787) . Donat Press release: * * * * * * * * * * * * Scientists Present a Collaborative Model for Accelerating Taxonomy A case study involving 1,700 ant specimens from Madagascar demonstrates how a combination of DNA barcoding, traditional morphology, and Web-based tools can help scientists quickly and accurately process large groups of specimens and make the results immediately available so that other researchers can readily incorporate the results into their work. SAN FRANCISCO (May 28, 2008) - Two hundred and fifty years after the publication of Linnaeus' Systema Naturae, which represents the official start of modern zoological nomenclature, an article published this week in PLoS ONE provides a glimpse of what the future of taxonomy could be in this brave new world of affordable DNA sequencing and the Internet. In the article, entomologist Brian Fisher of the California Academy of Sciences and M. Alex Smith of the University of Guelph, Richard Pyle from Zoobank, and Terry Catapano and Donat Agosti from Swiss-based Plazi present a collaborative approach to taxonomy in which collectors, morphologists, and DNA barcoders combine forces to accelerate the process of species identification and description. Their publication is openly accessible on the World Wide Web and offers not only the descriptions but also the primary specimen and genetic data upon which they are based. Such accelerated and openly accessible work is necessary to keep pace with climate change and other human-induced threats to biodiversity, which may eradicate species from the Earth before they are even recognized as rare or valuable. Insects contribute enormously to the biodiversity of most habitats, but often they are too numerous and too time-consuming to identify using only morphology-based methods. In the PLoS ONE article, Fisher and Smith were faced with the gargantuan task of identifying 1,700 ant specimens collected in Madagascar from 1992 through 2006. To tackle the problem with speed and efficiency, they employed DNA barcoding-in which they sequenced 600 base pairs of the cytochrome c oxidase 1 (CO1) gene-on a representative sample of 501 specimens, and measured the morphological characters of 209 specimens. With this combined data set, they were able to group the ants into five species of Anochetus (three of which are new species) and three species of Odontomachus. While the morphological data was useful in determining the species boundaries between specimens, the results from DNA barcoding-fast, inexpensive, and relatively easy to produce-were what allowed the authors to identify the specimens at a useful scale and speed, especially when members of the same species showed wildly different morphologies. This collaborative approach, anchored by DNA barcoding, will allow scientists to make more timely recommendations to conservation policymakers, the authors argue. For example, the ant data was used as part of a multi-taxon analysis of biodiversity in Madagascar that allowed Fisher and his colleagues to recommend future conservation areas on the island, well before a 2008 deadline set by the Malagasy government. The publishing model set forth in the PLoS ONE article also leverages the digital age-the traditional descriptive text is complemented with links to the underlying data, such as the gene sequences at GenBank, descriptions and images of specimens at AntWeb (www.antweb.org) and naming information at Zoobank, the registry of animal names. Furthermore, the authors have allowed open access to the publication, and offer enhanced machine- (XML-based) and human-readable versions on Plazi, a taxonomy website (http://plazi.org <http://plazi.org/> ). Plazi provides tools to convert and enhance existing publications and provides standardized, searchable access to taxonomic literature. It is already used by data harvesters like the Global Biodiversity Facility (http://gbif.org <http://gbif.org/> ) to enhance their 150 million specimen records. Education and Research at the California Academy of Sciences: The Academy is an international center for scientific education and research and is at the forefront of efforts to understand and protect the diversity of Earth's living things. The Academy has a staff of over 50 professional educators and Ph.D.-level scientists, supported by more than 100 Research and Field Associates and over 300 Fellows. It conducts research in 11 scientific fields: anthropology, aquatic biology, botany, comparative genomics, entomology, geology, herpetology, ichthyology, invertebrate zoology, mammalogy and ornithology. The California Academy of Sciences is home to Steinhart Aquarium, Morrison Planetarium and the Kimball Natural History Museum. The Academy is in the midst of an extensive rebuilding project in Golden Gate Park. Pritzker Prize-winning architect Renzo Piano designed the new Academy, which is scheduled to open on September 27, 2008. www.calacademy.org (415) 379-8000. Contact: Stephanie Stone California Academy of Sciences Email: sstone(a)calacademy.org Tel: +1 (415) 321-8119 Andrew Ng California Academy of Sciences Email: ang(a)calacademy.org Tel: +1 (415) 321-8121 Citation: Fisher BL, Smith MA (2008) A Revision of Malagasy Species of Anochetus Mayr and Odontomachus Latreille (Hymenoptera: Formicidae). PLoS ONE 3(5):e1787. doi:10.1371/journal.pone.0001787 Dr. Donat Agosti Science Consultant Research Associate, American Museum of Natural History and Naturmuseum der Burgergemeinde Bern Email: agosti(a)amnh.org Web: <http://antbase.org/> http://antbase.org Blog: <http://biodivcontext.blogspot.com/> http://biodivcontext.blogspot.com/ Skype: agostileu CV <http://antbase.org/agosticv_2003.html> Current Location <http://antbase.org/agosti_loc_bern.kmz> Dalmaziquai 45 3005 Bern Switzerland +41-31-351 7152 +1-202-558 0330

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[Biogeosdi] itinerary tool geospatial data analysis
by bmeganck 20 May '08

20 May '08

Dear all, RMCA is happy to announce an updated website dedicated to our "itinerary tool" for geospatial data analysis (expedition pathway reconstruction), with extensive documentation and demo, at : http://synthesys.africamuseum.be/itin/ The Tool will collaborate with the EDIT Geoportal and TDWG and GBIF services. The next big step will be requesting GBIF occurrence data and displaying it on the map to support/complement the uploaded data. As you will see from the documentation and the source code, the tool uses a very modular structure, with ideas developed within TDWG and GBIF collaborations, for which we are very grateful to you all. Coming up are some more texts on "spin-off", comprising a phylogeographic module (taking in a treefile, and producing a KML output), GBIF connection and links to the OpenstreetMap initiative. Any questions and/or comments are appreciated ! best regards, Bart. ########################################### This message has been scanned by ICT - Africa Museum ________________________________________ 20/5/2008 - Filtered through antispam by ICT

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[tdwg-tnc] ontological representation of taxonomies and phylogenies
by Hilmar Lapp 16 May '08

16 May '08

(apologies if you receive this multiple times - we are trying to reach as many interested researchers from the taxonomic/systematic community as possible) Under the umbrella of the Open Biomedical Ontologies project (OBO; http://obofoundry.org/) we have created a new mailing list, called obo-taxonomy, for the discussion of ontological representation of taxonomies and phylogenies. The OBO Foundry supports the development of orthogonal, interoperable reference ontologies for biological science. The Phenoscape project (http://phenoscape.org) develops methods and tools for using ontologies to integrate comparative morphological data with mutant phenotypes of genetic model organisms. As such we are very interested in participation from members of the evolutionary biology community to explore how best to integrate taxonomy into an ontological framework. Issues include proper semantics of the relationship between taxonomic groups, and between specimens and species. Subscribe to the mailing list: https://lists.sourceforge.net/lists/listinfo/obo-taxonomy Additional info: http://blog.phenoscape.org/2008/05/15/taxonomy-as-ontology-opening- the-debate/ Acknowledgments: The Phenoscape project (http://phenoscape.org/) is funded by NSF-BDI and supported by the National Evolutionary Synthesis Center (NESCent; http://nescent.org) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : ===========================================================

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[tdwg-lit] wiki on open access movement
by Donat Agosti 06 May '08

06 May '08

Attached a brief description of the new Open Acces Directory, a resource on Open Access. I think this is helpful, because we will not succeed with our effort to build a global biodiversity heritage libray which is up to date with the last new publication, unless our community moves to and adopts open access as a standard.s Donat .......... Open Access Directory: A wiki to organize information about the open access movement Boston, April 30, 2008. Peter Suber and Robin Peek have launched the Open Access Directory (OAD), a wiki where the open access community can create and maintain simple factual lists about open access to science and scholarship. Suber, a Research Professor of Philosophy at Earlham College, and Peek, an Associate Professor of Library and Information Science at Simmons College, conceived the project in order to collect OA-related lists for one-stop reference and searching. The wiki will start operating with about half a dozen lists --for example, conferences devoted to open access, discussion forums devoted to open access, and journal "declarations of independence"-- and add more over time. The goal is to harness the knowledge and energy of the open access community itself to enlarge and correct the lists. A list on a wiki, revised continuously by its users, can be more comprehensive and up to date than the same list maintained by an individual. By bringing many OA-related lists together in one place, OAD will make it easier for users, especially newcomers, to discover them and use them for reference. The easier they are to maintain and discover, the more effectively they can spread useful, accurate information about open access. The URL for the Open Access Directory is http://oad.simmons.edu <http://oad.simmons.edu/> . To contact us, email Athanasia Pontika, the Assistant Editor (OAD.contact(a)gmail.com) or the Editorial Board (OAD.editors(a)gmail.com) The wiki is represented by an editorial board consisting of prominent figures in the open access movement. The Graduate School of Library and Information Science (GSLIS) at Simmons College hosts and provides technical support to the OAD. http://www.simmons.edu/gslis/ Editors and administrators Robin Peek. Editor, Associate Professor, Graduate School of Library and Information Science, Simmons College Athanasia Pontika. Assistant Editor, Doctoral Student, Graduate School of Library and Information Science, Simmons College Terry Plum. Technical Coordinator, Assistant Dean for Technology and Director, Simmons GSLIS at Mount Holyoke College Editorial board members Charles Bailey. Publisher, Digital Scholarship Leslie Chan. Program Supervisor for New Media Studies, University of Toronto Scarborough Heather Joseph. Executive Director, Scholarly Publishing and Academic Resources Coalition (SPARC) Melissa Hagemann. Open Society Institute Peter Suber. Research Professor of Philosophy at Earlham College, Visiting Fellow at Yale Law School, and Senior Researcher at SPARC Alma Swan. Key Perspectives Ltd John Wilbanks. Vice President, Creative Commons Dr. Donat Agosti Science Consultant Research Associate, American Museum of Natural History and Naturmuseum der Burgergemeinde Bern Email: agosti(a)amnh.org Web: <http://antbase.org/> http://antbase.org Blog: <http://biodivcontext.blogspot.com/> http://biodivcontext.blogspot.com/ Skype: agostileu CV <http://antbase.org/agosticv_2003.html> Current Location <http://antbase.org/agosti_loc_bern.kmz> Dalmaziquai 45 3005 Bern Switzerland +41-31-351 7152 +1-202-558 0330

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[tdwg-img] Multimedia Resources in Biodiversity - Survey launched
by Donald.Hobern＠csiro.au 05 May '08

05 May '08

GBIF has recently established a Multimedia Resources Survey Task Group ( http://www.gbif.org/News/NEWS1205258694) The Task Group has now commissioned a Survey of Multimedia Resources in Biodiversity. This survey is now open for responses at http://www.surveymonkey.com/s.aspx?sm=3IfGMGfEI3SMm_2f5h3yNuAw_3d_3d. More information on the survey can be found at http://www.gbif.org/News/NEWS1209648731. I would encourage TDWG participants to contribute to this survey. Many thanks, Donald Donald Hobern, Director, Atlas of Living Australia CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601 Phone: (02) 62464352 Mobile: 0437990208 Email: Donald.Hobern(a)csiro.au

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