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      Is Open Access

      Taxonomic information exchange and copyright: the Plazi approach

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      1 , , 2

      BMC Research Notes

      BioMed Central

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          Abstract

          Background

          A large part of our knowledge on the world's species is recorded in the corpus of biodiversity literature with well over hundred million pages, and is represented in natural history collections estimated at 2 – 3 billion specimens. But this body of knowledge is almost entirely in paper-print form and is not directly accessible through the Internet. For the digitization of this literature, new territories have to be chartered in the fields of technical, legal and social issues that presently impede its advance. The taxonomic literature seems especially destined for such a transformation.

          Discussion

          Plazi was founded as an association with the primary goal of transforming both the printed and, more recently, "born-digital" taxonomic literature into semantically enabled, enhanced documents. This includes the creation of a test body of literature, an XML schema modeling its logic content (TaxonX), the development of a mark-up editor (GoldenGATE) allowing also the enhancement of documents with links to external resources via Life Science Identifiers (LSID), a repository for publications and issuance of bibliographic identifiers, a dedicated server to serve the marked up content (the Plazi Search and Retrieval Server, SRS) and semantic tools to mine information. Plazi's workflow is designed to respect copyright protection and achieves extraction by observing exceptions and limitations existent in international copyright law.

          Conclusion

          The information found in Plazi's databases – taxonomic treatments as well as the metadata of the publications – are in the public domain and can therefore be used for further scientific research without any restriction, whether or not contained in copyrighted publications.

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          Most cited references 15

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          Biodiversity informatics: the challenge of linking data and the role of shared identifiers.

           Roderic Page (2008)
          A major challenge facing biodiversity informatics is integrating data stored in widely distributed databases. Initial efforts have relied on taxonomic names as the shared identifier linking records in different databases. However, taxonomic names have limitations as identifiers, being neither stable nor globally unique, and the pace of molecular taxonomic and phylogenetic research means that a lot of information in public sequence databases is not linked to formal taxonomic names. This review explores the use of other identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnected facts in different databases. The structure of these links can also be exploited using the PageRank algorithm to rank the results of searches on biodiversity databases. The key to rich integration is a commitment to deploy and reuse globally unique, shared identifiers [such as Digital Object Identifiers (DOIs) and Life Science Identifiers (LSIDs)], and the implementation of services that link those identifiers.
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            A Revision of Malagasy Species of Anochetus Mayr and Odontomachus Latreille (Hymenoptera: Formicidae)

            Species inventories are essential for documenting global diversity and generating necessary material for taxonomic study and conservation planning. However, for inventories to be immediately relevant, the taxonomic process must reduce the time to describe and identify specimens. To address these concerns for the inventory of arthropods across the Malagasy region, we present here a collaborative approach to taxonomy where collectors, morphologists and DNA barcoders using cytochrome c oxidase 1 (CO1) participate collectively in a team-driven taxonomic process. We evaluate the role of DNA barcoding as a tool to accelerate species identification and description. This revision is primarily based on arthropod surveys throughout the Malagasy region from 1992 to 2006. The revision is based on morphological and CO1 DNA barcode analysis of 500 individuals. In the region, five species of Anochetus (A. boltoni sp. nov., A. goodmani sp. nov., A. grandidieri, and A. madagascarensis from Madagascar, and A. pattersoni sp. nov. from Seychelles) and three species of Odontomachus (O. coquereli, O. troglodytes and O. simillimus) are recognized. DNA barcoding (using cytochrome c oxidase 1 (CO1)) facilitated caste association and type designation, and highlighted population structure associated with reproductive strategy, biogeographic and evolutionary patterns for future exploration. This study provides an example of collaborative taxonomy, where morphology is combined with DNA barcoding. We demonstrate that CO1 DNA barcoding is a practical tool that allows formalized alpha-taxonomy at a speed, detail, precision, and scale unattainable by employing morphology alone.
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              A universal register for animal names.

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                Author and article information

                Journal
                BMC Res Notes
                BMC Research Notes
                BioMed Central
                1756-0500
                2009
                30 March 2009
                : 2
                : 53
                Affiliations
                [1 ]Plazi, Zinggstrasse 16, CH-3007, Bern, Switzerland
                [2 ]Advocomplex, Zinggstrasse 16, CH-3007, Bern, Switzerland
                Article
                1756-0500-2-53
                10.1186/1756-0500-2-53
                2673227
                19331688
                Copyright © 2009 Egloff et al; licensee BioMed Central Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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                Correspondence

                Medicine

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