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      Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects

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          Abstract

          With biodiversity research activities being increasingly shifted to the web, the need for a system of persistent and stable identifiers for physical collection objects becomes increasingly pressing. The Consortium of European Taxonomic Facilities agreed on a common system of HTTP-URI-based stable identifiers which is now rolled out to its member organizations. The system follows Linked Open Data principles and implements redirection mechanisms to human-readable and machine-readable representations of specimens facilitating seamless integration into the growing semantic web. The implementation of stable identifiers across collection organizations is supported with open source provider software scripts, best practices documentations and recommendations for RDF metadata elements facilitating harmonized access to collection information in web portals.

          Database URL: http://cetaf.org/cetaf-stable-identifiers

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          Darwin Core: An Evolving Community-Developed Biodiversity Data Standard

          John Wieczorek, David Bloom, Robert Guralnick … (2012)
          Biodiversity data derive from myriad sources stored in various formats on many distinct hardware and software platforms. An essential step towards understanding global patterns of biodiversity is to provide a standardized view of these heterogeneous data sources to improve interoperability. Fundamental to this advance are definitions of common terms. This paper describes the evolution and development of Darwin Core, a data standard for publishing and integrating biodiversity information. We focus on the categories of terms that define the standard, differences between simple and relational Darwin Core, how the standard has been implemented, and the community processes that are essential for maintenance and growth of the standard. We present case-study extensions of the Darwin Core into new research communities, including metagenomics and genetic resources. We close by showing how Darwin Core records are integrated to create new knowledge products documenting species distributions and changes due to environmental perturbations.
          Article 0 comments Cited 234 times – based on 0 reviews     Review now
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            Taverna: a tool for building and running workflows of services

            Duncan Hull, Katy Wolstencroft, Robert Stevens … (2006)
            Taverna is an application that eases the use and integration of the growing number of molecular biology tools and databases available on the web, especially web services. It allows bioinformaticians to construct workflows or pipelines of services to perform a range of different analyses, such as sequence analysis and genome annotation. These high-level workflows can integrate many different resources into a single analysis. Taverna is available freely under the terms of the GNU Lesser General Public License (LGPL) from .
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              The Global Genome Biodiversity Network (GGBN) Data Portal

              Gabriele Droege, Katharine Barker, Jonas Astrin … (2013)
              The Global Genome Biodiversity Network (GGBN) was formed in 2011 with the principal aim of making high-quality well-documented and vouchered collections that store DNA or tissue samples of biodiversity, discoverable for research through a networked community of biodiversity repositories. This is achieved through the GGBN Data Portal (http://data.ggbn.org), which links globally distributed databases and bridges the gap between biodiversity repositories, sequence databases and research results. Advances in DNA extraction techniques combined with next-generation sequencing technologies provide new tools for genome sequencing. Many ambitious genome sequencing projects with the potential to revolutionize biodiversity research consider access to adequate samples to be a major bottleneck in their workflow. This is linked not only to accelerating biodiversity loss and demands to improve conservation efforts but also to a lack of standardized methods for providing access to genomic samples. Biodiversity biobank-holding institutions urgently need to set a standard of collaboration towards excellence in collections stewardship, information access and sharing and responsible and ethical use of such collections. GGBN meets these needs by enabling and supporting accessibility and the efficient coordinated expansion of biodiversity biobanks worldwide.
              Article 0 comments Cited 45 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Database (Oxford)
                Journal ID (iso-abbrev): Database (Oxford)
                Journal ID (publisher-id): databa
                Title: Database: The Journal of Biological Databases and Curation
                Publisher: Oxford University Press
                ISSN (Electronic): 1758-0463
                Publication date Collection: 2017
                Publication date (Electronic): 26 February 2017
                Publication date PMC-release: 26 February 2017
                Volume: 2017
                Electronic Location Identifier: bax003
                Affiliations
                [1 ]Botanic Garden and Botanical Museum Berlin, Freie Universität Berlin, Berlin, Germany
                [2 ]Royal Botanic Garden Edinburgh, Edinburgh, UK
                [3 ]Museum für Naturkunde Berlin, Leibniz-Institute for Evolution and Biodiversity, Berlin, Germany
                [4 ]Museum National d'Histoire Naturelle Paris, Paris, France
                [5 ]CETAF-Consortium of European Taxonomic Facilities, Brussels, Belgium
                [6 ]Botanic Garden Meise, Meise, Belgium
                [7 ]Naturalis Biodiversity Center, Leiden, The Netherlands
                [8 ]Institute of Botany, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Bratislava, Slovakia
                [9 ]Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
                [10 ]Department of Botany, Faculty of Science, Charles University, Praha, Czech Republic
                [11 ]Biodiversity Informatics & Spatial Analysis, Royal Botanic Gardens, Kew, London, UK
                [12 ]Department of Life Sciences, The Natural History Museum, UK
                [13 ]SNSB IT Center, Staatliche Naturwissenschaftliche Sammlungen Bayerns, München, Germany
                Author notes
                [* ] Corresponding author: Tel: +49 30 838 50166, Fax: +49 30 838 458574, Email: a.guentsch@ 123456bgbm.org

                Citation details: Güntsch,A., Hyam,R., Hagedorn,G. et al. Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects. Database (2017) Vol. 2017: article ID bax003; doi:10.1093/database/bax003

                Article
                Publisher ID: bax003
                DOI: 10.1093/database/bax003
                PMC ID: 5467547
                PubMed ID: 28365724
                SO-VID: 8a112da2-788c-4516-b13e-80b0136f25b4
                Copyright © © The Author(s) 2017. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 09 August 2016
                Date revision received : 21 November 2016
                Date accepted : 11 January 2017
                Page count
                Pages: 9
                Categories
                Subject: Original Article

                ScienceOpen disciplines: Bioinformatics & Computational biology
                Data availability:
                ScienceOpen disciplines: Bioinformatics & Computational biology

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