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Retrieving useful information from connected specimen- and data collections
 

Retrieving useful information from connected specimen- and data collections

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Presentation to the Dutch delegation and their Chinese counterparts at the Beijing Genomics Institute in Shenzhen, PRC.

Presentation to the Dutch delegation and their Chinese counterparts at the Beijing Genomics Institute in Shenzhen, PRC.

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    Retrieving useful information from connected specimen- and data collections Retrieving useful information from connected specimen- and data collections Presentation Transcript

    • RETRIEVING USEFUL INFORMATION FROM CONNECTED SPECIMEN- AND DATA COLLECTIONS Rutger Vos Conceptual design of future databases: sense and nonsense,22 March 2012 how to proceed jointly?
    • Outline   NCB Naturalis   Collections of physical and digital objects   Examples of research and services   Linking specimens and data   Future developments   ConclusionsSpecimen- and data collections, Rutger Vos
    • NCB Naturalis   Netherlands Centre for Biodiversity and national natural history museum   37 million physical objects   In the global top 5 of natural history museumsSpecimen- and data collections, Rutger Vos
    • Biological specimen collections Natural history museums, which evolved from cabinets of curiosities, played an important role in the emergence of professional biological disciplines and research programs. Particularly in the 19th century, scientists began to use their natural history collections as teaching tools for advanced students and the basis for their own morphological research.Specimen- and data collections, Rutger Vos
    • Biological data Research on biological collections generates many kinds of publicly available data   Global molecular databases (NCBI)   Global biodiversity information facility (*BIF)   Barcode of life data system (BOLD)   Domain-specific databases (e.g. TreeBASE)Specimen- and data collections, Rutger Vos
    • Big data?   Large data sets of various types:   NGS sequence data   GIS occurrence data   Digitization   Identification keysSpecimen- and data collections, Rutger Vos
    • NCB services and research Research Services   Terrestrial and marine   Advice customs on zoology, geology and traded endangered botany species   Fundamental and   Identify birds from applied research plane crashes   Significant NGS   Identify hardwoods applications   Identify gemstonesSpecimen- and data collections, Rutger Vos
    • Example: orchid genomics   NCB Naturalis and BGI scientists are mapping the first fully sequenced orchid genome (Erycina pusilla)   Study of developmental genes coding for floral shape, symmetry, scent and senescence   Many genes found to have horticultural applicationsSpecimen- and data collections, Rutger Vos
    • Example: DNA Barcoding TCM   Orchids long since used in China and now also increasingly popular in Europe   Require identification to ensure they do not contain:   legally protected wild species   other species than mentioned on label (=adulteration)   life threatening poisons in case of toxic substitutesSpecimen- and data collections, Rutger Vos
    • Example: the biodiversity crisis 1400 modeled species distributions (red = loss; green = gain) — = 2050 2010 2050-2010Specimen- and data collections, Rutger Vos
    • Example: snake venom and medicine   NCB Naturalis scientists are mapping the King Cobra genome   Studying its evolution in broader comparative context   Many proteins in venom might have medical applicationsSpecimen- and data collections, Rutger Vos
    • Linking physical and digital objects   Physical objects are linked to digital data along along various axes:   Specimen identifiers   Georeferences   Classification   Characters   LiteratureSpecimen- and data collections, Rutger Vos
    • Links between data and specimens   Primary voucher identifier is: institution:collection:specimen   Several databases use these for cross-referencing   Unfortunately not (yet, universally) resolvable* * http://iphylo.blogspot.com/Specimen- and data collections, Rutger Vos
    • The future   Globally unique, resolvable identifiers   Resolution results in standards compliant open data   Data discoverable to all by its links to other dataSpecimen- and data collections, Rutger Vos
    • Conclusions   Stakeholders in neighbouring domains need to identify where physical and digital objects can be linked usefully   Stakeholders need to engage in community processes for standards development and adoption to enable data sharing   Complexity needs to be managed collaborativelySpecimen- and data collections, Rutger Vos
    • Acknowledgements   Thank you:   For your attention   To our gracious hosts today   To the organizers of this visit 謝謝!Specimen- and data collections, Rutger Vos