Retrieving useful information from connected specimen- and data collections
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
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