retrieving useful information from connected specimen- and data collections
DESCRIPTION
Presentation to the Dutch delegation and their Chinese counterparts at the Beijing Genomics Institute in Shenzhen, PRC.TRANSCRIPT
RETRIEVING USEFUL INFORMATION
FROM CONNECTED SPECIMEN- AND DATA
COLLECTIONS
Conceptual design of future databases: sense and nonsense, how to proceed jointly?
Rutger Vos 22 March 2012
Outline
NCB Naturalis Collections of physical and digital objects Examples of research and services Linking specimens and data Future developments Conclusions
Specimen- 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 museums
Specimen- 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 keys
Specimen- and data collections, Rutger Vos
NCB services and research
Terrestrial and marine zoology, geology and botany
Fundamental and applied research
Significant NGS applications
Advice customs on traded endangered species
Identify birds from plane crashes
Identify hardwoods Identify gemstones
Research Services
Specimen- 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 applications
Specimen- 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 substitutes
Specimen- and data collections, Rutger Vos
2050 2010 2050-2010
— =
Example: the biodiversity crisis
Specimen- and data collections, Rutger Vos
1400 modeled species distributions (red = loss; green = gain)
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 applications
Specimen- 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 Literature
Specimen- 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 data
Specimen- 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 collaboratively
Specimen- 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