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

1. 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?

2. 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

3. 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

4. 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

5. 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

6. Big data?
 Large data sets of
various types:
 NGS sequence data
 GIS occurrence data
 Digitization
 Identification keys
Specimen- and data collections, Rutger Vos

7. 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 gemstones
Specimen- and data collections, Rutger Vos

8. 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

9. 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

10. Example: the biodiversity crisis
1400 modeled species distributions
(red = loss; green = gain)
— =
2050 2010 2050-2010
Specimen- and data collections, Rutger Vos

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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