1. Biodiversity Informatics:
small pieces, loosely joined.
Dave Roberts
Natural History Museum, London
dmr@nomencurator.org
Contemporary Issues in Biodiversity
U. Oxford MSc in Conservation, Biodiversity and Management
20 Feb 2013

2. ViBRANT
Virtual Biodiversity
Addressing the challenges of taxonomy
Goal ...
Inventory the Earth’s species
Document their relationships
“Publish” & apply these data
Data set ...
1.8 M described spp. (17M names)
300M pages (over last 250 years)
1.5-3B specimens
People ...
4-6,000 taxonomists
30-40,000 “pro-amateurs”
Many more citizen scientists?
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3. ViBRANT
Virtual Biodiversity
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4. ViBRANT
Virtual Biodiversity
Biodiversity informatics landscape
GenBank MorphBank Interactions Geospatial Census
Biotic
Genotype Phenotype Environment Human Effects
Interactions
Pop. data IUCN
Niche & Pop. Biodiversity
Ecology Loss
TreeBase GBIF AquaMaps
Phylogenetic Geographic Conservation &
Trees Dsitributions management
IPNI, Zoobank Extent of Occurrence AquaMaps
Forecasts of Data
Taxonomy Range Maps
Change
Products
Key problems Systems
Landscape is complex, fragmented & hard to navigate
Many audiences (policy makers, scientists, amateurs, citizen scientists) Figure adapted from
Many scales (global solutions to local problems) Peterson et al 2010
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5. ViBRANT
Virtual Biodiversity
Addressing the challenges of biodiversity informatics
“…the field [of biodiversity informatics] appears to be growing in
a void of overarching, motivating questions, effectively making it
a set of technologies in search of questions to address.”
Peterson et al, Syst. & Biodiv. 2010
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6. ViBRANT
Virtual Biodiversity
Small pieces loosely joined
Has many potential meanings:
Joining contributors together to form
communities
Joining the data together that go towards
forming a Scratchpad
Joining Scratchpad content with the landscape of
biodiversity informatics data on the web
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7. ViBRANT
Virtual Biodiversity
Can technology help?
I The technology must largely embody the cause–effect
relationship connecting problem to solution.
II The effects of the technological fix must be assessable using
relatively unambiguous or uncontroversial criteria.
III Research and development is most likely to contribute
decisively to solving a social problem when it focuses on
improving a standardized technical core that already exists.
Sarewitz and Nelson (2008) Three rules for technological fixes. Nature, 456: 871-872
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8. ViBRANT
Virtual Biodiversity
Identifiers
A key to find
something in a
database.
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9. ViBRANT
Virtual Biodiversity
10.4289/0013-8797.115.1.75
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10. ViBRANT
Virtual Biodiversity
http://dx.doi.org/10.4289/0013-8797.115.1.75
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11. ViBRANT
Virtual Biodiversity
http://hdl.handle.net/10.4289/0013-8797.115.1.75
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12. ViBRANT
Virtual Biodiversity
http://www.google.co.uk/search?q=10.4289/0013-8797.115.1.75
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13. ViBRANT
Virtual Biodiversity
http://zoobank.org/10.4289/0013-8797.115.1.75
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14. ViBRANT
Virtual Biodiversity
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15. ViBRANT
Virtual Biodiversity
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16. ViBRANT
Virtual Biodiversity
Ecosystem
state
Herbivore
cohort
Abundance
Carnivore
cohort
Omnivore
cohort
Body mass
High biomass
Ecological
processes
Low biomass Reproduction Metabolism Dispersal
Eating Mortality Other
Variation in biomass across the world simulated by the Madingley model for terrestrial and marine
ecosystems. Fundamental ecological processes, encoded into simple computational forms,
determine the abundance and body mass of organisms (grouped into cohorts for simplicity) and
so indicate the state of ecosystems.
Purves, D., Scharlemann, J. P. W., Harfoot, M., Newbold, T., Tittensor, D.
P., Hutton, J. & Emmott, S. (2013). Ecosystems: Time to model all life on
Earth. Nature 493: 295–297. DOI: 10.1038/493295a
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17. ViBRANT
Virtual Biodiversity
DOI:10.1038/493597a
Length
85 cm
Maturation
9 years
t
Weigh
.1 kg Length
5
82 cm
Mat
aturation
7.7 years
We ight
.6 kg Length
4
73 cm SHRINKING FISH
2000s For Northeast Arctic
cod, the age, size and
spawners have fallen
Mat
aturation dramatically.
7 years
We ight
g
3.2 k
Borrell, B. (2013). Ocean conservation: A big fight over little fish. Nature 493: 597–598.
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18. ViBRANT
Virtual Biodiversity
Data mining.
The abundant microorganisms
in Earth’s soils perform myriad
ecosystem services, many of
which are still poorly understood
or remain unrecognized. The
best ways of identifying and
studying these processes is a
topic of debate in the ecology
community.
Jansson, J. K. & Prosser, J. I. (2013). Nature 494: 40–41. doi: 10.1038/494040a
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19. ViBRANT
Virtual Biodiversity
8 June 2012 14 June 2012
Relman, D. (2012) Nature, 486,194–195 Number of microbial species
doi:10.1038/486194a Number of genes
Modified from GBIF/GBIC –2-4 Jul 2012 –Copenhagen, ©2012, R. J. Robbins
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20. ViBRANT
Virtual Biodiversity
FUNGI ARCHAEA
BACTERIA
ANIMALS
If the goal of biodiversity
studies is to understand
all of the diversity in the
Earth’s biosphere…
PLANTS
Then the notion that we can EUKARYA
accomplish that goal only by
looking here is just plain wrong.
Modified from GBIF/GBIC –2-4 Jul 2012 –Copenhagen, ©2012, R. J. Robbins
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