GLOBAL BIODIVERSITY

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GLOBALBIODIVERSITY
INFORMATIONFACILITY
The magnitude of biodiversity data and the
imperative role of biodiversity
informatics Converging Sciences Trento, Italy, 17
December 2004
WWW.GBIF.ORG
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And now for something different

• So far, this conference has largely focused on
  molecular and genetic biology
• Will now move to higher levels of complexity
• With strong connections to climate change and
  environmental problems
• I will emphasise the role of global
  infrastructure as an enabler for biodiversity
  analysis and understanding

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What is biodiversity?

• The Convention on Biological Diversity recognises
  three levels of biodiversity
• Genetic ( molecular) diversity
• Species ( organismal) diversity
• Ecosystem ( ecological) diversity
• There are important emergent properties at each
  level
• Biodiversity has come to be associated with the
  species and ecosystem levels

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Fundamental properties of biodiversity at all
levels

• At all levels of organization, each biological
  entity is unique
• History (differentiation, development, phylogeny)
  must be taken into account
• Every biological entity has important contingent
  relations to all other entities

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The Fundamental Role of Informatics in Biology

• Therefore the law of large numbers does not hold
  in biology, since every living thing is genuinely
  unique
• Instead of calculus, the method for manipulating
  information about statistically large numbers of
  small, independent, equivalent things ...
• Biology needs informatics, the method for
  manipulating information about large numbers of
  dependent, historically contingent, individual
  things

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There is Lots of Biological Information to
Manipulate

• (factoids from Bob Robbins, Fred Hutchinson
  Cancer Institute)
• DNA is amazingly efficient at storing information
• Typed in 10-pitch font, the 3 billion base pairs
  of the human genome would stretch gt 8000 km
• Duplicating the information storage capacity of
  all the DNA in the biosphere would need 1027
  100-Gb hard disks
• Which would fill a volume gt that of the Earth

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Information overload at the species and specimen
level

• 1.8 million known species on Earth
• And estimates of the total number of species
  range from 10 million to 100 million
• On average, each species has 5 scientific names
• Billions of specimens in the worlds natural
  history museums
• Which provide an invaluable historical and
  contemporary record of biodiversity
• One of the major roles of the Global Biodiversity
  Information Facility (GBIF) is to liberate this
  species and specimen data

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GBIFs major goals are to

• Make the worlds biodiversity data freely and
  universally available via the Internet
• Share primary scientific biodiversity data
• Especially georeferenced data
• ... Promote the development of biodiversity
  informatics around the world
• GBIF-UNESCO Chairs in Biodiversity Informatics

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What do we mean by primary biodiversity data?

• Label data on 1.5 - 3.0 billion specimens in
  natural history collections, herbaria, botanical
  gardens, etc.

• Associated notes, recordings, publications, etc.
• Observational data (e.g. bird banding data)

• These data have been amassed over 300 years
  most not digital

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Other reasons for establishing GBIF

• to partner with other biodiversity
  organisations
• to establish and promote standards, protocols
  and ontologies for biodiversity data
• Create vigour and rigour
• to help deal with the unequal distribution of
  biodiversity information

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Biodiversity and information about it are
unevenly distributed.
biodiversity hotspot
holder of large amounts of biodiversity data
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How does GBIF work ?

• Was established in 2001
• Is an open-ended network of Participants
  (currently 70)
• 42 countries/economies -- newest is Indonesia
• 28 international organisations
• E.g. Species 2000, UNEPs World Conservation
  Monitoring Centre
• Each Participant agrees to
• Share biodiversity data
• Set up a computer node(s) for accessing those
  data
• Data providers retain control of their data
• GBIF asserts no IPR over the data

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GBIF uses a web-services approach

• Uses open-source software
• Data providers make their data known through our
  Registry of Shared Biodiversity data
• www.gbif.net currently serving gt 45 million
  specimen and observation records from gt 330
  collections
• Electronic catalogue of scientific names (ECAT)
  will be available as an authority file to any
  user
• GenBank was one of the inspirations for GBIF, but
  are clear differences

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GBIF plays a critical role in e-biodiversity
GBIF
Bioinformatics Molecular Informatics
Ecoinformatics
Biodiversity Informatics
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What can you do with georeferenced biodiversity
data

• 20 years ago, Mexicos CONABIO set out to make a
  comprehensive database of Mexican plants and
  animals
• Gathered data from the worlds natural history
  collections and herbaria
• Now have an unparalleled database that can be
  used in many ways, including
• Predict effects of climate change
• Determine safe sites for field trials of
  genetically modified organisms
• Predict best places to set up new protected areas
• GBIF working to be a reverse global CONABIO

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Essence of Ecological Niche Modeling
Geographic Space
Ecological Space
ecological niche modeling
occurrence points on native distribution
Native range prediction
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Example Predicting the spread of an invasive
disease vector

• From Townsend Peterson, University of Kansas, and
  his students
• The vector the mosquito Aedes albopictus
• The disease dengue fever
• Original vector for dengue fever was eradicated
  in US in 1970
• Invasion of A. albopictus has now brought the
  disease back to the US

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Aedes albopictus
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Aedes albopictus in the USA
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Aedes albopictus US Invasion
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Aedes albopictus World Risk Map
Levine, R. R., and M. Q. Benedict. In preparation.
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Conclusions

• Species- and specimen-level biodiversity are a
  distributed, largely non-digitised but valuable
  resource
• Large-scale megascience efforts are needed to
  mobilise these data
• Global approaches can produce infrastructures
  (like GenBank and GBIF) that act as essential
  underpinnings for whole new areas of science and
  economy