The Role of Online Biodiversity Databases

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The Role of Online Biodiversity Databases

• David E. Schindel, Executive Secretary
• National Museum of Natural History
• Smithsonian Institution
• SchindelD_at_si.edu http//www.barcoding.si.edu
• 202/633-0812 fax [phone]

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Encyclopedia of Life Taxonomic revisions, biotic
surveys Published species descriptions Public
database records Description/revision not yet
published Data not yet released Not yet
described Not yet in specimen catalog Not yet
examined Not yet curated Not yet collected
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Producers and Consumers of Taxonomy

• Taxonomists are both producers and consumers
• Produces tendency for taxonomy to be
  interest-driven
• Funding for taxonomy has been driven largely by
  basic research agencies
• Growth in funding will have to come from new
  sources

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Users
Taxonomists
Applied users
Funding sources
Support
Results
Providers
Taxonomists
What are the Returns on Investment for

• Description of new species?
• Phylogenetic analyses?
• Taxonomic revisions?
• Biotic inventories?

• Identification services?
• Collection curation?
• Creation of public databases?
• Education and outreach?

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TreeBase

• Assembling the Tree of Life
• Seven annual NSF competitions
• 40 project awards to US universities, museums and
  herbaria
• International participation
• 3322 authors, 1783 studies
• 4878 trees, 84907 taxa

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The Encyclopedia of Life (EOL)

• An online encyclopedia composed of 1.8 million
  web sites
• One for each known species
• EOL is developing two aspects of the original
  GBIF work programme
• SpeciesBank--assemblage of all kinds of
  information about species
• Digital library of biodiversity literature

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Components of theEncyclopedia of Life (EOL)

• Each site consists of several components
• Species page for the general public
• Draft pages assembled via mashup technology
• Drafts authenticated by experts (curators)
  using controlled wikis
• Information protected from being changed by
  anyone except the curators
• But anyone can comment on the information and or
  suggest things to add
• Curators will examine these suggestions and may
  move some of the information to the protected part

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Uses of Integrated Data

• Research tool
• GIS data layer for interdisciplinary research
• Predictive tool
• Spread of invasive species
• Undersampled areas relative to predicted
  biodiversity
• Anomalies relative to environmental data
• Analysis of biodiversity responses to climate
  change (back-casting to archival data)

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GEOSS Mission for Biodiversity Understanding,
monitoring and conserving biodiversity

• Issues in this area include the condition and
  extent of ecosystems, distribution and status of
  species, and genetic diversity in key
  populations.
• Implementing GEOSS will unify many disparate
  biodiversity observing systems and create a
  platform to integrate biodiversity data with
  other types of information.
• Taxonomic and spatial gaps will be filled, and
  the pace of information collection and
  dissemination will be increased.

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GEOSS Biodiversity Work Packages

• Capturing Historical Biodiversity Data (Led by
  GBIF)
• Biodiversity Observation Network (DIVERSITAS
  International)
• Invasive Species Monitoring System (USA)

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Example

• Illustration of Predictive Capacity of Ecological
  Niche Modeling regarding Species Invasions

A. Townsend Peterson University of Kansas
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Species Invasion
Accessibility
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Species Invasion
Accessibility
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Aedes albopictus

• Known as the Asian Tiger Mosquito
• Invader fastest spreading mosquito in the world
• Aggressive daytime biter and pest
• Known to transmit Dengue, La Crosse, St. Louis,
  Eastern Equine, Ross River, Rift Valley, and West
  Nile Viruses

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Aedes albopictus
Present predicted distribution, native range in
Asia
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Aedes albopictusUSA invasion
Projected Asian niche into USA present to create
invasion risk-map. How well did GARP perform...
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Aedes albopictus USA invasion
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Aedes albopictus world risk-map
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Example

• Historic museum collections and climate change

H. M. Kharouba J. T. Kerr Canadian Facility for
Ecoinformatics Research Department of Biology,
University of Ottawa
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Example

• Mexicos use of biodiversity data for resource
  management

Jorge Soberon M. CONABIO and University of Kansas
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Localities of Plant Specimens in different
Herbaria
TEX (Universidad de Texas en Austin)
UADY (University de Yucatan)
CIDIIR (Centro de Investigaciones Científicas de
Durango)
ARIZ (University de Arizona)
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Localities of Plant Specimens in different
Herbaria
XAL (Instituto de Ecología de Xalapa)
CAS (California Academy of Sciences)
CICY (Centro de Investigaciones Científicas de
Yucatan)
MEXU (Universidad Nacional Autónoma de México)
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Pool the data together...
The Virtual Herbarium of Mexico 700,000 registers
from 25 Herbaria In Mexico and the United States.
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The Biodiversity World Information Network
(REMIB)

• 28 nodes in six different countries
• 104 collections, more than 6.3 million data
  records
• DIGIR compliant, . Soon it will join the GBIF
  network

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Growth of the database
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I. The Cactus Moth Cactoblastis cactorum

• Devours every single species of prickley-pear
  that has been tried.
• In the US and Mexico there are more than 90
  species of Platyopuntia, many endangered, vital
  componente of arid ecosystems.
• In Mexico, Opuntia is the 10th product of
  agricultural importance

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Cactoblastis cactorum
Data points obtained from the NMNH, USA
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Climate surface obtained by Floramap (12 layers)
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Platyopuntia localities MNHSD, IBUNAM, ENCB,
MOBOT, NMNH, UAH
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Predicted number of species of Platyopuntia
Opuntia lagunae Fotografías de la planta y el
fruto de Jon Rebman Fotografía de las flores de
George Lindsay http//www.oceanoasis.org/fieldgui
de/opun-lag-sp.html
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Vulnerable areas to Cactoblastis (right climate
and right food)
Red isolines High similarity to climate in the
original Cactoblastis cactorum sites.
Blue regions Richness of species of
Platyopuntia.
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Selecting areas for new explorations

• The biological inventory of Mexico is far from
  finished
• Where to invest scarce resources?
• How much to invest?

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Non-agricultural, non-cattle and non-urban land
use
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Localities with plant species belonging to arid
vegetation
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An overlay of natural vegetation and arid
species
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Natural vegetation, arid species and roads
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Areas selected for floristic expeditions
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Stopping rules

• Accumulation curves are used.
• Negotiation with scientists are based on them.
• Formal stopping rules, based on decision theory
  are being developed.

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Monthly accesses to Conabios Web Page
Number of Hits in log10 Scale
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Monthly records provided to users through Remib
Numbero of records in Log10 Scale
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Distributions of type of user
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DNA BarcodesA Key Variable for Biodiversity
Informatics
Museum databases of associated data
Databases of species occurrences and distribution
(OBIS)
Authority files of taxonomic names
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Adoption by Regulators

• US Federal Aviation Administration All Birds
• US Environmental Protection Agency
• 250K pilot test, water quality bioassessment
• US Food and Drug Administration
• Reference barcodes for commercial fish
• FISH-BOL and fish regulatory agencies
• CBOL workshop in Taipei, September 2007
• FAO International Plant Protection Commission
• Proposal for Diagnostic Protocols for fruit flies
  
• CITES, National Agencies, Conservation NGOs
• International Steering Committee, identifying
  pilot projects

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Long-term data curationof BARCODE records
Data records assembled in BOLD
Community feedback
Compliant with BARCODE standards?
Update records (audit trail of species names
retained)
Data records released on INSDC
IDs consistent with other records?
GenBank adds BARCODE flag
CBOL control of BARCODE flag
Data records published in BOLD
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An Invitation

• International Conference on Biodiversity
  Informatics
• Spring 2009
• Convened by Encyclopedia of Life
• Co-organized by GBIF, TDWG, OBIS, EDIT, CBOL
• Showcase products, capabilities, uses
• Engage providers and users
• Discuss the next generation of efforts

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BARCODE Records in INSDC
Voucher Specimen
Species Name
Specimen Metadata
GeoreferenceHabitatCharacter setsImagesBehavio
rOther genes
Indices - Catalogue of Life -
GBIF/ECAT Nomenclators - Zoo Record - IPNI -
NameBank Publication links - New species
Barcode Sequence
Trace files
Primers
Other Databases
Literature(link to content or citation)
PhylogeneticPopn GeneticsEcological
Databases - Provisional sp.
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Structured Link to Vouchers
Institutional Acronym
Collection Code
Catalog ID


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Structured Link to Vouchers


NHM
LEP
123456


personal
DHJanzen
SRNP12345
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CBOL/GBIF/NCBI Registry of Biorepositories
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Link from GenBank to Museums
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Linkout from GenBank to Taxonomy