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The Role of Online Biodiversity Databases. David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution SchindelD@si.edu ; http://www.barcoding.si.edu 202/633-0812; fax 202/633-2938. Encyclopedia of Life Taxonomic revisions, biotic surveys

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the role of online biodiversity databases

The Role of Online Biodiversity Databases

David E. Schindel, Executive Secretary

National Museum of Natural History

Smithsonian Institution

SchindelD@si.edu;http://www.barcoding.si.edu

202/633-0812; fax 202/633-2938

slide2

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

producers and consumers of taxonomy
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
slide4

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?
treebase
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
the encyclopedia of life eol
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
components of the encyclopedia of life eol
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
uses of integrated data
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)
geoss mission for biodiversity understanding monitoring and conserving biodiversity
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.

geoss biodiversity work packages
GEOSS Biodiversity Work Packages
  • Capturing Historical Biodiversity Data(Led by GBIF)
  • Biodiversity Observation Network(DIVERSITAS International)
  • Invasive Species Monitoring System(USA)
example

Example

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

A. Townsend Peterson

University of Kansas

slide24

Abiotic niche

Accessibility

Biotic interactions

Species Invasion

Accessibility

slide25

Abiotic niche

Biotic interactions

Species Invasion

Accessibility

aedes albopictus
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
aedes albopictus1
Aedes albopictus

Present predicted distribution, native range in Asia

aedes albopictus usa invasion
Aedes albopictus:USA invasion

Projected Asian niche into USA present to create invasion risk-map. How well did GARP perform...

example1

Example

Historic museum collections and climate change

H. M. Kharouba & J. T. Kerr

Canadian Facility for Ecoinformatics Research

Department of Biology, University of Ottawa

example2

Example

Mexico’s use of biodiversity data for resource management

Jorge Soberon M.

CONABIO and University of Kansas

slide34

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)

slide35

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)

slide36

Pool the data together...

The Virtual Herbarium of Mexico

700,000 registers from 25 Herbaria

In Mexico and the United States.

slide37

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
i the cactus moth cactoblastis cactorum
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
slide40

Cactoblastis cactorum

Data points obtained from

the NMNH, USA

slide41

Climate surface obtained by

Floramap (12 layers)

slide43

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/fieldguide/opun-lag-sp.html

slide44

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.

selecting areas for new explorations
Selecting areas for new explorations
  • The biological inventory of Mexico is far from finished
  • Where to invest scarce resources?
  • How much to invest?
stopping rules
Stopping rules
  • Accumulation curves are used.
  • Negotiation with scientists are based on them.
  • Formal “stopping rules”, based on decision theory are being developed.
slide52

Monthly accesses to Conabio´s Web Page

Number of Hits in log10 Scale

slide53

Monthly records provided to users through Remib

Numbero of records in Log10 Scale

dna barcodes a key variable for biodiversity informatics
DNA Barcodes:A Key Variable for Biodiversity Informatics

Museum databases of associated data

Databases of species occurrences and distribution (OBIS)

Authority files of taxonomic names

adoption by regulators
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
long term data curation of barcode records
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

an invitation
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
slide60

BARCODE Records in INSDC

Specimen Metadata

Voucher Specimen

Species Name

GeoreferenceHabitatCharacter setsImagesBehaviorOther 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)

PhylogeneticPop’n GeneticsEcological

Databases - Provisional sp.

structured link to vouchers
Structured Link to Vouchers

Institutional Acronym

Collection Code

Catalog ID

:

:

structured link to vouchers1
Structured Link to Vouchers

:

:

NHM

LEP

123456

:

:

personal

DHJanzen

SRNP12345