From Field to Federation:

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From Field to Federation Challenges in
Biodiversity Informatics
Portal
Provider
Provider
Provider
Public Database
Public Database
Public Database
Collection Database
Collection Database
Collection Database
John Wieczorek Museum of Vertebrate
Zoology University of California, Berkeley
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Biodiversity Informatics
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Biodiversity Informatics First Use
1992, John Whiting Canadian Biodiversity
Informatics Consortium Canadian Museum of
Nature, GPS, GIS, RDBMS, environmental economics
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Biodiversity Informatics Definition
The creation, integration, analysis, and
understanding of information regarding biological
diversity.
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Biodiversity Informatics The Journal
Mammals of the World MaNIS as an example of data
integration in a distributed network
environment Uses and Requirements of Ecological
Niche Models and Related Distributional Models A
synecological framework for systematic
conservation planning Climate Change and
Biodiversity Some Considerations in Forecasting
Shifts in Species' Potential Distributions
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Biodiversity Informatics The Prize
Ebbe Nielsen Prize
offered by the Global Biodiversity Information
Facility (GBIF)
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Pieces of the Biodiversity Informatics Puzzle
Lane, M.A. 2003. Bulletin of the American Society
for Information Science and Technology.
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Biodiversity Informatics Challenges
Digitization Mobilization Applications Integrat
ion
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Biodiversity Informatics Solutions
Digitization Mobilization Applications Integrat
ion
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Work Programmes
ECAT
DIGIT
DADI
OCB
Digitization (DIGIT)
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Biodiversity Informatics Solutions
Digitization Mobilization Applications Integrat
ion
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Digitization
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Biodiversity Informatics Solutions
Digitization Mobilization Applications Integrat
ion
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Mobilization Standards
Information Standards
Darwin Core (DwC) ABCD
Communication Protocols
DiGIR BioCASE TAPIR
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Mobilization Information Standards
Darwin Core (DwC) and Extensions ABCD - Access
to Biological Collections Databases
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What data are being shared?
Who collector, researcher What taxonomy,
observations Where geography, locality When
date observed/collected
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Mobilization Communication Protocols
DiGIR Distributed Generic Information Retrieval
TAPIR TDWG Access Protocol for Information
Retrieval
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Darwin Core (DwC)
A list of concepts (data fields) needed for
questions based on biodiversity occurrence data.
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DiGIR and TAPIR

• protocols for retrieving structured data from
  multiple, heterogeneous databases across the
  Internet
• reference implementation of both provider and
  portal software

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A Simple DistributedDatabase Network
http//www.tdwg.org/activities/tapir/
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How are data being shared?
Distributed Data Network
Provider Software
Provider Software
Provider Software
Public Database Local Copy
Public Database Hosted Copy
Occurrence Database
Occurrence Database
Occurrence Database
Local Public Repository
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How are data being shared?
Distributed Data Network
Provider Software
Provider Software
Provider Software
Public Database Local Copy
Public Database Hosted Copy
Occurrence Database
Occurrence Database
Occurrence Database
Local Direct Access
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How are data being shared?
Distributed Data Network
Provider Software
Provider Software
Provider Software
Public Database Local Copy
Public Database Hosted Copy
Occurrence Database
Occurrence Database
Occurrence Database
Hosted Public Repository
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Biodiversity Informatics Challenges
Digitization Mobilization Applications Integrat
ion
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Applications Services
Taxonomic uBio
Geospatial BioGeomancer
Niche Modeling openModeller
Conservation ReBioMa
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BioGeomancer Geospatial Digitization
Data Validation
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Biodiversity Informatics Challenges
Digitization Mobilization Applications Integrat
ion
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Integration Species Pages
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AmphibiaWeb Species Descriptions
Literature, Media, etc.
Species Descriptive Data
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Integration Workflows
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Integration Collaborative Distributed Databases
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Case StudyA Network of Mammal Collections
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If you talk to a man in a language he
understands, that goes to his head. If you
talk to him in his own language, that goes to
his heart. Nelson Mandela
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Challenge Engender provider participation.

• Solution Gain the trust of collections.
• begin with collections that have no doubts
• lead by example
• preserve the integrity of the original data
• concede control to data providers
• promote the value of data providers

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Challenge Promote the importance of providers

• Solution Engage users, improve collections.
• preserve the identity of the data source
• accommodate the dynamic nature of data
• provide data validation tools
• provide data feedback mechanisms

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Challenge Maintain provider interest.

• Solution Increase value of collections
• through participation.
• increase visibility
• liberate resources
• enable providers to track data access
• provide tools for collection improvement
• provide tools to ask interesting questions

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Relatively well-known and stable taxonomy.
A Network of Mammal Collections
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Relatively well-known and stable taxonomy.
A Network of Mammal Collections
Willing community with a shared vision.
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Distributed Data Network Example
Distributed Data Network
Provider Software
Provider Software
Provider Software
Public Database Local Copy
Public Database Hosted Copy
Occurrence Database
Occurrence Database
Occurrence Database
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MaNIS Query
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MaNIS Query Summary
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MaNIS Result Map
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Global Coverage, Mammals, Specimens only
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MaNIS Data Accessibility, Georeferencing
30 institutions 2M specimens
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HerpNet Synonym Lookup
43 institutions 4.6M specimens
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ORNIS Data Validation
Data Validation
36 institutions 37M specimens and observations
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Museums Participating in MaNIS/HerpNET/ORNIS
(VertNet)
Multiple projects ORNIS HerpNET MaNIS
86 institutions 74 in North America, 12
others 70 available now on MHO for searching
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Biodiversity Informatics Current status
Digitization progress, bottle
necks Mobilization have solutions Applications
more every day Integration issues
(persistence, performance, management, IPR)
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Web Portal
John Wieczorek Lead Developer, REBIOMA Museum of
Vertebrate Zoology University of California,
Berkeley
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Case Study Network of Madagascar Occurrences
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Global Objective
To serve up-to-date, validated biodiversity
occurrence data for the conservation community in
Madagascar.
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Madagascar, All Taxa, All Occurrences
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Global Objective
To serve up-to-date, validated biodiversity
occurrence data for the conservation community in
Madagascar.
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What data are being shared?
Who collector, observer What taxon,
observation Where collection, locality When
date observed/collected
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Darwin Core (DwC)
A list of concepts (data fields) needed for
questions based on biodiversity occurrence data.
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Darwin Core (DwC)
Who?
GlobalUniqueIdentifier BasisOfRecord DateLastModif
ied ScientificName IdentifiedBy Collectors Collect
ingMethod Sex LifeStage Attributes IndividualCount
HigherGeography Locality DecimalLatitude DecimalLo
ngitude GeodeticDatum MaximumUncertainty Georefere
nceProtocol GeoreferenceSources EarliestDateCollec
ted LatestDateCollected InformationWithheld
http//wiki.tdwg.org/DarwinCore/
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Darwin Core (DwC)
What?
GlobalUniqueIdentifier BasisOfRecord DateLastModif
ied ScientificName IdentifiedBy Collectors Collect
ingMethod Sex LifeStage Attributes IndividualCount
HigherGeography Locality DecimalLatitude DecimalLo
ngitude GeodeticDatum MaximumUncertainty Georefere
nceProtocol GeoreferenceSources EarliestDateCollec
ted LatestDateCollected InformationWithheld
http//wiki.tdwg.org/DarwinCore/
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Darwin Core (DwC)
Where?
GlobalUniqueIdentifier BasisOfRecord DateLastModif
ied ScientificName IdentifiedBy Collectors Collect
ingMethod Sex LifeStage Attributes IndividualCount
HigherGeography Locality DecimalLatitude DecimalLo
ngitude GeodeticDatum MaximumUncertainty Georefere
nceProtocol GeoreferenceSources EarliestDateCollec
ted LatestDateCollected InformationWithheld
http//wiki.tdwg.org/DarwinCore/
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Darwin Core (DwC)
When?
GlobalUniqueIdentifier BasisOfRecord DateLastModif
ied ScientificName IdentifiedBy Collectors Collect
ingMethod Sex LifeStage Attributes IndividualCount
HigherGeography Locality DecimalLatitude DecimalLo
ngitude GeodeticDatum MaximumUncertainty Georefere
nceProtocol GeoreferenceSources EarliestDateCollec
ted LatestDateCollected InformationWithheld
http//wiki.tdwg.org/DarwinCore/
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Darwin Core (DwC)
Details
GlobalUniqueIdentifier BasisOfRecord DateLastModif
ied ScientificName IdentifiedBy Collectors Collect
ingMethod Sex LifeStage Attributes IndividualCount
HigherGeography Locality DecimalLatitude DecimalLo
ngitude GeodeticDatum MaximumUncertainty Georefere
nceProtocol GeoreferenceSources EarliestDateCollec
ted LatestDateCollected InformationWithheld
http//wiki.tdwg.org/DarwinCore/
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Darwin Core (DwC)
Record Metadata
GlobalUniqueIdentifier BasisOfRecord DateLastModif
ied ScientificName IdentifiedBy Collectors Collect
ingMethod Sex LifeStage Attributes IndividualCount
HigherGeography Locality DecimalLatitude DecimalLo
ngitude GeodeticDatum MaximumUncertainty Georefere
nceProtocol GeoreferenceSources EarliestDateCollec
ted LatestDateCollected InformationWithheld
http//wiki.tdwg.org/DarwinCore/
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A Simple DistributedDatabase Network
http//www.tdwg.org/activities/tapir/
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Conservation Applications
Models Database
User Queries, Visualization
Automated Modeling
Validated Occurrence Data
Human Expert Review
Automated Validation
Distributed Data Network
Occurrence Data
Occurrence Data
Occurrence Data
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Global Objective
To serve up-to-date, validated biodiversity
occurrence data for the conservation community in
Madagascar.
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Conservation Applications
Models Database
User Queries, Visualization
Automated Modeling
Validated Occurrence Data
Human Expert Review
Automated Validation
Distributed Data Network
Occurrence Data
Occurrence Data
Occurrence Data
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Automated Data Validation
Taxonomy Digital Taxonomic Thesaurus Geography
BioGeomancer
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Conservation Applications
Models Database
User Queries, Visualization
Automated Modeling
Validated Occurrence Data
Human Expert Review
Automated Validation
Distributed Data Network
Occurrence Data
Occurrence Data
Occurrence Data
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Conservation Applications
Models Database
User Queries, Visualization
Automated Modeling
Validated Occurrence Data
Human Expert Review
Automated Validation
Distributed Data Network
Occurrence Data
Occurrence Data
Occurrence Data
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Conservation Applications
Models Database
User Queries, Visualization
Automated Modeling
Validated Occurrence Data
Human Expert Review
Automated Validation
Distributed Data Network
Occurrence Data
Occurrence Data
Occurrence Data
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Conservation Applications
Models Database
User Queries, Visualization
Automated Modeling
Validated Occurrence Data
Human Expert Review
Automated Validation
Distributed Data Network
Occurrence Data
Occurrence Data
Occurrence Data
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Human Expert Review
Taxonomic Review Board Experts notified of new
records Experts flag suspect records
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Conservation Applications
Models Database
User Queries, Visualization
Automated Modeling
Validated Occurrence Data
Human Expert Review
Automated Validation
Distributed Data Network
Occurrence Data
Occurrence Data
Occurrence Data
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Conservation Applications
Models Database
User Queries, Visualization
Automated Modeling
Validated Occurrence Data
Human Expert Review
Automated Validation
Distributed Data Network
Occurrence Data
Occurrence Data
Occurrence Data
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Global Objective
To serve up-to-date, validated biodiversity
occurrence data for the conservation community in
Madagascar.
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Conservation Applications
Models Database
User Queries, Visualization
Automated Modeling
Validated Occurrence Data
Human Expert Review
Automated Validation
Distributed Data Network
Occurrence Data
Occurrence Data
Occurrence Data
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REBIOMA Result Map
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Conservation Applications
Models Database
User Queries, Visualization
Automated Modeling
Validated Occurrence Data
Human Expert Review
Automated Validation
Distributed Data Network
Occurrence Data
Occurrence Data
Occurrence Data
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Automated Modeling
Linked to environmental data Choice of model
algorithms Choice of scenarios Update models as
data change
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Conservation Applications
Models Database
User Queries, Visualization
Automated Modeling
Validated Occurrence Data
Human Expert Review
Automated Validation
Distributed Data Network
Occurrence Data
Occurrence Data
Occurrence Data
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User Queries,Visualization
Heteropsis parva
2000
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Conservation Applications
Models Database
User Queries, Visualization
Automated Modeling
Validated Occurrence Data
Human Expert Review
Automated Validation
Distributed Data Network
Occurrence Data
Occurrence Data
Occurrence Data
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Conservation Applications
Conservation Planning Protected Area
Design Planning for Climate Change Monitoring
Biodiversity Business Ecotourism Development
Plans Environmental Impact Statement Science Bi
ogeographic Analyses Identifying New Survey Areas
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