VegBank and the ESA Cyber-infrastructure for Vegetation Science

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VegBank and the ESA Cyber-infrastructure for
Vegetation Science
Robert K. Peet The Ecological Society of
America Vegetation Panel
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Background
The ESA Vegetation Classification Panel was
established in 1993 with a mandate to support the
emerging U.S. Vegetation Classification.
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ESA Guidelines forvegetation classification The
ESA Vegetation Panel has developed guidelines for
vegetation classification covering requirements
for

• Vegetation field plots.
• Documentation description of floristic types.
• Submission peer review of proposed types.
• Management, citation, archiving of vegetation
  data.

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North American Vegetation Classification

• Ecological Society of America Standards, peer
  review publication.
• US Federal Geographic Data Committee US
  government standards.
• NatureServe Maintenance and distribution of the
  Classification.
• USDA ITIS Taxonomic standards for organisms

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The new community ecology Intersection of 3 data
types

• Site data climate, soils, topography, etc.
• Taxon attribute data identification, phylogeny,
  distribution, life-history, functional attributes
  ...
• Co-occurrence data attributes of individuals
  (e.g., size, age, growth rate) and taxa (e.g.,
  cover, biomass) that co-occur at a site.

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• The Vegetation Plot
• The primary unit of vegetation observation.
• Universal attributes date, location, area,
  species list, species importance
• Optional attributes environment, soil,
  disturbance
• Protocols and formats many flexible
• Available data gt 106 plot records containing gt
  5x107 species occurrence records.

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• VegBank
• VegBank a public archive for vegetation plot
  observations (http//vegbank.org).
• VegBank functions in a manner analogous to
  GenBank.
• Plot data can be deposited, discovered, viewed,
  cited, annotated, downloaded.
• Plot data can be used for documentation
  validation and reanalysis.

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VegBank strategies

• Standard exchange format established through
  IAVS
• Supports multiple protocols.
• Flexible and expandable
• Tools for data discovery, integration, and
  summarization.
• Generalizable to most types of species
  co-occurrence data.
• Incentives to participate.

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US-NVC--- Proposed data flow
NatureServe Explorer
Extraction
NatureServe Biotics
Classification Mgt.
NVC Proceedings
US-NVC Panel
Peer Review
Proposal submission
Legend
External Action
Analysis Synthesis
Internal Action
VegBank other plot archives
Software Entity
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Biodiversity data structure
Observation or Community Type
Observation type database
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Core elements of VegBank
Project
Plot
Plot Observation
Taxon / Individual Observation
Taxon Interpretation
Plot Interpretation
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Taxonomic database challengeStandardizing
organisms and communities The problem
Integration of data potentially representing
different times, places, investigators and
taxonomic standards. The traditional solution
A standard list of organisms / communities.
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One concept ofAbies lasiocarpa
USDA Plants ITIS Abies lasiocarpa var.
lasiocarpa var. arizonica
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A narrow concept of Abies lasiocarpa
Flora North America Abies lasiocarpa Abies
bifolia
Partnership with USDA plants to provide plant
concepts for data integration
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High-elevation fir trees of western US
AZ NM CO WY MT AB eBC wBC WA OR
Distribution
Abies lasiocarpa
var. arizonica
var. lasiocarpa
USDA ITIS
Abies bifolia
Abies lasiocarpa
Flora North America
A. lasiocarpa sec USDA gt A. lasiocarpa sec
FNA A. lasiocarpa sec USDA gt A. bifolia sec
FNA A. lasiocarpa v. lasiocarpa sec USDA gt A.
lasiocarpa sec FNA A. lasiocarpa v. lasiocarpa
sec USDA gtlt A. bifolia sec FNA A. lasiocarpa v.
arizonica sec USDA lt A. bifolia sec FNA
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www.vegbank.org
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VegBank Lessionsfor community participation

• Usability (testing, training)
• Incentives
• Uploads (mandates, rewards, security)
• Downloads (opportunity)
• Citation (culture)
• Tools and integration
• Connectivity

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VegBank Lessionsfor data sharing

• Embrace established standards (e.g., TDWG, EML)
• Work to establish new standards
• Content, process, exchange
• Design for idiosyncratic data
• Anticipate distributed systems and connectivity
• Leverage agency mandates
• Repositories for archiving databases for access
• Respect intellectual property
• Embargos, licenses, confidentiality

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Roles ResponsibilitiesProfessional Societies

• Set standards
• Data content and exchange format
• Data archiving and access (discrete,
  well-circumscribed elements)
• Assure quality control (peer review)
• One of the 4 functions of publication
  Certification, Validation, Awareness, Archiving

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Roles ResponsibilitiesDigital repositories and
libraries

• Archive and provide access to publications and
  data
• Institutional responsibilities to granting
  agencies. Driven by lawyers and paid for by
  overhead
• Potential security for databases

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Roles Responsibilities Granting Agencies

• Set requirements for data archiving and sharing,
  but perhaps delegate implementation to societies
• Pay for archiving and publication, directly or
  through overhead

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Roles Responsibilities Data Centers

• Maintain a portfolio of critical,
  discipline-specific database systems
• Maintain key infrastructure content
• Digital identifiers
• Common objects (e.g. taxa, publications)
• Data registries

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Roles ResponsibilitiesPublishers

• Require that specific types of data be archived
  (e.g., GenBank, VegBank)
• Imbed deep links as a form of citation for
  standard elements such as taxon concepts and data
  elements
• Provide archives for and links to supporting
  documentation

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Roles ResponsibilitiesGovernment Agencies

• Formulate federal standards and policies (in
  context of disciplinary standards).
• Mandate and implement federal standards (e.g.,
  FGDC standards)
• Assure critical infrastructure exists

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Conclusions

• VegBank is an example of a discipline-specific
  but public data archive (functions for deposit,
  discovery, withdrawal, citation, annotation)
• Standards for data content, data exchange, and
  archiving
• Standards for reference to standard elements such
  as taxonomic data
• Work with a broader community to avoid
  institutional fragility.