VegBank and the ESA Cyber-infrastructure for Vegetation Science

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VegBank and the ESA Cyber-infrastructure for
Vegetation Science
R.K. Peet, Don Faber-Langendoen, Michael
Jennings, Michael Lee Ecological Society of
America Vegetation Panel
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We are pleased to acknowledge the support and
cooperation of
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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, cited, discovered,
  referenced, viewed, shared, annotated, updated,
  downloaded.
• Plot data can be used for documentation
  validation and reanalysis.

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VegBank strategies

• Standard exchange format
• 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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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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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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www.vegbank.org
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Requirements exchange standards for plot data

• Standard data structure (draft by VegBank team)
  in implementation.
• XML Schema (draft by VegBank team, modification
  proposed by the German team).
• International standards and compatibility (Active
  Working Group within the International
  Association for Vegetation Science).

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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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• Standardized taxon lists fail
• to allow dataset integration
• The reasons include
• Taxonomic concepts are not defined (just lists),
• Relationships among concepts are not defined
• The user cannot reconstruct the database as
  viewed at an arbitrary time in the past,
• Multiple party perspectives on taxonomic concepts
  and names cannot be supported or reconciled.

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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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Relationships among conceptsallow comparisons
and conversions

• Congruent, equal ()
• Includes (gt)
• Included in (lt)
• Overlaps (gtlt)
• Disjunct ()
• and others

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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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• Party Perspective
• VegBank supports selection of Party perspective
  at an arbitrary date by tracking
• Status Standard, Nonstandard, Undetermined
• Correlation with other concepts Equal,
  Greater, Lesser, Overlap, Undetermined
• Start Stop dates.

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Taxon/community interpretationDocumenting the
users informal working concept

• Multiple concepts can be linked simultaneously by
  concept relationship notation.
• Degree of fit for each can be indicated by fuzzy
  logic notation
• Subsequent interpretations supported.

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Scale for concept fit

• 1 Absolutely wrong. Unambiguously incorrect.
• 2 Understandable but wrong. Doesn't fit but is
  close. Not a good answer.
• 3 Reasonable or acceptable answer
• 4 Good answer. Unambiguously correct
• 5 Absolutely correct. Perfect fit.

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Documenting identifications

• Always show the concept not just the name!!
• Relationships added for identification
• Indicates identification
• (or aff.) Indicates similarity
• gt,lt,gtlt, As with concept relationships
• Example of complex identification
• lt Potentilla sec. Cronquist 1991
• Potentilla simplex sec Cronquist 1991
• Potentilla canadensis sec Cronquist 1991

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Conclusion The new community ecology depends on
standards and connectivity

• Standard for co-occurrence data
• Standards for data exchange
• Public data archives (functions for deposit,
  discovery, withdrawal, citation, annotation)
• Standards for data archiving
• Standards for reference to taxonomic data