The VegBank

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The VegBank taxonomic datamodel Robert K. Peet
Sponsored by The Ecological Society of America
US National Science Foundation Produced at The
National Center for Ecological Analysis and
Synthesis
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1. The Intended User Groups

• Specifically
• Ecologists who record species composition of
  vegetation.
• Ecologists who use records of vegetation
  composition.
• In general
• Creators and distributors of data wherein
  organisms need to be labeled.
• Users and consolidators of data wherein organisms
  are labeled.

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• VegBank
• The ESA Vegetation Panel is currently
  developingVegBank (www.vegbank.org) as a public
  vegetation plot archive
• VegBank is expected to function for vegetation
  plot data in a manner analogous to GenBank.
• Primary data will be deposited for reference,
  novel synthesis, and reanalysis, particularly for
  classification.

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2. Intended Functionality

• Ecologists, like most users of organism names,
  care about how to label organisms, and how to
  interpret labels others have placed on organisms.
• We wish for ease in combining datasets.
• We abhor name changes and ambiguity

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Plot
Core elements of VegBank
Plot Observation
Taxon Observation
Taxon Interpretation
Plot Interpretation
Taxon Assignment
Plot Assignment
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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 checklists of organisms.
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Standard lists are available for
Taxa Representative examples for higher plants
in North America / US USDA Plants
http//plants.usda.gov ITIS
http//www.itis.usda.gov NatureServe http//ww
w.natureserve.org BONAP Flora North
America These are intended to be checklists
wherein the taxa recognized perfectly partition
all plants. The lists can be dynamic.
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• Most taxon checklists fail to allow effective
  dataset integration
• The reasons include
• The user cannot reconstruct the database as
  viewed at an arbitrary time in the past,
• Taxonomic concepts are not defined (just lists),
• Multiple party perspectives on taxonomic concepts
  and names cannot be supported or reconciled.

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Intended functionality

• Organisms are labeled by reference to concept
  (name-reference combination),
• Party perspectives on concepts and names can be
  dynamic,
• User can select which party perspective to
  follow,
• Party perspectives are perfectly archived,
• Different names systems are supported,
• Enhanced stability in recognized concepts by
  separating name assignment and rank from concept,

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3. Taxonomic theory A taxon concept represents a
unique combination of a name and a
reference Taxon concept roughly equivalent to
Potential taxon assertion
Name
Reference
Concept
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A usage represents a unique association of a
concept with a name.
Name
Concept
Usage

• Usage does not appear in the IOPI model, but
  instead is a special case of concept
• Usage can be used to apply multiple name systems
  to a concept
• Desirable for stability in recognized concepts

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Six shagbark hickory concepts Possible synonyms
are listed together
Names Carya ovata Carya carolinae-septentrionalis
Carya ovata v. ovata Carya ovata v. australis
Concepts (One shagbark)C. ovata sec Gleason
52 C. ovata sec FNA 97 (Southern shagbark)C.
carolinae-s. sec Radford 68C. ovata v.
australis sec FNA 97 (Northern shagbark) C.
ovata sec Radford 68 C. ovata (v. ovata) sec FNA
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References Gleason 1952. Britton Brown Radford
et al. 1968. Flora Carolinas Stone 1997. Flora
North America
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Data relationshipsVegBank taxonomic data model
Name
Concept Start, Stop ConceptStatus Level, Parent
Usage Start, Stop NameStatus Name system
Reference
Single party, dynamic perspective
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• Party Perspective
• The Party Perspective on a concept includes
• Status Standard, Nonstandard, Undetermined
• Correlation with other concepts Equal,
  Greater, Lesser, Overlap, Undetermined.
• Lineage Predecessor and Successor concepts.
• Start Stop dates.

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Application of Party Perspective
Party
Concept
ITIS FNA CommitteeNatureServe
Carya ovata sec Gleason 1952 Carya ovata sec FNA
1997 Carya ovata sec Radford 1968 Carya
carolinae sec Radford 1968 Carya ovata (ovata)
sec FNA 1997 Carya ovata australis sec FNA 1997
Status
Party Concept Status Start UsageSciName ITIS
ovata G52 NS 1996 ITIS ovata R68
St 1996 C. ovata ITIS carolinae-s R68
St 1996 C. carolinae-sept. ITIS carolinae-s R68
NS 2000 ITIS ovata aust FNA St 2000 C.
carolinae-sept. ITIS ovata R68
NS 2000 ITIS ovata ovata FNA St 2000 C. ovata
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Data relationshipsVegBank taxonomic data model
Name
Concept
Usage Start, Stop NameStatus Name system
Status Start, Stop ConceptStatus Level, Parent
Party
Reference
Multiple parties, dynamic perspectives
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Data relationshipsVegBank taxonomic data model
Name
Concept
Usage Start, Stop NameStatus Name system
Correlation
Party
Status Start, Stop ConceptStatus Level, Parent
Lineage
Reference
With party correlations and lineages
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• Primary differences between the VegBank and IOPI
  models
• The IOPI model is optimized for
• describing taxonomic decisions represented in
  literature.
• The VB model is optimized for
• stability in accepted concepts (super concepts),
• support of multiple dynamic party perspectives,
• support of multiple name systems.

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Core elements of the IOPI model
Name
Concept
Is author
SourceType Lit, Org
Correlation
Reference
Assigns status
Status
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4. State of Development

• 1. VegBank
• 2. Collaborators
• NatureServe Biotics4
• USDA PLANTS ITIS

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Status of VegBank

• Working Prototype open for deposit Jan 1
• Production version July 2004
• Access version on VegBranch today
• Efficient data exchange by July 2004
• Functionality mandated in draft FGDC standards
• IAVS working group established for data exchange
  standards established 2003

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VegBank data content

• Prototype populated with USDA PLANTS lists and
  synonyms weak concepts.
• Contract with NatureServe and John Kartesz
• Develop reference-based concepts for 14000 by
  July 2004 of the 32000 vascular plant taxa at
  species level and below
• List of unambiguous taxa (6000?)
• Treatment of most ambiguous taxa
• Demonstration mapping to FNA
• A few demonstration groups in depth

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Concept workbench

• Concept workbench for both plant concepts and
  community concepts is planned.

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NatureServe Biotics 4

• In production
• Loading the same initial concepts
• Already using concepts where strong differences
  between state programs
• Routine data exchange with Vegbank under
  development.

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PLANTS ITIS

• Frequent communication during redesign.
• Design documents for conversion to concept-based
  system complete
• Collaboration to assure that the concepts we
  develop will be employed in the new system
• Uncertainties about funding