Vegetation databases

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Vegetation databases

• Lessons from VegBank, SEEK, TDWG, IAVS, NCEAS

Robert Peet University of North Carolina
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Biodiversity data structure
SynTaxon
Community type databases
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Topics

• Introduction
• Taxonomic data
• Observation data
• Identification
• Vegetation data standards
• VegBank
• Data archiving and sharing

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1. Taxonomic database challengeStandardizing
taxa 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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Taxonomic theory A taxon concept represents a
unique combination of a name and a reference.
Report -- name sec reference.
.
Name
Reference
Concept
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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 A. bifolia sec FNA A. lasiocarpa v.
arizonica sec USDA lt A. bifolia sec FNA
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Andropogon virginicus complex in the Carolinas 9
elemental units 17 base concepts
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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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Toward a new Atlas
http//herbarium.unc.edu/seflora/firstviewer.htm
How to integrate new sources of data??
Carya carolinae-septentrionalis, Radford et al.
1968
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Add USDA PLANTS records CVS vegetation plot
data
NCU RAB USDA CVS
Carya carolinae-septentrionalis
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But wait !There is a concept issue

• According to Radford 1968, USDA PLANTS v 4.0,
  Weakley 2005
• Carya carolinae-septentrionalis
• Carya ovata
• According to Stone 1997 in FNA
• Carya ovata var australis
• Carya ovata var. ovata

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How to merge records that may be based on
different concepts??

• Weakley 2005 Reference concepts
• Radford 1968 Concepts mapped
• NC Heritage Program Weakley concepts
• CVS Weakley concepts (mostly)
• USDA Kartesz 1999 concepts (mostly)
• NCU NCSC Nominal concepts only
• Most museum collection identifications must be
  interpreted as nominal concepts!! To do otherwise
  would be to introduce false positives.

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How have things changed? Concept relationships of
Southeastern US plants treated in different
floras.
Based on gt 50,000 concept relationshipshttp//her
barium.unc.edu/flora.htm
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Taxonomic standards

• TDWG, TCS
• SEEK, TOS
• GUIDs, DOIs, LSISs
• IPNI

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2. Observation data

• TDWG proposal
• NatureServe EOs Cornell bird data
• Basics
• Place, time, protocol, taxa, attributes
• Plots constitute a subset
• Museum collections constitute a subset

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3. Identifications

• A name in a publication could be either a concept
  or an identification.
• Identifications should include linkage to at
  least one concept, but need not be limited to a
  single concept.
• Eg. --
• lt Potentilla sec. Cronquist 1991
• Potentilla simplex sec Cronquist 1991
• Potentilla canadensis sec Cronquist 1991

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Uncertainty

• Absolutely wrong
• Understandable but wrong
• Acceptable but not typical
• Good fit
• Ideal, typical

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4. Vegetation data standards

• FGDC, ESA, IAVS
• VegBank XML
• VegetWeb
• IAVS 24-27 April _at_ NESCent
• EML
• Supports blocks of data
• No concepts, no identification uncertainty

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• 5 .VegBank
• The ESA Vegetation Panel has developed VegBank--
  a public archive for vegetation plots
  (http//vegbank.org).
• VegBank is expected to function for vegetation
  plot data in a manner analogous to GenBank.
• Primary data will be archived for future
  reference, novel synthesis, and reanalysis.
• The database architecture is compatable with most
  types of species co-occurrence data.

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VegBank data are open access

• All data placed in VegBank are available to the
  public at no charge (unless the plot contributor
  places restrictions to protect location
  information for rare and endangered species or
  private lands).
• Key data can be viewed by a simple web link.
• The following link shows information for two
  VegBank plots
• http//vegbank.org/get/std/observation/5153,5906

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Core elements of VegBank
Project
Plot
Plot Observation
Taxon / Individual Observation
Taxon Interpretation
Plot Interpretation
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http//www.vegbank.org
http//www.vegbank.org
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• T

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http//vegbank.org/get/std/observation/'VB.Ob.2601
3.027020404
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• T

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• T

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• T

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VegBank design issues

• Idiosyncratic ecologists
• Soils and environment
• Intellectual property confidentiality
• Notes
• Input and output
• Stems
• Change tracking
• Multiple name records
• Stem databases?

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New directions
Data archiving sharing

• ESA data sharing and ease of discovery
• Data sharing trends ESA, NSF, NIH
• Institutional repositories

Taxon attributes

• BiolFlor, LEDA, USDA
• TraitNet RCN