Vegetation databasesVegetation databases

Lessons from Lessons from VegBank, SEEK, VegBank, SEEK,

TDWG, IAVS, & NCEASTDWG, IAVS, & NCEAS

Robert PeetRobert Peet

University of North University of North CarolinaCarolina

Biodiversity data structure

Taxonomic databases

Plot/Inventory databases

Object databases

Observation/CollectionEvent

Object or specimen

BioTaxon

Locality

SynTaxon

Community type databases

Topics

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

1. Taxonomic database 1. Taxonomic database challenge:challenge:

Standardizing taxaStandardizing taxa

The problem:The problem: Integration of data potentially Integration of data potentially

representing different times, places, representing different times, places, investigators and taxonomic standards.investigators and taxonomic standards.

The traditional solution:The traditional solution: A standard list of organisms / A standard list of organisms /

communities.communities.

USDA Plants & ITIS

Abies lasiocarpa

var. lasiocarpa

var. arizonica

One concept ofAbies lasiocarpa

Flora North America

Abies lasiocarpa

Abies bifolia

A narrow concept of Abies lasiocarpa

Partnership with USDA plants to provide plant concepts for data integration

Name ReferenceConcept

Taxonomic theoryTaxonomic theory

A taxon concept represents a unique combination of a name and a reference.

Report -- name sec reference.

.

Relationships among concepts

allow comparisons and conversions

• Congruent, equal (=)• Includes (>)• Included in (<)• Overlaps (><)• Disjunct (|)• and others …

High-elevation fir trees of western US

AZ NM CO WY MT AB eBC wBC WA OR

var. arizonica

Abies lasiocarpa

Distribution

USDA & ITIS

Flora North America

Abies bifolia Abies lasiocarpa

A. lasiocarpa sec USDA > A. lasiocarpa sec FNA

A. lasiocarpa sec USDA > A. bifolia sec FNA

A. lasiocarpa v. lasiocarpa sec USDA > A. lasiocarpa sec FNA

A. lasiocarpa v. lasiocarpa sec USDA | A. bifolia sec FNA

A. lasiocarpa v. arizonica sec USDA < A. bifolia sec FNA

var. lasiocarpa

Andropogon virginicusAndropogon virginicus complex in the complex in the CarolinasCarolinas

9 elemental units; 17 base concepts9 elemental units; 17 base concepts

Standardized taxon lists Standardized taxon lists failfail

to allow dataset integrationto allow dataset integration

The reasons include:The reasons include:

• Taxonomic concepts are not defined (just Taxonomic concepts are not defined (just lists), lists),

• Relationships among concepts are not Relationships among concepts are not defineddefined

• The user cannot reconstruct the database as The user cannot reconstruct the database as viewed at an arbitrary time in the past, viewed at an arbitrary time in the past,

• Multiple party perspectives on taxonomic Multiple party perspectives on taxonomic concepts and names cannot be supported or concepts and names cannot be supported or reconciled.reconciled.

Toward a new AtlasToward a new Atlas

Carya carolinae-septentrionalisCarya carolinae-septentrionalis, Radford et al. 1968, Radford et al. 1968

How to How to integrate integrate new new sources of sources of data??data??

http://herbarium.unc.edu/seflora/firstviewer.htm

Carya carolinae-septentrionalisCarya carolinae-septentrionalis

NCUNCU

RABRAB

USDAUSDA

CVSCVS

Add USDA PLANTS records & Add USDA PLANTS records & CVS vegetation plot dataCVS vegetation plot data

But wait !But wait !There is a concept issueThere is a concept issue

• According to Radford 1968, USDA According to Radford 1968, USDA PLANTS v 4.0, & Weakley 2005PLANTS v 4.0, & Weakley 2005– Carya carolinae-septentrionalisCarya carolinae-septentrionalis– Carya ovataCarya ovata

• According to Stone 1997 in FNAAccording to Stone 1997 in FNA– Carya ovata var australisCarya ovata var australis– Carya ovata var. ovataCarya ovata var. ovata

How to merge records that may be based on different concepts??• Weakley 2005 – Reference conceptsWeakley 2005 – Reference concepts• Radford 1968 – Concepts mappedRadford 1968 – Concepts mapped• NC Heritage Program – Weakley conceptsNC Heritage Program – Weakley concepts• CVS – Weakley concepts (mostly)CVS – Weakley concepts (mostly)• USDA – Kartesz 1999 concepts (mostly)USDA – Kartesz 1999 concepts (mostly)• NCU & NCSC – Nominal concepts onlyNCU & NCSC – Nominal concepts only

Most museum collection identifications Most museum collection identifications must be interpreted as nominal must be interpreted as nominal concepts!! To do otherwise would be to concepts!! To do otherwise would be to introduce false positives.introduce false positives.

How have things changed?How have things changed?Concept relationships of Southeastern US Concept relationships of Southeastern US

plants treated in different floras.plants treated in different floras.

Based on > 50,000 concept Based on > 50,000 concept relationshipsrelationships

http://herbarium.unc.edu/flora.htmhttp://herbarium.unc.edu/flora.htm

Taxonomic standards

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

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

• 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. --< Potentilla sec. Cronquist 1991 +~ Potentilla simplex sec Cronquist 1991 +~ Potentilla canadensis sec Cronquist 1991

3. Identifications

1. Absolutely wrong2. Understandable but wrong3. Acceptable but not typical4. Good fit5. Ideal, typical

Uncertainty

• FGDC, ESA, IAVS• VegBank XML• VegetWeb• IAVS: 24-27 April @ NESCent• EML

– Supports blocks of data– No concepts, no identification

uncertainty

4. Vegetation data standards

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.

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

Project

PlotPlot

Observation

Taxon / Individual Observation

Taxon Interpretation

PlotInterpretation

Core elements of VegBank

http://www.vegbank.org

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http://vegbank.org/get/std/observation/'VB.Ob.26013.027020404

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

VegBank design issues

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

Data archiving & sharing

Taxon attributes

New directions

• BiolFlor, LEDA, USDA• TraitNet RCN