the vegbank taxonomic datamodel robert k. peet sponsored by: the ecological society of america us...

The VegBank taxonomic datamodel

Robert K. PeetSponsored by:

The Ecological Society of America US National Science Foundation

Produced at:The National Center for Ecological Analysis and Synthesis

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.

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.

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

Plot

PlotObservation

Taxon Observation

Taxon Interpretation

Plot Interpretation

Core elements of VegBank

Taxon Assignment

Plot Assignment

Taxonomic database challenge:Standardizing 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.

Standard lists are available for Taxa

Representative examples for higher plants in North America / US

USDA Plants http://plants.usda.govITIS http://www.itis.usda.gov NatureServe http://www.natureserve.orgBONAP Flora North America

These are intended to be checklists wherein the taxa recognized perfectly partition all plants. The lists can be dynamic.

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.

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,

Name ReferenceConcept

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 ConceptUsage

A usage represents a unique association of a concept with a

name.

• 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

Name ConceptStart, StopConceptStatusLevel, Parent

UsageStart, StopNameStatusName system

Reference

Data relationshipsVegBank taxonomic data model

Single party, dynamic perspective

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.

Name Concept

Party

UsageStart, StopNameStatusName system

StatusStart, StopConceptStatusLevel, Parent

Reference

Data relationshipsVegBank taxonomic data model

Multiple parties, dynamic perspectives

Name Concept

Party

UsageStart, StopNameStatusName system

StatusStart, StopConceptStatusLevel, Parent

Correlation

Reference

Lineage

Data relationshipsVegBank taxonomic data model

With party correlations and lineages

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.

4. State of Development

1. VegBank2. Collaborators• NatureServe Biotics4

• USDA PLANTS & ITIS

Status of VegBank• Working Prototype; open for deposit Nov 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

VegBank data contentPrototype 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 demosntration groups in depth

Concept workbench

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

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.

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

NamesCarya ovata Carya carolinae-septentrionalisCarya ovata v. ovataCarya ovata v. australis

Concepts(One shagbark)C. ovata sec Gleason ’52C. ovata sec FNA ‘97

(Southern shagbark)C. carolinae-s. sec Radford ‘68C. ovata v. australis sec FNA ‘97

(Northern shagbark)C. ovata sec Radford ‘68C. ovata (v. ovata) sec FNA ‘97

ReferencesGleason 1952. Britton & BrownRadford et al. 1968. Flora CarolinasStone 1997. Flora North America

Six shagbark hickory conceptsPossible synonyms are listed together

ITISFNA CommitteeNatureServe

Carya ovata sec Gleason 1952Carya ovata sec FNA 1997 Carya ovata sec Radford 1968Carya carolinae sec Radford 1968Carya ovata (ovata) sec FNA 1997Carya ovata australis sec FNA 1997

Party Concept

Party Concept Status Start Usage:SciName

ITIS ovata –G52 NS 1996ITIS ovata –R68 St 1996 C. ovataITIS carolinae-s –R68 St 1996 C. carolinae-sept.ITIS carolinae-s –R68 NS 2000ITIS ovata aust –FNA St 2000 C. carolinae-sept.ITIS ovata – R68 NS 2000ITIS ovata ovata –FNA St 2000 C. ovata

Status

Application of Party Perspective

Name Concept

Party

UsageStart, StopNameStatusName system

StatusStart, StopConceptStatusLevel, Parent

Correlation

Reference

Lineage

Data relationshipsVegBank taxonomic data model

With party correlations and lineages

Name Concept

SourceType: Lit, Org Correlation

Status

Reference

Core elements of the IOPI model

Is author

Assigns status