The challenge of biodiversity:Plot, organism, and taxonomic databases

Robert K. PeetUniversity of North Carolina

The National Plots Database Committee

John HarrisNCEAS

A case study: VegBank - The ESA Vegetation Plot Archive

Project supported by:National Center for Ecological Analysis & SynthesisU.S. National Science FoundationUSGS-BRD Gap Analysis ProgramABI / The Nature Conservancy

Project organized and directed by:Robert K. Peet, University of North CarolinaMarilyn Walker, USDA Forest Service & U. AlaskaDennis Grossman, The Nature Conservancy / ABIMichael Jennings, USGS-BRD & UCSB

Observation/CollectionEvent

Object or specimen

Taxon

Locality

Biodiversity data structure

Taxonomic databases

Plot/Inventory databases

Specimen databases

Web-interface

Veg Classification Database

VegBank

Proposal

Raw Plot Data

Vegetation/Biodiversity

Information flow in the US National Vegetation Classification

TaxonomicDatabase

Proposal

Taxonomic database challengeThe problem:

Integration of data potentially representing different times, places, investigators and taxonomic standards

The traditional solution: A standard list of kinds of organisms.

There exist numerous compilations of organism names.

For example:

• Species 2000http://www.sp2000.org/default.html(Composed of 18 participant databases)

• All Species http://www.all-species.org

• ITIS http://www.itis.usda.gov/(The US government standard list, plus Canada & Mexico)

• Index to organism nameshttp://www.biosis.org.uk/triton/indexfm.htm

Taxon-specific standard lists are available. Representative examples for higher plants include:North America / US

USDA Plants http://plants.usda.gov/ITIS http://www.itis.usda.gov/ NatureServe http://www.natureserve.org

WorldIPNI International Plant Names Checklist

http://www.ipni.org/IOPI Global Plant Checklist

http://www.bgbm.fu-berlin.de/IOPI/GPC/

Most standardized taxon lists fail to allow effective integration of datasets.

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.

Current standards• Biological organisms are named following international rules of nomenclature.

• Database standards are being developed by TDWG, GBIF, IOPI, etc.

• Metadata standards have been developed. For example, the Darwin Core is a profile describing the minimum set of standards for search and retrieval of natural history collections and observation databases. (http://tsadev.speciesanalyst.net/DarwinCore/)

Carya ovata(Miller)K. Koch

Carya carolinae-sept.(Ashe) Engler & Graebner

Carya ovata(Miller)K. Koch

sec. Gleason 1952 sec. Radford et al. 1968

Three concepts of shagbark hickorySplitting one species into two illustrates the ambiguity often associated with scientific names. If you encounter the name “Carya ovata (Miller) K. Koch” in a database, you cannot be sure which of two meanings applies.

R. plumosa

R. plumosa

R plumosav. intermedia

R. plumosav. plumosa

R. intermedia

R. plumosav. interrupta R. pineticola

R. plumosa R. sp. 1

R. plumosav. plumosa

R. plumosav. pineticola

Multiple concepts of Rhynchospora plumosa s.l.

Elliot 1816

Gray 1834

Kral 1998

Peet 2002?

1

2

3

Chapman1860

Name ReferenceAssertion

An assertion represents a unique combination of a name and a reference

“Assertion” is equivalent to “Potential taxon” & “taxonomic concept”

NamesCarya ovata Carya carolinae-septentrionalisCarya ovata v. australis

Assertions(One shagbark)C. ovata sec Gleason ’52C. ovata (sl) 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 assertionsPossible taxonomic synonyms are listed together

Name AssertionUsage

A usage represents a unique combination of an assertion and a name.

Usages can be used to track nomenclatural synonyms

1. Carya ovata2. C. carolinae3. C. ovata var. australis

A. ovata sec. GleasonB. ovata sl sec. FNAC. carolinae sec. RadfordD. ovata australis sec. FNAE. ovata sec. RadfordF. ovata ovata sec. FNA

1-F OK2-D OK3-D Syn

Names AssertionsITIS Usage

ITIS likely views the linkage of the assertion “Carya ovata var. australis sec. FNA 1997” with the name “Carya ovata var. australis” as a nomenclatural synonym.

Name AssertionUsage

A usage (name assignment) and assertion (taxon concept) can be

combined in a single model

Reference

Party Perspective

The Party Perspective on an Assertion includes:

•Status – Standard, Nonstandard, Undetermined

• Correlation with other assertions – Equal, Greater, Lesser, Overlap,

Undetermined.

•Lineage – Predecessor and Successor assertions.

•Start & Stop dates.

ITISFNA CommitteeNatureServeUSDA Plants

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

Party Assertion

Party Assertion Status Start Name

ITIS ovata – G52 NS 1996ITIS ovata – R68 St 1996 ovataITIS carolinae – R68 St 1996 carolinaeITIS carolinae – R68 NS 2000ITIS ovata aust – FNA St 2000 carolinaeITIS ovata – R68 NS 2000ITIS ovata ovata – FNA St 2000 ovata

Status

VegBank taxonomic data model

Concept-based taxonomy is coming! • All organisms/specimens in databases should be identified by linkage to an assertion = name and reference!

• Various standards are being developed by FGDC, TDWG, IOPI, GBIF, etc.

• Most major databases are working toward inclusion of assertions (e.g. ITIS, IOPI, HDMS).

• Until standard assertion lists are available, databases that track organisms should include couplets containing both a scientific name and a reference.

(Inter)National Taxonomic Database?

• Concept-based• Party-neutral• Synonymy and lineage tracking• Perfectly archived

An upgrade for ITIS & Species 2000?

Specimen/object/occurrence databases

Information on specimens/objects/occurrence-observations should be tracked by reference to

• Place (place or collection)

• Unique identifier (accession number)

• Time

A museum is a place

Annotation should be by assertion (concept)!

Database systems for tracking specimens

The following are a few of the many available• BioLink http://www.ento.csiro.au/biolink/index.html

• Specify http://usobi.org/specify/default.htm

• Biota http://viceroy.eeb.uconn.edu/Biota

• Taxis http://taxis.virtualave.net/

TDWG maintains links to multiple software systemshttp://www.bgbm.fu-berlin.de/TDWG/acc/Software.htm

Plots Database SystemsSeveral plot database systems are available. Among the best know and widely used are:

• TurboVeg (over 1,000,000 plots stored) http://www.alterra.nl/onderzoek/producten/websites/turboveg/

• Plots (NatureServe NPS Mapping Project)

A vegetation plot archive?

There is currently no standard repository for plot data.

A repository is needed for:

• Plot storage

• Plot access and identification

• Plot documentation in literature/databases

This would be equivalent to GenBank for vegetation.

Project

Plot PlotObservation

Taxon Observation

Taxon Interpretation

PlotInterpretation

Core elements of VegBank

Interface tools•Desktop client for data preparation and local use.

•Flexible data inport, including XML.

•Tools for linking taxonomic and community concepts.

•Standard query, flexible query, SQL query.

•Flexible data export, including XML.

•Local data refresh

•Easy web access to central archive

Conclusions for database designers1. Records of organisms should always contain

(or point to) couplets consisting of a scientific name and a reference where the name was used.

2. Design for future annotation of organism and community concepts.

3. Track specimens/objects by unique identifier with metadata including location, annotation & time.

4. Design for reobservation. Separate permanent from transient attributes.

5. Archival databases should support time-specific views.

Infrastructural needs1. A national or international database of taxon concepts

with support for at least one (ITIS?) party perspective.

2. Software tools for development and documentation of taxonomic concepts (including irregular concepts) and party perspectives.

3. Completion and long-term support for a national or international archive for vegetation plot data (VegBank) and similar community observations.

4. A national or international database of community concepts with support for at least the FGDC party perspective.