The challenge of biodiversity: Plot, organism and taxonomic databases Robert K. Peet

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: The US National Plots Database

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 databases

Specimen databases

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.

Current standards• Biological organisms are names 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/)

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)

• 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

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

WorldIPNI International Plant Names Checklist

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

http://iopi.csu.edu.au/iopi/iopigpc1.html

Most standardized plant 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 often not defined,

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

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 hickory

Splitting 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 var. australis

Assertions(One shagbark)C. ovata sec Gleason ‘52

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

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

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

Five shagbark hickory assertions

Possible taxonomic synonyms are listed together

Name TaxonUsage

A usage represents a unique combination of a taxon and a name.

Usages can be used to track nomenclatural synonyms

1. Carya ovata2. C. carolinae-septentrionalis3. C. ovata var. australis

A. One shagbarkB. Southern shagbarkC. Northern shagbark

1-A1-C2-B3-B

Published names Species conceptsUsage

An example of a nomenclatural synonym is the linkage of the assertion “Carya ovata var. australis sec. FNA 1997” with the name “Carya carolinae-septentrionalis” by both ITIS and ABI.

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 CommitteeABI

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

Party Assertion

Party Assertion Status Start Name

ITIS ovata – G52 S 1996ITIS ovata – R68 A 1996 ovataITIS carolinae – R68 A 1996 carolinaeITIS carolinae – R68 S 2000ITIS ovata aust – FNA A 2000 carolinae

Status

Concept-based taxonomy is coming soon• All organisms 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, ABI).

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

National Taxonomic Database?

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

An upgrade for ITIS & Species 2000?

Specimen/object databases

Information on specimens/objects should be tracked by reference to

• Place (place or collection)

• Unique identifier (accession number)

• Time

A museum is a place

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 systems

http://www.bgbm.fu-berlin.de/TDWG/acc/Software.htm

Project

PlotPlot

Observation

Taxon Observation

Taxon Interpretation

PlotInterpretation

Core elements of the National Plots Database

Support multiple interpretations of which concept applies to an organism or community.

Various observers will associate different taxonomic concepts with records in a database

Provision must be made for inclusion of these taxonomic interpretations.

Minimal attributes include

• Concept applied

• Date applied

• Who made the interpretation

• Links to supporting information

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

•Loaders for legacy data.

•Data export.

•Tools for linking taxonomic concepts.

•Standard query, flexible query, SQL query.

•Flexible export.

•Local data refresh

•Easy web access with consistent interface

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 concepts.

3. Track specimens/objects by location, unique identifier & time.

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

5. Archival databases should provide time-specific views.