The challenge of biodiversity:

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The challenge of biodiversity Plot, organism and
taxonomic databases Robert K. Peet University
of North Carolina The National Plots Database
Committee John Harris NCEAS
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A case study The US National Plots Database
Project organized and directed by Robert K.
Peet, University of North Carolina Marilyn
Walker, USDA Forest Service U. Alaska Dennis
Grossman, The Nature Conservancy / ABI Michael
Jennings, USGS-BRD UCSB
Project supported by National Center for
Ecological Analysis Synthesis U.S. National
Science Foundation USGS-BRD Gap Analysis
Program ABI / The Nature Conservancy
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Biodiversity data structure
Locality
Observation/Collection Event
Plot databases
Object or specimen
Specimen databases
Taxon
Taxonomic databases
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Taxonomic database challenge The problem
Integration of data potentially representing
different times, places, investigators and
taxonomic standards The traditional solution
A standard list of kinds of organisms.
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• 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.speciesanaly
  st.net/DarwinCore/)

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• There exist numerous compilations of organism
  names. For example
• Species 2000 http//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 names http//www.biosis.org.u
  k/triton/indexfm.htm

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Taxon-specific standard lists are available.
Representative examples for higher plants
includeNorth America USDA Plants http//plants.
usda.gov/ ITIS http//www.itis.usda.gov/
ABI http//www.natureserve.org World IPNI
International Plant Names Checklist
http//www.ipni.org/ IOPI Global Plant
Checklist http//iopi.csu.edu.au/iopi/iopigpc1.
html
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• 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.

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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.
Carya carolinae-sept. (Ashe) Engler Graebner
Carya ovata (Miller)K. Koch
Carya ovata (Miller)K. Koch
sec. Gleason 1952
sec. Radford et al. 1968
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Multiple concepts of Rhynchospora plumosa s.l.
Elliot 1816
Gray 1834
Kral 1998
Peet 2002
Chapman 1860
R. plumosa
R. plumosa v. plumosa
R. plumosa
R. sp. 1
1
R. plumosa v. plumosa
R. plumosa
R plumosa v. intermedia
R. intermedia
2
R. plumosa v. interrupta
R. pineticola
R. plumosa v. pineticola
3
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An assertion represents a unique combination of a
name and a reference Assertion is equivalent to
Potential taxon taxonomic concept
Name
Reference
Assertion
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Five shagbark hickory assertions Possible
taxonomic synonyms are listed together
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
68 C. ovata sec FNA 97
Names Carya ovata Carya carolinae-septentrionalis
Carya ovata var. australis
References Gleason 1952 Britton Brown Radford
et al. 1968 Flora Carolinas Stone 1997 Flora
North America
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A usage represents a unique combination of a
taxon and a name. Usages can be used to track
nomenclatural synonyms
Name
Taxon
Usage
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Species concepts
Usage
Published names
1. Carya ovata 2. C. carolinae-septentrionalis 3.
C. ovata var. australis
A. One shagbark B. Southern shagbark C. Northern
shagbark
1-A 1-C 2-B 3-B
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.
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A usage (name assignment) and assertion (taxon
concept) can be combined in a single model
Name
Assertion
Usage
Reference
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• 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.

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Party
Assertion
ITIS FNA CommitteeABI
Carya ovata sec Gleason 1952 Carya ovata sec
Radford 1968 Carya carolinae sec Radford
1968 Carya ovata sec FNA 1997 Carya ovata
australis sec FNA 1997
Status
Party Assertion Status Start Name ITIS ovata
G52 S 1996 ITIS ovata R68
A 1996 ovata ITIS carolinae R68
A 1996 carolinae ITIS carolinae R68
S 2000 ITIS ovata aust FNA A 2000 carolinae
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• 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.

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National Taxonomic Database?

• Concept-based
• Party-neutral
• Synonymy and lineage tracking
• Perfectly archived
• An upgrade for ITIS Species 2000?

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• 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

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• 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.ht
  m

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Core elements of the National Plots Database
Project
Plot
Plot Observation
Taxon Observation
Taxon Interpretation
Plot Interpretation
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• 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

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• 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

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• Conclusions for database designers
• Records of organisms should always contain (or
  point to) couplets consisting of a scientific
  name and a reference where the name was used.
• Design for future annotation of organism
  concepts.
• Track specimens/objects by location, unique
  identifier time.
• Design for reobservation! Separate permanent from
  transient attributes.
• Archival databases should provide time-specific
  views.