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 VegBank - The ESA Vegetation Plot
Archive
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/Inventory databases
Object or specimen
Specimen databases
Taxon
Taxonomic databases
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Web-interface
Information flow in the US National Vegetation
Classification
Veg Classification Database
Proposal
Taxonomic Database
VegBank
Raw Plot Data
Proposal
Vegetation/Biodiversity
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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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• 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, plus Canada Mexico)
• 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 / US USDA
Plants http//plants.usda.gov/ ITIS http//www.i
tis.usda.gov/ NatureServe http//www.natureserv
e.org World IPNI International Plant Names
Checklist http//www.ipni.org/ IOPI Global
Plant Checklist http//www.bgbm.fu-berlin.de/IO
PI/GPC/
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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 not defined (just lists),
• Multiple party perspectives on taxonomic concepts
  and names cannot be supported or reconciled.

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• 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.speciesanaly
  st.net/DarwinCore/)

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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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Six shagbark hickory assertions Possible
taxonomic synonyms are listed together
Assertions (One shagbark)C. ovata sec Gleason
52 C. 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 68 C. ovata (v.
ovata) sec FNA 97
Names Carya ovata Carya carolinae-septentrionalis
Carya ovata v. 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 an
assertion and a name. Usages can be used to track
nomenclatural synonyms
Name
Assertion
Usage
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ITIS Usage
Assertions
Names
1. Carya ovata 2. C. carolinae 3. C. ovata var.
australis

• ovata sec. Gleason
• ovata sl sec. FNA
• carolinae sec. Radford
• ovata australis sec. FNA
• ovata sec. Radford
• ovata ovata sec. FNA

1-F OK 2-D OK 3-D Syn
ITIS views the linkage of the assertion Carya
ovata var. australis sec. FNA 1997 with the name
Carya ovata var. australis as a nomenclatural
synonym.
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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 (sl) sec
FNA 1997 Carya ovata sec Radford 1968 Carya
carolinae sec Radford 1968 Carya ovata (ovata)
sec FNA 1997 Carya ovata australis sec FNA 1997
Status
Party Assertion Status Start Name ITIS ovata
G52 NS 1996 ITIS ovata R68
St 1996 ovata ITIS carolinae R68
St 1996 carolinae ITIS carolinae R68
NS 2000 ITIS ovata aust FNA
St 2000 carolinae ITIS ovata R68
NS 2000 ITIS ovata ovata FNA St 2000 ovata
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VegBank taxonomic data model
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• 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.

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(Inter)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
• Annotation should be by assertion (concept)!

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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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Plots Database Systems Several plot database
systems are available. Among the best know and
widely used are TurboVeg http//www.alterra.nl/on
derzoek/producten/websites/turboveg/Over
1,000,000 plots stored using TurboVeg Plots (ABI
NPS Mapping Project)
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• 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 science

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Core elements of the VegBank
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 client for data preparation and local
  use.
• Loaders for legacy data.
• Flexible data inport.
• Tools for linking to taxonomic and community
  concepts.
• Standard query, flexible query, SQL query.
• Flexible data 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 multiple or
  continuous time-specific views.