Transcript Taxonomic plot and specimen databases.

The challenge of biodiversity:
Plot, organism, and taxonomic databases
Robert K. Peet
University of North Carolina
The National Plots Database Committee
John Harris
NCEAS
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
Biodiversity data structure
Locality
Observation/Collection
Event
Plot/Inventory databases
Object or specimen
Specimen databases
Taxon
Taxonomic databases
Information
flow in the
US National
Vegetation
Classification
Web-interface
Veg Classification Database
Proposal
VegBank
Taxonomic
Database
Raw Plot Data
Proposal
Vegetation/Biodiversity
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.
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.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
World
IPNI 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/)
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
Multiple concepts of Rhynchospora plumosa s.l.
Elliot
1816
Gray
1834
R. plumosa
R. plumosa
Chapman
1860
Kral
1998
Peet
2002?
R. plumosa
v. plumosa
R. plumosa
R. sp. 1
1
R. plumosa
v. plumosa
2
R. plumosa
v. pineticola
3
R plumosa
v. intermedia
R. intermedia
R. plumosa
v. interrupta
R. pineticola
An assertion represents a unique
combination of a name and a reference
“Assertion” is equivalent to
“Potential taxon” & “taxonomic concept”
Name
Assertion
Reference
Six shagbark hickory assertions
Possible taxonomic synonyms are listed together
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
Assertions
(One shagbark)
C. ovata sec Gleason ’52
C. ovata (sl) sec FNA ‘97
(Southern shagbark)
C. carolinae-s. sec Radford ‘68
C. ovata v. australis sec FNA ‘97
(Northern shagbark)
C. ovata sec Radford ‘68
C. ovata (v. ovata) sec FNA ‘97
A usage represents a unique combination of
an assertion and a name.
Usages can be used to track nomenclatural synonyms
Name
Usage
Assertion
Names
1. Carya ovata
2. C. carolinae
3. C. ovata var. australis
ITIS
Usage
1-F OK
2-D OK
3-D Syn
Assertions
A.
B.
C.
D.
E.
F.
ovata sec. Gleason
ovata sl sec. FNA
carolinae sec. Radford
ovata australis sec. FNA
ovata sec. Radford
ovata ovata sec. FNA
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.
A usage (name assignment) and
assertion (taxon concept) can be
combined in a single model
Name
Usage
Reference
Assertion
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.
Party
Assertion
ITIS
FNA Committee
NatureServe
USDA Plants
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
ITIS
ITIS
ITIS
ITIS
ITIS
ITIS
ITIS
ovata – G52
NS
ovata – R68
St
carolinae – R68
St
carolinae – R68
NS
ovata aust – FNA St
ovata – R68
NS
ovata ovata – FNA St
1996
1996
1996
2000
2000
2000
2000
Name
ovata
carolinae
carolinae
ovata
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/occurrenceobservations 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 systems
http://www.bgbm.fu-berlin.de/TDWG/acc/Software.htm
Plots Database Systems
Several 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
Core elements of
VegBank
Plot
Observation
Taxon
Observation
Taxon
Interpretation
Plot
Interpretation
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 designers
1. 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 needs
1. 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.