Data models forCommunity information
Robert K. Peet, University of North CarolinaJohn Harris, Nat. Center for Ecol. Analysis & SynthesisMichael D. Jennings, U.S. Geological SurveyDennis Grossman, NatureServeMarilyn D. Walker, USDA Forest Service
New Directions forCommunity Ecology?
Massive datasets and databases are becoming available which will provide unprecedented access to:
• Spatially explicit environmental & spectral data.
• Species occurrences & co-occurrences.• Species attributes.• Species distributions.
EcoInformatics ?
Massive co-occurrence data have the potential to create new disciplines and allow critical syntheses.
• Theoretical community ecology. Who occurs together, and where, and following what rules?
• Vegetation & species modeling. Where should we expect species & communities to occur after environmental changes?
• Remote sensing. What is really on the ground?
• Monitoring & restoration. What changes are really taking place in the communities?
How do we get there from here?
• Public data archives (deposit, withdraw, cite).• Standard data structures. • Standard exchange formats.• Tools for semantic mediation.• Standard protocols.
Biodiversity data structure
Taxonomic databases
Plot/Inventory databases
Specimen databases
Observation/CollectionEvent
Object or specimen
BioTaxon
Locality
SynTaxon
Community type databases
A co-occurrence archive?
There is currently no standard repository for community composition data.
A repository is needed for:
• Record storage and preservation
• Record access and identification
• Record documentation in literature/databases
VegBank
• The ESA Vegetation Panel is currently developing a public archive for vegetation plots known as VegBank (www.vegbank.org).
• VegBank is expected to function for vegetation plot data in a manner analogous to GenBank.
• Primary data will be deposited for reference, novel synthesis, and reanalysis.
• The database architecture is generalizable to most types of species co-occurrence data.
Project
PlotPlot
Observation
Taxon Observation
Taxon Interpretation
PlotInterpretation
Core elements of VegBank
ESA standards for plot data
• Four levels of standards:
• Pick lists (48 and counting)
• Conversion to common units
• Method protocols
• Concept-based interpretations
• “Painless” metadata
VegBank Interface Tools
• Desktop client for data preparation and local use.
• Flexible data import, including XML.
• Standard query, flexible query, SQL query.
• Flexible data export, including XML.
• Easy web access to central archive
The Taxonomic database challenge:Standardizing organisms and communities
The problem: Integration of data potentially representing
different times, places, investigators and taxonomic standards.
The traditional solution: A standard list of organisms / communities.
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.
The single largest impediment to large-scale synthesis in community ecology
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.
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. ovataCarya ovata v. australis
Assertions(One shagbark)C. ovata sec Gleason ’52C. ovata 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
Name AssertionUsage
A usage (name assignment) and assertion (taxon concept) can be
combined in a single model
Reference
1. Carya ovata2. C. carolinae3. C. ovata var. ovata3. C. ovata var. australis
A. ovata sec. GleasonB. ovata sec. FNAC. carolinae sec. RadfordD. ovata australis sec. FNAE. ovata sec. RadfordF. ovata (ovata) sec. FNA
1-F OK2-D OK3-F Syn4-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.
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.
(Inter)National Taxonomic Database?
An upgrade for ITIS & USDA PLANTS?
• Concept-based.• Party-neutral.• Perfectly archived.• Synonymy and lineage tracking.• Alternate names systems & hierarchies.
A few conclusions
1. EcoInformatics is developing as a large and important new subfield of community ecology
2. Public archives are needed for co-occurrence data.
3. Standard data structures and exchange formats are needed.
4. Records of organisms should always contain a scientific name and a reference!
5. Design for future annotation of organism and community concepts.
6. Archival databases should provide time-specific views.
We are pleased to acknowledge the support and cooperation of:
Ecological Society of America
Gap Analysis Program
National Center for Ecological Analysis and Synthesis
National Biological Information Infrastructure
Federal Geographic Data Committee
National Science Foundation