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Acknowledgements
• Presentation by Robert Peet, 2003 & 2004 IAVS conference
• TurboVeg logo
• www.vegbank.org
• www.salvias.net
• www.ctfs.si.edu
• Powerpoint by Martin Kleikamp, VegetWeb
Major data types
• Site data: climate, soils, topography, etc.
• Taxon attribute data: identification, phylogeny, distribution, life-history, functional attributes, etc.
• Occurrence data: attributes of individuals (e.g., size, age, growth rate) and taxa (e.g., cover, biomass) that co-occur at a site.
• Demographic data: tagged individuals
EcoInformatics opportunitiesThe availability of massive quantities of data (and co-occurrence data in particular) has the potential to create new directions and allow critical syntheses in ecology.
•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?
• Standard data structures
• Public data archives (deposit, withdraw, cite, annotate)
• Standard exchange formats
• Standard protocols
• Tools for data discovery
Symposia from last 3 years
• 2003 Naples “Databases and information systems for vegetation science”
• 2004 Hilo “Databases and information systems for vegetation science”
• 2005 Lisbon “Long-term datasets: from descriptive to predictive data using eco-informatics”
• Database management system for relevé data
• Is standard relevé storage database software for vegetation ecologist worldwide (except the US)
• Developed for Dutch vegetation classification project.
• Core is species checklist for an area, e.g. Netherlands, USA, Switzerland
• Easy to export data to other vegetation software.
• Software free for students.
• The ESA Vegetation Panel has developed a public archive for vegetation plots known as VegBank (http://vegbank.org).
• VegBank is expected to function for vegetation plot data in a manner analogous to GenBank.
• Primary data is deposited for reference, novel synthesis, and reanalysis.
• The database architecture is generalizable to most types of species co-occurrence data.
VegBank data sourcesvegbank.org natureserve.org
plants.usda.gov
communities
plants
VegBankCommunity of
Users
plots
Search for data in VegBank
vegbank.org
VegBankCommunity of
Users
plot
s
plan
ts
com
mun
itie
s
Interpretation&
Annotation:Adding information to data
already in VegBank(i.e. interpreting a plant on a
plot, assigning a plot to a community, notes)
vegbank.org
Adding plots to VegBank
VegBankCommunity of
Users
VegBranch: A MS Access Database on your own computer that allows you to interact with VegBank on the web
•Load data to VegBank
•Download data from VegBank enter plots
importplots
vegbank.org
Downloading plots from VegBank
VegBank Community of
Users
Query plots from VegBank,
Then download to VegBranch
Query
Download
vegbank.org
Analysis of plot data
VegBankCommunity of
Users
VegBank&VegBranch have no analysis tools.
Other software and organizations can provide these tools, e.g. PC-ORD
Does provide data downloads that can be used for analysis.
query
spreadsheets
Analysis in PC-Ord or
similar program}
VegetWeb
• Online databank by Germany's Federal Agency for Nature Conservation
• Common data pool for German phytosociologists
• Data contributed from regional databases
• New plots published in Tuexenia are transferred to VegetWeb
• > 7000 forest plots
Tropical efforts
• SALVIAS manages data from > 3,500 studies, [14,000 plots]
• emphasis on the New World tropics
• Most inventories are one-time samples
• growing number of permanent 1 ha plots
(1) Assemble plot data and network with existing global databases of local tree community inventories
(2) “Ecoinformatics Tools” to embellish existing data sources and to standardize taxonomy.
Standardized Baseline Standardized Baseline for assessing local community diversity and dynamics.
SALVIAS Proximate Goals
MBG, RAINFOR, Vegbank etc.
(3) Web accessible database and ecoinformatics tools
SALVIAS ‘Taxon scrubber’
• Splits name into components:
“Quercus alba L.” “Quercus” “alba” “L.”
• Recognises & removes “cf” “aff” “?”
• Standardises spelling using reference lists
• Standardises families
• Flags invalid names using world ref. list
• Beginning to incorporate synonymised ref. lists
Local Inventory DataCount
Taxonomy ((A)A)SizeGeog. Data
Herbaria LinksGeographic DistributionPhenology
((B)B)
Analyze cross linkages between Diversity Patterns and Functional
Attributes of Forests on Local, Regional and Global Scales
Calculate Diversity MeasuresBioass, ProductionDistribution, Endemism
Site ‘Ecosystem’ DataGPPBiomass, Carbon
NPP ((C)C)Climate
Remotelysensed Data (MODIS)Environmental data
Canopy flux ((D)D)Landscape metrics
Ultimate GoalsAssemble
Salvias. Outline_plotmap
A. Gentry MBG
B. Boyle MBG, OTS
O. Phillips RAINFOR
USGS
TEAM CI
Enquist Lab UA
Many others . . .
Baseline of 0.1 ha Inventory Plots
~300 to 1,000
Spans latitudinal and elevational gradients
What is NZ-NVS?• A physical repository and archive for plot-
based vegetation data from throughout New Zealand (includes field data sheets, maps, photographs)
• An electronic archive of vegetation data from these plot sheets.
• Concentrates on indigenous plant communities, but increasingly represents vegetation from agricultural and other landscapes.
50 000+ relevé plots
12 000+ permanent plots
Major themes
• NVS serves as a major information source for understanding and reporting on status and trends in NZ biodiversity
• This requires • state-of-the-art data management of a
continually growing resource
• anticipating and meeting the needs of end-users
• leadership in data integration and synthesis
2003 Charge to the IAVS Working Group
1. Develop international data exchange standard including XML schema.
2. Recommend standards and requirements for archiving plot data.
3. Communicate with TDWG, IOPI, GBIF, ITIS and others regards our taxonomic database needs.
4. Address issues related to requirements for extended queries, intellectual property rights, & confidentiality.
ARC-NZ Network for Vegetation Function &
Terrestrial & Freshwater Biodiversity Information Systems
International exchange schema workshop
• April 2007
• All major databases described here
• Also TDWG observations group, EML
• Goal is to draft international exchange schema for plot-based vegetation data
Recommend standards and requirements for archiving plot data
• VegBank/IAVS perspective on requiring plot archiving presented at NCEAS workshop
• Need to develop a formal position paper to distribute to professional societies
Communicate with TDWG, IOPI, GBIF, ITIS and others regards our taxonomic database
needs
• Presentations were made to the Oct 2003 and Oct 2006 meetings of TDWG
• the SEEK project developed an international XML exchange standard for taxonomic concept data
Address issues related to requirements for extended queries, intellectual
property rights, & confidentiality
Databank Citation requirement
Access levels
VegBank SALVIAS NZ-NVS STRI VegetWeb ? ?