Transcript Plant communities on montane rock outcrops of Banks Peninsula

Overview of progress in
Ecoinformatics
Susan Wiser
Landcare Research, Lincoln
New Zealand
Acknowledgements
• Presentation by Robert Peet, 2003 & 2004 IAVS
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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 opportunities
The 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?
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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”
Major vegetation plot databases
• 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.
• Across databases stores > 1 million records
• Between 1000-1500 users
• 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 sources
natureserve.org
vegbank.org
communities
plots
VegBank
Community of
Users
plants.usda.gov
Search for data in VegBank
communities
plants
plots
vegbank.org
VegBank
Community of
Users
Interpretation
&
Annotation:
Adding information to data
already in VegBank
(i.e. interpreting a plant on a
plot, assigning a plot to a
community, notes)
Adding plots to VegBank
vegbank.org
VegBranch: A MS Access
Database on your own
computer that allows you to
interact with VegBank on
the web
VegBank
Community of
Users
•Load data to VegBank
import
plots
enter
plots
•Download data from VegBank
Downloading plots from
VegBank
vegbank.org
 Query plots from VegBank,
 Then download to VegBranch
Query
VegBank
Community of
Users
Analysis of plot data
vegbank.org
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
VegBank
Community of
Users
}
Analysis in PC-Ord or
similar program
~22,000 plots
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
VPRO: BC Biogeographic Ecosystem Classification
>30,000 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
SALVIAS
Proximate Goals
(1) Assemble plot data and network with existing
global databases of local tree community inventories
MBG, RAINFOR, Vegbank etc.
Standardized Baseline for assessing
local community diversity and dynamics.
(2) “Ecoinformatics Tools” to embellish existing
data sources and to standardize taxonomy.
(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
Ultimate Goals
Assemble
Local Inventory Data
Count
Taxonomy
(A)
Size
Geog. Data
Calculate
Diversity Measures
Bioass, Production
Distribution, Endemism
Herbaria Links
Geographic
Distribution
Phenology
(B)
Site ‘Ecosystem’ Data
GPP
Biomass, Carbon
NPP
(C)
Climate
Remotely
sensed Data (MODIS)
Environmental data
Canopy flux
(D)
Landscape metrics
Analyze cross linkages between
Diversity Patterns and Functional
Attributes of Forests on Local,
Regional and Global Scales
Baseline of 0.1 ha Inventory Plots
~300 to 1,000
Spans latitudinal and elevational gradients
A. Gentry MBG
B. Boyle MBG, OTS
O. Phillips RAINFOR
USGS
TEAM CI
Enquist Lab UA
Many others . . .
Salvias. Outline_plotmap
Centre for Tropical Forest Studies &
Smithsonian Tropical Research Institute
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
Distribution of plots in NZ-NVS
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 endusers
• 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.
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+ VegetWeb
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
Draft exchange schema
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
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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
VegBank
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SALVIAS
NZ-NVS
STRI
VegetWeb
Access levels
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Themes for informatics
sessions
• Databases and software
• Large-scale data syntheses
• Data syntheses across time