Overview of progress in Ecoinformatics

Susan Wiser

Landcare Research, LincolnNew Zealand

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”

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 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}

~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

(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

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 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.

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 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 ? ?

Themes for informatics sessions

• Databases and software

• Large-scale data syntheses

• Data syntheses across time