Overview of progress in Ecoinformatics

1. Overview of progress in Ecoinformatics Susan Wiser Landcare Research, Lincoln New Zealand

2. 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

3. 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

4. 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?

5. How do we get there? • Standard data structures • Public data archives (deposit, withdraw, cite, annotate) • Standard exchange formats • Standard protocols • Tools for data discovery

6. 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”

8. Major vegetation plot databases

10. 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.

11. Across databases stores > 1 million records • Between 1000-1500 users

13. 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.

14. vegbank.org natureserve.org plants.usda.gov VegBankCommunity of Users VegBank data sources communities plots plants

15. vegbank.org Interpretation& Annotation:Adding information to data already in VegBank(i.e. interpreting a plant on a plot, assigning a plot to a community, notes) VegBankCommunity of Users Search for data in VegBank plots plants communities

16. vegbank.org VegBankCommunity of Users Adding plots to VegBank • 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 importplots enter plots

17. vegbank.org VegBank Community of Users Downloading plots from VegBank • Query plots from VegBank, • Then download to VegBranch Query Download

18. vegbank.org VegBankCommunity of Users Analysis of plot data 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

19. ~22,000 plots

20. 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

21. VPRO: BC Biogeographic Ecosystem Classification >30,000 plots

22. 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

23. 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

24. 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

25. 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

26. 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 Salvias. Outline_plotmap

27. Centre for Tropical Forest Studies &Smithsonian Tropical Research Institute

28. 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

29. Distribution of plots in NZ-NVS

30. 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

31. 2003 Charge to the IAVS Working Group • Develop international data exchange standard including XML schema. • Recommend standards and requirements for archiving plot data. • Communicate with TDWG, IOPI, GBIF, ITIS and others regards our taxonomic database needs. • Address issues related to requirements for extended queries, intellectual property rights, & confidentiality.

34. VegetWeb + +

35. ARC-NZ Network for Vegetation Function & Terrestrial & Freshwater Biodiversity Information SystemsInternational 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

36. Draft exchange schema

37. 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

38. 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

39. Address issues related to requirements for extended queries, intellectual property rights, & confidentiality

40. Themes for informatics sessions • Databases and software • Large-scale data syntheses • Data syntheses across time