EcoInformatics & Vegetation Science

1. EcoInformatics & Vegetation Science

2. The symposium message Plant community ecology is on the brink of a dramatic transformation that will be made possible by the emergence of the new field of ecoinformatics. An important role for IAVS is to encourage, facilitate, and direct this transformation.

3. The challenge “… ecology is a science of contingent generalizations, where future trends depend (much more than in the physical sciences) on past history and on the environmental and biological setting.” Robert May 1986.

4. Traditional Community Ecology The questions: • How are communities structured? • How do taxa interact? The solutions : • Simple observations. • Simple experiments. The scale: • Stand or landscape.

5. 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.

6. 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?

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

8. What next? • International data exchange standard – IAVS • Requirement for data archiving – JVS and other journals • Requirement for documentation of taxonomic concepts • Linked system of international databases

9. 2003 Charge to the 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. • IAVS EcoInformatics Working Group website: http://www.bio.unc.edu/faculty/peet/vegdata/

10. An information infrastructure for vegetation science in North America • Robert K. Peet • University of North Carolina • in collaboration with Don Faber-Langendoen, Michael Jennings, Dennis Grossman, Michael Lee, & Mark Anderson

11. Ecological Society of America National Science Foundation Gap Analysis Program National Center for Ecological Analysis and Synthesis National Biological Information Infrastructure Federal Geographic Data Committee I am pleased to acknowledge the support and cooperation of:

12. The North American Initiative • Ecological Society of America – Development of standards and implementation of peer review; maintenance of VegBank archive. • US Federal Geographic Data Committee – Establishment of US government standards. • NatureServe – Maintenance and distribution of the “International Classification of Ecological Communities.” • USDA PLANTS & ITIS – Maintenance of a standard taxonomic database for organisms.

13. Physiognomic categories CategoryExample Class . . . . . . . . . . Woodlands Subclass . . . . . . .Mainly Evergreen Woodlands Group . . . . . . . . .Evergreen Needle‑leaved Woodlands Subgroup . . . . . Natural/Seminatural Formation . . . . Evergreen Coniferous Woodland with Rounded Crowns Floristic categories Alliance . . . . . . Juniperus occidentalis Association . . . . Juniperus occidentalis / Artemesia tridentata

14. Guidelines for Vegetation Classification The ESA Vegetation Panel and its partners have collaborated to develop guidelines for the floristic levels of the classification covering: • Requirements for vegetation field plots. • Documentation & description of floristic types. • Submission & peer review of proposed types. • Management, citation, & archiving of vegetation data.

15. Guidelines for describing the associations and alliances of the U.S. National Vegetation Classification. Michael Jennings, Don Faber-Langendoen, Robert Peet, Orie Loucks, David Glenn-Lewin, Antoni Damman, Michael Barbour, Robert Pfister, Dennis Grossman, David Roberts, David Tart, Marilyn Walker, Stephen Talbot, Joan Walker, Gary Hartshorn, Gary Waggoner, Marc Abrams, Alison Hill, Marcel Rejmanek The Ecological Society of America Vegetation Classification Panel. Version 4.0. July, 2004 http://www.esa.org/vegweb/ Under review by FGDC as a U.S. federal standard

16. vegbank.org natureserve.org TBA plants.usda.gov Overview of online resources Stores plots and makes them publicly accessible Stores current communities in the NVC Allows people to change and update NVC and plants Stores current plant taxonomy

17. NatureServe Explorer US-NVC--- Proposed data flow Extraction NatureServe Biotics Classification Mgt. NVC Proceedings US-NVC Panel Peer Review Revision Proposal Legend External Action Analysis & Synthesis Internal Action VegBank & other plot archives Entity

18. VegBank • The ESA Vegetation Panel is developing 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 will be deposited for reference, novel synthesis, and reanalysis. • The database architecture is generalizable to most types of species co-occurrence data.

19. Challenges • Distributed databases and data exchange formats • Data ownership, intellectual property rights, & confidentiality • Multiple classifications of organsms and communities • Multiple plot types (relevés & Hubbell plots) • Data entry & submission tools • Perfect archiving • Plot and taxon interpretation

20. Locality Observation/Collection Event Plot/Inventory databases Object or specimen Specimen databases BioTaxon Taxonomic databases Biodiversity data structure SynTaxon Community type databases

21. Core elements of VegBank Project Plot Plot Observation Taxon / Individual Observation Taxon Interpretation Plot Interpretation

22. http://www.vegbank.org

26. VegBank Interface Tools • Desktop client (VegBranch) for data preparation and local use. • Flexible XML data import supporting VegBranch & TurboVeg formats. • Flexible data export. • Easy web access to central archive

27. VegBranch can be used for converting legacy data, entering data, and maintaining a local plot database.

28. 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.

29. 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

30. Three concepts of shagbark hickory Splitting 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. Carya carolinae-sept. (Ashe) Engler & Graebner Carya ovata (Miller)K. Koch Carya ovata (Miller)K. Koch sec. Gleason 1952 sec. Radford et al. 1968

31. A taxonon concept represents a unique combination of a name and a reference “taxon concept” is equivalent to “Potential taxon” & “taxonomic assertion” Name Concept Reference

32. Six shagbark hickory assertions Possible taxonomic synonyms are listed together Names Carya ovata Carya carolinae-septentrionalis Carya ovata v. ovata Carya ovata v. australis Taxon concepts (One shagbark)C. ovata sec Gleason ’52 C. ovata sec FNA ‘97 (Southern shagbark)C. carolinae-s. sec Radford ‘68C. ovata v. australis sec FNA ‘97 (Northern shagbark) C. ovata sec Radford ‘68 C. ovata (v. ovata) sec FNA ‘97 References Gleason 1952 Britton & Brown Radford et al. 1968 Flora Carolinas Stone 1997 Flora North America

33. 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.

34. http://www.natureserve.org/explorer

37. Coming soon – direct links to views of typal and occurrence plots in VegBank

41. Concluding remarks • Much of what we are doing in the US is common to the vegetation classification enterprise worldwide, but much is also novel. We need and encourage greater international communication and collaboration. • Public plot archives, initially driven by the classification enterprise, have the potential to radically change the development of vegetation science in general.