1. Data models for Community information Robert K. Peet, University of North Carolina John Harris, Nat. Center for Ecol. Analysis & Synthesis Michael D. Jennings, U.S. Geological Survey Dennis Grossman, NatureServe Marilyn D. Walker, USDA Forest Service

2. New Directions for Community Ecology? Massive datasets and databases are becoming available which will provide unprecedented access to: Spatially explicit environmental & spectral data. Species occurrences & co-occurrences. Species attributes. Species distributions.

3. EcoInformatics ? Massive co-occurrence data have the potential to create new disciplines and allow critical syntheses. 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?

4. How do we get there from here? Public data archives (deposit, withdraw, cite). Standard data structures. Standard exchange formats. Tools for semantic mediation. Standard protocols.

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

6. A co-occurrence archive? There is currently no standard repository for community composition data. A repository is needed for: Record storage and preservation Record access and identification Record documentation in literature/databases

7. VegBank The ESA Vegetation Panel is currently developing a public archive for vegetation plots known as VegBank (www.vegbank.org).www.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.

8. Project Plot Observation Taxon Observation Taxon Interpretation Plot Interpretation Core elements of VegBank

9. ESA standards for plot data Four levels of standards: Pick lists (48 and counting) Conversion to common units Method protocols Concept-based interpretations “Painless” metadata

10. VegBank Interface Tools Desktop client for data preparation and local use. Flexible data import, including XML. Standard query, flexible query, SQL query. Flexible data export, including XML. Easy web access to central archive

11. 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.

12. Standard lists are available Representative examples for higher plants include: * North America / US USDA Plants http://plants.usda.gov/ ITIS http://www.itis.usda.gov/ NatureServe http://www.natureserve.org * World IPNI International Plant Names Checklist http://www.ipni.org/ IOPI Global Plant Checklist http://www.bgbm.fu-berlin.de/IOPI/GPC/

13. 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

14. Carya ovata (Miller)K. Koch Carya carolinae-sept. (Ashe) Engler & Graebner Carya ovata (Miller)K. Koch sec. Gleason 1952sec. Radford et al. 1968 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.

15. NameReferenceAssertion An assertion represents a unique combination of a name and a reference “Assertion” is equivalent to “Potential taxon” & “taxonomic concept”

16. Names Carya ovata Carya carolinae-septentrionalis Carya ovata v. ovata Carya ovata v. australis Assertions (One shagbark) C. ovata sec Gleason ’52 C. ovata sec FNA ‘97 (Southern shagbark) C. carolinae-s. sec Radford ‘68 C. 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 Six shagbark hickory assertions Possible taxonomic synonyms are listed together

17. NameAssertionUsage A usage represents a unique combination of an assertion and a name. Usages can be used to track nomenclatural synonyms

18. NameAssertionUsage A usage (name assignment) and assertion (taxon concept) can be combined in a single model Reference

19. 1. Carya ovata 2. C. carolinae 3. C. ovata var. ovata 3. C. ovata var. australis A.ovata sec. Gleason B.ovata sec. FNA C.carolinae sec. Radford D.ovata australis sec. FNA E.ovata sec. Radford F.ovata (ovata) sec. FNA 1-F OK 2-D OK 3-F Syn 4-D Syn Names Assertions ITIS Usage ITIS likely views the linkage of the assertion “Carya ovata var. australis sec. FNA 1997” with the name “Carya ovata var. australis” as a nomenclatural synonym.

20. 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.

21. (Inter)National Taxonomic Database? An upgrade for ITIS & USDA PLANTS? Concept-based. Party-neutral. Perfectly archived. Synonymy and lineage tracking. Alternate names systems & hierarchies.

22. A few conclusions 1.EcoInformatics is developing as a large and important new subfield of community ecology 2.Public archives are needed for co-occurrence data. 3.Standard data structures and exchange formats are needed. 4.Records of organisms should always contain a scientific name and a reference! 5.Design for future annotation of organism and community concepts. 6.Archival databases should provide time-specific views.

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