VegBank and the ESA Cyber-infrastructure for Vegetation Science R.K. Peet, Don Faber-Langendoen, Michael Jennings, & Michael Lee Ecological Society of America Vegetation Panel

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

The new community ecology Intersection of 3 data types Site data: climate, soils, topography, etc.Site data: climate, soils, topography, etc. Taxon attribute data: identification, phylogeny, distribution, life-history, functional attributes...Taxon attribute data: identification, phylogeny, distribution, life-history, functional attributes... Co-occurrence data: attributes of individuals (e.g., size, age, growth rate) and taxa (e.g., cover, biomass) that co-occur at a site.Co-occurrence data: attributes of individuals (e.g., size, age, growth rate) and taxa (e.g., cover, biomass) that co-occur at a site.

The Vegetation Plot The primary unit of vegetation observation. Universal attributes: date, location, area, species list, species importanceUniversal attributes: date, location, area, species list, species importance Optional attributes: environment, soil, disturbanceOptional attributes: environment, soil, disturbance Protocols and formats: many & flexibleProtocols and formats: many & flexible Available data: > 10 6 plot records containing > 5x10 7 species occurrence records.Available data: > 10 6 plot records containing > 5x10 7 species occurrence records.

VegBank VegBank – a public archive for vegetation plot observations ( – a public archive for vegetation plot observations ( VegBank functions in a manner analogous to GenBank.VegBank functions in a manner analogous to GenBank. Plot data can be deposited, cited, discovered, referenced, viewed, shared, annotated, updated, & downloaded.Plot data can be deposited, cited, discovered, referenced, viewed, shared, annotated, updated, & downloaded. Plot data can be used for documentation validation and reanalysis.Plot data can be used for documentation validation and reanalysis.

VegBank strategies Standard exchange formatStandard exchange format Supports multiple protocols.Supports multiple protocols. Flexible and expandableFlexible and expandable Tools for data discovery, integration, and summarization.Tools for data discovery, integration, and summarization. Generalizable to most types of species co-occurrence data.Generalizable to most types of species co-occurrence data. Incentives to participate.Incentives to participate.

The ESA Vegetation Classification Panel was established in 1993 with a mandate to support the emerging U.S. Vegetation Classification. Background

Vegetation field plots.Vegetation field plots. Documentation & description of floristic types.Documentation & description of floristic types. Submission & peer review of proposed types.Submission & peer review of proposed types. Management, citation, & archiving of vegetation data.Management, citation, & archiving of vegetation data. ESA Guidelines for vegetation classification The ESA Vegetation Panel has developed guidelines for vegetation classification covering requirements for:

North American Vegetation Classification Ecological Society of America – Standards, peer review & publication.Ecological Society of America – Standards, peer review & publication. US Federal Geographic Data Committee – US government standards.US Federal Geographic Data Committee – US government standards. NatureServe – Maintenance and distribution of the Classification.NatureServe – Maintenance and distribution of the Classification. USDA & ITIS – Taxonomic standards for organismsUSDA & ITIS – Taxonomic standards for organisms

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

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Biodiversity data structure Taxonomic database Observation database Occurrence database Observation/ Collection Event Specimen or Object Bio-Taxon Locality Observation or Community Type Observation type database

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

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Requirements: exchange standards for plot data Standard data structure (draft by VegBank team) in implementation.Standard data structure (draft by VegBank team) in implementation. XML Schema (draft by VegBank team, modification proposed by the German team).XML Schema (draft by VegBank team, modification proposed by the German team). International standards and compatibility (Active Working Group within the International Association for Vegetation Science).International standards and compatibility (Active Working Group within the International Association for Vegetation Science).

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.

Standardized taxon lists fail to allow dataset integration The reasons include: Taxonomic concepts are not defined (just lists),Taxonomic concepts are not defined (just lists), Relationships among concepts are not definedRelationships among concepts are not defined The user cannot reconstruct the database as viewed at an arbitrary time in the past,The user cannot reconstruct the database as viewed at an arbitrary time in the past, Multiple party perspectives on taxonomic concepts and names cannot be supported or reconciled.Multiple party perspectives on taxonomic concepts and names cannot be supported or reconciled.

USDA Plants & ITIS Abies lasiocarpa var. lasiocarpa var. arizonica One concept ofAbies lasiocarpa

Flora North America Abies lasiocarpa Abies bifolia A narrow concept of Abies lasiocarpa Partnership with USDA plants to provide plant concepts for data integration

Relationships among concepts allow comparisons and conversions Congruent, equal (=)Congruent, equal (=) Includes (>)Includes (>) Included in (<)Included in (<) Overlaps (> <) Disjunct (|)Disjunct (|) and others …and others …

High-elevation fir trees of western US AZ NM CO WY MT AB eBC wBC WA OR var. arizonica Abies lasiocarpa Distribution USDA & ITIS Flora North America Abies bifoliaAbies lasiocarpa A. lasiocarpa sec USDA > A. lasiocarpa sec FNA A. lasiocarpa sec USDA >A. bifolia sec FNA A. lasiocarpa v. lasiocarpa sec USDA >A. lasiocarpa sec FNA A. lasiocarpa v. lasiocarpa sec USDA > <A. bifolia sec FNA A. lasiocarpa v. arizonica sec USDA <A. bifolia sec FNA var. lasiocarpa

Party Perspective VegBank supports selection of Party perspective at an arbitrary date by tracking: Status – Standard, Nonstandard, Undetermined Correlation with other concepts – Equal, Greater, Lesser, Overlap, Undetermined Correlation with other concepts – Equal, Greater, Lesser, Overlap, Undetermined Start & Stop dates. Start & Stop dates.

Taxon/community interpretation Documenting the user’s informal working concept Multiple concepts can be linked simultaneously by concept relationship notation.Multiple concepts can be linked simultaneously by concept relationship notation. Degree of fit for each can be indicated by fuzzy logic notationDegree of fit for each can be indicated by fuzzy logic notation Subsequent interpretations supported.Subsequent interpretations supported.

Scale for concept fit 1 = Absolutely wrong. Unambiguously incorrect. 2 = Understandable but wrong. Doesn't fit but is close. Not a good answer. 3 = Reasonable or acceptable answer 4 = Good answer. Unambiguously correct 5 = Absolutely correct. Perfect fit 5 = Absolutely correct. Perfect fit.

Documenting identifications Always show the concept – not just the name!! Relationships added for identification =Indicates identification ~(or aff.) Indicates similarity >,, <,|As with concept relationships Example of complex identification < Potentilla sec. Cronquist ~ Potentilla simplex sec Cronquist ~ Potentilla canadensis sec Cronquist 1991

Conclusion: The new community ecology depends on standards and connectivity Standard for co-occurrence dataStandard for co-occurrence data Standards for data exchangeStandards for data exchange Public data archives (functions for deposit, discovery, withdrawal, citation, annotation)Public data archives (functions for deposit, discovery, withdrawal, citation, annotation) Standards for data archivingStandards for data archiving Standards for reference to taxonomic dataStandards for reference to taxonomic data