VegBank and the ESA Cyber-infrastructure for Vegetation Science Robert K. Peet & The Ecological Society of America Vegetation Panel

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

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, discovered, viewed, cited, annotated, & downloaded.Plot data can be deposited, discovered, viewed, cited, annotated, & 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 format – established through IAVSStandard exchange format – established through IAVS 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.

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

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

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.

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

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

T

T

T

T

T

T

VegBank Lessions for community participation Usability (testing, training)Usability (testing, training) IncentivesIncentives –Uploads (mandates, rewards, security) –Downloads (opportunity) –Citation (culture) –Tools and integration ConnectivityConnectivity

VegBank Lessions for data sharing Embrace established standards (e.g., TDWG, EML)Embrace established standards (e.g., TDWG, EML) Work to establish new standardsWork to establish new standards –Content, process, exchange Design for idiosyncratic dataDesign for idiosyncratic data Anticipate distributed systems and connectivityAnticipate distributed systems and connectivity Leverage agency mandatesLeverage agency mandates Repositories for archiving; databases for accessRepositories for archiving; databases for access Respect intellectual propertyRespect intellectual property –Embargos, licenses, confidentiality

Roles & Responsibilities Professional Societies Set standardsSet standards –Data content and exchange format –Data archiving and access (discrete, well-circumscribed elements) Assure quality control (peer review)Assure quality control (peer review) –One of the 4 functions of publication: Certification, Validation, Awareness, Archiving

Roles & Responsibilities Digital repositories and libraries Archive and provide access to publications and dataArchive and provide access to publications and data Institutional responsibilities to granting agencies. Driven by lawyers and paid for by overheadInstitutional responsibilities to granting agencies. Driven by lawyers and paid for by overhead Potential security for databasesPotential security for databases

Roles & Responsibilities Granting Agencies Set requirements for data archiving and sharing, but perhaps delegate implementation to societiesSet requirements for data archiving and sharing, but perhaps delegate implementation to societies Pay for archiving and publication, directly or through overheadPay for archiving and publication, directly or through overhead

Roles & Responsibilities Data Centers Maintain a portfolio of critical, discipline-specific database systemsMaintain a portfolio of critical, discipline-specific database systems Maintain key infrastructure contentMaintain key infrastructure content –Digital identifiers –Common objects (e.g. taxa, publications) –Data registries

Roles & Responsibilities Publishers Require that specific types of data be archived (e.g., GenBank, VegBank)Require that specific types of data be archived (e.g., GenBank, VegBank) Imbed deep links as a form of citation for standard elements such as taxon concepts and data elementsImbed deep links as a form of citation for standard elements such as taxon concepts and data elements Provide archives for and links to supporting documentationProvide archives for and links to supporting documentation

Roles & Responsibilities Government Agencies Formulate federal standards and policies (in context of disciplinary standards).Formulate federal standards and policies (in context of disciplinary standards). Mandate and implement federal standards (e.g., FGDC standards)Mandate and implement federal standards (e.g., FGDC standards) Assure critical infrastructure existsAssure critical infrastructure exists

Conclusions VegBank is an example of a discipline- specific but public data archive (functions for deposit, discovery, withdrawal, citation, annotation)VegBank is an example of a discipline- specific but public data archive (functions for deposit, discovery, withdrawal, citation, annotation) Standards for data content, data exchange, and archivingStandards for data content, data exchange, and archiving Standards for reference to standard elements such as taxonomic dataStandards for reference to standard elements such as taxonomic data Work with a broader community to avoid institutional fragility.Work with a broader community to avoid institutional fragility.