VegBank and the ESA VegBank and the ESA Cyber-infrastructure Cyber-infrastructure

for Vegetation Science for Vegetation Science

Robert K. PeetRobert K. Peet

&&

The Ecological Society of America Vegetation The Ecological Society of America Vegetation PanelPanel

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

BackgrouBackgroundnd

• Vegetation field plots.Vegetation field plots.• Documentation & description of floristic Documentation & description of floristic

types.types.• Submission & peer review of proposed Submission & peer review of proposed

types.types.• Management, citation, & archiving of Management, citation, & archiving of

vegetation data.vegetation data.

ESA Guidelines forESA Guidelines forvegetationvegetation classificationclassification

The ESA Vegetation Panel has developed The ESA Vegetation Panel has developed guidelines for vegetation classification guidelines for vegetation classification covering requirements for:covering requirements for:

North American North American Vegetation ClassificationVegetation Classification

• Ecological Society of AmericaEcological Society of America – – Standards, peer review & publication.Standards, peer review & publication.

• US Federal Geographic Data CommitteeUS Federal Geographic Data Committee –US government standards.–US government standards.

• NatureServeNatureServe – Maintenance and – Maintenance and distribution of the Classification.distribution of the Classification.

• USDA & ITISUSDA & ITIS – Taxonomic standards for – Taxonomic standards for organismsorganisms

The new community ecology The new community ecology

Intersection of 3 data typesIntersection of 3 data types• Site dataSite data:: climate, soils, climate, soils,

topography, etc.topography, etc.

• Taxon attribute dataTaxon attribute data: : identification, phylogeny, identification, phylogeny, distribution, life-history, functional distribution, life-history, functional attributes ...attributes ...

• Co-occurrence dataCo-occurrence data:: attributes of attributes of individuals (e.g., size, age, growth individuals (e.g., size, age, growth rate) and taxa (e.g., cover, rate) and taxa (e.g., cover, biomass) that co-occur at a site.biomass) that co-occur at a site.

The Vegetation PlotThe Vegetation Plot

The primary unit of vegetation The primary unit of vegetation observation.observation.

• Universal attributesUniversal attributes: date, location, area, : date, location, area, species list, species importance species list, species importance

• Optional attributesOptional attributes: environment, soil, : environment, soil, disturbancedisturbance

• Protocols and formatsProtocols and formats: many & flexible: many & flexible

• Available dataAvailable data: > 10: > 1066 plot records plot records containing > 5x10containing > 5x1077 species occurrence species occurrence records.records.

VegBankVegBank

• VegBankVegBank – a public archive for – a public archive for vegetation plot observations (vegetation plot observations (http://vegbank.org))..

• VegBankVegBank functions in a manner functions in a manner analogous to analogous to GenBankGenBank. .

• Plot data can be deposited, Plot data can be deposited, discovered, viewed, cited, annotated, discovered, viewed, cited, annotated, & downloaded.& downloaded.

• Plot data can be used for Plot data can be used for documentation validation and documentation validation and reanalysis.reanalysis.

VegBank strategiesVegBank strategies• Standard exchange format – established Standard exchange format – established

through IAVS through IAVS • Supports multiple protocols.Supports multiple protocols.• Flexible and expandableFlexible and expandable• Tools for data discovery, integration, and Tools for data discovery, integration, and

summarization.summarization.• Generalizable to most types of species co-Generalizable to most types of species co-

occurrence data.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 flowExtraction

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

PlotPlot

Observation

Taxon / Individual Observation

Taxon Interpretation

PlotInterpretation

Core Core elements of elements of

VegBankVegBank

Taxonomic database Taxonomic database challenge:challenge:

Standardizing organisms and Standardizing organisms and communitiescommunities

The problem:The problem: Integration of data potentially Integration of data potentially

representing different times, places, representing different times, places, investigators and taxonomic standards.investigators and taxonomic standards.

The traditional solution:The traditional solution: A standard list of organisms / A standard list of organisms /

communities.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

DistributionDistribution

USDA & ITISUSDA & ITIS

Flora North AmericaFlora North America

Abies bifolia Abies lasiocarpa

A. lasiocarpaA. lasiocarpa secsec USDA USDA > > A. lasiocarpaA. lasiocarpa secsec FNAFNA

A. lasiocarpaA. lasiocarpa secsec USDAUSDA > > A. bifoliaA. bifolia secsec FNAFNA

A. lasiocarpa v. lasiocarpaA. lasiocarpa v. lasiocarpa secsec USDAUSDA > > A. lasiocarpaA. lasiocarpa secsec FNAFNA

A. lasiocarpa v. lasiocarpaA. lasiocarpa v. lasiocarpa secsec USDAUSDA >< >< A. bifoliaA. bifolia secsec FNAFNA

A. lasiocarpa v. arizonicaA. lasiocarpa v. arizonica secsec USDAUSDA < < A. bifoliaA. bifolia secsec FNAFNA

var. lasiocarpa

www.vegbank.orgwww.vegbank.org

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VegBank LessionsVegBank Lessionsfor community for community participationparticipation

• Usability (testing, training)Usability (testing, training)

• IncentivesIncentives– Uploads (mandates, rewards, Uploads (mandates, rewards,

security)security)

– Downloads (opportunity)Downloads (opportunity)

– Citation (culture)Citation (culture)

– Tools and integrationTools and integration

• ConnectivityConnectivity

VegBank LessionsVegBank Lessionsfor data sharingfor data sharing

• Embrace established standards Embrace established standards (e.g., TDWG, EML)(e.g., TDWG, EML)

• Work to establish new standards Work to establish new standards – Content, process, exchangeContent, 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, confidentialityEmbargos, licenses, confidentiality

Roles & ResponsibilitiesRoles & ResponsibilitiesProfessional SocietiesProfessional Societies

• Set standardsSet standards– Data content and exchange formatData content and exchange format

– Data archiving and access (discrete, Data archiving and access (discrete, well-circumscribed elements)well-circumscribed elements)

• Assure quality control (peer Assure quality control (peer review)review)– One of the 4 functions of publication: One of the 4 functions of publication:

Certification, Certification, ValidationValidation, Awareness, , Awareness, ArchivingArchiving

Roles & ResponsibilitiesRoles & ResponsibilitiesDigital repositories and Digital repositories and

librarieslibraries

• Archive and provide access to Archive and provide access to publications and datapublications and data

• Institutional responsibilities to Institutional responsibilities to granting agencies. Driven by granting agencies. Driven by lawyers and paid for by overheadlawyers and paid for by overhead

• Potential security for databasesPotential security for databases

Roles & Responsibilities Roles & Responsibilities Granting AgenciesGranting Agencies

• Set requirements for data Set requirements for data archiving and sharing, but archiving and sharing, but perhaps delegate perhaps delegate implementation to societiesimplementation to societies

• Pay for archiving and publication, Pay for archiving and publication, directly or through overheaddirectly or through overhead

Roles & Responsibilities Roles & Responsibilities Data CentersData Centers

• Maintain a portfolio of critical, Maintain a portfolio of critical, discipline-specific database systemsdiscipline-specific database systems

• Maintain key infrastructure contentMaintain key infrastructure content– Digital identifiersDigital identifiers

– Common objects (e.g. taxa, Common objects (e.g. taxa, publications)publications)

– Data registriesData registries

Roles & ResponsibilitiesRoles & ResponsibilitiesPublishersPublishers

• Require that specific types of data Require that specific types of data be archived (e.g., GenBank, be archived (e.g., GenBank, VegBank)VegBank)

• Imbed deep links as a form of Imbed deep links as a form of citation for standard elements such citation for standard elements such as taxon concepts and data as taxon concepts and data elementselements

• Provide archives for and links to Provide archives for and links to supporting documentationsupporting documentation

Roles & ResponsibilitiesRoles & ResponsibilitiesGovernment AgenciesGovernment Agencies

• Formulate federal standards and Formulate federal standards and policies (in context of disciplinary policies (in context of disciplinary standards).standards).

• Mandate and implement federal Mandate and implement federal standards (e.g., FGDC standards)standards (e.g., FGDC standards)

• Assure critical infrastructure Assure critical infrastructure exists exists

ConclusionsConclusions

• VegBank is an example of a discipline-VegBank is an example of a discipline-specific but public data archive specific but public data archive (functions for deposit, discovery, (functions for deposit, discovery, withdrawal, citation, annotation)withdrawal, citation, annotation)

• Standards for data content, data Standards for data content, data exchange, and archivingexchange, and archiving

• Standards for reference to standard Standards for reference to standard elements such as taxonomic dataelements such as taxonomic data

• Work with a broader community to Work with a broader community to avoid institutional fragility.avoid institutional fragility.