VegBank and the ESA Cyber-infrastructure for Vegetation Science

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

for Vegetation Science for Vegetation Science

R.K. Peet, Don Faber-R.K. Peet, Don Faber-Langendoen, Michael Jennings, Langendoen, Michael Jennings,

& Michael Lee& Michael Lee

Ecological Society of America Vegetation PanelEcological Society of America Vegetation Panel

We are pleased to We are pleased to acknowledge the support acknowledge the support

and cooperation ofand 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 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, biomass) rate) and taxa (e.g., cover, biomass) that co-occur at a site.that co-occur at a site.

The Vegetation PlotThe Vegetation PlotThe 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, cited, Plot data can be deposited, cited, discovered, referenced, viewed, discovered, referenced, viewed, shared, annotated, updated, & shared, annotated, updated, & 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 formatStandard exchange format• 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.

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

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

LegendExternal Action

Internal Action

Software Entity

T

T

T

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 PlotObservation

Taxon / Individual Observation

Taxon Interpretation

PlotInterpretation

Core Core elements of elements of VegBankVegBank

www.vegbank.orgwww.vegbank.org

T

T

T

Requirements: exchange Requirements: exchange standards for plot datastandards for plot data

• Standard data structure (draft by Standard data structure (draft by VegBank team) in implementation.VegBank team) in implementation.

• XML Schema (draft by VegBank XML Schema (draft by VegBank team, modification proposed by the team, modification proposed by the German team).German team).

• International standards and International standards and compatibility (Active Working Group compatibility (Active Working Group within the International Association within the International Association for Vegetation Science).for Vegetation Science).

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.

Standardized taxon lists Standardized taxon lists failfailto allow dataset integrationto allow dataset integration

The reasons include:The reasons include:• Taxonomic concepts are not defined (just Taxonomic concepts are not defined (just

lists), lists), • Relationships among concepts are not Relationships among concepts are not

defineddefined• The user cannot reconstruct the database as The user cannot reconstruct the database as

viewed at an arbitrary time in the past, viewed at an arbitrary time in the past, • Multiple party perspectives on taxonomic Multiple party perspectives on taxonomic

concepts and names cannot be supported or concepts and names cannot be supported or reconciled.reconciled.

USDA Plants & ITISAbies lasiocarpa

var. lasiocarpavar. arizonica

One concept ofAbies lasiocarpa

Flora North AmericaAbies lasiocarpa Abies bifolia

A narrow concept of Abies lasiocarpa

Partnership with USDA plants to provide plant concepts for data integration

Relationships among Relationships among conceptsconcepts

allow comparisons and allow comparisons and conversionsconversions

• Congruent, equal (=)Congruent, equal (=)• Includes (>)Includes (>)• Included in (<)Included in (<)• Overlaps (><)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. arizonicaAbies lasiocarpa

DistributionDistribution

USDA & ITISUSDA & ITIS

Flora North AmericaFlora North America

Abies bifolia Abies lasiocarpa

A. lasiocarpaA. lasiocarpa secsec USDA USDA > > A. lasiocarpaA. lasiocarpa secsec FNAFNAA. lasiocarpaA. lasiocarpa secsec USDAUSDA > > A. bifoliaA. bifolia secsec FNAFNAA. lasiocarpa v. lasiocarpaA. lasiocarpa v. lasiocarpa secsec USDAUSDA > > A. lasiocarpaA. lasiocarpa secsec FNAFNAA. lasiocarpa v. lasiocarpaA. lasiocarpa v. lasiocarpa secsec USDAUSDA >< >< A. bifoliaA. bifolia secsec FNAFNAA. lasiocarpa v. arizonicaA. lasiocarpa v. arizonica secsec USDAUSDA < < A. bifoliaA. bifolia secsec FNAFNA

var. lasiocarpa

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

Taxon/community Taxon/community interpretationinterpretationDocumenting the user’s informal Documenting the user’s informal working conceptworking concept

• Multiple concepts can be linked Multiple concepts can be linked simultaneously by concept simultaneously by concept relationship notation.relationship notation.

• Degree of fit for each can be Degree of fit for each can be indicated by fuzzy logic notationindicated by fuzzy logic notation

• Subsequent interpretations Subsequent interpretations supported.supported.

Scale for concept fitScale for concept fit

1 = Absolutely wrong. Unambiguously 1 = Absolutely wrong. Unambiguously incorrect.incorrect.

2 = Understandable but wrong. Doesn't 2 = Understandable but wrong. Doesn't fit but is close. Not a good answer. fit but is close. Not a good answer.

3 = Reasonable or acceptable answer3 = Reasonable or acceptable answer4 = Good answer. Unambiguously 4 = Good answer. Unambiguously

correctcorrect5 = Absolutely correct. Perfect fit5 = Absolutely correct. Perfect fit.

Documenting Documenting identificationsidentifications

Always show the concept – not just the name!!Always show the concept – not just the name!!Relationships added for identificationRelationships added for identification== Indicates identificationIndicates identification~~ (or aff.) Indicates similarity(or aff.) Indicates similarity>,<,><,|>,<,><,| As with concept relationshipsAs with concept relationshipsExample of complex identificationExample of complex identification< < Potentilla sec. Cronquist 1991 +Potentilla sec. Cronquist 1991 +~ ~ Potentilla simplex sec Cronquist 1991 +Potentilla simplex sec Cronquist 1991 +~ ~ Potentilla canadensis sec Cronquist 1991Potentilla canadensis sec Cronquist 1991

Conclusion: The new Conclusion: The new community ecology community ecology

depends on standards depends on standards and connectivityand connectivity

• Standard for co-occurrence dataStandard for co-occurrence data• Standards for data exchange Standards for data exchange • Public data archives (functions Public data archives (functions

for deposit, discovery, for deposit, discovery, withdrawal, citation, annotation)withdrawal, citation, annotation)

• Standards for data archivingStandards for data archiving• Standards for reference to Standards for reference to

taxonomic datataxonomic data