Collections

Vegetation sampling

We observe and collect data on soil

More soil. . .

Once a plot is set up, the fun begins!

Marl outcrop – Lake Waccamaw, Columbus Co, NC

Fall line rock outcrop vegetation , with

Amphianthus pusillus and Diamorpha smallii

- Forty Acre Rock HP, Lancaster Co, SC

Determining DBHDetermining DBHwith d-tapewith d-tape

And more trees. . .

It’s a plant id party!!

VegBankVegBank ------

Data Model & XML Data Model & XML schemaschema

Why an exchange Why an exchange standard?standard?

• Many research questions require Many research questions require lots of datalots of data

• Facilitate exchange !Facilitate exchange !• Write input/output just onceWrite input/output just once• Encourage others to participate Encourage others to participate

(eg US Forest Service)(eg US Forest Service)• Safe & documented long-term Safe & documented long-term

storage of plot datastorage of plot data

www.vegbank.orgwww.vegbank.org

T

T

Key design featuresKey design features

• Many kinds of plots !!!Many kinds of plots !!!• Easy search Easy search • Easy citation and linkageEasy citation and linkage• Easy downloadEasy download• XML input and output optionsXML input and output options• Users can annotate plots and Users can annotate plots and

determinationsdeterminations• Support of taxon conceptsSupport of taxon concepts

Biodiversity data structure

Taxonomic database

Plot/Inventory database

Occurrence database

Plot Observation/Collection Event

Specimen or Object

Bio-Taxon

Locality

Vegetation Type

Vegetation type database

Project

PlotPlot

Observation

Taxon / Individual Observation

Taxon Interpretation

PlotInterpretation

Core Core elements of elements of VegBankVegBank

VegBank VegBank consists of consists of three integrated three integrated

databasesdatabases

1.1. The Plot DatabaseThe Plot Database

2.2. The Plant DatabaseThe Plant Database

3.3. The Community DatabaseThe Community Database

The VegBank ERDThe VegBank ERD

• Available at: Available at: http://vegbank.org/vegdocs/design/erd/vegbank_erd.pdf

• Click tables for data dictionary and Click tables for data dictionary and constrained vocabularyconstrained vocabulary

PlotPlot

• EmbargosEmbargos

• Named PlaceNamed Place

ObservationObservation

• ProjectProject

• Disturbance ObsDisturbance Obs

• Soil Obs Soil Obs

• Soil taxonSoil taxon

• GraphicGraphic

• Observation Observation SynonymSynonym

Taxon ObservationTaxon Observation

• Importance valuesImportance values

• Author nameAuthor name

Taxon InterpretationTaxon Interpretation

• Which taxonWhich taxon

• Who decided and whyWho decided and why

• Stem or collectiveStem or collective

• Voucher informationVoucher information

Strata & Strata & CoverCover

• Stratum methodStratum method

• Stratum typeStratum type

• StratumStratum

• Cover methodCover method

• Cover IndexCover Index

InterpretatioInterpretationncontinued continued

PlantsPlants

• Tax Tax InterpretationInterpretation

• Taxon AltTaxon Alt

CommunitiesCommunities

• ClassClass

• InterpretationInterpretation

Problematic taxa of ecological datasets

• Carex sp.• Crustose lichen• Hairy sedge #6.• Sporobolus sp. #1• Picea glauca – engelmannii complex• Potentilla simplex or P. canadensis• Carya ovata sec. Gleason 1952

PartyParty• Project Project Contr.Contr.

• Obs Contr.Obs Contr.

• RoleRole

ReferencReferenceses

UtilitiesUtilities• User definedUser defined

• NotesNotes

• RevisionsRevisions

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 failfail

to 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.

Abies lasiocarpa

Abies bifolia

Abies lasiocarpa

sec.sec. Little Littlesec.sec. USDA PLANTS USDA PLANTS

sec.sec. Flora North America Flora North America

Three concepts of subalpine fir

Splitting one species into two illustrates the ambiguity often associated with scientific names.

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 High-elevation fir trees of western North Americawestern North America

AZ NM CO WY MT AB eBC wBC WA OR

Abies lasiocarpa

var. arizonica

Abies lasiocarpa var. lasiocarpa

DistributionDistribution

USDA - ITISUSDA - ITIS

Flora North AmericaFlora North America

Abies bifolia Abies lasiocarpa

Minimal conceptsMinimal concepts

A B C

Andropogon virginicusAndropogon virginicus complex in the complex in the CarolinasCarolinas

9 elemental units; 17 base concepts, 27 scientific names9 elemental units; 17 base concepts, 27 scientific names

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 …

Party PerspectiveParty Perspective

The Party Perspective on a concept includes:The Party Perspective on a concept includes:

• Status – Standard, Nonstandard, Status – Standard, Nonstandard, UndeterminedUndetermined

• Correlation with other concepts – Correlation with other concepts – Equal, Greater, Lesser, Overlap, Equal, Greater, Lesser, Overlap,

Undetermined.Undetermined.

• Start & Stop dates for tracking changesStart & Stop dates for tracking changes

Intended functionalityIntended functionality

• Organisms are labeled by reference to Organisms are labeled by reference to concept (name-reference combination),concept (name-reference combination),

• Party perspectives on concepts and names Party perspectives on concepts and names can be dynamic, but remain perfectly can be dynamic, but remain perfectly archived,archived,

• User can select which party perspective to User can select which party perspective to follow,follow,

• Different names systems are supported,Different names systems are supported,

• Enhanced stability in recognized concepts Enhanced stability in recognized concepts by separating name assignment and rank by separating name assignment and rank from concept.from concept.