Collections. Vegetation sampling We observe and collect data on soil.
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Transcript of Collections. Vegetation sampling We observe and collect data on soil.
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Collections
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Vegetation sampling
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We observe and collect data on soil
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More soil. . .
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Once a plot is set up, the fun begins!
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Marl outcrop – Lake Waccamaw, Columbus Co, NC
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Fall line rock outcrop vegetation , with
Amphianthus pusillus and Diamorpha smallii
- Forty Acre Rock HP, Lancaster Co, SC
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Determining DBHDetermining DBHwith d-tapewith d-tape
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And more trees. . .
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It’s a plant id party!!
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VegBankVegBank ------
Data Model & XML Data Model & XML schemaschema
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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
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www.vegbank.orgwww.vegbank.org
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T
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T
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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
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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
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Project
PlotPlot
Observation
Taxon / Individual Observation
Taxon Interpretation
PlotInterpretation
Core Core elements of elements of VegBankVegBank
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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
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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
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PlotPlot
• EmbargosEmbargos
• Named PlaceNamed Place
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ObservationObservation
• ProjectProject
• Disturbance ObsDisturbance Obs
• Soil Obs Soil Obs
• Soil taxonSoil taxon
• GraphicGraphic
• Observation Observation SynonymSynonym
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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
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Strata & Strata & CoverCover
• Stratum methodStratum method
• Stratum typeStratum type
• StratumStratum
• Cover methodCover method
• Cover IndexCover Index
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InterpretatioInterpretationncontinued continued
PlantsPlants
• Tax Tax InterpretationInterpretation
• Taxon AltTaxon Alt
CommunitiesCommunities
• ClassClass
• InterpretationInterpretation
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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
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PartyParty• Project Project Contr.Contr.
• Obs Contr.Obs Contr.
• RoleRole
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ReferencReferenceses
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UtilitiesUtilities• User definedUser defined
• NotesNotes
• RevisionsRevisions
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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.
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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.
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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.
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USDA Plants & ITIS
Abies lasiocarpa
var. lasiocarpa
var. arizonica
One concept ofAbies lasiocarpa
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Flora North America
Abies lasiocarpa
Abies bifolia
A narrow concept of Abies lasiocarpa
Partnership with USDA plants to provide plant concepts for data integration
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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
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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
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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 …
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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
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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.