- VegCore data dictionary
- Tables
- Source
- DataOwner
- Dataset
- Record
- Occurrence
- ?Observation
- Method
- Project
- Event
- Coordinates
- decimalLatitude
- acceptedDecimalLatitude
- decimalLongitude
- acceptedDecimalLongitude
- realLatitude
- realLongitude
- longitude_DMS
- latitude_DMS
- verbatimCoordinates
- verbatimLatitude
- verbatimLongitude
- verbatimCoordinateSystem
- verbatimSRS
- geodeticDatum
- coordinateUncertaintyInMeters
- coordinatePrecision_deg
- pointRadiusSpatialFit
- footprintWKT
- footprintSRS
- footprintSpatialFit
- georeferencedBy
- georeferencedDate
- georeferenceProtocol
- georeferenceSources
- georeferenceVerificationStatus
- georeferenceRemarks
- Placename
- Geovalidation
- Location
- LocationObservation
- locationRemarks
- ?elevation
- ?minimumElevation
- ?maximumElevation
- ?depth
- ?minimumDepth
- ?maximumDepth
- distanceAboveSurfaceInMeters
- minimumDistanceAboveSurfaceInMeters
- maximumDistanceAboveSurfaceInMeters
- ?plotArea
- slopeAspect
- minSlopeAspect
- maxSlopeAspect
- slopeGradient
- minSlopeGradient
- maxSlopeGradient
- landform
- ?temperature
- ?precipitation
- ?PlotObservation
- Subplot
- SubplotObservation
- SoilObservation
- GeologicalContext
- geologicalContextID
- earliestEonOrLowestEonothem
- latestEonOrHighestEonothem
- earliestEraOrLowestErathem
- latestEraOrHighestErathem
- earliestPeriodOrLowestSystem
- latestPeriodOrHighestSystem
- earliestEpochOrLowestSeries
- latestEpochOrHighestSeries
- earliestAgeOrLowestStage
- latestAgeOrHighestStage
- lowestBiostratigraphicZone
- highestBiostratigraphicZone
- lithostratigraphicTerms
- group
- formation
- member
- bed
- Community
- Taxon
- taxonID
- parentTaxonID
- scientificNameID
- parentScientificNameID
- parentNameUsageID
- namePublishedInID
- scientificName
- taxonName
- taxonNameOrEpithet
- taxonNameWithMorphospecies
- speciesBinomial
- speciesBinomialWithMorphospecies
- parentNameUsage
- namePublishedIn
- namePublishedInYear
- higherClassification
- higherPlantGroup
- kingdom
- phylum
- class
- order
- family
- genus
- subgenus
- specificEpithet
- ?species
- morphospeciesSuffix
- ?morphospecies
- infraspecificRank
- infraspecificEpithet
- subspecies
- variety
- forma
- cultivar
- taxonRank
- verbatimTaxonRank
- scientificNameAuthorship
- vernacularName
- nomenclaturalCode
- taxonomicStatus
- taxonIsCanonical
- nomenclaturalStatus
- taxonRemarks
- threatened
- concatenatedScientificName
- TaxonConcept
- TaxonOccurrence
- TaxonDetermination
- OriginalTaxonDetermination
- originalNameUsageID
- originalNameUsage
- originalTaxonName
- originalScientificName
- morphoname
- originalKingdom
- originalPhylum
- originalClass
- originalOrder
- originalFamily
- originalGenus
- originalSpecificEpithet
- originalInfraspecificEpithet
- originalSubspecies
- originalVariety
- originalForma
- originalCultivar
- originalTaxonRank
- originalScientificNameAuthorship
- originalIdentificationQualifier
- MatchedTaxonDetermination
- matchedScientificNameID
- matchedTaxonName
- matchedScientificName
- matchedKingdom
- matchedPhylum
- matchedClass
- matchedOrder
- matchedFamily
- matchedGenus
- matchedSpecificEpithet
- matchedMorphospecies
- matchedInfraspecificEpithet
- matchedSubspecies
- matchedVariety
- matchedForma
- matchedCultivar
- matchedTaxonRank
- matchedScientificNameAuthorship
- matchedIdentificationQualifier
- matchedTaxonConfidence_fraction
- matchedFamilyConfidence_fraction
- matchedGenusConfidence_fraction
- matchedSpeciesConfidence_fraction
- AcceptedTaxonDetermination
- acceptedNameUsageID
- acceptedNameUsage
- acceptedScientificNameID
- acceptedTaxonName
- acceptedScientificName
- acceptedKingdom
- acceptedPhylum
- acceptedClass
- acceptedOrder
- acceptedFamily
- acceptedGenus
- acceptedSpecificEpithet
- acceptedInfraspecificEpithet
- acceptedSubspecies
- acceptedVariety
- acceptedForma
- acceptedCultivar
- acceptedTaxonRank
- acceptedScientificNameAuthorship
- acceptedIdentificationQualifier
- TaxonObservation
- AggregateObservation
- Individual
- IndividualObservation
- Stem
- StemObservation
- Collection
- Specimen
- Voucher
- Measurement
- ResourceRelationship
- Special terms
- Sources
- Editing
- Related pages
VegCore data dictionary¶
VegCore is a vegetation exchange schema which combines 370+ terms and 34 tables from existing exchange schemas
Examples¶
Example specimen data¶
See ACAD.Specimen.csv1, which contains well-formed Darwin Core data.
1 The dataset is from ACAD, a Canadensys herbarium, so it's public domain.
Data dictionary notes¶
- A leading
?indicates an ambiguous term - Copying a term name gives you a permalink to that term, which can be pasted into an HTML-formatted e-mail
- For a term's preferred name, the sources are only those which inspired that name for the term.
The term's concept, on the other hand, comes from all sources for the term, including those of synonyms. - Some links contain a URL fragment (the part after the
#) which indicates a section within the linked resource. Mouse over the link to view this fragment.
See also: Special terms | Editing guide | Sources
VegCore format notes¶
- In the data dictionary, terms are placed in the table they are most applicable to.
In a VegCore export, they can also be placed in any other table they apply to, according to how the data is normalized.
Forming IDs¶
- An ID should always be globally unique to allow appending data from arbitrary datasets.
A local ID can be made global by prepending the institution's ID. - An ID must permanently and unambiguously identify the record
- Domain identifiers are usually permanent, while autogenerated primary keys often aren't.
However, domain identifiers are sometimes duplicated, in which case another ID, such as a primary key, must be used to distinguish them.
- Domain identifiers are usually permanent, while autogenerated primary keys often aren't.
- When multiple IDs are available, include all of them (in separate columns) to allow looking up the record by any of them
Note that these globally unique IDs are not the same as UUIDs, which are randomly generated
Forming preferred IDs¶
- Choose one ID to serve as the preferred ID. This becomes the database primary key.
- Choose the ID which is most directly associated with the identified object:
- a domain identifier
- a permanent URL
- a permanent primary key
- Within these categories, choose the shortest string which is globally unique
Downloads¶
Tables¶
Source
DataOwner
Dataset
Record
Occurrence
Method
Project
Event
Coordinates
Placename
Geovalidation
Location
LocationObservation
Subplot
SubplotObservation
SoilObservation
GeologicalContext
Community
Taxon
TaxonConcept
TaxonOccurrence
TaxonDetermination
OriginalTaxonDetermination
MatchedTaxonDetermination
AcceptedTaxonDetermination
TaxonObservation
AggregateObservation
Individual
IndividualObservation
Stem
StemObservation
Collection
Specimen
Voucher
Measurement
ResourceRelationship
Source 
¶
a "reference[...] cited within the database" (VegBank)
Datasource ¶
DataProvider ¶
Reference ¶
sourceType ¶
Values: herbarium, primary database, aggregator, ...
referenceType ¶
aggregatorOrPrimary ¶
Components:
isHerbarium ¶
source ¶
Where this database got the data
"the proximate data provider" (Brad Boyle)
"Can an aggregator (such as GBIF or SALVIAS) or an original source (a herbarium such as ARIZ or a person such as Bob Peet)" (Brad Boyle)
proximateDataProvider ¶
dataProvider ¶
dataSource ¶
dataSourceName ¶
creator ¶
Who originally created the data. This is who created the data record, rather than the collector of the specimen or measurement.
"The dataprovider that first provides electronic access to a dataset. The dataprovider must not have obtained the data from another dataprovider; they either digitized the dataset themselves, or are making available a digital copy of the dataset prepared by someone else but not previously made available." (Brad Boyle)
primaryDataProvider ¶
dataPublisher ¶
distributors¶
The data distributors through which the record passed, starting with the source and ending with the creator
references ¶
dcterms_references ¶
DataOwner ¶
dataOwner ¶
datasetOwner ¶
Dataset ¶
dataset ¶
"a dataset belonging to a designated primary data owner, either a person or an institution. For a specimen record provided to BIEN by an aggregator, datasource<>(dataset=institutionCode). For a specimen record provided to BIEN by the herbarium which holds that specimen, datasource= dataset =institutionCode. For a plot provided by the data owner, datasource= dataset <>(institutionCode=NULL). For a plot provided by an aggregator, datasource<> dataset <>(institutionCode=NULL)." (Brad Boyle)
"a set of records that can be traced to a single party or group of parties who are the owners of the data. For specimens, all records from a single herbarium (as identified by the herbarium acronym) would constitute a dataset. For plot, a set of plot provided at one time by a particular owner typically constitute a dataset. Note that the dataset is not the same as the datasetOwnerID; while one dataset traces only to a single datasetauthor (which can be a group of authors), a single datasetauthor my own multiple datasets." (Brad Boyle)
dataResource ¶
datasetName ¶
datasetURL ¶
datasetID ¶
Record ¶
recordID ¶
dataProviderRecordID ¶
ID within dataProvider
"Unique ID (primary key) within datasource database. Will be same as datasetRecordID if dataset and datasource are the same." (Brad Boyle)
Scope: dataProvider
datasourceRecordID ¶
ID_Canadensys ¶
globalUniqueIdentifier_SpeciesLink ¶
?ID ¶
Alternative: ID_Canadensys¶
Alternative: ID_TEAM¶
datasetRecordID ¶
"Unique ID (database primary key) for the specimen or observation in the dataset, if provided." (Brad Boyle)
Scope: dataset
type¶
dcterms_type ¶
modified¶
"an internal timestamp indicat[ing] when record last modified, not necessarily when determination (taxon name) last modified" (Brad Boyle)
dcterms_modified ¶
dateLastModified ¶
language¶
dcterms_language ¶
rights¶
dcterms_rights ¶
rightsHolder¶
dcterms_rightsHolder ¶
accessRights¶
dcterms_accessRights ¶
bibliographicCitation¶
dcterms_bibliographicCitation ¶
informationWithheld ¶
dataGeneralizations ¶
dynamicProperties ¶
Occurrence ¶
An observation of any entity, biological or otherwise
Observation_VegCore ¶
occurrenceID ¶
"A globally unique identifier for the specimen or observation, formed by combining the [...] unique identifier of the collection with the locally unique identifier of the specimen. For specimens, construct as follows: "urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber]". If a properly formed occurrenceID is provided by the data provider, use it. For plots, construct as follows: "urn:observation:[datasource]:[dataset]:[catalogNumber]. Replace any spaces in dataset name with hyphens." (Brad Boyle)
globalUniqueIdentifier_DwC ¶
?globalUniqueIdentifier ¶
Alternative: globalUniqueIdentifier_DwC¶
Alternative: globalUniqueIdentifier_SpeciesLink¶
basisOfRecord ¶
occurrenceRemarks ¶
recordedBy ¶
"A list (concatenated and separated) of names of people, groups, or organizations responsible for recording the original Occurrence. The primary collector or observer, especially one who applies a personal identifier (recordNumber), should be listed first." (DwC)
collector ¶
Components:
recordedBy_givenName ¶
"The given name" (VegX)
recordedBy_middleName ¶
The "middle name or initial" (VegBank)
recordedBy_surName ¶
"The last name" (VegX)
associatedMedia ¶
associatedReferences ¶
associatedOccurrences ¶
associatedSequences ¶
?Observation ¶
Alternative: Observation_VegCore¶
Alternative: Observation_VegBank¶
Method ¶
"A specific method definition followed in the creation of the dataset. Each method links to a protocol and literature citation reference. A protocol may have many method or steps." (VegX)
SamplingProtocol ¶
Related: VegBank:stratumMethod, VegBank:coverMethod
samplingProtocolID ¶
samplingProtocol ¶
method¶
Named like: Method
methodology¶
plotMethodology ¶
samplingEffort ¶
?observationType ¶
Alternative: observationType_SALVIAS¶
Alternative: observationType_BIEN2¶
observationGranularity¶
Values: plot, specimen
observationType_BIEN2 ¶
observationMeasure ¶
Values: count, cover, presence, points-intercepted, distance-intercepted
observationType_SALVIAS ¶
Project ¶
A "project established to collect vegetation plot data. Each plot originates as part of a project." (VegBank)
projectID ¶
"A reference to a specific 'project'" (VegX)
projectName¶
"Title of the project" (VegX)
projectTitle ¶
Named like: plotName
projectStartDate ¶
"Project start date" (VegBank)
Named like: startDate
projectEndDate ¶
"Project stop date" (VegBank)
Named like: endDate
Event ¶
"an action that occurs at a place and during a period of time" (DwC)
eventID ¶
censusID ¶
eventDate ¶
"The date-time or interval during which an Event occurred" (DwC)
startDate¶
"The start date" (VegX) of the "interval during which an Event occurred" (DwC)
obsStartDate ¶
Related: eventDate
endDate¶
"The end date" (VegX) of the "interval during which an Event occurred" (DwC)
obsEndDate ¶
Related: eventDate
eventTime ¶
timeOfDay ¶
startDayOfYear ¶
julianDay ¶
endDayOfYear ¶
year ¶
month ¶
day ¶
verbatimEventDate ¶
habitat ¶
authorEventCode¶
"the code or name that the author uses to identify [the] event" (VegBank)
authorObsCode ¶
plotCensusNumber ¶
fieldNumber_DwC_terms ¶
eventRemarks ¶
"the text of notes taken in the field about the Event" (DwC)
fieldNotes_DwC_terms ¶
Coordinates ¶
A numerically-defined point
decimalLatitude ¶
latitude ¶
acceptedDecimalLatitude¶
Related: decimalLatitude, acceptedNameUsage
decimalLongitude ¶
longitude ¶
acceptedDecimalLongitude¶
Related: decimalLongitude, acceptedNameUsage
realLatitude ¶
Replace with: PRIVATE¶
realLongitude ¶
Replace with: PRIVATE¶
longitude_DMS¶
Related: DwC:longitude
latitude_DMS¶
Related: DwC:latitude
verbatimCoordinates ¶
verbatimLatitude ¶
verbatimLongitude ¶
verbatimCoordinateSystem ¶
verbatimSRS ¶
geodeticDatum ¶
coordinateUncertaintyInMeters ¶
coordinatePrecision_deg¶
Related: coordinatePrecision
pointRadiusSpatialFit ¶
footprintWKT ¶
boundingBox ¶
shapeOfSite ¶
footprintSRS ¶
footprintSpatialFit ¶
georeferencedBy ¶
georeferencedDate ¶
georeferenceProtocol ¶
georeferenceProtocol_bien ¶
georeferenceSources ¶
Where the coordinates came from
Values: source data, GPS, georeferencing, ...
coordinateSource ¶
coordinateSource_bien ¶
georeferenceVerificationStatus ¶
georeferenceRemarks ¶
Placename¶
A named region
NamedPlace ¶
higherGeographyID ¶
higherGeography ¶
continent ¶
continentOcean ¶
waterBody ¶
islandGroup ¶
island ¶
country ¶
countryName ¶
acceptedCountry¶
Related: country, acceptedNameUsage
countryCode ¶
stateProvince ¶
state ¶
acceptedStateProvince¶
Related: stateProvince, acceptedNameUsage
county ¶
acceptedCounty¶
Related: county, acceptedNameUsage
municipality ¶
locality ¶
locationNarrative ¶
descriptionOfSite ¶
verbatimLocality ¶
Geovalidation¶
The accuracy of the Coordinates, taking into account the Placename
Geoscrub ¶
Named like: geovalid
geovalid¶
isGeovalid ¶
latLongDomainValid¶
Whether the coordinates are in the range of valid decimal values
isValidLatLong ¶
latLongDomainInvalid¶
Whether the coordinates are not in the range of valid decimal values
isBadLatLong ¶
Named like: isValidLatLong
latLongInCountry¶
isInCountry ¶
Named like: isValidLatLong, country
?distanceToCountry ¶
?distErrCountry ¶
Named like: country
distanceToCountry_m¶
distanceToCountry_km¶
latLongInStateProvince¶
isInStateProvince ¶
Named like: isValidLatLong, stateProvince
?distanceToStateProvince ¶
?distErrStateProvince ¶
Named like: stateProvince
distanceToStateProvince_m¶
distanceToStateProvince_km¶
latLongInCounty¶
isInCountyParish ¶
Named like: isValidLatLong, county
isNewWorld ¶
isNewWorld_bien ¶
Location ¶
"A spatial region" (DwC) or point
Plot ¶
PlotLocation ¶
locationID ¶
plotID ¶
plotUniqueIdentifierID ¶
locationName¶
"Name or label for a plot" (VegX)
plotName ¶
authorPlotCode ¶
locationNumber¶
Named like: recordNumber
parentLocationID ¶
Related: locationID, VegBank:PARENT_ID
parentPlotName¶
"Name or label" (VegX) for "the parent plot when plot is nested within another plot" (VegBank)
Related: VegX:plotName, VegBank:PARENT_ID
locationAccordingTo ¶
LocationObservation¶
A sampling of a Location
PlotObservation_VegX ¶
Observation_VegBank ¶
PlotInventory ¶
Related: Location, VegBank:plot
locationRemarks ¶
plotNotes¶
plotNote ¶
notes_Madidi ¶
?elevation ¶
elevationInMeters¶
verbatimElevation ¶
Value must include units
verbatimElevation_m¶
Components:
?minimumElevation ¶
minimumElevationInMeters ¶
minimumElevation_verbatim¶
Value must include units
?maximumElevation ¶
maximumElevationInMeters ¶
maximumElevation_verbatim¶
Value must include units
?depth ¶
verbatimDepth ¶
Components:
?minimumDepth ¶
minimumDepthInMeters ¶
minimumDepth_verbatim¶
Value must include units
?maximumDepth ¶
maximumDepthInMeters ¶
maximumDepth_verbatim¶
Value must include units
distanceAboveSurfaceInMeters¶
Components:
minimumDistanceAboveSurfaceInMeters ¶
maximumDistanceAboveSurfaceInMeters ¶
?plotArea ¶
"Total area of the plot" (VegX)
?area ¶
plotArea_m2¶
plotArea_ha ¶
slopeAspect ¶
"Representative azimuth of slope gradient (0-360 degrees) or as a cardinal direction (e.g. N, S, NE)" (VegX)
minSlopeAspect ¶
maxSlopeAspect ¶
slopeGradient ¶
"Representative inclination of slope in degrees" (VegX)
minSlopeGradient ¶
maxSlopeGradient ¶
landform ¶
"A recognizable physical feature on the surface of the earth, often including consideration of the natural cause of its formation" (VegX)
?temperature ¶
"Temperature during observation" (VegX)
"Mean annual temperature" (SALVIAS)
temperature_C¶
temp_C ¶
temperature_F¶
?precipitation ¶
precipitation_m¶
precipitation_mm¶
precip_mm ¶
?PlotObservation ¶
Alternative: PlotObservation_VegX¶
Alternative: PlotObservation_SALVIAS¶
Subplot¶
"subplot, line, or any other subsample or subdivision of plot" (SALVIAS)
Related: SALVIAS:subplot
subplotID ¶
quadratID ¶
Related: locationID, SALVIAS:subplot
subplot ¶
Scope: locationID
quadratName ¶
subplotX¶
"The X-coordinate of the related items position in meters. The user will enter the relative position of related item with respect to the plot origin (in meters) with the x-axis defined by the plot azimuth." (VegX)
plotRelativeX ¶
startX ¶
subplotY¶
"The Y-coordinate of the related items position in metres. The user will enter the relative position of related item with respect to the plot origin (in meters) with the y-axis defined by the plot azimuth." (VegX)
plotRelativeY ¶
startY ¶
SubplotObservation¶
A sampling of a Subplot
Related: Subplot, LocationObservation
SoilObservation¶
A sampling of a Location's soil
AbioticObservation ¶
SoilObs ¶
?phosphorus ¶
"Phosphorus of soil" (VegX)
phosphorus_fraction¶
phosphorus_percent¶
?potassium ¶
"Pottasium of soil" (VegX)
?pottasium ¶
potassium_fraction¶
potassium_percent¶
?magnesium ¶
"Magnesium of soil" (VegX)
magnesium_fraction¶
magnesium_percent¶
?nitrogen ¶
"Nitrogen of soil" (VegX)
nitrogen_fraction¶
nitrogen_percent¶
?carbon ¶
?soilC ¶
carbon_fraction¶
carbon_percent¶
?calcium ¶
?soilCa ¶
calcium_fraction¶
calcium_percent¶
?sodium ¶
?soilNa ¶
sodium_fraction¶
sodium_percent¶
?acidity ¶
?soilAcidity ¶
acidity_fraction¶
acidity_percent¶
?organic ¶
?soilOrganic ¶
organic_fraction¶
organic_percent¶
texture¶
soilTexture ¶
?sand ¶
?soilSand ¶
sand_fraction¶
sand_percent¶
?silt ¶
?soilSilt ¶
silt_fraction¶
silt_percent¶
?clay ¶
?soilClay ¶
clay_fraction¶
clay_percent¶
ph ¶
"The pH of the soil" (VegX)
?cationExchangeCapacity ¶
?exchangeCapacity ¶
?soilCationCap ¶
cationExchangeCapacity_cmol_kg ¶
cationExchangeCapacity_meq_100g ¶
?baseSaturation ¶
baseSaturation_fraction¶
baseSaturation_percent¶
conductivity¶
soilConductivity ¶
GeologicalContext ¶
"information pertaining to a location within a geological context, such as stratigraphy" (DwC)
geologicalContextID ¶
earliestEonOrLowestEonothem ¶
latestEonOrHighestEonothem ¶
earliestEraOrLowestErathem ¶
latestEraOrHighestErathem ¶
earliestPeriodOrLowestSystem ¶
latestPeriodOrHighestSystem ¶
earliestEpochOrLowestSeries ¶
latestEpochOrHighestSeries ¶
earliestAgeOrLowestStage ¶
latestAgeOrHighestStage ¶
lowestBiostratigraphicZone ¶
highestBiostratigraphicZone ¶
lithostratigraphicTerms ¶
group ¶
formation ¶
member ¶
bed ¶
Community¶
communityID ¶
"A community type is an abstract grouping of organisms that tend to co-occur on the landscape due to shared ecological requirements or preferences. May be designated by syntaxon or physiognomic types." (VegX)
Related: VegX:communityConcept, occurrenceID
communityName¶
"A textual label for a community type" (VegX)
communityConceptName ¶
Taxon ¶
"a group of one (or more) populations of organism(s), which a taxonomist adjudges to be a unit" (Wikipedia)
TaxonName ¶
PlantName ¶
taxonID ¶
parentTaxonID ¶
Related: taxonID, VegBank:plantParent_ID
scientificNameID ¶
parentScientificNameID ¶
Related: scientificNameID, VegBank:plantParent_ID
parentNameUsageID ¶
namePublishedInID ¶
scientificName ¶
Taxonomic name with author
Compare to: taxonName
taxonName¶
Taxonomic name without author
Compare to: scientificName
Named like: Taxon
taxonNameOrEpithet¶
Related: higherClassification, taxonName
Named like: specificEpithet
taxonNameWithMorphospecies ¶
It doesn't make sense to include infraspecific ranks when using morphospecies.
Use speciesBinomialWithMorphospecies instead.
Related: taxonName, morphospecies
speciesBinomial ¶
species_VegBank ¶
speciesBinomialWithMorphospecies ¶
"To be safe, we always combine the `taxon` plus `morphospecies` to produce a unique string, `taxonMorphospecies`" (Brad Boyle)
# Reconstruct morphospecies using accepted names UPDATE observations SET morphospecies= TRIM( IF(acceptedSpecies IS NOT NULL,acceptedSpecies, IF(acceptedGenus IS NOT NULL,CONCAT(acceptedGenus," ",unmatchedTerms), IF(acceptedFamily IS NOT NULL,CONCAT(acceptedFamily," ",unmatchedTerms), IF(unmatchedTerms IS NOT NULL,unmatchedTerms,nameSubmitted) ) ) ) );
taxonMorphospecies ¶
morphospecies_Brad_2 ¶
Related: speciesBinomial, morphospeciesSuffix
parentNameUsage ¶
namePublishedIn ¶
namePublishedInYear ¶
higherClassification ¶
higherPlantGroup ¶
higherPlantGroup_bien ¶
Related: higherClassification
kingdom ¶
phylum ¶
class ¶
order ¶
family ¶
genus ¶
subgenus ¶
specificEpithet ¶
species_DwC ¶
speciesName ¶
?species ¶
Alternative: species_DwC¶
Alternative: species_VegBank¶
morphospeciesSuffix ¶
"the non-standard part of the name. The morphospecies string enables accurate counting of species within a plot, even if standard species names are not known. `morphospecies` strings in theory are of two types: "dependent" morphospecies must be combined with `taxon` to be unique. Most names in the above example are of this type. "standalone" morphospecies string are unique on their own. [...] "Boyle 6155" (a citation of a voucher specimen) is standalone. "Fuzzy Miconia" and Monsterleaf are also probably standalone names as well." (Brad Boyle)
morphospecies_Brad_1 ¶
Compare to: morphoname
?morphospecies ¶
Alternative: morphospecies_Brad_1¶
Alternative: morphospecies_Brad_2¶
infraspecificRank ¶
infraspecificEpithet ¶
subspecies ¶
ssp ¶
subspeciesName ¶
variety ¶
var ¶
forma ¶
fm ¶
cultivar ¶
cv ¶
Notes: "The epithet is usually output in single quotes and may contain multiple words, see ICBN §28" (TCS)
taxonRank ¶
verbatimTaxonRank ¶
scientificNameAuthorship ¶
scientificNameAuthor ¶
vernacularName ¶
nomenclaturalCode ¶
taxonomicStatus ¶
taxonIsCanonical¶
taxonIsAccepted ¶
Named like: Taxon
nomenclaturalStatus ¶
taxonRemarks ¶
threatened ¶
concatenatedScientificName ¶
Name input to taxonomic scrubbing, which is derived from other Taxon fields
TaxonConcept ¶
A Taxon described by a specific Reference
PlantConcept ¶
Related: taxonConceptID
taxonConceptID ¶
parentTaxonConceptID ¶
Related: taxonConceptID, VegBank:plantParent_ID
nameAccordingTo ¶
"Information about the authorship of this concept which uses the Name in their sense (i.e. secundum, sensu)" (TCS)
accordingTo ¶
nameAccordingToID ¶
TaxonOccurrence¶
Any entity on which TaxonDeterminations can be made
"A taxon name string occurring within the dataset. This is a usage concept defined by the dataset author which may follow, or be according to, an additional third party. It may be further related to a published name (taxon name, tcs:TaxonName) and or taxonomic name (taxon concept, tcs:TaxonConcept) in taxonDetermination." (VegX)
Requirements: Should be at the finest level of granularity possible, i.e. each specimen, plant, size class, etc. gets its own TaxonOccurrence
TaxonNameUsageConcept ¶
Named like: Occurrence
authorTaxonCode¶
authorPlantName ¶
Related: recordNumber, VegBank:authorPlotCode, VegBank:stemCode, Taxon
taxonOccurrencePkey ¶
Related: taxonOccurrenceID
taxonOccurrenceID ¶
taxonNameUsageConceptID ¶
Related: VegBank:taxonObservation
dateCollected¶
Related: DwC:EarliestDateCollected-2007-04-17
collectedDate ¶
yearCollected ¶
monthCollected ¶
dayCollected ¶
growthForm¶
habit ¶
Related: VegBank:growthform1Type, habitClassIncluded
oldGrowth ¶
TaxonDetermination ¶
An assertion that a TaxonOccurrence is a particular Taxon
Identification ¶
TaxonInterpretation ¶
identificationID ¶
identificationType¶
interpretationType ¶
Named like: Identification
identifiedBy ¶
dateIdentified ¶
identifiedDate ¶
yearIdentified ¶
monthIdentified ¶
dayIdentified ¶
identificationQualifier ¶
fit ¶
taxonFit ¶
cf_aff ¶
annotations ¶
identificationVerificationStatus ¶
confidence ¶
taxonConfidence ¶
identificationReferences ¶
identificationRemarks ¶
typeStatus ¶
"Indicates whether this specimen served as type for taxon name" (Brad Boyle)
previousIdentifications ¶
associatedTaxa ¶
OriginalTaxonDetermination ¶
originalNameUsageID ¶
originalNameUsage ¶
originalTaxonName ¶
originalScientificName ¶
morphoname ¶
The name assigned in the field, which is unique within the plot
originalKingdom ¶
originalPhylum ¶
originalClass ¶
originalOrder ¶
originalFamily ¶
originalGenus ¶
originalSpecificEpithet ¶
originalInfraspecificEpithet ¶
originalSubspecies ¶
originalVariety ¶
originalForma ¶
originalCultivar ¶
originalTaxonRank ¶
originalScientificNameAuthorship ¶
originalIdentificationQualifier ¶
MatchedTaxonDetermination ¶
matchedScientificNameID ¶
Name_matched_url ¶
matchedTaxonName ¶
Name_matched ¶
matchedScientificName ¶
matchedKingdom ¶
matchedPhylum ¶
matchedClass ¶
matchedOrder ¶
matchedFamily ¶
Family_matched ¶
matchedGenus ¶
Genus_matched ¶
matchedSpecificEpithet ¶
Specific_epithet_matched ¶
matchedMorphospecies ¶
Unmatched_terms ¶
matchedInfraspecificEpithet ¶
Infraspecific_epithet_matched ¶
matchedSubspecies ¶
matchedVariety ¶
matchedForma ¶
matchedCultivar ¶
matchedTaxonRank ¶
Name_matched_rank ¶
matchedScientificNameAuthorship ¶
Name_matched_author ¶
Author_matched ¶
matchedIdentificationQualifier ¶
matchedTaxonConfidence_fraction¶
overallScore ¶
Related: taxonConfidence, TNRS:Name_matched
matchedFamilyConfidence_fraction¶
familyScore ¶
Related: taxonConfidence, TNRS:Family_matched
matchedGenusConfidence_fraction¶
genusScore ¶
Related: taxonConfidence, TNRS:Genus_matched
matchedSpeciesConfidence_fraction¶
specificEpithetScore ¶
Related: taxonConfidence, TNRS:Specific_epithet_matched
Named like: species
AcceptedTaxonDetermination ¶
acceptedNameUsageID ¶
acceptedNameUsage ¶
acceptedScientificNameID ¶
acceptedTaxonName ¶
acceptedScientificName ¶
acceptedKingdom ¶
acceptedPhylum ¶
acceptedClass ¶
acceptedOrder ¶
acceptedFamily ¶
acceptedGenus ¶
acceptedSpecificEpithet ¶
acceptedInfraspecificEpithet ¶
acceptedSubspecies ¶
acceptedVariety ¶
acceptedForma ¶
acceptedCultivar ¶
acceptedTaxonRank ¶
acceptedScientificNameAuthorship ¶
acceptedIdentificationQualifier ¶
TaxonObservation ¶
An observation of just a Taxon's presence
SpeciesInventory ¶
taxonObservationID ¶
speciesInvID ¶
occurrenceStatus ¶
AggregateObservation¶
"An observation applying to all occurrences of an organism based on an aggregation factor" (VegX)
"the importance (i.e. cover, basal area, biomass) of [a] taxon observed on a plot" (VegBank)
AggregateOrganismObservation ¶
AggregateOccurrence ¶
TaxonImportance ¶
Related: VegBank:stemCount, IndividualObservation
aggregateOrganismObservationID ¶
aggregateOccurrenceID¶
individualCount ¶
coverPercent ¶
"Average cover of the index in percent" (VegX)
?intercept ¶
intercept_m¶
intercept_cm ¶
individualCount_1cm_or_more¶
abund1cm ¶
Related: individualCount
individualCount_2_5cm_or_more¶
abund2_5cm ¶
Related: individualCount
individualCount_10cm_or_more¶
abund10cm ¶
Related: individualCount
Individual¶
A distinct biological organism
IndividualOrganism ¶
Organism¶
Tree ¶
Related: IndividualObservation
individualID ¶
tag¶
identificationLabel ¶
tag2 ¶
IndividualObservation¶
An observation of an Individual
IndividualOrganismObservation ¶
OrganismObservation¶
PlotObservation_SALVIAS ¶
Related: Individual
individualObservationID ¶
The unique identifier for the observation of an individual
Requirements: Must be unique within the datasource
individualOrganismObservationID ¶
ID_TEAM ¶
Related: individualID
Suggestions: Usually set to a database primary key
individualCode ¶
authorPlantCode¶
Named like: authorPlotCode, PlantConcept
organismX_m¶
"The X-coordinate of the related item position in m. The user will enter the relative position of related item with respect to the plot origin (in meters) with the x-axis defined by the plot azimuth." (VegX)
individualOrganismObservationRelativeX ¶
organismY_m¶
"The Y-coordinate of the relatedSpatialItem position in m. The user will enter the relative position of relatedSpatialItems with respect to the plot origin (in meters) with the y-axis defined by the plot azimuth." (VegX)
individualOrganismObservationRelativeY ¶
censusNumber¶
censusNo ¶
stemCount ¶
sex ¶
lifeStage ¶
reproductiveCondition ¶
phenology ¶
behavior ¶
establishmentMeans ¶
cultivated ¶
cultivated_bien ¶
cultivatedBasis¶
Related: cultivated
cultivatedBasis_bien ¶
canopyForm¶
stemCanopyForm ¶
canopyPosition¶
stemCanopyPosition ¶
lianaInfestation¶
stemLianaInfestation ¶
organismNotes¶
fieldNotes_DwC_curatorial ¶
remarks ¶
notes_SALVIAS ¶
?fieldNotes ¶
Alternative: fieldNotes_DwC_curatorial¶
Alternative: fieldNotes_DwC_terms¶
?notes ¶
Alternative: notes_SALVIAS¶
Alternative: notes_Madidi¶
Stem ¶
An "individual tree stem" (VegBank)
StemLocation ¶
Related: StemObservation, Individual
stemID ¶
stemTag¶
stemTag2 ¶
StemObservation¶
An observation of a Stem
Related: Stem, IndividualObservation
authorStemCode¶
"Name or code applied to a specific stem in the plot. This is generally a numeric label to associate a field data entry with a stem in the database." (VegBank)
stemCode ¶
Named like: authorPlotCode
?height ¶
"The measured height of the stem" (VegBank)
?stemHeight ¶
height_m¶
height_ft¶
?heightFirstBranch ¶
heightFirstBranch_m¶
htFirstBranch_m ¶
heightFirstBranch_ft¶
?diameterBreastHeight ¶
?stemDbh ¶
?DBH ¶
diameterBreastHeight_m¶
diameterBreastHeight_cm¶
diameterBreastHeight_in¶
?diameterBreastHeightGentry ¶
?gentryDbh ¶
diameterBreastHeightGentry_m¶
diameterBreastHeightGentry_cm¶
diameterBreastHeightGentry_in¶
?basalDiameter ¶
?basalDiam ¶
basalDiameter_m¶
basalDiameter_cm¶
basalDiameter_in¶
stemNotes ¶
Collection ¶
"the collection within the institution where a specimen is held" (Brad Boyle)
A type of dataset that applies only to specimens
collection ¶
"the collection within the institution where a specimen is held. This is not an important field for herbaria because the herbarium acronym (institutionCode) is already globally unique. Herbaria typically use a word describing the type of collection, such as "herbarium", although I have also seen the acronym repeated here. Needed for animal collections where institutionCode is the name of a university and collectionCode distinguishes one of several collections (e.g., institutionCode="University of Colorado", collectionCode="Mammals"). In general, use whatever the data provider provides, unless badly formed." (Brad Boyle)
collectionCode ¶
collectionURL ¶
collectionID ¶
Specimen ¶
A "part of a plant" (Wikipedia) which was collected from it
Related: Occurrence
specimenHolders ¶
The institution(s) holding a copy of the specimen
"Identifies the institution where a specimen is held. For herbaria, this will be the acronym of the herbarium. In general, use the verbatim value provided by the data provider, unless this is incorrect. For an aggregator such as GBIF, this column will contain many values corresponding to different data providers. For a primary source (e.g., New York Botanical Garden), all values should be the same (e.g., "NY"). Some herbaria incorrectly list the acronym that sent them the specimen if it was an exchange or trade. This is incorrect. Only the acronym of the herbarium providing the data should be listed here, regardless of whether they collected the specimen themselves or received it as a duplicate from another herbarium." (Brad Boyle)
specimenHolder ¶
institutionCode_DwC ¶
Compare to: specimenIndexer
specimenHolderURL ¶
institutionID ¶
?institutionCode ¶
Alternative: institutionCode_DwC¶
Alternative: institutionCode_UNCC¶
specimenIndexer ¶
The institution that stamped an accession number or barcode on the specimen
"The name or acronym in use by the institution that donated the collection" (Bob Peet)
"the acronym [of the donor institution] that sent [...] the specimen if it was an exchange or trade" (Brad Boyle)
specimenDonor ¶
institutionCode_UNCC ¶
specimenOwner ¶
The institution which owns the specimen. This is specimenHolder if the specimen was donated or specimenIndexer if it was lent.
ownerInstitutionCode ¶
barcode ¶
"a bar code, machine-generated and glued or stamped to the specimen and recorded in the database" (Brad Boyle)
"IF a herbarium provides a field labelled "barCode" (or similar) that value goes here, otherwise NULL. Should be locally unique within the dataset (it may also be unique within the datasource if datasource=dataset)." (Brad Boyle)
Scope: specimenIndexer (not custodialInstitution) + collection
If the specimenIndexer is not provided, the custodialInstitution may be substituted instead. If multiple custodialInstitutions are specified, this assumes that they all share the same barcode.
accessionNumber ¶
"an accession number stamped physically on the specimen [...] The accession number is the most widely used, but is not guaranteed to be unique because of the physical stamping process, human error, etc." (Brad Boyle)
"Whatever the data provider provides, as long as catalogNumber is unique within the dataset. If no catalogNumber provided, use accessionNumber, but only if it is unique within the dataset. If no accession number, use datasetRecordID, else use barCode, else use datasourceRecordID. This usage differs from DwC in that catalogNumber is constrained to be unique within the dataset. It is populated for plot data as well as specimens." (Brad Boyle)
Scope: specimenIndexer (not custodialInstitution) + collection
If the specimenIndexer is not provided, the specimenHolder may be substituted instead. If multiple specimenHolders are specified, this assumes that they all share the same catalogNumber.
accession ¶
museumAccessionNumber ¶
catalogNumber ¶
collectorNumber ¶
Scope: none
collectionNumber ¶
recordNumber ¶
fieldNumber_DwC_classic ¶
?fieldNumber ¶
Alternative: fieldNumber_DwC_classic¶
Alternative: fieldNumber_DwC_terms¶
preparations ¶
preparationType ¶
preparation ¶
disposition ¶
otherCatalogNumbers ¶
previousCatalogNumber ¶
Voucher¶
voucherType¶
Values: direct, indirect
detType ¶
Measurement¶
An attribute of any type of Occurrence
MeasurementOrFact ¶
TraitObservation ¶
Trait¶
measurementID ¶
measurementName¶
measurementType ¶
traitName ¶
measurementValue ¶
traitValue ¶
measurementAccuracy ¶
measurementUnit ¶
unit ¶
measurementDeterminedDate ¶
measurementDeterminedBy ¶
measurementMethod ¶
measurementRemarks ¶
ResourceRelationship ¶
"information pertaining to relationships between resources (instances of data records, such as Occurrences, Taxa, Locations, Events)" (DwC)
resourceRelationshipID ¶
resourceID ¶
relatedResourceID ¶
relatedCatalogItem ¶
relationshipOfResource ¶
relationshipType ¶
relationshipAccordingTo ¶
relationshipEstablishedDate ¶
relationshipRemarks ¶
Special terms¶
OMIT¶
The field contains data but should be omitted
The reason for omission should be described in the mapping's comments
PRIVATE¶
The field contains private data which should be omitted from a public database
UNUSED¶
The field does not contain any data
The following query should return no rows: SELECT * FROM table WHERE field IS NOT NULL
Sources¶
Mouse over a source's acronym to see its full name
Exchange schemas¶
DwC¶
VegCore includes all Darwin Core terms (some have been renamed)
DwC-terms¶
DwC-history¶
DwC-MaNIS¶
DwC-classic¶
DwC-dwcore¶
TCS¶
VegX¶
Aggregators¶
VegBank¶
SALVIAS¶
BIEN2¶
BIEN2-web¶
BIEN2-core¶
BIEN2-DB¶
Primary databases¶
TNRS¶
CTFS¶
CTFS-DB¶
CTFS-v5¶
Data dictionaries¶
Brad Boyle¶
Brad Boyle's BIEN database entities related to data provenance and ownership¶
Brad Boyle's DwC ID terms from 2013-2-7¶
Brad Boyle's DwC ID terms from 2013-1-31¶
Editing¶
- To get the Redmine syntax for linking to a term, copy the portion of that term's header with the form
[[VegCore#term_anchor|term_name]] - After adding or renaming a term, be sure to regenerate the VegCore downloads, using the steps in README.TXT > Maintenance > VegCore data dictionary
Note: This section must stay on the same page as the data dictionary so that its templates are refactored along with it
Naming¶
- A term name should always be unambiguous to allow seamlessly combining data from arbitrary datasets
- The preferred name for a term is the shortest name which unambiguously identifies the concept
- Determine the shortest name using the following factors, in order:
- the number of syllables
- the number of characters
- the number of uncommon characters (i.e. the complexity of the spelling)
Tables¶
- Table names are capitalized
- Table names should always be singular, not plural
Table template:¶
All sections are optional
h1. [[VegCore#Table|Table]] !{padding-left: 1em; font-size: small; font-weight: normal;}_(from)! !{font-size: small;}_(Source)!:URL#TableAsSpelledBySource
p(((. definition
h3((. !{padding: 0 0.3em 3pt 0.75em; font-weight: normal;}_(Synonym:)! [[VegCore#Table|Table]] !{padding-left: 1em; font-size: small; font-weight: normal;}_(from)! !{font-size: small;}_(Source)!:URL#SynonymAsSpelledBySource
[fields...]
Fields¶
- Field names start with a lowercase letter
Field template:¶
All sections are optional
h2((. [[VegCore#field|field]] !{padding-left: 1em; font-size: small; font-weight: normal;}_(from)! !{font-size: small;}_(Source)!:URL#fieldAsSpelledBySource
p(((((. definition
p(((((. Scope: [[VegCore#uniqueWithinTerm1|uniqueWithinTerm1]] + [[VegCore#uniqueWithinTerm2|uniqueWithinTerm2]]
h3((((. !{padding: 0 0.3em 3pt 0.65em; font-weight: normal;}_(Synonym:)! [[VegCore#synonym|synonym]] !{padding-left: 1em; font-size: small; font-weight: normal;}_(from)! !{font-size: small;}_(Source)!:URL#synonymAsSpelledBySource
p(((((. Related: [[VegCore#relatedTerm|relatedTerm]]
p(((((. Named like: [[VegCore#similarlyNamedTerm|similarlyNamedTerm]]
ID template:¶
- See also Forming IDs
h2((. [[VegCore#ID|ID]] !{padding-left: 1em; font-size: small; font-weight: normal; font-style: italic;}_(globally unique)! !{padding-left: 1em; font-size: small; font-weight: normal;}_(from)! !{font-size: small;}_(Source)!:URL#fieldAsSpelledBySource
[...]
Ambiguous terms¶
- Ambiguous term names must start with
?(this is required by scripts that parse the data dictionary page) - Except for fields requiring units, each alternative should also be listed as a synonym of an unambiguous term.
All such synonyms must occur before the ambiguous term itself to ensure that the alternatives' anchors link to their definition rather than to their appearance in the alternatives list. - Term and synonym headers have the form
[[VegCore#term|?term]]. The leading ? will be displayed in the data dictionary but won't be part of the HTML anchor, which allows the term to be permalinked using just its name.
Ambiguous table template:¶
h1. [[VegCore#AmbiguousTable|?AmbiguousTable]] !{padding-left: 1em; font-size: small; font-weight: normal; font-style: italic;}_(AMBIGUOUS)!
h3(((. Alternative: [[VegCore#AmbiguousTable_Source1|AmbiguousTable_Source1]]
h3(((. Alternative: [[VegCore#AmbiguousTable_Source2|AmbiguousTable_Source2]]
[...]
h1. [[VegCore#Alternative1UnambiguousName|Alternative1UnambiguousName]] [...]
[...]
h3((. !{padding: 0 0.3em 3pt 0.75em; font-weight: normal;}_(Synonym:)! [[VegCore#AmbiguousTable_Source1|AmbiguousTable_Source1]] !{padding-left: 1em; font-size: small; font-weight: normal;}_(from)! [...] !{padding-left: 1em; font-size: small; font-weight: normal;}_(alternative of)! !{font-size: small;}_(?AmbiguousTable)!:https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#AmbiguousTable
Ambiguous field template:¶
h2((. [[VegCore#ambiguousTerm|?ambiguousTerm]] !{padding-left: 1em; font-size: small; font-weight: normal; font-style: italic;}_(AMBIGUOUS)!
h3(((((. Alternative: [[VegCore#ambiguousTerm_Source1|ambiguousTerm_Source1]]
h3(((((. Alternative: [[VegCore#ambiguousTerm_Source2|ambiguousTerm_Source2]]
[...]
h2((. [[VegCore#alternative1UnambiguousName|alternative1UnambiguousName]] [...]
[...]
h3((((. !{padding: 0 0.3em 3pt 0.65em; font-weight: normal;}_(Synonym:)! [[VegCore#ambiguousTerm_Source1|ambiguousTerm_Source1]] !{padding-left: 1em; font-size: small; font-weight: normal;}_(from)! [...] !{padding-left: 1em; font-size: small; font-weight: normal;}_(alternative of)! !{font-size: small;}_(?ambiguousTerm)!:https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#ambiguousTerm
Field requiring units template:¶
This also includes enums (picklists). In this case, the units are the name of a vocabulary (which is often the name of the source which defines it).
Synonyms sections are optional
h2((. [[VegCore#fieldRequiringUnits|?fieldRequiringUnits]] !{padding-left: 1em; font-size: small; font-weight: normal; font-style: italic;}_(requires units)!
h3((((. !{padding: 0 0.3em 3pt 0.65em; font-weight: normal;}_(Synonym:)! [[VegCore#synonym|?synonym]] !{padding-left: 1em; font-size: small; font-weight: normal; font-style: italic;}_(requires units)! !{padding-left: 1em; font-size: small; font-weight: normal;}_(from)! !{font-size: small;}_(Source)!:URL#synonymAsSpelledBySource
h3((((. !{padding: 0 0.3em 3pt 0.65em; font-weight: normal;}_(Unit alternative:)! [[VegCore#fieldRequiringUnits_units1|fieldRequiringUnits_units1]]
h3((((((. !{padding: 0 0.3em 3pt 0.65em; font-weight: normal;}_(Synonym:)! [[VegCore#synonym_units1|synonym_units1]] !{padding-left: 1em; font-size: small; font-weight: normal;}_(from)! !{font-size: small;}_(Source)!:URL#synonymAsSpelledBySource
h3((((. !{padding: 0 0.3em 3pt 0.65em; font-weight: normal;}_(Unit alternative:)! [[VegCore#fieldRequiringUnits_units2|fieldRequiringUnits_units2]]
Related pages¶
ACAD.Specimen.csv 
(12 KB)
vegbien_identifier_examples.xlsx (28.6 KB)
vegbien_identifiers.xlsx (30.1 KB)
BIEN database entities related to data provenance and ownership.docx (157 KB)