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VegCore data dictionary

VegCore is a vegetation exchange schema which combines 380+ terms and 38 tables from existing exchange schemas

Examples

Example specimen data

See ACAD.Specimen.csv1, which contains well-formed Darwin Core data.

1 This public domain dataset is from ACAD, a Canadensys herbarium
 

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.

Downloads

Vocabulary | Thesaurus


normalized VegCore schema

The schema makes extensive use of inheritance, which can be implemented in several ways. The tables are shown in the ERD using class table inheritance (option 3 in the link), which is considered the best practice for most database engines. However, if and only if PostgreSQL-style inheritance ever supports foreign keys3, it may then be better to use concrete table inheritance (option 2), which avoids both the need to insert into each superclass table separately, and the need to join to superclass tables when selecting2. Until this is available, you can also get these benefits via single table inheritance (option 1, which is the denormalized, full_occurrence format) at the expense of being messier (not having separate tables for the separate subclasses).

2 at the cost of slightly slower index scans when there is a large number of subclasses and rows are evenly distributed between them (because each subclass index needs to be scanned separately).
also, when inserting into a subclass, you need to explicitly check that the pkey doesn't exist in any superclass (or sibling subclass), because unique indexes don't include superclass rows.

3 "A serious limitation of the inheritance feature is that indexes (including unique constraints) and foreign key constraints only apply to single tables, not to their inheritance children. This is true on both the referencing and referenced sides of a foreign key constraint." (PostgreSQL: Inheritance > Caveats)
however, you can simulate a foreign key using a domain type with a CHECK constraint that SELECTs on the referenced table. this SELECT statement will also query subclass tables, making this a suitable way of implementing foreign keys to superclass tables.

VegCore schema: click for hyperlinked version


denormalized VegCore entities

Source
Dataset
Record
Occurrence
Method
Stratum
Project
Event
EventParticipant
Coordinates
Placename
Geovalidation
Location
LocationObservation
Subplot
SubplotObservation
SoilObservation
GeologicalContext
Community
TaxonName
TaxonConcept
QualifiedTaxonName
MatchedTaxon
AcceptedTaxon
TaxonOccurrence
TaxonDetermination
OriginalTaxonDetermination
AggregateObservation
Individual
IndividualObservation
Stem
StemObservation
Collection
Specimen
Voucher
Measurement
ResourceRelationship


Source from BIEN2 | Brad Boyle

a "reference[...] cited within the database" (VegBank)

Synonym: Datasource from BIEN2 | Brad Boyle

Synonym: DataProvider from Brad Boyle

Synonym: Reference from VegBank

sourceType from VegBank

Values: herbarium, primary database, aggregator, ...

Synonym: referenceType from VegBank

Synonym: aggregatorOrPrimary from BIEN2

Components:

isHerbarium from BIEN2

source text ID from BIEN2 | Brad Boyle

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)

Synonym: proximateDataProvider from Brad Boyle

Synonym: dataProvider from Brad Boyle

Synonym: dataSource from BIEN2 | Brad Boyle

Synonym: dataSourceName from BIEN2

firstPublisher text ID from Brad Boyle

Who initially published the data. This is usually an institution.

"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)

Synonym: primaryDataProvider from Brad Boyle

Synonym: dataPublisher from Brad Boyle

distributors

The data distributors through which the record passed, starting with the source and ending with the firstPublisher

The entities that "provide electronic access to a dataset" (Brad Boyle)

Synonym: dataProviders from Brad Boyle

Synonym: references from DwC

Synonym: dcterms_references from DwC

data_authors text ID from Brad Boyle

Who made the observation the data record is based on. This is usually a person. For a specimen or measurement, this is the collector.

"The persons or institutions who created the data on which a dataset is based. Note that digitization of data (for example, digitization of a specimen by a herbarium) does not by itself constitute authorship. A herbarium that digitizes a specimen is the datapublisher, not a dataauthor, of that specimen. The dataauthor of a specimen is the collector." (Brad Boyle)

Synonym: data_author from Brad Boyle

dataOwners text ID from Brad Boyle

"A dataauthor who retains at least minimum ownership rights. A test of minimum ownership rights is acknowledgement: if you are obliged to cite a dataauthor, they they are also a dataowner. Collectors of individuals specimens are not considered data owners as they are not typically acknowledged. Dataowner may have more extensive ownership rights, including the right to restrict access to their data and the right to be offer coauthorship in publications which use their data." (Brad Boyle)

Synonym: dataOwner from Brad Boyle

Synonym: rightsHolder from DwC

Synonym: dcterms_rightsHolder from DwC

Synonym: datasetOwner from Brad Boyle

source__version from conference call

Synonym: edition from VegBank

source__modified_date from Brad Boyle

This applies to the source rather than the data record

Synonym: pubDate from VegBank

Compare to: modified

Dataset from DwC | Brad Boyle

Synonym: DataResource from Brad Boyle

dataset text ID from DwC | Brad Boyle

"One or more data records managed together as a unit, and limited in scope in one or more ways, for example, to a particular region ("Madidi National Park forest plots"), a particular author ("Alwyn Gentry Transect Dataset"), a particular taxon ("University of Arizona Mycological Collection"), a particular research project ("La Selva secondary forest plots") or a particular data publisher (typically, a herbarium, such as New York Botanical Garden)" (Brad Boyle)

"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)

Synonym: dataResource from Brad Boyle

Synonym: datasetName from DwC

datasetURL text ID from DwC | Brad Boyle

Synonym: datasetID from DwC | Brad Boyle

Record from DwC

recordID text ID analogous to occurrenceID

dataProviderRecordID from Brad Boyle

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

Synonym: datasourceRecordID from Brad Boyle

Synonym: ID_Canadensys from Canadensys | U alternative of ?ID

Synonym: globalUniqueIdentifier_SpeciesLink from SpeciesLink alternative of ?globalUniqueIdentifier

?ID AMBIGUOUS

Alternative: ID_Canadensys

Alternative: ID_TEAM

datasetRecordID from Brad Boyle

"Unique ID (database primary key) for the specimen or observation in the dataset, if provided." (Brad Boyle)

Scope: dataset

type

Synonym: dcterms_type from DwC

modified

"an internal timestamp indicat[ing] when record last modified, not necessarily when determination (taxon name) last modified" (Brad Boyle)

Synonym: dcterms_modified from DwC

Synonym: dateLastModified from DwC

language

Synonym: dcterms_language from DwC

rights

Synonym: dcterms_rights from DwC

accessRights

Synonym: dcterms_accessRights from DwC

bibliographicCitation

Synonym: dcterms_bibliographicCitation from DwC

informationWithheld from DwC

dataGeneralizations from DwC

dynamicProperties from DwC

Occurrence from DwC | DwC ToC

An observation of any entity, biological or otherwise

Synonym: Observation_VegCore alternative of ?Observation

occurrenceID text ID from DwC

"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)

Synonym: globalUniqueIdentifier_DwC from DwC alternative of ?globalUniqueIdentifier

?globalUniqueIdentifier AMBIGUOUS

Alternative: globalUniqueIdentifier_DwC

Alternative: globalUniqueIdentifier_SpeciesLink

basisOfRecord from DwC

occurrenceRemarks from DwC

Synonym: organismNotes from VegX

Synonym: fieldNotes_DwC_curatorial from DwC alternative of ?fieldNotes

Synonym: remarks from DwC

Synonym: notes_SALVIAS from SALVIAS alternative of ?notes

?fieldNotes AMBIGUOUS

Alternative: fieldNotes_DwC_curatorial

Alternative: fieldNotes_DwC_terms

?notes AMBIGUOUS

Alternative: notes_SALVIAS

Alternative: notes_Madidi

recordedBy from DwC

"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)

Synonym: collector from DwC

Components:

recordedBy_givenName from VegX

"The given name" (VegX)

recordedBy_middleName from VegBank

The "middle name or initial" (VegBank)

recordedBy_surName from VegX

"The last name" (VegX)

associatedMedia from DwC

associatedReferences from DwC

associatedOccurrences from DwC

associatedSequences from DwC

?Observation AMBIGUOUS

Alternative: Observation_VegCore

Alternative: Observation_VegBank

Method from VegX

"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)

Synonym: SamplingProtocol from DwC

Related: VegBank:stratumMethod, VegBank:coverMethod

samplingProtocolID text ID

samplingProtocol from DwC

Synonym: method

Named like: Method

Synonym: methodology

Synonym: plotMethodology from SALVIAS

samplingEffort from DwC

?observationType AMBIGUOUS

Alternative: observationType_SALVIAS

Alternative: observationType_BIEN2

observationGranularity

Values: plot, specimen

Synonym: observationType_BIEN2 from BIEN2 alternative of ?observationType

observationMeasure from Brad Boyle's method attribute examples spreadsheet

Values: count, cover, presence, points-intercepted, distance-intercepted

Synonym: observationType_SALVIAS from SALVIAS alternative of ?observationType

Stratum from VegX | VegBank

a non-horizontal way of subdividing a plot

stratum__name from VegX | VegBank

Project from VegX | VegBank

A "project established to collect vegetation plot data. Each plot originates as part of a project." (VegBank)

projectID text ID from VegX

"A reference to a specific 'project'" (VegX)

projectName

"Title of the project" (VegX)

Synonym: projectTitle from VegX

Named like: plotName

projectStartDate from VegBank

"Project start date" (VegBank)

Named like: startDate

projectEndDate from VegBank

"Project stop date" (VegBank)

Named like: endDate

Event from DwC | DwC ToC

"an action that occurs at a place and during a period of time" (DwC)

eventID text ID from DwC

Synonym: censusID from CTFS

eventDate from DwC

"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)

Synonym: obsStartDate from VegX

Related: eventDate

endDate

"The end date" (VegX) of the "interval during which an Event occurred" (DwC)

Synonym: obsEndDate from VegX

Related: eventDate

eventTime from DwC

Synonym: timeOfDay from DwC

dayOfYear from DwC

the day of the month

Synonym: julianDay from DwC

startDayOfYear from DwC

endDayOfYear from DwC

year from DwC

month from DwC

day from DwC

verbatimEventDate from DwC

authorEventCode

"the code or name that the author uses to identify [the] event" (VegBank)

Synonym: authorObsCode from VegBank

Synonym: plotCensusNumber from CTFS

Synonym: fieldNumber_DwC_terms from DwC alternative of ?fieldNumber

eventRemarks from DwC

"the text of notes taken in the field about the Event" (DwC)

Synonym: fieldNotes_DwC_terms from DwC alternative of ?fieldNotes

EventParticipant

A participant in an Event

Synonym: ObservationContributor from VegBank

event__participant from VegBank

project_participant from VegBank

Coordinates from CTFS

A numerically-defined point

?latitude requires units from DwC

Unit alternative: decimalLatitude from DwC

Unit alternative: verbatimLatitude from DwC

Unit alternative: latitude_DMS

Components:

latitude_deg from REMIB

latitude_min from REMIB

latitude_sec from REMIB

?longitude requires units from DwC

Unit alternative: decimalLongitude from DwC

Unit alternative: verbatimLongitude from DwC

Unit alternative: longitude_DMS

Components:

longitude_deg from REMIB

longitude_min from REMIB

longitude_sec from REMIB

acceptedDecimalLatitude analogous to decimalLatitude

acceptedDecimalLongitude analogous to decimalLongitude

realLatitude from VegBank

Replace with: PRIVATE

realLongitude from VegBank

Replace with: PRIVATE

verbatimCoordinates from DwC

coordinateUnits from DwC

Synonym: ?verbatimCoordinateSystem from DwC

?verbatimCoordinateSystem AMBIGUOUS

Alternative: coordinateUnits

Alternative: geodeticDatum

verbatimSRS from DwC

geodeticDatum from DwC

Synonym: ?verbatimCoordinateSystem from conference call on 2013-2-28

?coordinateUncertainty requires units from DwC

Synonym: ?coordinatePrecision from DwC

Unit alternative: coordinateUncertaintyInMeters from DwC

Unit alternative: coordinatePrecision_deg from DwC

pointRadiusSpatialFit from DwC

footprintWKT from DwC

Synonym: boundingBox from DwC

Synonym: shapeOfSite from CTFS

footprintSRS from DwC

footprintSpatialFit from DwC

georeferencedBy from DwC

georeferencedDate from DwC

georeferenceProtocol from DwC

Synonym: georeferenceProtocol_bien from Brad Boyle

georeferenceSources from DwC

Where the coordinates came from

Values: source data, GPS, georeferencing, ...

Synonym: coordinateSource from Brad Boyle

Synonym: coordinateSource_bien from Brad Boyle

georeferenceVerificationStatus from DwC

georeferenceRemarks from DwC

Placename

A named region

Synonym: NamedPlace from VegBank

higherGeographyID text ID from DwC

higherGeography from DwC

continent from DwC

Synonym: continentOcean from DwC

waterBody from DwC

islandGroup from DwC

island from DwC

country from DwC

Synonym: countryName from CTFS

acceptedCountry

Related: country, acceptedNameUsage

countryCode from DwC

stateProvince from DwC

Synonym: state from NCU-NCSC | REMIB | UNCC

acceptedStateProvince

Related: stateProvince, acceptedNameUsage

county from DwC

acceptedCounty

Related: county, acceptedNameUsage

municipality from DwC

locality from DwC

Synonym: verbatimLocality from DwC

Synonym: locationNarrative from VegX

Synonym: descriptionOfSite from CTFS

Geovalidation

The accuracy of the Coordinates, taking into account the Placename

Synonym: Geoscrub from BIEN2

Named like: geovalid

geovalid

Synonym: isGeovalid from BIEN2

latLongDomainValid

Whether the coordinates are in the range of valid decimal values

Synonym: isValidLatLong from BIEN2

latLongDomainInvalid

Whether the coordinates are not in the range of valid decimal values

Synonym: isBadLatLong from BIEN2

Named like: isValidLatLong

latLongInCountry

Synonym: isInCountry from BIEN2

Named like: isValidLatLong, country

?distanceToCountry requires units

Synonym: ?distErrCountry requires units from BIEN2

Named like: country

Unit alternative: distanceToCountry_m

Unit alternative: distanceToCountry_km

latLongInStateProvince

Synonym: isInStateProvince from BIEN2

Named like: isValidLatLong, stateProvince

?distanceToStateProvince requires units

Synonym: ?distErrStateProvince requires units from BIEN2

Named like: stateProvince

Unit alternative: distanceToStateProvince_m

Unit alternative: distanceToStateProvince_km

latLongInCounty

Synonym: isInCountyParish from BIEN2

Named like: isValidLatLong, county

isNewWorld from BIEN2

Synonym: isNewWorld_bien from Brad Boyle

Location from DwC | DwC ToC

"A spatial region" (DwC) or point

Synonym: Plot from VegX | VegBank

Synonym: PlotLocation from Madidi

locationID text ID from DwC

Synonym: plotID from VegX

Synonym: plotUniqueIdentifierID from VegX

locationName

"Name or label for a plot" (VegX)

Synonym: plotName from VegX

Synonym: authorPlotCode from VegBank

Synonym: locationNumber

Named like: recordNumber

parentLocationID text ID

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 from DwC

LocationObservation

A sampling of a Location

Synonym: PlotObservation_VegX from VegX alternative of ?PlotObservation

Synonym: Observation_VegBank from VegBank alternative of ?Observation

Synonym: PlotInventory from Madidi

Related: Location, VegBank:plot

locationRemarks from DwC

Synonym: plotNotes

Synonym: plotNote from VegX

Synonym: notes_Madidi from Madidi#Notes alternative of ?notes

?elevation requires units from DwC | CTFS

Unit alternative: elevationInMeters

Unit alternative: elevation_ft

Unit alternative: verbatimElevation from DwC

Value must include units

Unit alternative: verbatimElevation_m

Components:

?minimumElevation requires units from DwC

Unit alternative: minimumElevationInMeters from DwC

Unit alternative: minimumElevation_verbatim

Value must include units

?maximumElevation requires units from DwC

Unit alternative: maximumElevationInMeters from DwC

Unit alternative: maximumElevation_verbatim

Value must include units

?depth requires units

Unit alternative: verbatimDepth from DwC

Components:

?minimumDepth requires units from DwC

Unit alternative: minimumDepthInMeters from DwC

Unit alternative: minimumDepth_verbatim

Value must include units

?maximumDepth requires units from DwC

Unit alternative: maximumDepthInMeters from DwC

Unit alternative: maximumDepth_verbatim

Value must include units

distanceAboveSurfaceInMeters

Components:

minimumDistanceAboveSurfaceInMeters from DwC

maximumDistanceAboveSurfaceInMeters from DwC

?plotArea requires units

"Total area of the plot" (VegX)

Synonym: ?area requires units from VegX

Unit alternative: plotArea_m2

Unit alternative: plotArea_ha from SALVIAS

slopeAspect from VegX

"Representative azimuth of slope gradient (0-360 degrees) or as a cardinal direction (e.g. N, S, NE)" (VegX)

minSlopeAspect from VegBank

maxSlopeAspect from VegBank

slopeGradient from VegX

"Representative inclination of slope in degrees" (VegX)

minSlopeGradient from VegBank

maxSlopeGradient from VegBank

landform from VegX

"A recognizable physical feature on the surface of the earth, often including consideration of the natural cause of its formation" (VegX)

?temperature requires units from VegX

"Temperature during observation" (VegX)
"Mean annual temperature" (SALVIAS)

Unit alternative: temperature_C

Synonym: temp_C from SALVIAS

Unit alternative: temperature_F

?precipitation requires units

Unit alternative: precipitation_m

Unit alternative: precipitation_mm

Synonym: precip_mm from SALVIAS

habitat from DwC

?PlotObservation AMBIGUOUS

Alternative: PlotObservation_VegX

Alternative: PlotObservation_SALVIAS

Subplot

"subplot, line, or any other subsample or subdivision of plot" (SALVIAS)

Related: SALVIAS:subplot

subplotID text ID

Synonym: quadratID from CTFS

Related: locationID, SALVIAS:subplot

subplot from SALVIAS

Scope: locationID

Synonym: quadratName from CTFS

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)

Synonym: plotRelativeX from VegX

Synonym: startX from CTFS

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)

Synonym: plotRelativeY from VegX

Synonym: startY from CTFS

SubplotObservation

A sampling of a Subplot

Related: Subplot, LocationObservation

SoilObservation

A sampling of a Location's soil

Synonym: AbioticObservation from VegX

Synonym: SoilObs from VegBank

?phosphorus requires units from VegX

"Phosphorus of soil" (VegX)

Unit alternative: phosphorus_fraction

Unit alternative: phosphorus_percent

?potassium requires units

"Pottasium of soil" (VegX)

Synonym: ?pottasium requires units from VegX

Unit alternative: potassium_fraction

Unit alternative: potassium_percent

?magnesium requires units from VegX

"Magnesium of soil" (VegX)

Unit alternative: magnesium_fraction

Unit alternative: magnesium_percent

?nitrogen requires units from VegX

"Nitrogen of soil" (VegX)

Unit alternative: nitrogen_fraction

Unit alternative: nitrogen_percent

?carbon requires units

Synonym: ?soilC requires units from SALVIAS

Unit alternative: carbon_fraction

Unit alternative: carbon_percent

?calcium requires units

Synonym: ?soilCa requires units from SALVIAS

Unit alternative: calcium_fraction

Unit alternative: calcium_percent

?sodium requires units

Synonym: ?soilNa requires units from SALVIAS

Unit alternative: sodium_fraction

Unit alternative: sodium_percent

?acidity requires units

Synonym: ?soilAcidity requires units from SALVIAS

Unit alternative: acidity_fraction

Unit alternative: acidity_percent

?organic requires units

Synonym: ?soilOrganic requires units from VegBank

Unit alternative: organic_fraction

Unit alternative: organic_percent

texture

Synonym: soilTexture from VegBank

?sand requires units

Synonym: ?soilSand requires units from VegBank

Unit alternative: sand_fraction

Unit alternative: sand_percent

?silt requires units

Synonym: ?soilSilt requires units from VegBank

Unit alternative: silt_fraction

Unit alternative: silt_percent

?clay requires units

Synonym: ?soilClay requires units from VegBank

Unit alternative: clay_fraction

Unit alternative: clay_percent

ph from VegX

"The pH of the soil" (VegX)

?cationExchangeCapacity requires units from Wikipedia

Synonym: ?exchangeCapacity from VegBank

Synonym: ?soilCationCap from SALVIAS

Unit alternative: cationExchangeCapacity_cmol_kg from Wikipedia

Unit alternative: cationExchangeCapacity_meq_100g from Wikipedia

?baseSaturation requires units from VegBank

Unit alternative: baseSaturation_fraction

Unit alternative: baseSaturation_percent

conductivity

Synonym: soilConductivity from SALVIAS

GeologicalContext from DwC | DwC ToC

"information pertaining to a location within a geological context, such as stratigraphy" (DwC)

geologicalContextID text ID from DwC

earliestEonOrLowestEonothem from DwC

latestEonOrHighestEonothem from DwC

earliestEraOrLowestErathem from DwC

latestEraOrHighestErathem from DwC

earliestPeriodOrLowestSystem from DwC

latestPeriodOrHighestSystem from DwC

earliestEpochOrLowestSeries from DwC

latestEpochOrHighestSeries from DwC

earliestAgeOrLowestStage from DwC

latestAgeOrHighestStage from DwC

lowestBiostratigraphicZone from DwC

highestBiostratigraphicZone from DwC

lithostratigraphicTerms from DwC

group from DwC

formation from DwC

member from DwC

bed from DwC

Community from VegX | VegBank

communityID text ID

"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)

Synonym: communityConceptName from VegX

?Taxon AMBIGUOUS from Wikipedia

Alternative: TaxonName

Alternative: TaxonPath

Alternative: TaxonConcept

TaxonName from Wikipedia | DwC | DwC ToC

"a group of one (or more) populations of organism(s), which a taxonomist adjudges to be a unit" (Wikipedia)

Synonym: TaxonName from VegX

Synonym: PlantName from VegBank

taxonID text ID from DwC

parentTaxonID text ID

Related: taxonID, VegBank:plantParent_ID

scientificNameID text ID from DwC

parentScientificNameID text ID

Related: scientificNameID, VegBank:plantParent_ID

parentNameUsageID text ID from DwC

namePublishedInID text ID from DwC

scientificName from DwC

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 DEPRECATED

It doesn't make sense to include infraspecific ranks when using morphospecies.
Use speciesBinomialWithMorphospecies instead.

Related: taxonName, morphospecies

speciesBinomial from Wikipedia

genus+specificEpithet

Synonym: species_VegBank from VegBank alternative of ?species

taxonMorphospecies from BIEN2 | Brad Boyle

"To be safe, we always combine the `taxon` plus `morphospecies` to produce a unique string, `taxonMorphospecies`" (Brad Boyle)

e-mail from Brad:

# 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)
)
)
)
);

Synonym: speciesBinomialWithMorphospecies from BIEN2 | Brad Boyle | Brad Boyle

Synonym: morphospecies_Brad_2 from Brad Boyle alternative of ?morphospecies

Related: speciesBinomial, morphospeciesSuffix

parentNameUsage from DwC

namePublishedIn from DwC

namePublishedInYear from DwC

higherClassification from DwC

higherPlantGroup from BIEN2

Synonym: higherPlantGroup_bien from Brad Boyle

Related: higherClassification

kingdom from DwC

phylum from DwC

class from DwC

order from DwC

family from DwC

genus from DwC

subgenus from DwC

specificEpithet from DwC

Synonym: species_DwC from DwC alternative of ?species

Synonym: speciesName from CTFS

?species AMBIGUOUS

Alternative: species_DwC

Alternative: species_VegBank

morphospeciesSuffix from Brad Boyle

"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)

Synonym: morphospecies_Brad_1 from Brad Boyle alternative of ?morphospecies

Compare to: morphoname

?morphospecies AMBIGUOUS

Alternative: morphospecies_Brad_1

Alternative: morphospecies_Brad_2

infraspecificRank from TNRS

infraspecificEpithet from DwC

subspecies from TCS | Wikipedia

Synonym: ssp from TCS

Synonym: subspeciesName from CTFS

variety from TCS | Wikipedia

Synonym: var from TCS

forma from TCS | Wikipedia

Synonym: fm from TCS

cultivar from TCS

Synonym: cv from TCS

Notes: "The epithet is usually output in single quotes and may contain multiple words, see ICBN §28" (TCS)

taxonRank from DwC

verbatimTaxonRank from DwC

scientificNameAuthorship from DwC

Synonym: scientificNameAuthor from DwC

vernacularName from DwC

Synonym: commonName from SALVIAS

nomenclaturalCode from DwC

taxonRemarks from DwC

threatened from IUCN

concatenatedScientificName analogous to scientificName

Name input to taxonomic scrubbing, which is derived from other Taxon fields

TaxonConcept from VegX

A Taxon described by a specific Reference

Synonym: PlantConcept from VegBank

Related: taxonConceptID

taxonConceptID text ID from DwC

parentTaxonConceptID text ID

Related: taxonConceptID, VegBank:plantParent_ID

nameAccordingTo from DwC

"Information about the authorship of this concept which uses the Name in their sense (i.e. secundum, sensu)" (TCS)

Synonym: accordingTo from TCS

nameAccordingToID text ID from DwC

QualifiedTaxonName from DwC

identificationQualifier from DwC

Synonym: cf_aff from SALVIAS

Synonym: annotations from TNRS

MatchedTaxon from TNRS

matchedScientificNameID text ID analogous to scientificNameID

Synonym: Name_matched_url from TNRS

matchedTaxonName analogous to taxonName

Synonym: Name_matched from TNRS

matchedScientificName analogous to scientificName

matchedKingdom analogous to kingdom

matchedPhylum analogous to phylum

matchedClass analogous to class

matchedOrder analogous to order

matchedFamily analogous to family

Synonym: Family_matched from TNRS

matchedGenus analogous to genus

Synonym: Genus_matched from TNRS

matchedSpecificEpithet analogous to specificEpithet

Synonym: Specific_epithet_matched from TNRS

matchedMorphospecies analogous to morphospecies

Synonym: Unmatched_terms from TNRS

matchedInfraspecificEpithet analogous to infraspecificEpithet

Synonym: Infraspecific_epithet_matched from TNRS

matchedSubspecies analogous to subspecies

matchedVariety analogous to variety

matchedForma analogous to forma

matchedCultivar analogous to cultivar

matchedTaxonRank analogous to taxonRank

Synonym: Name_matched_rank from TNRS

matchedScientificNameAuthorship analogous to scientificNameAuthorship

Synonym: Name_matched_author from TNRS

Synonym: Author_matched from TNRS

taxonomicStatus from DwC

Synonym: matchedTaxonomicStatus from DwC

taxonIsCanonical

Synonym: taxonIsAccepted from DwC

Named like: Taxon

nomenclaturalStatus from DwC

matchedIdentificationQualifier analogous to identificationQualifier

matchedTaxonConfidence_fraction

Synonym: overallScore from TNRS

Related: taxonConfidence, TNRS:Name_matched

matchedFamilyConfidence_fraction

Synonym: familyScore from TNRS

Related: taxonConfidence, TNRS:Family_matched

matchedGenusConfidence_fraction

Synonym: genusScore from TNRS

Related: taxonConfidence, TNRS:Genus_matched

matchedSpeciesConfidence_fraction

Synonym: specificEpithetScore from TNRS

Related: taxonConfidence, TNRS:Specific_epithet_matched

Named like: species

AcceptedTaxon from DwC

acceptedNameUsageID text ID from DwC

acceptedNameUsage from DwC

acceptedScientificNameID text ID analogous to scientificNameID

acceptedTaxonName analogous to taxonName

acceptedScientificName analogous to scientificName

acceptedKingdom analogous to kingdom

acceptedPhylum analogous to phylum

acceptedClass analogous to class

acceptedOrder analogous to order

acceptedFamily analogous to family

acceptedGenus analogous to genus

acceptedSpecificEpithet analogous to specificEpithet

acceptedInfraspecificEpithet analogous to infraspecificEpithet

acceptedSubspecies analogous to subspecies

acceptedVariety analogous to variety

acceptedForma analogous to forma

acceptedCultivar analogous to cultivar

acceptedTaxonRank analogous to taxonRank

acceptedScientificNameAuthorship analogous to scientificNameAuthorship

acceptedIdentificationQualifier analogous to identificationQualifier

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

Synonym: TaxonNameUsageConcept from VegX

Synonym: SpeciesInventory from CTFS

Named like: Occurrence

authorTaxonCode

Synonym: authorPlantName from VegBank

Related: recordNumber, VegBank:authorPlotCode, VegBank:stemCode, Taxon

taxonOccurrencePkey text ID

Related: taxonOccurrenceID

taxonOccurrenceID text ID

Synonym: taxonNameUsageConceptID from VegX

Synonym: taxonObservationID from VegBank

Synonym: speciesInvID from CTFS

Related: VegBank:taxonObservation

dateCollected

Related: DwC:EarliestDateCollected-2007-04-17 (dwcore)

Synonym: collectedDate from BIEN2

yearCollected from DwC

monthCollected from DwC

dayCollected from DwC

occurrenceStatus from DwC

growthForm

Synonym: habit from SALVIAS

Related: VegBank:growthform1Type, habitClassIncluded

oldGrowth from BIEN2

TaxonDetermination from VegX

An assertion that a TaxonOccurrence is a particular Taxon

Synonym: Identification from DwC | DwC ToC

Synonym: TaxonInterpretation from VegBank

identificationID text ID from DwC

identificationType from VegBank

Synonym: interpretationType from VegBank

Named like: Identification

taxon_determination__is_current from VegBank

Synonym: currentInterpretation from VegBank

taxon_determination__is_original from VegBank

Synonym: originalInterpretation from VegBank

identifiedBy from DwC

dateIdentified from DwC

Synonym: identifiedDate from BIEN2

yearIdentified from DwC

monthIdentified from DwC

dayIdentified from DwC

fit from VegX

Synonym: taxonFit from VegBank

confidence from VegX

Synonym: taxonConfidence from VegBank

identificationVerificationStatus from DwC

identificationReferences from DwC

identificationRemarks from DwC

typeStatus from DwC

"Indicates whether this specimen served as type for taxon name" (Brad Boyle)

previousIdentifications from DwC

associatedTaxa from DwC

OriginalTaxonDetermination from DwC

originalNameUsageID text ID from DwC

originalNameUsage from DwC

originalTaxonName analogous to taxonName

originalScientificName analogous to scientificName

morphoname from SALVIAS

The name assigned in the field, which is unique within the plot

originalKingdom analogous to kingdom

originalPhylum analogous to phylum

originalClass analogous to class

originalOrder analogous to order

originalFamily analogous to family

originalGenus analogous to genus

originalSpecificEpithet analogous to specificEpithet

originalInfraspecificEpithet analogous to infraspecificEpithet

originalSubspecies analogous to subspecies

originalVariety analogous to variety

originalForma analogous to forma

originalCultivar analogous to cultivar

originalTaxonRank analogous to taxonRank

originalScientificNameAuthorship analogous to scientificNameAuthorship

originalIdentificationQualifier analogous to identificationQualifier

TaxonObservation from VegBank DEPRECATED

denormalized VegCore doesn't distinguish between taxon occurrences and taxon observations of them.
use TaxonOccurrence instead.

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)

Synonym: AggregateOrganismObservation from VegX

Synonym: AggregateOccurrence from meeting on 2012-1-11

Synonym: TaxonImportance from VegBank

Related: VegBank:stemCount, IndividualObservation

aggregateOrganismObservationID text ID from VegX

Synonym: aggregateOccurrenceID

individualCount from DwC

coverPercent from VegX

"Average cover of the index in percent" (VegX)

?intercept requires units

Unit alternative: intercept_m

Unit alternative: intercept_cm from SALVIAS

individualCount_1cm_or_more

Synonym: abund1cm from BIEN2

Related: individualCount

individualCount_2_5cm_or_more

Synonym: abund2_5cm from BIEN2

Related: individualCount

individualCount_10cm_or_more

Synonym: abund10cm from BIEN2

Related: individualCount

Individual

A distinct biological organism

Synonym: IndividualOrganism from VegX

Synonym: Organism

Synonym: Tree from CTFS

Related: IndividualObservation

individualID text ID from DwC

tag

Synonym: identificationLabel from VegX

Synonym: tag2 from SALVIAS

IndividualObservation

An observation of an Individual

Synonym: IndividualOrganismObservation from VegX

Synonym: OrganismObservation

Synonym: PlotObservation_SALVIAS from SALVIAS | Madidi alternative of ?PlotObservation

Related: Individual

individualObservationID text ID

The unique identifier for the observation of an individual

Requirements: Must be unique within the datasource

Synonym: individualOrganismObservationID from VegX

Synonym: ID_TEAM from TEAM alternative of ?ID

Related: individualID

Suggestions: Usually set to a database primary key

individualCode from SALVIAS

Synonym: 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)

Synonym: individualOrganismObservationRelativeX from VegX

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)

Synonym: individualOrganismObservationRelativeY from VegX

censusNumber

Synonym: censusNo from SALVIAS

stemCount from VegBank

sex from DwC

lifeStage from DwC

reproductiveCondition from DwC

Synonym: phenology from SALVIAS

Components:

flower from UNCC

fruit from UNCC

behavior from DwC

establishmentMeans from DwC

cultivated from DwC

Synonym: cultivated_bien from Brad Boyle

cultivatedBasis

Related: cultivated

Synonym: cultivatedBasis_bien from Brad Boyle

canopyForm

Synonym: stemCanopyForm from SALVIAS

canopyPosition

Synonym: stemCanopyPosition from SALVIAS

lianaInfestation

Synonym: stemLianaInfestation from SALVIAS

Stem from CTFS

An "individual tree stem" (VegBank)

Synonym: StemLocation from VegBank

Related: StemObservation, Individual

stemID text ID from SALVIAS

stemTag

Synonym: stemTag2 from SALVIAS

StemObservation

An observation of a Stem

Related: Stem, IndividualObservation

This is an immovable type of TaxonOccurrence

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)

Synonym: stemCode from VegBank

Named like: authorPlotCode

?height requires units from VegX

"The measured height of the stem" (VegBank)

Synonym: ?stemHeight requires units from VegBank

Unit alternative: height_m

Unit alternative: height_ft

?heightFirstBranch requires units

Unit alternative: heightFirstBranch_m

Synonym: htFirstBranch_m from SALVIAS

Unit alternative: heightFirstBranch_ft

?diameterBreastHeight requires units

Synonym: ?stemDbh requires units from SALVIAS

Synonym: ?DBH requires units from CTFS

Unit alternative: diameterBreastHeight_m

Unit alternative: diameterBreastHeight_cm

Unit alternative: diameterBreastHeight_in

?diameterBreastHeightGentry requires units

Synonym: ?gentryDbh requires units from SALVIAS

Unit alternative: diameterBreastHeightGentry_m

Unit alternative: diameterBreastHeightGentry_cm

Unit alternative: diameterBreastHeightGentry_in

?basalDiameter requires units

Synonym: ?basalDiam requires units from SALVIAS

Unit alternative: basalDiameter_m

Unit alternative: basalDiameter_cm

Unit alternative: basalDiameter_in

stemNotes from SALVIAS

Collection from DwC | Brad Boyle

"the collection within the institution where a specimen is held" (Brad Boyle)

A type of dataset that applies only to specimens

collection text ID from DwC | Brad Boyle

"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)

Synonym: collectionCode from DwC | Brad Boyle

collectionURL text ID from DwC

Synonym: collectionID text ID from DwC

Specimen from Wikipedia | CTFS

A "part of a plant" (Wikipedia) which was collected from it

This is a movable type of TaxonOccurrence

Related: Occurrence

specimen_duplicate_institutions from Brad Boyle

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)

Synonym: specimenHolderInstitutions from Brad Boyle

Synonym: specimenHolderInstitution from Brad Boyle

Synonym: institutionCode_DwC from DwC alternative of ?institutionCode

Compare to: specimenDonorInstitution

specimenHolderURL text ID from DwC | Brad Boyle

Synonym: institutionID from DwC

?institutionCode AMBIGUOUS

Alternative: institutionCode_DwC

Alternative: institutionCode_UNCC

specimenDonorInstitution text ID from Bob Peet | Brad Boyle

"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)

Synonym: institutionCode_UNCC from Bob Peet alternative of ?institutionCode

specimenOwner text ID from DwC

The institution which owns the specimen. This is specimenHolderInstitution if the specimen was donated or specimenDonorInstitution if it was lent.

Synonym: ownerInstitutionCode from DwC

specimenStampingInstitution text ID from Bob Peet | Brad Boyle

The institution that stamped an accession number or barcode on the specimen

barcode from Brad Boyle | NCU | U

"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 from Brad Boyle | REMIB

"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.

Synonym: accession from UNCC

Synonym: museumAccessionNumber from VegBank

Synonym: catalogNumber from DwC

collectorNumber from DwC

Scope: none

Synonym: collectionNumber from VegBank

Synonym: recordNumber from DwC

Synonym: fieldNumber_DwC_classic from DwC alternative of ?fieldNumber

?fieldNumber AMBIGUOUS

Alternative: fieldNumber_DwC_classic

Alternative: fieldNumber_DwC_terms

preparations from DwC

Synonym: preparationType from DwC

Synonym: preparation from REMIB

specimenDescription from Brad Boyle analogous to occurrenceRemarks

disposition from DwC

otherCatalogNumbers from DwC

Synonym: previousCatalogNumber from DwC

Voucher

voucherType

Values: direct, indirect

Synonym: detType from SALVIAS

Measurement

An attribute of any type of Occurrence

Synonym: MeasurementOrFact from DwC | DwC ToC

Synonym: TraitObservation from BIEN2

Synonym: Trait

measurementID text ID from DwC

measurementName

Synonym: measurementType from DwC

Synonym: traitName from BIEN2

measurementValue from DwC

Synonym: traitValue from BIEN2

measurementAccuracy from DwC

measurementUnit from DwC

Synonym: unit from BIEN2

measurementDeterminedDate from DwC

measurementDeterminedBy from DwC

measurementMethod from DwC

measurementRemarks from DwC

ResourceRelationship from DwC | DwC ToC

"information pertaining to relationships between resources (instances of data records, such as Occurrences, Taxa, Locations, Events)" (DwC)

resourceRelationshipID text ID from DwC

resourceID text ID from DwC

relatedResourceID text ID from DwC

Synonym: relatedCatalogItem from DwC

relationshipOfResource from DwC

Synonym: relationshipType from DwC

relationshipAccordingTo from DwC

relationshipEstablishedDate from DwC

relationshipRemarks from DwC


Special terms

A distinguishing suffix must be appended to each special term in the format special_term#suffix to make the resulting column name unique within the staging table. This suffix is usually the original column name.

OMIT

The field contains data but should be omitted

The reason for omission should be described in the mapping's comments

Use the format OMIT#this_field

When possible, use one of the more specific terms below:

UNUSED

The field does not contain any data

The following query should return no rows:

SELECT * FROM table WHERE field IS NOT NULL

DUPLICATE

The field contains the same data as another field (so that both do not need to be mapped)

The following query should return no rows: (requires ?>=)
(The values do not need to be exactly the same if the other field is more complete than this field)

SELECT * FROM table WHERE NOT dup_field ?>= this_field

The field is also an exact duplicate if the following query returns no rows:

SELECT * FROM table WHERE NOT dup_field IS NOT DISTINCT FROM this_field

Use the format DUPLICATE#of:dup_field#this_field (with original column names)

EQUIV

The field contains data that is equivalent to another field (so that both do not need to be mapped)

The following query should return no rows: (requires ?*>=)

SELECT * FROM table WHERE NOT equiv_field ?*>= this_field

Use the format EQUIV#to:equiv_field#this_field (with original column names)

PRIVATE

The field contains private data which should be omitted from a public database


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, eg. to clarify what kind of entity a term is referring to, since this might not be a specimen)

DwC-terms

DwC-history

DwC-MaNIS

DwC-classic

DwC-dwcore

TCS

VegX

Aggregators

TNRS

VegBank

SALVIAS

VegBIEN

BIEN2

BIEN2-web

BIEN2-core

BIEN2-DB

Primary databases

CTFS

CTFS-DB

CTFS-v5

People

Brad Boyle

Brad Boyle-data provenance

Brad Boyle-DwC IDs-2013-2-7

Brad Boyle-DwC IDs-2013-1-31


Editing

Note: This section must stay on the same page as the data dictionary so that its templates are refactored along with it

  • 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

Naming

  • A term name should always be a u-name (unambiguous and with a standard format) to allow seamlessly combining data from arbitrary datasets
  • It should ideally be the c-name (as short as possible)

Tables

  • Table names are capitalized (this is required by scripts that parse the data dictionary page)
  • 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 (this is required by scripts that parse the data dictionary page)

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:

h2((. [[VegCore#ID|ID]] !{padding-left: 1em; font-size: small; font-weight: normal; font-style: italic;}_(text ID)!:https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Text_IDs !{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.
    These synonyms must not have the same HTML anchor as the ambiguous term itself, to ensure that the ambiguous term's anchor links to it rather than to its first alternative. The templates below, which differ from ordinary synonyms, will ensure this.
  • 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.

In the templates below, note that there are two forms of synonym definitions, depending on whether the synonym has a from clause or not. These are needed to form the HTML anchor properly.

Ambiguous table template:

h1. [[VegCore#AmbiguousTable|?AmbiguousTable]] !{padding-left: 1em; font-size: small; font-weight: normal; font-style: italic;}_(AMBIGUOUS)!

h3(((. Alternative: [[VegCore#Alternative1_withFrom|Alternative1_withFrom]]

h3(((. Alternative: [[VegCore#Alternative2_withoutFrom|Alternative2_withoutFrom]]

[...]

h1. [[VegCore#Alternative1_withFrom|Alternative1_withFrom]] [...]

h3((((. !{padding: 0 0.3em 3pt 0.65em; font-weight: normal;}_(Synonym:)! [[VegCore#AmbiguousTable|?AmbiguousTable]] !{padding: 0 0 3pt 1em; font-size: small; font-weight: normal;}_(from)! "Source":URL#AmbiguousTableAsSpelledBySource

[...]

h1. [[VegCore#Alternative2_withoutFrom|Alternative2_withoutFrom]] [...]

h3((((. !{padding: 0 0 3pt 0.65em; font-weight: normal;}_(Synonym)!: [[VegCore#AmbiguousTable|?AmbiguousTable]]

Ambiguous field template:

h2((. [[VegCore#ambiguousTerm|?ambiguousTerm]] !{padding-left: 1em; font-size: small; font-weight: normal; font-style: italic;}_(AMBIGUOUS)!

h3(((((. Alternative: [[VegCore#alternative1_withFrom|alternative1_withFrom]]

h3(((((. Alternative: [[VegCore#alternative2_withoutFrom|alternative2_withoutFrom]]

[...]

h2((. [[VegCore#alternative1_withFrom|alternative1_withFrom]] [...]

h3((((. !{padding: 0 0.3em 3pt 0.65em; font-weight: normal;}_(Synonym:)! [[VegCore#ambiguousTerm|?ambiguousTerm]] !{padding: 0 0 3pt 1em; font-size: small; font-weight: normal;}_(from)! "Source":URL#ambiguousTermAsSpelledBySource

[...]

h2((. [[VegCore#alternative2_withoutFrom|alternative2_withoutFrom]] [...]

h3((((. !{padding: 0 0 3pt 0.65em; font-weight: normal;}_(Synonym)!: [[VegCore#ambiguousTerm|?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 View (12 KB) Aaron Marcuse-Kubitza, 12/05/2012 09:21 AM

vegbien_identifier_examples.xlsx (28.6 KB) Aaron Marcuse-Kubitza, 01/31/2013 04:40 PM

vegbien_identifiers.xlsx (30.1 KB) Aaron Marcuse-Kubitza, 02/12/2013 12:27 AM

BIEN database entities related to data provenance and ownership.docx (157 KB) Aaron Marcuse-Kubitza, 02/14/2013 04:44 PM