Darwin Core Terms

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This quick guide provides a list of all current Darwin Core terms we are using in Species Product Discovery Service.

Darwin Core Archive is used to export taxonomic (species) data, while Simple Darwin Core is used to export species occurrences.

Darwin Core Archive

DarwinCore Archive (DwC-A) is a Biodiversity informatics data standard that makes use of the DarwinCore terms to produce a single, self contained dataset for taxonomic (species) data. The GBIF GNA format consists of a set of files where one (or more) files represents the 'core' taxonomic data where a single row represents a single taxon reference. The DarwinCore Taxon class provides the majority of concepts supported in the format that enable taxonomic and nomenclatural semantics and syntax (classification, taxonomic and nomenclatural synonymy, status, etc.) to be expressed.

Other files represent "extensions" to this core table and allow additional data elements to be linked to a taxon in the core table with a many to one relationship. The overall topology of one or more of these extensions to the core table is referred to as a "star schema" and provides a compromise between an overly simple flat-file representation of data and more complex multi-related files. In addition to these files, an additional descriptor file serves as a key to the other files. Collectively, these files can be further zipped into a single compressed archive file for portability. This compressed file is known as a DarwinCore Archive (DwCA) file.

DwC-A Components

Example: Sarda from OBIS

The example represents the sarda species checklist from OBIS.

The process to create a Darwin Core Archive is simple:

  • Identify the standard terms and extensions required to map the biodiversity data you wish to share in your archive;

Sarda4.png

  • Export your data as a set of one or more text files;
taxonID		parentNameUsageID	scientificName		scientificNameAuthorship	kingdom		phylum		class		   order		taxonRank	
__________________________________________________________________________________________________________________________________________________________________________________
OBIS:506000	OBIS:758818		Sarda			Cuvier, 1829			Animalia	Chordata	Actinopterygii	   Perciformes	        genus		
OBIS:758818	OBIS:755264		Scombridae						Animalia	Chordata	Actinopterygii	   Perciformes          family	
OBIS:755264	OBIS:737387		Perciformes						Animalia	Chordata	Actinopterygii                          order	
OBIS:737387	OBIS:755917		Actinopterygii						Animalia        Chordata                                                class	
.........
  • Add XML descriptor files to inform others how your files are organized;
  • Zip the folder into a single archive and you are done!

Files

A DarwinCore Archive file generated by SPD Service (in our case representing Darwin Core Taxa) contains the following files:

  • a metadata file (eml.xml) that describes the data resource;
  • a metafile (meta.xml) file that describes the content and relationship of the text data files;
  • a core data file in CSV (taxa.txt) consisting of a standard set of DarwinCore terms;
  • a vernacular names extension file (VernacularName.txt) that supports the description of common name properties that might be related to a species described in the core data file.


Metafile (meta.xml)

The DarwinCore Archive format relies on a special file - an XML descriptor file, called the "metafile" (typically named meta.xml). The metafile is used as a map to describe the core taxon file and any extensions that collectively form the specific data profile that will be produced by the user. 

<?xml version='1.0' encoding='utf-8'?>
<archive xmlns="http://rs.tdwg.org/dwc/text/" metadata="eml.xml">
	<core encoding="UTF-8" linesTerminatedBy="\n" fieldsTerminatedBy="\t" fieldsEnclosedBy="" ignoreHeaderLines="1" rowType="http://rs.tdwg.org/dwc/terms/Taxon">
		<files>
			<location>taxa.txt</location>
		</files>
		<id index="0"/>
		<field index="0" term="http://rs.tdwg.org/dwc/terms/taxonID"/>
		<field index="1" term="http://rs.tdwg.org/dwc/terms/acceptedNameUsageID"/>
		<field index="2" term="http://rs.tdwg.org/dwc/terms/parentNameUsageID"/>
		<field index="3" term="http://rs.tdwg.org/dwc/terms/scientificName"/>
		<field index="4" term="http://rs.tdwg.org/dwc/terms/scientificNameAuthorship"/>
		<field index="5" term="http://rs.tdwg.org/dwc/terms/nameAccordingTo"/>
		<field index="6" term="http://rs.tdwg.org/dwc/terms/kingdom"/>
		<field index="7" term="http://rs.tdwg.org/dwc/terms/phylum"/>
		<field index="8" term="http://rs.tdwg.org/dwc/terms/class"/>
		<field index="9" term="http://rs.tdwg.org/dwc/terms/order"/>
		<field index="10" term="http://rs.tdwg.org/dwc/terms/family"/>
		<field index="11" term="http://rs.tdwg.org/dwc/terms/genus"/>
		<field index="12" term="http://rs.tdwg.org/dwc/terms/subgenus"/>
		<field index="13" term="http://rs.tdwg.org/dwc/terms/specificEpithet"/>
		<field index="14" term="http://rs.tdwg.org/dwc/terms/infraspecificEpithet"/>
		<field index="15" term="http://rs.tdwg.org/dwc/terms/verbatimTaxonRank"/>
		<field index="16" term="http://rs.tdwg.org/dwc/terms/taxonRank"/>
		<field index="17" term="http://rs.tdwg.org/dwc/terms/taxonomicStatus"/>
		<field index="18" term="http://purl.org/dc/terms/modified"/>
		<field index="19" term="http://purl.org/dc/terms/bibliographicCitation"/>
		<field index="20" term="http://rs.tdwg.org/dwc/terms/taxonRemarks"/>
		<field index="21" term="http://rs.tdwg.org/dwc/terms/scientificNameID"/>
	</core>
	<extension encoding="UTF-8" linesTerminatedBy="\n" fieldsTerminatedBy="\t" fieldsEnclosedBy="" ignoreHeaderLines="1" rowType="http://rs.gbif.org/terms/1.0/VernacularName">
		<files>
			<location>VernacularName.txt</location>
		</files>
		<coreid index="0"/>
		<field index="1" term="http://rs.tdwg.org/dwc/terms/vernacularName"/>
		<field index="2" term="http://purl.org/dc/terms/language"/>
		<field index="3" term="http://rs.tdwg.org/dwc/terms/locality"/>
	</extension>
</archive>

Core Data File (taxa.txt)

A required core data file consisting of a standard set of DarwinCore terms.

A data file is formatted as fielded text, where data records are expressed as rows of text, and data fields (column) are separated with a standard delimiter (a tab).

In a DarwinCore data file the first row of the file contains the names of the DarwinCore terms represented in the succeeding rows of the data.

Repository URL: http://rs.gbif.org/core/dwc_taxon.xml


Field Description DwC term
taxonID A ‘taxonID’ value may be any string, it is not required to be numeric. An accepted name should have a unique ‘taxonID’ value. A synonym (or similar name linked to a taxon) should ideally have an identifier in the ‘taxonID’ field.

Data Type: string

http://rs.tdwg.org/dwc/terms/taxonID
acceptedNameUsageID The field ‘acceptedNameUsageID’ should be used to link a synonym record to its corresponding accepted name (which will have a matching ‘taxonID’ value).

An accepted name should have an empty ‘acceptedNameUsageID’ field.

Data Type: string

http://rs.tdwg.org/dwc/terms/acceptedNameUsageID
parentNameUsageID The field ‘parentNameUsageID’ of the accepted name record for a taxon is used to refer to the ‘taxonID’ value of the parent taxon at the next higher taxonomic rank included in the checklist.

If there is no parent included in the checklist, because the “top of the tree” has been reached, then this field should be empty to indicate this.

Data Type: string

http://rs.tdwg.org/dwc/terms/parentNameUsageID
scientificName The scientific name of taxon with or without authorship information depending on the format of the source database.

Examples: "Coleoptera" , "Vespertilionidae”, "Manis" , "Ctenomys sociabilis", "Ambystoma tigrinum diaboli", "Quercus agrifolia var.oxyadenia (Torr.)"

Data Type: string

http://rs.tdwg.org/dwc/terms/scientificName
scientificNameAuthorship If the authority is known and can be separated from the rest of the scientific name, the authority string should also be placed in the ‘scientificNameAuthorship’ field.

If authorship is included in the scientificName field, this field is optional. Example: "(Torr.) J.T. Howell", "(Martinovsk ) Tzvelev", "(Linnaeus 1768)"

Data Type: string

http://rs.tdwg.org/dwc/terms/scientificNameAuthorship
nameAccordingTo A citation representing the concept or sense in which the name is used.

Data Type: string

http://rs.tdwg.org/dwc/terms/nameAccordingTo
kingdom The full scientific name of the kingdom in which the taxon is classified.

Example: "Animalia", "Plantae"

Data Type: string

http://rs.tdwg.org/dwc/terms/kingdom
phylum The full scientific name of the phylum in which the taxon is classified.

Example: "Chordata" (phylum), "Bryophyta" (division)

Data Type: string

http://rs.tdwg.org/dwc/terms/phylum
class The full scientific name of the class in which the taxon is classified.

Example: "Mammalia", "Hepaticopsida"

Data Type: string

http://rs.tdwg.org/dwc/terms/class
order The full scientific name of the order in which the taxon is classified.

Example: "Carnivora", "Monocleales"

Data Type: string

http://rs.tdwg.org/dwc/terms/order
family The full scientific name of the family in which the taxon is classified.

Example: "Felidae", "Monocleaceae"

Data Type: string

http://rs.tdwg.org/dwc/terms/family
genus The full scientific name of the genus in which the taxon is classified.

Example: "Puma", "Monoclea"

Data Type: string

http://rs.tdwg.org/dwc/terms/genus
subgenus The full scientific name of the subgenus in which the taxon is classified. Values should include the genus to avoid homonym confusion.

Example: Puma (Puma); Loligo (Amerigo); Hieracium subgen. Pilosella

Data Type: string

http://rs.tdwg.org/dwc/terms/subgenus
specificEpithet 2nd word in a scientific name (species), es. Acer saccharum, saccharum is the specificEpithet.

Example: scientificName: Carex viridula subsp. brachyrrhyncha var. elatior (Schltdl.) Crins specificEpithet: viridula

Data Type: string

http://rs.tdwg.org/dwc/terms/specificEpithet
infraspecificEpithet Terminal word in a scientific name.

Example: scientificName: Carex viridula subsp. brachyrrhyncha var. elatior (Schltdl.) Crins infraspecificEpithet: elatior

Data Type: string

http://rs.tdwg.org/dwc/terms/infraspecificEpithet
verbatimTaxonRank The taxonomic rank of the most specific name in the scientificName.

Example: scientificName: Carex viridula subsp. brachyrrhyncha var. elatior (Schltdl.) Crins verbatimTaxonRank: var.

Data Type: string

http://rs.tdwg.org/dwc/terms/verbatimTaxonRank
taxonRank The taxonomic rank of the most specific name in the scientificName. Recommended best practice is to use a controlled vocabulary: http://rs.gbif.org/vocabulary/gbif/rank.xml.

Examples: "subspecies", "varietas", "forma", "species", "genus".

Data Type: string

http://rs.tdwg.org/dwc/terms/taxonRank
taxonomicStatus The status of the use of the scientificName as a label for a taxon. Controlled vocabulary:

"accepted", "invalid", "misapplied", "provisional", “synonym”, “valid” “unknown” has also been suggested, but often an empty value is expected to indicate an unknown value.

Data Type: string

http://rs.tdwg.org/dwc/terms/taxonomicStatus
modified The most recent date-time on which the resource was changed.

It is recommended this format: “YYYY-MM-DD”.

Data Type: date

http://purl.org/dc/terms/modified
bibliographicCitation Citation information specified by the data publisher.

Data Type: string

http://purl.org/dc/terms/bibliographicCitation
taxonRemarks Comments or notes about the taxon or name.

Data Type: string

http://rs.tdwg.org/dwc/terms/taxonRemarks
scientificNameID Exclusively used to reference an external and resolvable identifier that returns nomenclatural (not taxonomic) details of a name. Use taxonID to refer to taxa. Use to explicitly refer to an external nomenclatural record.

Example: “urn:lsid:ipni.org:names:37829-1:1.3”

Data Type: string

http://rs.tdwg.org/dwc/terms/scientificNameID


Vernacular Names Extension File (VernacularName.txt)

Extension file are also simple text files that can visualised as a spreadsheet. They are tied to the core taxon file through a copy of the taxonID used in the core taxon file that is repeated once for each row in the extension file in a manner similar to foreign keys in a relational database. An extension file may include Darwin Core terms as well as terms defined through other means.

The use of extension files allows checklist information to be represented in a one-to-many relation ship between the core taxon file and the extension. For example, Vernacular Names Extension provides the means to share information related to common (vernacular) names linked to taxa in the core data file. Multiple vernacular names can be linked to the same taxon via the taxonID.


Repository: http://rs.gbif.org/extension/gbif/1.0/vernacular.xml


Field Description DwC term
taxonID The first field in the data file should be the taxonID representing the taxon in the core data file to which this vernacular name points. This identifier provides the link between the core data record and the extension record.

Data Type: string

'http://rs.tdwg.org/dwc/terms/taxonID
vernacularName A common or vernacular name.

Example: Andean Condor", "Condor Andino", "American Eagle", "Gönsegeier"

Data Type: string

http://rs.tdwg.org/dwc/terms/vernacularName
language ISO 639-1 language code used for the vernacular name value.

Example: “ES”, “Spanish”, “Español”

Data Type: string

http://purl.org/dc/terms/language
locality The specific description of the area from which the vernacular name usage originates. Vernacular names may have very specific regional contexts. A name used for a species in one area may refer to a different species in another.

Example: "Southeastern coastal New England from Buzzards Bay through Rhode Island"

Data Type: string

http://rs.tdwg.org/dwc/terms/locality

Validating

You can test your archive for structural or data problems by checking it with the GBIF Darwin Core Archive Validator.

This tool will perform several tests:

  • ensure the archive is valid by decompressing it and confirming the presence of a meta.xml descriptor file;
  • validate the meta.xml file according to the DwC-A meta file XML Schema;
  • verify that required fields are included;
  • validate certain field values such as data types and licenses;
  • perform some data type-specific validation such as verify text object contain descriptions and images contain accessURIs.

Simple Darwin Core

The Simple Darwin Core has minimal restrictions on which fields are required (none). By having no required field restriction, the Simple Darwin Core can be used to share any meaningful combination of fields - in our case, occurrences.

The following schema specifies the fields contained in a Simple Darwin Core file.

Field Description DwC term
occurrenceID The ID is supposed to (globally) uniquely identify an occurrence record, whether it is a specimen-based occurrence, a one-time observation of a species at a location, or one of many occurrences of an individual who is being tracked, monitored, or recaptured. Making it globally unique is quite a trick, one for which we don't really have good solutions in place yet, but one which ontologists insist is essential.

Data Type: string

http://rs.tdwg.org/dwc/terms/occurrenceID
scientificNameAuthorship The authorship information for the scientificName formatted according to the conventions of the applicable nomenclaturalCode.

Example: "(Torr.) J.T. Howell", "(Martinovský) Tzvelev", "(Györfi, 1952)".

Data Type: string

http://rs.tdwg.org/dwc/terms/scientificNameAuthorship
language The language of the parent resource. Recommended best practice is to use a controlled vocabulary such as ISO 693.

Example: "eng"

Data Type: string

http://purl.org/dc/terms/language
modified The most recent date-time on which the resource was changed. Recommended format: "yyyy-MM-dd'T'HH:mm:ss"

Data Type: string

http://purl.org/dc/terms/modified


basisOfRecord The specific nature of the data record - a subtype of the dcterms:type. Recommended best practice is to use a controlled vocabulary such as the Darwin Core Type Vocabulary (http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm).

Examples: "PreservedSpecimen", "FossilSpecimen", "LivingSpecimen", "HumanObservation", "MachineObservation".

Data Type: string

http://rs.tdwg.org/dwc/terms/basisOfRecord
institutionCode The name (or acronym) in use by the institution having custody of the object(s) or information referred to in the record.

Examples: "MVZ", "FMNH", "AKN-CLO", "University of California Museum of Paleontology (UCMP)".

Data Type: string

http://rs.tdwg.org/dwc/terms/institutionCode


collectionCode The name, acronym, coden, or initialism identifying the collection or data set from which the record was derived.

Examples: "Mammals", "Hildebrandt", "eBird".

Data Type: string

http://rs.tdwg.org/dwc/terms/collectionCode
catalogNumber An identifier (preferably unique) for the record within the data set or collection.

Examples: "2008.1334", "145732a", "145732".

Data Type: string

http://rs.tdwg.org/dwc/terms/catalogNumber


identified A list of names of people, groups, or organizations responsible for recording the original Occurrence.

Example: "Oliver P. Pearson; Anita K. Pearson".

Data Type: string

http://rs.tdwg.org/dwc/terms/identifiedBy


scientificName The scientific name of taxon with or without authorship information depending on the format of the source database.

Examples: "Coleoptera", "Vespertilionidae".

Data Type: string

http://rs.tdwg.org/dwc/terms/scientificName
kingdom The full scientific name of the kingdom in which the taxon is classified.

Example: "Animalia", "Plantae".

Data Type: string

http://rs.tdwg.org/dwc/terms/kingdom


family The full scientific name of the family in which the taxon is classified.

Example: "Felidae", "Monocleaceae".

Data Type: string

http://rs.tdwg.org/dwc/terms/family


locality The specific description of the place.

Example: "Bariloche, 25 km NNE via Ruta Nacional 40".

Data Type: string

http://rs.tdwg.org/dwc/terms/locality


eventDate The date-time or interval during which an Event occurred. For occurrences, this is the date-time when the event was recorded.

Examples: "1963-03-08T14:07-0600".

Data Type: date

http://rs.tdwg.org/dwc/terms/eventDate


year The four-digit year in which the Event occurred, according to the Common Era Calendar.

Example: "2008".

Data Type: date

http://rs.tdwg.org/dwc/terms/year


decimalLatitude The geographic latitude.

Data Type: float

http://rs.tdwg.org/dwc/terms/decimalLatitude
decimalLongitude The geographic longitude.

Data Type: float

http://rs.tdwg.org/dwc/terms/decimalLongitude


coordinateUncertaintyInMeters As close an approximation to the standard deviation of the coordinates expressed in meters.

Data Type: float

http://rs.tdwg.org/dwc/terms/coordinateUncertaintyInMeters
maximumDepthInMeters The greater depth of a range of depth below the local surface, in meters.

Data Type: float

http://rs.tdwg.org/dwc/terms/maximumDepthInMeters
minimumDepthInMeters The lesser depth of a range of depth below the local surface, in meters.

Data Type: float

http://rs.tdwg.org/dwc/terms/minimumDepthInMeters


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