Difference between revisions of "Darwin Core Terms"

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===Example===
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===Files===
  
 
A DarwinCore Archive file generated by SPD Service (in our case representing [http://rs.tdwg.org/dwc/terms/#Taxon Darwin Core Taxa]) contains the following files:
 
A DarwinCore Archive file generated by SPD Service (in our case representing [http://rs.tdwg.org/dwc/terms/#Taxon Darwin Core Taxa]) contains the following files:

Revision as of 12:46, 22 March 2013

This quick guide provides a list of all current terms of the Darwin core we are using in SPD Service.

Names that begin with dcterms: are terms managed by the Dublin Core Metadata Initiative [DCMI], which are reproduced here and which may include a description and comments adapted for the biodiversity community.

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 species occurrence or 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


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)

<?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>

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