Difference between revisions of "Darwin Core Terms"
(→Darwin Core Archive Format) |
(→Darwin Core Archive Format) |
||
Line 6: | Line 6: | ||
==Darwin Core Archive Format== | ==Darwin Core Archive Format== | ||
− | Darwin Core Archive (DwC-A) is a Biodiversity informatics data standard that makes use of the Darwin Core terms to produce a single, self contained dataset for species occurrence or taxonomic (species) data. | + | Darwin Core Archive (DwC-A) is a Biodiversity informatics data standard that makes use of the Darwin Core 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 Darwin Core Archive (DwCA) file. | ||
[[Image:dwca.png|center| DwC-A Components]] | [[Image:dwca.png|center| DwC-A Components]] | ||
Revision as of 19:23, 14 March 2013
This document is targeted toward those who need a reference (lists and definitions) to the essential information about the current recommended Darwin Core terms. 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.
Contents
Darwin Core Archive Format
Darwin Core Archive (DwC-A) is a Biodiversity informatics data standard that makes use of the Darwin Core 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 Darwin Core Archive (DwCA) file.
The Core Taxon File
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
This 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 |
Simple Darwin Core
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
|