Difference between revisions of "Darwin Core Terms"

Revision as of 11:58, 15 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.

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.

Three componentes are required:

• 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 file(s) and
• text data file(s) in CSV or Tab format, containing the data itself.

Metadata Document

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>

The Core Taxon File

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

Vernacular Names Extension

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

Validate the Archive

Use the GBIF Darwin Core Archive Validator to check that the archive validates. The validator will provide feedback if the archive does not validate.

Simple Darwin Core

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