Darwin Core Text Guide
This document provides guidelines for formatting and sharing Darwin Core
terms [TERMS] in fielded text formats,
such as one or more comma separated value (CSV) files. Data conforming to the
Simple Darwin Core [SIMPLEDWC] (CSV
format and having the first row include Darwin Core standard term names) can
be shared in a single file, while a non-standard text file can be understood
using an [XML] metafile to describe its
contents and formatting.
More complex structure can be shared in multiple related files. The description of content and relationships between files can be achieved using the metafile. This guideline makes recommendations for the simple case of a core file, upon which Darwin Core records are based, and extensions that are linked to records in that core file. Specifically, extension records have a many-to-one relationship with records in the core file. For example, a core file might contain specimen records, with one specimen per row in the file, while an extension file contains one or more identifications for those specimens, with one identification per row in the extension file, and with an identifier to the specimen for each identification row. This example would allow many identifications to be associated with each specimen.
ID,Species,Count 123,"Cryptantha gypsophila Reveal & C.R. Broome",12 124,"Buxbaumia piperi",2can be described with the following Darwin Core metafile:
<?xml version="1.0" encoding="UTF-8"?> <archive xmlns="http://rs.tdwg.org/dwc/text/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:schemaLocation="http://rs.tdwg.org/dwc/text/ http://rs.tdwg.org/dwc/text/tdwg_dwc_text.xsd"> <core rowType="http://rs.tdwg.org/dwc/xsd/simpledarwincore/SimpleDarwinRecord" ignoreHeaderLines="1"> <files> <location>http://data.gbif.org/download/specimens.csv</location> </files> <field index="0" term="http://rs.tdwg.org/dwc/terms/catalogNumber" /> <field index="1" term="http://rs.tdwg.org/dwc/terms/scientificName" /> <field index="2" term="http://rs.tdwg.org/dwc/terms/individualCount" /> <!-- A constant value has no index, but applies to all rows --> <field term="http://rs.tdwg.org/dwc/terms/datasetID" default="urn:lsid:tim.lsid.tdwg.org:collections:1"/> </core> </archive>
These same data could be understood without the metafile if the first row of the CSV file contained the term names:
type,institutionCode,collectionCode,catalogNumber,scientificName,individualCount,datasetID PhysicalObject,ANSP,PH,123,"Cryptantha gypsophila Reveal & C.R. Broome",12,urn:lsid:tim.lsid.tdwg.org:collections:1 PhysicalObject,ANSP,PH,124,"Buxbaumia piperi",2,urn:lsid:tim.lsid.tdwg.org:collections:1
Many resources exist on the web describing the advantages of Extensible
Markup Language [XML] over less
structured content such as fielded text. The Darwin Core Text Guide
(this document) is not meant to promote the use of fielded text over
XML for data exchange, but rather to provide recommendations for how to
handle such data files when necessary.
Two scenarios that might benefit from the use of fielded text are:
The text metafile schema [TEXTSCHEMA] provides technical details for the structure of a metafile by defining the elements and attributes required to describe the contents and relationships between text files. These elements and attributes, with descriptions and specifications for their use in a metafile, are described in the following table.
|metadata||Contains a qualified Uniform Resource Locator (URL) defining the location of a metadata description of the entire archive. The format of the metadata is not prescribed, but a standardized format such as Ecological Metadata Language (EML), Federal Geographic Data Committee (FGDC), or ISO 19115 family is recommended.|
An <archive> must contain exactly one <core> element, representing the data entity
(the actual file and its column header mappings to Darwin Core terms)
upon which records are based.
If extensions are being used, each record in the core data must have a unique identifier. The field for this identifier must be specified in an explicit <id> field in order to associate extension records with the core record.
|<extension>||An <archive> may define zero or more <extension> elements, each representing an individual extension entity directly related to the core. In addition to the general file attributes described below, every extension entity must have an explicit <coreId> field to relate the extension record to a row in the core entity. The extension itself does not have to have a unique ID field and many rows can point to the same core record.|
A Unified Resource Identifier (URI) for the term identifying the
class of data represented by each row, for example,
http://rs.tdwg.org/dwc/terms/Occurrence for Occurrence records or
http://rs.tdwg.org/dwc/terms/Taxon for Taxon records. Additional
classes may be referenced by URI and defined outside the Darwin Core
specification. The row type defaults to the ambiguous
SimpleDarwinRecord. For convenience the URIs for classes defined by
the Darwin Core are listed below:
|fieldsTerminatedBy||Specifies the delimiter between fields. Typical values might be "," or "\t" for CSV or Tab files respectively.||,|
|linesTerminatedBy||Specifies the row separator character.||\n|
|fieldsEnclosedBy||Specifies the character used to enclose (mark the start and end of) each field. CSV files frequently use the double quote character ("), but the default is no enclosing character. Note that a comma separated value file that has commas within the content of any field must have an enclosing character.||"|
Specifies the character
encoding for the data file. The encoding is extremely important,
but often ignored. The most frequently used encodings are:
|ignoreHeaderLines||Specifies the number lines to ignore from the beginning of the file. This can be used to ignore files with column headings or preamble comments for example.||0|
When verbatim dates are consistent in format, this field can be used
to indicate the format represented. It is recommended to use the
date, dateTime and time for field formats wherever possible, but
where verbatim dates are required, a format may be specified here.
This should be considered a 'hint' for consumers. It is recommended
that consumers support the minimum combinations of DD MM and YYYY
with the separators / and -. Examples:
|<files>||<core> or <extension> element must contain one <files> element to locate the data being described.|
|<id>||If extensions are being used, the <core> must contain an <id> element that indicates the identifier for a record.|
|<coreId>||If extensions are being used, the <extension> element must contain a <coreId> element that indicates the column in the extension file that contains the core record identifier (the matching <id> in the core file).|
|<field>||A <core> or <extension> element must contain one or more <field> elements, each representing a 'column' in the row.|
The files element must contain one or more <location> elements, each defining where a file resides. Each core or extension entity can be composed from one or more files. If an entity has data in more than one file, use the <location> element multiple times, once for each file that makes up the entity.Elements
Specifies the location of the file being described, which may take
either of the following forms:
|index||Specifies the position of the column in the row. The first column has an index of 0, the second column 1, etc. If no column index is specified, then the term and the default may be used to define a constant value for all rows.|
|term||A Unified Resource Identifier (URI) for the term represented by this field. For example, a field containing the scientific name would have term="http://rs.tdwg.org/dwc/terms/scientificName". Terms outside of the Darwin Core specification may be used, such as those from the Dublin Core Metadata Initative, for example, dcterms:modified would be term="http://purl.org/dc/terms/modified".||✓|
|default||Specifies value to use if one is not supplied for the field in a given row. If no index is supplied, the default can be used to define a constant for all rows for a field that is not in the data file.|
|vocabulary||A Unified Resource Identifier (URI) for a vocabulary that the source values for this field are based on. The URI ideally should resolve to some machine readable definition like SKOS, RDF or at least some simple text or html file often found for ISO or RFC standards. For example http://rs.gbif.org/vocabulary/gbif/nomenclatural_code.xml, http://www.ietf.org/rfc/rfc3066.txt or http://www.iso.org/iso/list-en1-semic-3.txt .|
<?xml version="1.0" encoding="UTF-8"?> <archive xmlns="http://rs.tdwg.org/dwc/text/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:schemaLocation="http://rs.tdwg.org/dwc/text/ http://rs.tdwg.org/dwc/text/tdwg_dwc_text.xsd"> <core encoding="UTF-8" fieldsTerminatedBy="\t" linesTerminatedBy="\n" ignoreHeaderLines="1" rowType="http://rs.tdwg.org/dwc/terms/Taxon"> <files> <location>whales.txt</location> </files> <id index="0" /> <field index="0" term="http://rs.tdwg.org/dwc/terms/taxonID" /> <field index="1" term="http://purl.org/dc/terms/modified" /> <field index="2" term="http://rs.tdwg.org/dwc/terms/scientificName"/> <field index="3" term="http://rs.tdwg.org/dwc/terms/acceptedNameUsageID"/> <field index="4" term="http://rs.tdwg.org/dwc/terms/parentNameUsageID"/> <field index="5" term="http://rs.tdwg.org/dwc/terms/originalNameUsageID"/> </core> <extension encoding="UTF-8" fieldsTerminatedBy="," linesTerminatedBy="\n" fieldsEnclosedBy='"' ignoreHeaderLines="1" rowType="http://rs.gbif.org/terms/1.0/Types"> <files> <location>types.csv</location> </files> <coreId index="0" /> <field index="1" term="http://purl.org/dc/terms/bibliographicCitation"/> <field index="2" term="http://rs.tdwg.org/dwc/terms/catalogNumber"/> <field index="3" term="http://rs.tdwg.org/dwc/terms/collectionCode"/> <field index="4" term="http://rs.tdwg.org/dwc/terms/institutionCode"/> <field index="5" term="http://rs.tdwg.org/dwc/terms/typeStatus"/> </extension> <extension encoding="UTF-8" fieldsTerminatedBy="," linesTerminatedBy="\n" fieldsEnclosedBy='"' ignoreHeaderLines="1" rowType="http://rs.gbif.org/terms/1.0/Distribution"> <files> <location>distribution.csv</location> </files> <coreId index="0" /> <field index="1" term="http://rs.tdwg.org/dwc/terms/countryCode"/> <field index="2" term="http://rs.gbif.org/terms/1.0/threatStatus"/> <field index="3" term="http://rs.tdwg.org/dwc/terms/occurrenceStatus"/> </extension> </archive>
SELECT INTO outfilecommand from MySQL. The encoding of the resulting file will depend on the server variables and collations used, and might need to be modified before the operation is done. Note that MySQL will export NULL values as \N by default. Use the IFNULL() function as shown in the following example to avoid this.
SELECT IFNULL(id, ''), IFNULL(scientific_name, ''), IFNULL(count,'') INTO outfile '/tmp/dwc.txt' FIELDS TERMINATED BY ',' OPTIONALLY ENCLOSED BY '"' LINES TERMINATED BY '\n' FROM dwc;
For tools and applications, including a Java-based application to read Darwin Core text archives, see the Darwin Core Tools and Applications page [TOOLS].
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