Revision as of 10:11, 11 September 2012

Darwin Core extension for genebanks

The Darwin Core extension for genebanks (DwC-germplasm) was developed to provide a bridge between the established standards in use by the genebank community for plant genetic resources for food and agriculture (PGRFA) and the standards maintained by the Biodiversity Information Standards/Taxonomic Databases Working Group (TDWG). The DwC germplasm provides an extension to the Darwin Core standard of the TDWG for occurrences. Darwin Core can be seen as an extension to the Dublin Core Metadata Data Initiative (DCMI) terms.

The primary objective for creating the DwC-germplasm was to describe the additional terminology required for exchange of genebank datasets using the GBIF Integrated Publishing Toolkit (IPT). The terms included in the DwC germplasm are from the Multi-Crop Passport Descriptors (MCPD) and the proposed descriptors for germplasm characterization and evaluation data (C&E) (see: [1] and [2]) from the EPGRIS3 group of the European Cooperative Programme for Plant Genetic Resources (ECPGR). Version 0.1 (http://rs.nordgen.org/dwc/germplasm/0.1/terms/) of the DwC germplasm was developed by the Nordic Genetic Resources Center (NordGen) and Bioversity International (CGIAR) in 2009 (2009-08-24). It is licensed as CC0 (http://creativecommons.org/publicdomain/zero/1.0/).

The Darwin Core extension for genebanks is a vocabulary and is declared as rdf:type skos:ConceptScheme). The preferred namespace prefix is "germplasm" with namespace URI = "http://purl.org/germplasm/terms#". Each term will have it's own Wiki page with the description of the term. Terms are presented here organized alphabetical by their group (skos:Collection). The first step when setting up a new vocabulary (with external namespace URIs) is to import the term identifier URIs to the Wiki. This is done using a special wiki page in the "MediaWiki" wiki-namespace and starting with "Smw_import_" followed by the local namespace prefix to be used by the Wiki. For the germplasm terms we use: MediaWiki:Smw_import_germplasm.

Collection of Terms (skos:Collection)

Overview of the groups for organizing the Germplasm Terms (groups are of rdf:type = skos:Collection). These can be seen as classes (rdfs:Class, owl:Class) or the typical types of entities supported by the Darwin Core extension for genebanks. In a Darwin Core Archive (DwC-A) these terms can be used to indicate the row-type for an DwC-A extension.

Dataset :: dcmitype:Dataset
Taxon name :: dwc:Taxon
Germplasm accession :: (see also: dsw:Specimen, dsw:LivingSpecimen)
Collecting event :: (see also: dwc:Event)
Breeding event
Acquisition event
Safety duplication
Treaty or regulation
Measurement method
Measurement experiment
Measurement score :: dwc:MeasurementOrFact
In situ conservation :: (PROPOSED)

Controlled vocabularies of codes (controlled values)

Biological status type
Acquisition type
Storage type

Germplasm Terms

Minting the individual Terms here (terms are of rdf:type = skos:Concept). The germplasm terms can be seen as describing the relationship between entities, individuals, resources (comparable to owl:ObjectProperty, owl:DatatypeProperty, rdfs:Property).

Controlled vocabularies of codes (TESTING)

Biological status type

Acquisition type

Most of these could be replaced by their term in the Environmental Ontology (EnvO) before included into the Germplasm Vocabulary of Terms.

Storage type