View source for Germplasm

{{Concept scheme
|description=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 ([http://www.tdwg.org/ TDWG]). The DwC germplasm provides an extension to the [http://rs.tdwg.org/dwc/terms Darwin Core] standard of the TDWG for occurrences. Darwin Core can be seen as an extension to the Dublin Core Metadata Data Initiative ([http://dublincore.org/documents/dcmi-terms/ DCMI]) terms.

The primary objective for creating the DwC-germplasm was to describe the additional terminology required for the exchange of genebank datasets using the GBIF Integrated Publishing Toolkit ([http://code.google.com/p/gbif-providertoolkit/ IPT]). The terms included in the DwC germplasm are from the Multi-Crop Passport Descriptors ([http://www.bioversityinternational.org/index.php?id=19&user_bioversitypublications_pi1&#91;showUid&#93;=2192 MCPD]) and the proposed descriptors for germplasm characterization and evaluation data (C&E) (see: [http://www.epgris3.eu/EPGRIS3%2020090507workshop.htm ] and [http://www.epgris3.eu/docs/activities/2-05/Inclusion%20of%20C&E%20data.pdf ]) from the [http://www.epgris3.eu/ EPGRIS3] group of the European Cooperative Programme for Plant Genetic Resources ([http://www.ecpgr.cgiar.org/Index.htm%27 ECPGR]). Version 0.1 ([[dcterms:replaces::http://rs.nordgen.org/dwc/germplasm/0.1/terms/]]) of the DwC germplasm was developed by the [[dc:creator:=Nordic Genetic Resources Center]] ([http://www.nordgen.org/ NordGen]) and [[dc:creator:=Bioversity International]] ([http://www.bioversityinternational.org/ CGIAR]) in 2009 ([[dcterms:issued:=2009-08-24]]). It is licensed as CC0 ([[dcterms:license::http://creativecommons.org/publicdomain/zero/1.0/]]).
|contributors=
|preferred namespace uri=http://purl.org/germplasm/terms#
|preferred namespace prefix=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|Dataset]] :: [[dcmitype:Dataset]]
* [[#Taxon|Taxon name]] :: [[dwc:Taxon]]
* [[#GermplasmAccession|Germplasm accession]] :: (see also: [[dsw:Specimen]], [[dsw:LivingSpecimen]])
* [[#CollectingEvent|Collecting event]] :: (see also: [[dwc:Event]])
* [[#BreedingEvent|Breeding event]]
* [[#AcquisitionEvent|Acquisition event]]
* [[#SafetyDuplication|Safety duplication]]
* [[#TreatyOrRegulation|Treaty or regulation]]
* [[#MeasurementMethod|Measurement method]]
* [[#MeasurementExperiment|Measurement experiment]]
* [[#MeasurementOrFact|Measurement score]] :: [[dwc:MeasurementOrFact]]
* [[#InSituConservation|In situ conservation]] :: (PROPOSED)

Controlled vocabularies of codes (controlled values)
* [[#BiologicalStatusType|Biological status type]]
* [[#AcquisitionType|Acquisition type]]
* [[#StorageType|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).


=== [http://purl.org/dc/dcmitype/Dataset dcmitype:Dataset] [http://dublincore.org/documents/dcmi-terms/#dcmitype-Dataset ] [http://code.google.com/p/darwincore-germplasm/wiki/DatasetTerms ] ===
<div id="Dataset"></div>
[[dwc:datasetID]], 
[[dwc:datasetName]], 
[[dwc:collectionID]], 
[[dwc:collectionCode]], 
[[dwc:institutionID]], 
[[dwc:institutionCode]] (mcpd:INSTCODE)

=== [http://rs.tdwg.org/dwc/terms/Taxon dwc:Taxon] [http://rs.tdwg.org/dwc/terms/#Taxon ] [http://code.google.com/p/darwincore-germplasm/wiki/Taxon ] ===
<div id="Taxon"></div>
[[dwc:taxonID]], 
[[dwc:scientificNameID]], 
[[dwc:scientificName]], 
[[dwc:genus]] (mcpd:GENUS), 
[[dwc:specificEpithet]] (mcpd:SPECIES), 
[[dwc:scientificNameAuthorship]] (mcpd:SPAUTHOR, mcpd:SUBTAUTHOR), 
[[dwc:vernacularName]] (mcpd:CROPNAME)

=== [[germplasm:GermplasmAccession|GermplasmAccession]] (see also: [[dsw:Specimen]]) [http://code.google.com/p/darwincore-germplasm/wiki/GermplasmAccession ] ===
<div id="GermplasmAccession"></div>
[[dwc:occurrenceID]], 
[[dwc:catalogNumber]] (mcpd:ACCENUMB), 
[[germplasm:germplasmID|germplasmID]], 
[[germplasm:germplasmIdentifier|germplasmIdentifier]] (mcpd:ACCENAME), 
[[germplasm:biologicalStatus|biologicalStatus]] (mcpd:SAMPSTAT), 
[[germplasm:storageCondition|storageCondition]] (mcpd:STORAGE),
[[dwc:otherCatalogNumbers]] (mcpd:OTHERNUMB), 
[[dwc:occurrenceDetails]] (eurisco:ACCEURL), 
[[dwc:occurrenceRemarks]]

=== [[germplasm:CollectingEvent|CollectingEvent]] (see also: [[dwc:Event]]) [http://code.google.com/p/darwincore-germplasm/wiki/CollectingEvent ] ===
<div id="CollectingEvent"></div>
[[dwc:eventID]], 
[[dwc:recordNumber]] (mcpd:COLLNUMB), 
[[geo:location]],
[[geo:lat]], 
[[geo:long]], 
[[geo:alt]], 
[[dwc:decimalLatitude]], 
[[dwc:decimalLongitude]], 
[[dwc:geodeticDatum]], 
[[dwc:minimumElevationInMeters]] (mcpd:ELEVATION), 
[[dwc:eventDate]] (mcpd:COLLDATE), 
[[dwc:locality]] (mcpd:COLLSITE), 
[[dwc:countryCode]] (mcpd:ORIGCTY), 
[[dwc:verbatimLatitude]] (mcpd:LATITUDE), 
[[dwc:verbatimLongitude]] (mcpd:LONGITUDE), 
[[dwc:verbatimCoordinateSystem]],
[[germplasm:collectingInstituteID|collectingInstituteID]] (mcpd:COLLCODE), 
[[dwc:recordedBy]], 
[[dwc:eventRemarks]]

=== [[germplasm:BreedingEvent|BreedingEvent]] [http://code.google.com/p/darwincore-germplasm/wiki/BreedingEventTerms ] ===
<div id="BreedingEvent"></div>
[[germplasm:breedingID|breedingID]], 
[[germplasm:breedingIdentifier|breedingIdentifier]] (mcpd:ACCENAME), 
[[germplasm:breedingYear|breedingYear]], 
[[germplasm:breedingCountry|breedingCountry]], 
[[germplasm:breedingCountryCode|breedingCountryCode]], 
[[germplasm:breedingInstituteID|breedingInstituteID]] (mcpd:BREDCODE), 
[[germplasm:breedingInstitute|breedingInstitute]] (eurisco:BREDDESCR), 
[[germplasm:breedingPerson|breedingPerson]], 
[[germplasm:ancestralData|ancestralData]] (mcpd:ANCEST), 
[[germplasm:purdyPedigree|purdyPedigree]], 
[[germplasm:breedingRemarks|breedingRemarks]]

=== [[germplasm:AcquisitionEvent|AcquisitionEvent]] [http://code.google.com/p/darwincore-germplasm/wiki/AcquisitionEvent ] ===
<div id="AcquisitionEvent"></div>
[[germplasm:acquisitionID|acquisitionID]], 
[[germplasm:donorsID|donorsID]], 
[[germplasm:donorsIdentifier|donorsIdentifier]] (mcpd:DONORNUMB), 
[[germplasm:donorInstituteID|donorInstituteID]] (mcpd:DONORCODE), 
[[germplasm:donorInstitute|donorInstitute]] (eurisco:DONORDESCR), 
[[germplasm:acquisitionDate|acquisitionDate]] (mcpd:ACQDATE), 
[[germplasm:acquisitionSource|acquisitionSource]] (mcpd:COLLSRC), 
[[germplasm:acquisitionRemarks|acquisitionRemarks]]

=== [[germplasm:SafetyDuplication|SafetyDuplication]] [http://code.google.com/p/darwincore-germplasm/wiki/SafetyDuplicationTerms ] ===
<div id="SafetyDuplication"></div>
[[germplasm:safetyDuplicationID|safetyDuplicationID]], 
[[germplasm:safetyDuplicationDate|safetyDuplicationDate]], 
[[germplasm:safetyDuplicationInstituteID|safetyDuplicationInstituteID]] (mcpd:DUPLSITE)
[[germplasm:safetyDuplicationInstitute|safetyDuplicationInstitute]],
[[germplasm:safetyDuplicationRemarks|safetyDuplicationRemarks]]

=== [[germplasm:TreatyOrRegulation|TreatyOrRegulation]] [http://code.google.com/p/darwincore-germplasm/wiki/TreatiesAndRegulationsTerms ] ===
<div id="TreatyOrRegulation"></div>
[[germplasm:treatyOrRegulationID|treatyOrRegulationID]], 
[[germplasm:treatyOrRegulationName|treatyOrRegulationName]], 
[[germplasm:treatyOrRegulationGoverningBody|treatyOrRegulationGoverningBody]], 
[[germplasm:mlsStatus|mlsStatus]]

=== [[germplasm:MeasurementMethod|MeasurementMethod]] [http://code.google.com/p/darwincore-germplasm/wiki/MeasurementMethod ] ===
<div id="MeasurementMethod"></div>
[[germplasm:measurementMethodID|measurementMethodID]] (epgris3:TRAIT_NUMBER), 
[[germplasm:measurementMethodName|measurementMethodName]] (epgris3:TRAIT_NAME), 
[[germplasm:measurementMethodCategory|measurementMethodCategory]], 
[[germplasm:measurementMethodScale|measurementMethodScale]], 
[[germplasm:measurementMethodSource|measurementMethodSource]], 
[[germplasm:measurementMethodRemarks|measurementMethodRemarks]] (epgris3:TRAIT_REMARK)
[[dwc:measurementType]], 
[[dwc:measurementMethod]]

=== [[germplasm:MeasurementExperiment|MeasurementExperiment]] [http://code.google.com/p/darwincore-germplasm/wiki/MeasurementExperiment ] ===
<div id="MeasurementExperiment"></div>
[[germplasm:measurementEperimentID|measurementExperimentID]], 
[[germplasm:measurementExperimentIdentifier|measurementExperimentIdentifier]], 
[[germplasm:measurementExperimentYear|measurementExperimentYear]], 
[[geo:location]],
[[geo:lat]], 
[[geo:long]], 
[[geo:alt]], 
[[germplasm:measurementExperimentReport|measurementExperimentReport]], 
[[germplasm:measurementExperimentRemarks|measurementExperimentRemarks]]

=== [[dwc:MeasurementOrFact|MeasurementOrFact]] [http://code.google.com/p/darwincore-germplasm/wiki/MeasurementOrFact ] (Score) ===
<div id="MeasurementOrFact"></div>
[[dwc:measurementID]], 
[[dwc:measurementValue]], 
[[dwc:measurementUnit]], 
[[dwc:measurementAccuracy]], 
[[dwc:measurementDeterminedDate]], 
[[dwc:measurementDeterminedBy]],
[[germplasm:measurementByInstituteID|measurementByInstituteID]], 
[[germplasm:measurementGrowthStage|measurementGrowthStage]],
[[germplasm:measurementEperimentID|measurementExperimentID]], 
[[germplasm:measurementMethodID|measurementMethodID]]

=== [[germplasm:InSituConservation|In situ conservation (PROPOSED)]] [http://code.google.com/p/darwincore-germplasm/wiki/ConservationTraitsTerms ] ===
<div id="InSituConservation"></div>

''These terms are not yet included in the germplasm vocabulary. You may help providing the appropriate description of the proposed terms, and to open the discussion in the germplasm community.''

IUCNCategory,
NumberOfSeeds,
BioRegion,
InSituCountry,
InSituRecoveryDateStarted,
InSituRecoveryInstitute,
InSituRecoveryRemarks

== Controlled vocabularies of codes (TESTING) ==

=== [[germplasmType:BiologicalStatusType|Biological status type]] ===
<div id="BiologicalStatusType"></div>
[[germplasmType:wild|wild]] (100) | 
[[germplasmType:natural|natural]] (110) |
[[germplasmType:semiNaturalWild|semiNaturalWild]] (120) |
[[germplasmType:semiNaturalSown|semiNaturalSown]] (130) |
[[germplasmType:weedy|weedy]] (200) |
[[germplasmType:landrace|landrace]] (300) |
[[germplasmType:breedingResearchMaterial|breedingResearchMaterial]] (400) |
[[germplasmType:breedersLine|breedersLine]] (410) |
[[germplasmType:syntheticPopulation|syntheticPopulation]] (411) |
[[germplasmType:hybrid|hybrid]] (412) |
[[germplasmType:founderStock|founderStock]] (413) |
[[germplasmType:inbredLine|inbredLine]] (414) |
[[germplasmType:segregatingPopulation|segregatingPopulation]] (415) |
[[germplasmType:clonalSelection|clonalSelection]] (416) |
[[germplasmType:geneticStock|geneticStock]] (420) |
[[germplasmType:mutant|mutant]] (421) |
[[germplasmType:cytogeneticStock|cytogeneticStock]] (422)
[[germplasmType:otherGeneticStock|otherGeneticStock]] (423) |
[[germplasmType:advancedCultivar|advancedCultivar]] (500) |
[[germplasmType:GMO|GMO]] (600) |
[[germplasmType:otherBiologicalStatus|otherBiologicalStatus]] (999)

=== [[germplasmType:AcquisitionType|Acquisition type]] ===
<div id="AcquisitionType"></div>
Most of these could be replaced by their term in the [http://bioportal.bioontology.org/ontologies/1069 Environmental Ontology (EnvO)] before included into the Germplasm Vocabulary of Terms.

[[germplasmType:wildHabitat|wildHabitat]] (10) |
[[germplasmType:forest|forest]] (11) |
[[germplasmType:shrubland|shrubland]] (12) |
[[germplasmType:grassland|grassland]] (13) |
[[germplasmType:desertOrTundra|desertOrTundra]] (14) |
[[germplasmType:aquaticHabitat|aquaticHabitat]] (15) |
[[germplasmType:cultivatedHabitat|cultivatedHabitat]] (20) |
[[germplasmType:field|field]] (21) |
[[germplasmType:orchard|orchard]] (22) |
[[germplasmType:backyard|backyard]] (23) |
[[germplasmType:fallowLand|fallowLand]] (24) |
[[germplasmType:pasture|pasture]] (25) |
[[germplasmType:farmStore|farmStore]] (26) |
[[germplasmType:threshingFloor|threshingFloor]] (27) |
[[germplasmType:park|park]] (28) |
[[germplasmType:marketOrShop|marketOrShop]] (30) |
[[germplasmType:instituteOrGenebank|instituteOrGenebank]] (40) |
[[germplasmType:seedCompany|seedCompany]] (50) |
[[germplasmType:ruderalHabitat|ruderalHabitat]] (60) |
[[germplasmType:roadside|roadside]] (61) |
[[germplasmType:fieldMargin|fieldMargin]] (62) |
[[germplasmType:otherAcquisition|otherAcquisition]] (99)

=== [[germplasmType:StorageType|Storage type]] ===
<div id="StorageType"></div>
[[germplasmType:seedCollection|seedCollection]] (10) |
[[germplasmType:shortTerm|shortTerm]] (11) |
[[germplasmType:mediumTerm|mediumTerm]] (12) |
[[germplasmType:longTerm|longTerm]] (13) |
[[germplasmType:fieldCollection|fieldCollection]] (20) |
[[germplasmType:inVitro|inVitro]] (30) |
[[germplasmType:cryopreserved|cryopreserved]] (40) |
[[germplasmType:DNA|DNA]] (50) |
[[germplasmType:otherStorage|otherStorage]] (99)



----

=== Darwin Core extension for genebanks (germplasm) === 

{| style="color:black; background-color:#ffffee;" cellpadding="10" cellspacing="0" border="1"
!align="right" width="120px"|Description
|colspan="1"|[[rdfs:comment::The Darwin Core extension for genebanks is based on the Darwin Core vocabulary and is designed as an extension to this vocabulary.]]
|-
!align="right"|Comment
|[[skos:editorialNote::The base URI of the Darwin Core extension for genebanks is "http://purl.org/germplasm/terms#". Please make sure that you are only using element identifiers in this namespace, e.g. "http://purl.org/germplasm/terms#CollectingInstituteCode". There may be copies of the ontology file on the Web which can be retrieved from other locations, but those locations should not be used as the basis of identifiers.]]
|}

=== Links ===
* Project home page: [[foaf:homepage::http://code.google.com/p/darwincore-germplasm/]]
* Discussion forum: [[rdfs:seeAlso::http://kos.gbif.org/wiki/Germplasm]]
* Namespace: [[vann:preferredNamespaceUri::http://rs.nordgen.org/dwc/germplasm/0.1/]]
* Namespace (version 0.1): [[rdfs:seeAlso::http://rs.nordgen.org/dwc/germplasm/0.1/]] (deprecated)
* EPGRIS3 wiki: [[rdfs:seeAlso::http://www.nordgen.org/epgris3/wiki/index.php/DwC_Germplasm]] (deprecated)
* Darwin Core terms: http://rs.tdwg.org/dwc/terms
* Dublin Core terms: http://dublincore.org/documents/dcmi-terms/

=== References ===
* Alercia, A., S. Diulgheroff, and T. Metz (2001). FAO/IPGRI Multi-crop passport descriptors, December 2001. International Plant Genetic Resources Institute (IPGRI) / Food and Agriculture Organization of the United Nations (FAO), Rome, Italy. Available at http://apps3.fao.org/wiews/mcpd/MCPD_Dec2001_EN.pdf, verified 21 Feb 2012; and at http://www.bioversityinternational.org/nc/publications/publication/issue/faoipgri_multi_crop_passport_descriptors.html, verified 21 Feb 2012.

* Alercia A., S. Diulgheroff, and M. Mackay (2012). FAO/Bioversity Multi-crop passport descriptors v.2 [MCPD v.2]. Food and Agriculture Organization of the United Nations (FAO), and Bioversity International, Rome, Italy. 11 pp. Available at [http://www.bioversityinternational.org/index.php?id=19&user_bioversitypublications_pi1&#91;showUid&#93;=6901].

* Berendsohn, W. and H. Knüpffer (2006). Draft mapping of Eurisco descriptors to ABCD 2.06. Available at http://www.bgbm.org/tdwg/codata/Schema/Mappings/EURISCO-2-ABCD.pdf, verified 21 Feb 2012.

* Bioversity International (2007). Guidelines for the development of crop descriptor lists. Bioversity Technical Bulletin Series. Bioversity International, Rome, Italy. ISBN: 978-92-9043-792-1. Available at http://www.bioversityinternational.org/index.php?id=19&user_bioversitypublications_pi1&#91;showUid&#93;=3070, verified 21 Feb 2012.

* Endresen, D., S. Gaiji, and T. Robertson (2009). DarwinCore Germplasm Extension and deployment in the GBIF infrastructure. Proceedings of TDWG 2009, Montpellier, France. Bioversity Information Standards (TDWG). Available at http://www.tdwg.org/proceedings/article/view/464, verified 21 Feb 2012.

* Endresen, D.T.F. and H. Knüpffer (2011). The Darwin Core extension for genebanks opens up new opportunities for sharing genebank datasets. p. 119-142. In: Endresen, D.T.F. Utilization of Plant Genetic Resources: A Lifeboat to the Gene Pool. PhD Thesis, Department of Agriculture and Ecology, Faculty of Life Sciences, Copenhagen University, Denmark. ISBN: 978-91-628-8268-6. Available online at http://goo.gl/pYa9x, verified 21 Feb 2012.

* Endresen, D.T.F. and H. Knüpffer (2012). The Darwin Core extension for genebanks opens up new opportunities for sharing genebank data sets. Biodiversity Informatics 8:11-29. Available online at https://journals.ku.edu/index.php/jbi/article/view/4095, verified 16 July 2012.

* Hazekamp, T., J. Serwinski, and A. Alercia (1997). Appendix II. Multicrop passport descriptors (final version). p. 97-90. In: Lipman, E., M.W.M. Jongen, Th.J.L. van Hintum, T. Grass, and L. Maggioni (eds). Central crop databases: Tools for plant genetic resources management. International Plant Genetic Resources Institute (IPGRI), Rome, Italy/CGN, Wageningen, Netherlands. ISBN 92-9043- 320-5.

* Generation Challenge Program (2007). GCP Informatics, Web services, Schema [online]. Generation Challenge Programme, c/o CIMMYT, El Batán Texcoco, Mexico. Available online at http://gcpcr.grinfo.net/include/webservices/schema-documentation.php, verified 21 Feb 2012.

* Gotor, E., A. Alercia, V. Ramanatha Rao, J. Watts, and F. Caracciolo (2008). The scientific information activity of Bioversity International: the descriptor lists. Genetic Resources and Crop Evolution 55(5): 757-772. DOI: 10.1007/s10722-008-9342-x.

* Kell, S.P., J.D. Moore, J.M. Iriondo, M.A.Scholten, B.V. Ford-Lloyd, and N. Maxted, (2008). CWRIS: a tool for managing and accessing crop wild relative information. In: Maxted, N., Ford-Lloyd, B.V., Kell, S.P., Iriondo, J., Dulloo, E. and Turok, J. (eds.) Crop Wild Relative Conservation and Use. Pp. 469-489. CAB International, Wallingford. 

* Moore, J.D., S.P. Kell, J.M. Iriondo, B.V. Ford-Lloyd, and N. Maxted (2008). CWRML: representing crop wild relative conservation and use data in XML. BMC Bioinformatics, 9: 116. [http://dx.doi.org/10.1186/1471-2105-9-116 doi:10.1186/1471-2105-9-116] [http://wrap.warwick.ac.uk/547/ ]

== Import/Export RDF ==
* [[MediaWiki:Smw_import_germplasm|Import URI identifiers for the Germplasm terms]]
* [http://kos.gbif.org/wiki/Special:ExportRDF?pages=Germplasm Export RDF description for this Vocabulary]
* [http://kos.gbif.org/wiki/Special:ExportRDF?pages=Category:Germplasm_term&backlinks=1 Export an RDF overview list of Germplasm Terms]
* [http://kos.gbif.org/wiki/Special:ExportRDF?pages=Category:Germplasm_term&backlinks=1 Export an RDF overview list of all Germplasm Terms and Properties declared here]

For the germplasm terms we use: [[MediaWiki:Smw_import_germplasm]].

[[Category:Germplasm_terms]]