Germplasm

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The Darwin Core germplasm extension (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 the 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 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/).

Namespace URI: http://purl.org/germplasm/germplasmTerm# with preferred namespace prefix “germplasm”.



 



All Concepts in Germplasm:
By label: biological status
By concept name: germplasm:biologicalStatus


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.

Controlled vocabularies of codes (controlled values)

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).


dcmitype:Dataset [3] [4]

dwc:datasetID, dwc:datasetName, dwc:collectionID, dwc:collectionCode, dwc:institutionID, dwc:institutionCode (mcpd:INSTCODE)

dwc:Taxon [5] [6]

dwc:taxonID, dwc:scientificNameID, dwc:scientificName, dwc:genus (mcpd:GENUS), dwc:specificEpithet (mcpd:SPECIES), dwc:scientificNameAuthorship (mcpd:SPAUTHOR, mcpd:SUBTAUTHOR), dwc:vernacularName (mcpd:CROPNAME)

GermplasmAccession (see also: dsw:Specimen) [7]

dwc:occurrenceID, dwc:catalogNumber (mcpd:ACCENUMB), germplasmID, germplasmIdentifier (mcpd:ACCENAME), biologicalStatus (mcpd:SAMPSTAT), storageCondition (mcpd:STORAGE), dwc:otherCatalogNumbers (mcpd:OTHERNUMB), dwc:occurrenceDetails (eurisco:ACCEURL), dwc:occurrenceRemarks

CollectingEvent (see also: dwc:Event) [8]

dwc:eventID, dwc:recordNumber (mcpd:COLLNUMB), [[9]], [[10]], [[11]], [[12]], 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, collectingInstituteID (mcpd:COLLCODE), dwc:recordedBy, dwc:eventRemarks

BreedingEvent [13]

breedingID, breedingIdentifier (mcpd:ACCENAME), breedingYear, breedingCountry, breedingCountryCode, breedingInstituteID (mcpd:BREDCODE), breedingInstitute (eurisco:BREDDESCR), breedingPerson, ancestralData (mcpd:ANCEST), purdyPedigree, breedingRemarks

AcquisitionEvent [14]

acquisitionID, donorsID, donorsIdentifier (mcpd:DONORNUMB), donorInstituteID (mcpd:DONORCODE), donorInstitute (eurisco:DONORDESCR), acquisitionDate (mcpd:ACQDATE), acquisitionSource (mcpd:COLLSRC), acquisitionRemarks

SafetyDuplication [15]

safetyDuplicationID, safetyDuplicationDate, safetyDuplicationInstituteID (mcpd:DUPLSITE) safetyDuplicationInstitute, safetyDuplicationRemarks

TreatyOrRegulation [16]

treatyOrRegulationID, treatyOrRegulationName, treatyOrRegulationGoverningBody, mlsStatus

MeasurementTrait [17] (measurement methodology, descriptor)

measurementTraitID, measurementTraitIdentifier (epgris3:TRAIT_NUMBER), measurementTraitName (epgris3:TRAIT_NAME), measurementTraitCategory, measurementTraitScale, measurementTraitSource, measurementTraitRemarks (epgris3:TRAIT_REMARK) dwc:measurementType, dwc:measurementMethod

MeasurementTrial [18] (experiment trial season)

measurementTrialID, measurementTrialIdentifier, measurementTrialYear, [[19]], [[20]], [[21]], [[22]], measurementTrialReport, measurementTrialRemarks

MeasurementScore [23] (dwc:MeasurementOrFact)

dwc:measurementID, dwc:measurementType, dwc:measurementValue, dwc:measurementAccuracy, dwc:measurementUnit, dwc:measurementDeterminedDate, dwc:measurementDeterminedBy, dwc:measurementMethod, dwc:measurementRemarks, measurementByInstituteID, measurementGrowthStage, dwc:occurrenceID, dwc:catalogNumber, germplasmID, germplasmIdentifier, measurementExperimentID, measurementExperimentIdentifier, measurementMethodID, measurementMethodIdentifier


In situ conservation (PROPOSED) [24]

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)

Biological status type

wild (100) | natural (110) | semiNaturalWild (120) | semiNaturalSown (130) | weedy (200) | landrace (300) | breedingResearchMaterial (400) | breedersLine (410) | syntheticPopulation (411) | hybrid (412) | founderStock (413) | inbredLine (414) | segregatingPopulation (415) | clonalSelection (416) | geneticStock (420) | mutant (421) | cytogeneticStock (422) otherGeneticStock (423) | advancedCultivar (500) | GMO (600) | otherBiologicalStatus (999)

Acquisition type

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

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

Storage type

seedCollection (10) | shortTerm (11) | mediumTerm (12) | longTerm (13) | fieldCollection (20) | inVitro (30) | cryopreserved (40) | DNA (50) | otherStorage (99)



Darwin Core extension for genebanks (germplasm)

Description The Darwin Core extension for genebanks is based on the Darwin Core vocabulary and is designed as an extension to this vocabulary.
Comment The base URI of the Darwin Core extension for genebanks is "http://purl.org/germplasm/germplasmTerm#". Please make sure that you are only using element identifiers in this namespace, e.g. "http://purl.org/germplasm/germplasmTerm#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

References

  • Arnaud E, Castañeda-Álvarez NP, Cossi JG, Endresen D, Jahanshiri E, and Vigouroux Y (2016). Report of the Task Group on GBIF Data Fitness for Use in Agrobiodiversity. Global Biodiversity Information Facility, Copenhagen, Denmark, and Bioversity International, Rome, Italy. http://www.gbif.org/resource/82283
  • 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.
  • Faberova I (2010). Standard descriptors and EURISCO development. Czech Journal of Genetics and Plant Breeding 46: S106-S109.
  • 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.
  • 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.
  • 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. doi:10.1186/1471-2105-9-116 [25]
  • Robertson T, Döring M, Guralnick R, Bloom D, Braak K, Otegui J, Russell L, and Desmet P (2014) The GBIF Integrated Publishing Toolkit: Facilitating the efficient publishing of biodiversity data on the Internet. PLOS ONE 9(8):e102623. doi:10.1371/journal.pone.0102623
  • TDWG (2009). Darwin Core. Darwin Core Task Group, Biodiversity Information Standards (TDWG). http://rs.tdwg.org/dwc/ (accessed on 2015-09-19).
  • Thormann I, Alercia A, and Dulloo ME (2013). Core descriptors for in situ conservation of crop wild relatives v.1. Bioversity International, Rome, Italy. 28pp. ISBN-13: 978-92-9043-935-6.
  • Wieczorek J, Bloom D, Guralnick R, Blum S, Döring M, Giovanni R, Robertson T, and Vieglais D (2012). Darwin Core: An Evolving Community-Developed Biodiversity Data Standard. PLoS ONE 7(1): e29715. doi:10.1371/journal.pone.0029715


Import/Export RDF

For the germplasm terms we use: MediaWiki:Smw_import_germplasm.