Difference between revisions of "Germplasm"
Dag Endresen (Talk | contribs) (→dcmitype:Dataset [http://dublincore.org/documents/dcmi-terms/#dcmitype-Dataset ] [http://code.google.com/p/darwincore-germplasm/wiki/DatasetTerms ]) |
Dag Endresen (Talk | contribs) (→GermplasmAccession (see also: dsw:Specimen) [http://code.google.com/p/darwincore-germplasm/wiki/GermplasmAccession ]) |
||
| Line 54: | Line 54: | ||
=== [[germplasm:GermplasmAccession|GermplasmAccession]] (see also: [[dsw:Specimen]]) [http://code.google.com/p/darwincore-germplasm/wiki/GermplasmAccession ] === | === [[germplasm:GermplasmAccession|GermplasmAccession]] (see also: [[dsw:Specimen]]) [http://code.google.com/p/darwincore-germplasm/wiki/GermplasmAccession ] === | ||
<div id="GermplasmAccession"></div> | <div id="GermplasmAccession"></div> | ||
| − | dwc:occurrenceID, | + | [[dwc:occurrenceID]], |
| − | dwc:catalogNumber (mcpd:ACCENUMB), | + | [[dwc:catalogNumber]] (mcpd:ACCENUMB), |
[[germplasm:germplasmID|germplasmID]], | [[germplasm:germplasmID|germplasmID]], | ||
[[germplasm:germplasmIdentifier|germplasmIdentifier]] (mcpd:ACCENAME), | [[germplasm:germplasmIdentifier|germplasmIdentifier]] (mcpd:ACCENAME), | ||
[[germplasm:biologicalStatus|biologicalStatus]] (mcpd:SAMPSTAT), | [[germplasm:biologicalStatus|biologicalStatus]] (mcpd:SAMPSTAT), | ||
[[germplasm:storageCondition|storageCondition]] (mcpd:STORAGE), | [[germplasm:storageCondition|storageCondition]] (mcpd:STORAGE), | ||
| − | dwc:otherCatalogNumbers (mcpd:OTHERNUMB), | + | [[dwc:otherCatalogNumbers]] (mcpd:OTHERNUMB), |
| − | dwc:occurrenceDetails (eurisco:ACCEURL), | + | [[dwc:occurrenceDetails]] (eurisco:ACCEURL), |
| − | dwc:occurrenceRemarks | + | [[dwc:occurrenceRemarks]] |
=== [[germplasm:CollectingEvent|CollectingEvent]] (see also: [[dwc:Event]]) [http://code.google.com/p/darwincore-germplasm/wiki/CollectingEvent ] === | === [[germplasm:CollectingEvent|CollectingEvent]] (see also: [[dwc:Event]]) [http://code.google.com/p/darwincore-germplasm/wiki/CollectingEvent ] === | ||
Revision as of 08:57, 11 September 2012
Contents
- 1 Darwin Core extension for genebanks
- 1.1 Collection of Terms (skos:Collection)
- 1.2 Germplasm Terms
- 1.2.1 dcmitype:Dataset [3] [4]
- 1.2.2 dwc:Taxon [5] [6]
- 1.2.3 GermplasmAccession (see also: dsw:Specimen) [7]
- 1.2.4 CollectingEvent (see also: dwc:Event) [8]
- 1.2.5 BreedingEvent [9]
- 1.2.6 AcquisitionEvent [10]
- 1.2.7 SafetyDuplication [11]
- 1.2.8 TreatyOrRegulation [12]
- 1.2.9 MeasurementMethod [13]
- 1.2.10 MeasurementExperiment [14]
- 1.2.11 MeasurementOrFact [15]
- 1.2.12 In situ conservation (PROPOSED) [16]
- 1.3 Controlled vocabularies of codes (TESTING)
- 1.4 Import/Export RDF
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)
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), geo:lat, geo:long, geo:alt, geo:location, 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 [9]
breedingID, breedingIdentifier (mcpd:ACCENAME), breedingYear, breedingCountry, breedingCountryCode, breedingInstituteID (mcpd:BREDCODE), breedingInstitute (eurisco:BREDDESCR), breedingPerson, ancestralData (mcpd:ANCEST), purdyPedigree, breedingRemarks
AcquisitionEvent [10]
acquisitionID, donorsID, donorsIdentifier (mcpd:DONORNUMB), donorInstituteID (mcpd:DONORCODE), donorInstitute (eurisco:DONORDESCR), acquisitionDate (mcpd:ACQDATE), acquisitionSource (mcpd:COLLSRC), acquisitionRemarks
SafetyDuplication [11]
safetyDuplicationID, safetyDuplicationDate, safetyDuplicationInstituteID (mcpd:DUPLSITE) safetyDuplicationInstitute, safetyDuplicationRemarks
TreatyOrRegulation [12]
treatyOrRegulationID, treatyOrRegulationName, treatyOrRegulationGoverningBody, mlsStatus
MeasurementMethod [13]
measurementMethodID (epgris3:TRAIT_NUMBER), measurementMethodName (epgris3:TRAIT_NAME), measurementMethodCategory, measurementMethodScale, measurementMethodSource, measurementMethodRemarks (epgris3:TRAIT_REMARK) dwc:measurementType, dwc:measurementMethod
MeasurementExperiment [14]
measurementEperimentID, measurementExperimentIdentifier, measurementExperimentYear, measurementExperimentReport, measurementExperimentRemarks
MeasurementOrFact [15]
dwc:measurementID, dwc:measurementValue, dwc:measurementUnit, dwc:measurementAccuracy, dwc:measurementDeterminedDate, dwc:measurementDeterminedBy, measurementByInstituteID, measurementGrowthStage
In situ conservation (PROPOSED) [16]
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/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: http://code.google.com/p/darwincore-germplasm/
- Discussion forum: http://kos.gbif.org/wiki/Germplasm
- Namespace: http://rs.nordgen.org/dwc/germplasm/0.1/
- Namespace (version 0.1): http://rs.nordgen.org/dwc/germplasm/0.1/ (deprecated)
- EPGRIS3 wiki: 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 [17].
- 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%5BshowUid%5D=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. doi:10.1186/1471-2105-9-116 [18]
