Germplasm Vocabulary
The Germplasm Vocabulary (Darwin Core extension for germplasm) provides a vocabulary of terms for describing and annotating germplasm information resources.
Creative Commons Public Domain license; see http://creativecommons.org/publicdomain/zero/1.0/. You are free to copy, distribute and transmit the work; to remix/adapt the work (e.g. to import the ontology and create specializations of its elements), all without asking permissions. If you wish to provide attribution you may include the statement: "This work is based on the Darwin Core extension for genebanks".
Endresen DTF, and Knüpffer H (2012). The Darwin Core extension for genebanks opens up new opportunities for sharing genebank data sets. Biodiversity Informatics 8:11-29. Available at "https://journals.ku.edu/index.php/jbi/article/view/4095".
Endresen DTF, Gaiji S, and Robertson T (2009). DarwinCore Germplasm Extension and deployment in the GBIF infrastructure. Proceedings of TDWG, 2009. Available at "http://www.tdwg.org/proceedings/article/view/464".
Alercia A, Diulgheroff S, Mackay M (2012). FAO/Bioversity Multi-Crop Passport Descriptors V.2 [MCPD V.2]. Available at "http://www.bioversityinternational.org/e-library/publications/single-details-publication/?tx_news_pi1[news]=1350&cHash=d953e45ada3ab285d635593b5068a38f" and "http://www.bioversityinternational.org/uploads/tx_news/1526.pdf".
Alercia A, Diulgheroff S, Metz T (2001). FAO/IPGRI Multi-Crop Passport Descriptors [MCPD]. Available at "http://www.bioversityinternational.org/e-library/publications/single-details-publication/?tx_news_pi1[news]=177&cHash=a8d7778e9e4077f1047996a639a51a19" and "http://www.bioversityinternational.org/uploads/tx_news/124.pdf".
Notice that 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#TERM". There may be copies of the vocabulary file on the Web which can be retrieved from other locations, but those locations should not be used as the basis of identifiers.
The germplasm vocabulary of terms is an extension of the Darwin Core terms. Only the established germplasm terms that does not match Darwin Core terms are declared here.
Dataset
Data set with specimens (accessions) from genebank collections.
Taxon
The category of information pertaining to taxonomic names, taxon name usages, or taxon concepts.
Taxon names for specimens (accessions) in genebank collections.
Germplasm accession
Genebank specimen or accession is the unit for storing germplasm material in an ex situ genebank collection.
genebank accession
collecting event
Collecting event when the germplasm specimen was collected from a natural habitat (in situ) including the farmers field for cultivated germplasm material.
breeding event
Breeding event for domesticated and cultivated germplasm material.
Acquisition event
The acquisition event for inclusion of germplasm material into a genebank collection.
Safety duplication
Safety duplication of germplasm material stored under blackbox conditions at other locations.
Treaty or regulation
Treaty or regulation concerning germplasm material and plant genetic resources for food and agriculture.
Trait descriptor
Measurement trait used for the evaluation of crop trait properties (characterization and evaluation data).
The measurement trait terms should be evaluated for possible overlapping definitions in relation to the Crop Ontology (CO). These terms have further not been tested in the "wild" for sharing real data yet, and are therefore declared as status "unstable".
Measurement trial season
Measurement trial conducted to collect evaluation data on trait properties (characterization and evaluation data).
The measurement experiment terms should be evaluated for possible overlapping definitions in relation to the Crop Ontology (CO). These terms have further not been tested in the "wild" for sharing real data yet, and are therefore declared as status "unstable".
Measurement score
The category of information pertaining to measurements, facts, characteristics, or assertions about a resource (instance of data record, such as Occurrence, Taxon, Location, Event).
Measurement values and scores for trait properties (characterization and evaluation data).
Notice that the GBIF IPT toolkit require a unique URI for rowTypes between extensions, and we thus need a separate _germplasm_ MeasurementOrFact class. This term is intended in other aspects to be seen to be the same as the _Darwin-Core_ MeasurementOrFact term. The measurement terms should be evaluated for possible overlapping definitions in relation to the Crop Ontology (CO). These terms have further not been tested in the "wild" for sharing real data yet, and are therefore declared as status "unstable".
germplasm ID
A persistent identifier for a germplasm accession maintained as part of an ex situ genebank collection. Best practice is to use a globally unique and persistent identifier (PID).
Local identifiers such as the catalog number (accessions number) is best reported using the dwc:catalogNumber term.
germplasm PID
germplasm identifier
Accession name. Either a registered or other formal designation given to the accession.
Rheinische Vorgebirgstrauben; Emma; Avlon
biological status
The biological status for a germplasm accession describes the cultivation status and distinguish wild and primitive cultivars from modern cultivars and breeding lines (material under development).
Wild; Crop wild relative (CWR); Primitive; Traditional cultivar; Landrace; Breeding line; Genetic stock; Modern cultivar; GMO; 100; 110; 120; 130; 200; 300; 400; 410; 411; 412; 413; 414; 415; 416; 420; 421; 422; 423; 500; 600; 999
Recommended best practice is to follow a controlled vocabulary, such as the code list defined by the MCPD term, SAMPSTAT.
storage conditions
Type of germplasm storage conditions.
Recommended best practice is to use a controlled vocabulary such as the code list defined by the MCPD term STORAGE. Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.
collecting institute ID
Collecting institute ID.
SWE054; urn:lsid:biocol.org:col:35293; an established institute code for the collecting/gathering institute.
Recommended best practice is to use institute codes from the FAO WIEWS information system, "http://apps3.fao.org/wiews/institute_query.htm?i_l=EN" or the Biodiversity Collections Index (BCI), "http://www.biodiversitycollectionsindex.org/".
breeders ID
Persistent identifier for the source germplasm developed by a plant breeder.
Persistent identifier (PID) such as a URI, DOI, LSID or similar.
Local identifiers used by the breeder is best reported using the breedingIdentifier term.
breeders PID
breeders identifier
The germplasm name or accession number used by the plant breeder.
Could be the breeders catalog number, or the name under which a cultivar was marketed.
Recommended best practice is to report using the breedingID term whenever possible.
breeders accession number
breeding year
The year a germplasm accession was developed by a plant breeder. Could be the year the cultivar was released.
The four-digit year in which the breeding event was conducted.
breeding country
Name of the country in which the breeding event was conducted.
Denmark; Finland; Iceland; Norway; Sweden
Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
breeding country code
Code for the country in which the breeding event was conducted.
DNK; FIN; ISL; NOR; SWE
Recommended best practice is to use a controlled vocabulary such or the ISO 3166-1-alpha-3 country codes.
breeder institute ID
Breeding institute code.
SWE006; urn:lsid:biocol.org:col:35293
Recommended to use institute codes from the FAO WIEWS information system, "http://apps3.fao.org/wiews/institute_query.htm?i_l=EN" or the Biodiversity Collections Index (BCI), "http://www.biodiversitycollectionsindex.org/".
breeder institute
Breeder institute name. If the FAO WIEWS institute code is available, this term is not to be reported.
Svalöf Weibull AB Cereal Breeding Department
Recommended best practice is using the breederInstituteID term whenever possible.
breeder
Name of the plant breeder.
Gregor Mendel; Luther Burbank; Nils Herman Nilsson-Ehle
Name of the person conducting the breeding event.
ancestral pedigree data
Ancestral data, ANCEST. Information about either pedigree or other description of ancestral information.
Hanna/7*Atlas//Turk/8*Atlas; mutation found in Hanna; selection from Irene
Recommended best practice is to report using the PurdyPedigree term whenever possible.
Purdy pedigree
Ancestral information following the purdy pedigree format.
Hanna/7*Atlas//Turk/8*Atlas
Purdy et al. (1968), Crop Science 8(4):405-406; doi:10.2135/cropsci1968.0011183X000800040002x.
breeding remarks
Remarks to the breeding event.
Supplementary comments and remarks related to the breeding event
The breeding event is related to the development of germplasm by a breeder or through cultivation by a farmer depending on the biological status of the germplasm accession.
acquisition ID
An identifier for the event when germplasm material was acquired and included in the genebank collection.
URI; DOI; LSID or similar
The identifier used by the donor to identify the germplasm specimen is reported using the donorsID term.
donors accession ID
An identifier for the source germplasm material that was included in your genebank collection.
http://data.gbif.org/occurrences/164390781/; URI; DOI; LSID or similar
Local identifiers used by the donor is best reported using the donorsIdentifier term.
donors accession identifier
An identifier for the source accession donated to your genebank collection. Could be an unique and stable local identifier specific to the dataset.
NGB11
Recommended best practice is to report using the donorsID term whenever possible.
donor institute ID
Donor institute code.
DEU146; NLD037; SWE054; urn:lsid:biocol.org:col:35293
donor institute
Donor institute name. If the FAO WIEWS institute code is available, this term is not to be reported.
Nordic Genetic Resources Center (NordGen)
Recommended best practice is to report using the donorInstituteID term whenever possible.
acquisition date
Acquisition date. Date when the germplasm material (accession) entered the genebank collection.
Accessions can be acquired by a collecting event or from other genebank collections by an acquisition event. For either event this terms describes the date the accession was included into the receiving genebank collection.
acquisition source
Collecting/acquisition source.
Recommended to use the MCPD coding scheme. Wild habitat (10), Farm or cultivated habitat (20), Market or shop (30), Institute, experimental station, research organization, genebank (40), Seed company (50), Weedy, disturbed or ruderal habitat (60).
acquisition remarks
Remarks to the acquisition event.
General remarks related to the acquisition of the germplasm accession.
The acquisition terms relates to the immediate step or the germplasm holder before the accession was included in the genebank collection. Information related to the collecting event and the breeding event are not reported here.
safety duplication ID
Persistent identifier for the genebank accession in the safety duplication storage.
URI, DOI, LSID or similar.
Could also be an unique and stable identifier specific to the safety storage collection.
safety duplication date
Date of safety duplication.
Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
safety duplication institute ID
Location of safety duplicates. Persistent identifier for the institute where a safety duplicate of the accession is maintained.
NOR051; urn:lsid:biocol.org:col:35294
safety duplication institute
Location or institute for storage of safety duplicates.
The name of the institute holding the safe duplication germplasm material.
Recommended best practice is to use the safetyDuplicationInstituteID term whenever possible.
safety duplication remarks
Remarks to the safety duplication event.
General remarks related to the safety duplication of the germplasm material.
Genebank material will normally be stored in multiple locations, with safe backup material designated as safety duplication.
treaty or regulation ID
An identifier for the regulation or treaty.
Recommended best practice is to report a persistent identifier for the treaty or regulation.
treaty or regulation
Regulation or treaty name.
The International Treaty for Plant Genetic Resources for Food and Agriculture (ITPGRFA)
Recommended best practice is to use the treatyOrRegulationID term when possible.
governing body
Governing body for the regulation or treaty.
URI, DOI, WIEWS institute code or similar
Multilateral status (MLS)
The status of a germplasm accession with regards to the Multilateral System (MLS) of the International Treaty on Plant Genetic Resources for Food and Agriculture.
No, Yes, Other
trait ID
Persistent identifier for a trait descriptor used to identify the description of the measurement method. This could be the persistent URL to an external ontology where the trait term is declared.
URI, DOI, LSID or similar
Recommended best practice is to use a persistent identifier for trait descriptors, and a controlled and curated ontology such as the Plant Ontology (http://www.plantontology.org).
Trait id number
trait identifier
Number locally unique within the dataset used to identify the trait descriptor.
Local identifier for the experiment trait methodology.
This number should be unique and persistent for the data provider. Recommended best practice is to use the measurementTraitID term whenever possible.
Trait number
trait name
English name used to identify the trait measurement descriptor.
stem rust susceptibility; powdery mildew susceptibility; plant height; ear density; etc
Recommended best practice is to use the measurementTraitID term whenever possible, and to use a controlled vocabulary such as the Plant Ontology (http://www.plantontology.org).
English name of the trait
trait category
Classification type for the trait descriptor.
agrobotanical; morphological; chemical; phenological; molecular biology; disease susceptibility/-resistance; tolerance (abiotic); utilization.
Recommended best practice is to use a controlled vocabulary such as the Plant Ontology (http://www.plantontology.org).
trait scale
Measurement scale used to score the measurement values.
absolute; interval; nominal; ordinal; ratio; relative
Recommended best practice is to use a controlled vocabulary. The theory of scale types was developed by Stanley S. Stevens (1946) in Science 103(2684):677–680.
trait source
Reference to a standard germplasm descriptor. For example the UPOV descriptor or the Bioversity Crop Descriptor identifier.
UPOV TG/198/1 (april 2003)
Recommended best practice is to use a controlled vocabulary of source trait descriptors.
trait remarks
Remarks related to the trait measurement descriptor.
inflorescences after cutting; measured three days after heading date
Any general remark that helps interpret the trait measurement descriptor.
trial ID
Persistent identifier used to identify a trait measurement trial season.
Recommended best practice is to use a persistent identifier for trait measurement trial seasons.
trial identifier
Unique number in the dataset for the trial season.
Local identifier for the trial season.
This number should be unique and persistent for the data provider. Recommended best practice is to use the measurementTrialID term whenever possible.
Trial number
trial year
The year when the trait measurement trial was conducted.
For the more detailed experiment date, best practice is to use the dwc:measurementDeterminedDate term.
trial report
A reference to the report of the trait trial experiment, either supplied as the file name or the URL of the report.
URL or reference citation
Recommended best practice is to provide the URL to the report.
Trial season report
trial remarks
Information relevant for the interpretation of the scores from the trial season.
Experimental design, location, experimentor, weather, etc.
General remarks related to the experimental conditions or experiment design of a trial season.
Trial description
measurement by instituteID
Trait observation determined by institute code, INSTCODE. FAO WIEWS institute code for the institute performing the observation/measurement.
measurement at growth stage
The growth stage of the plant when the trait observation or measurement was made.
flowering; heading; ripening; etc.
A more general modifier of the TDWG SDD style could be applied here and include modifiers such as part of the plant where the observation was made (eg. leaf, stem, seeds).