brapi_put_traits_traitDbId: put /traits/{traitDbId}

In mverouden/brapir: Client to Access BrAPI Compliant Plant Breeding Databases

put /traits/{traitDbId}

Description

Update an existing Trait

Usage

brapi_put_traits_traitDbId(
  con = NULL,
  traitDbId = "",
  alternativeAbbreviations = "",
  attribute = "",
  class = "",
  description = "",
  entity = "",
  mainAbbreviation = "",
  ontologyReference = list(),
  status = "",
  synonyms = "",
  traitName = "",
  xref = ""
)

Arguments

con	list; required: TRUE; BrAPI connection object
traitDbId	character; required: TRUE; the internal database identifier of the trait to be updated; default: ""
alternativeAbbreviations	vector of type character; required: FALSE; Other frequent abbreviations of the trait, if any. These abbreviations do not have to follow a convention; default: "", when using multiple values supply as c("value1", "value2").
attribute	character; required: FALSE; A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour"; default: "".
class	character; required: FALSE; Trait class. (examples: "morphological trait", "phenological trait", "agronomical trait", "physiological trait", "abiotic stress trait", "biotic stress trait", "biochemical trait", "quality traits trait", "fertility trait", etc.); default: "".
description	character; required: FALSE; The description of a trait; default: "".
entity	character; required: FALSE; A trait can be decomposed as "Trait" = "Entity" + "Attribute", the entity is the part of the plant that the trait refers to e.g., for "grain colour", entity = "grain"; default: "".
mainAbbreviation	character; required: FALSE; Main abbreviation for trait name. (examples: "Carotenoid content" => "CC"); default: "".
ontologyReference	list; required: FALSE; The ontologyReference list should contain links to various ontology documentation (URL and type) supplied as a dataframe, an unique ontology database identifier, an ontology name and an ontology version (no specific format). In the Examples section an example on how to specify this list is provided; default: list()
status	character; required: FALSE; Trait status (examples: "recommended", "obsolete", "legacy", etc.); default: "".
synonyms	vector of type character; required: FALSE; Other trait names; default: "", when using multiple values supply as c("value1", "value2").
traitName	character; required: FALSE; The human readable name of a trait; default: "".
xref	character; required: FALSE; Cross reference of the trait to an external ontology or database term e.g., Xref to a trait ontology (TO) term; default: "".

Details

Update an existing trait

Value

data.frame

Author(s)

brapir generator package

References

BrAPI SwaggerHub

See Also

Other brapi_1.3: brapi_get_allelematrices_search(), brapi_get_allelematrices(), brapi_get_attributes_categories(), brapi_get_attributes(), brapi_get_breedingmethods_breedingMethodDbId(), brapi_get_breedingmethods(), brapi_get_calls(), brapi_get_commoncropnames(), brapi_get_germplasm_germplasmDbId_attributes(), brapi_get_germplasm_germplasmDbId_markerprofiles(), brapi_get_germplasm_germplasmDbId_mcpd(), brapi_get_germplasm_germplasmDbId_pedigree(), brapi_get_germplasm_germplasmDbId_progeny(), brapi_get_germplasm_germplasmDbId(), brapi_get_germplasm(), brapi_get_images_imageDbId(), brapi_get_images(), brapi_get_lists_listDbId(), brapi_get_lists(), brapi_get_locations_locationDbId(), brapi_get_locations(), brapi_get_maps_mapDbId_positions_linkageGroupName(), brapi_get_maps_mapDbId_positions(), brapi_get_maps_mapDbId(), brapi_get_maps(), brapi_get_markerprofiles_markerProfileDbId(), brapi_get_markerprofiles(), brapi_get_markers_markerDbId(), brapi_get_markers(), brapi_get_methods_methodDbId(), brapi_get_methods(), brapi_get_observationlevels(), brapi_get_observationunits(), brapi_get_ontologies(), brapi_get_people_personDbId(), brapi_get_people(), brapi_get_programs(), brapi_get_samples_sampleDbId(), brapi_get_samples(), brapi_get_scales_scaleDbId(), brapi_get_scales(), brapi_get_search_germplasm_searchResultsDbId(), brapi_get_search_images_searchResultsDbId(), brapi_get_search_markers_searchResultsDbId(), brapi_get_search_observationtables_searchResultsDbId(), brapi_get_search_observationunits_searchResultsDbId(), brapi_get_search_programs_searchResultsDbId(), brapi_get_search_samples_searchResultsDbId(), brapi_get_search_studies_searchResultsDbId(), brapi_get_search_variables_searchResultsDbId(), brapi_get_seasons(), brapi_get_studies_studyDbId_germplasm(), brapi_get_studies_studyDbId_layouts(), brapi_get_studies_studyDbId_observations(), brapi_get_studies_studyDbId_observationunits(), brapi_get_studies_studyDbId_observationvariables(), brapi_get_studies_studyDbId_table(), brapi_get_studies_studyDbId(), brapi_get_studies(), brapi_get_studytypes(), brapi_get_traits_traitDbId(), brapi_get_traits(), brapi_get_trials_trialDbId(), brapi_get_trials(), brapi_get_variables_observationVariableDbId(), brapi_get_variables(), brapi_get_vendor_orders_orderId_plates(), brapi_get_vendor_orders_orderId_results(), brapi_get_vendor_orders_orderId_status(), brapi_get_vendor_orders(), brapi_get_vendor_plates_submissionId(), brapi_get_vendor_specifications(), brapi_post_allelematrices_search(), brapi_post_images(), brapi_post_lists_listDbId_items(), brapi_post_lists(), brapi_post_methods(), brapi_post_people(), brapi_post_phenotypes(), brapi_post_scales(), brapi_post_search_germplasm(), brapi_post_search_images(), brapi_post_search_markers(), brapi_post_search_observationtables(), brapi_post_search_observationunits(), brapi_post_search_programs(), brapi_post_search_samples(), brapi_post_search_studies(), brapi_post_search_variables(), brapi_post_studies_studyDbId_table(), brapi_post_traits(), brapi_post_vendor_orders(), brapi_post_vendor_plates(), brapi_put_images_imageDbId_imagecontent(), brapi_put_images_imageDbId(), brapi_put_lists_listDbId(), brapi_put_methods_methodDbId(), brapi_put_people_personDbId(), brapi_put_samples(), brapi_put_scales_scaleDbId(), brapi_put_studies_studyDbId_layouts(), brapi_put_studies_studyDbId_observations(), brapi_put_studies_studyDbId_observationunits()

Other Observation Variables: brapi_get_methods_methodDbId(), brapi_get_methods(), brapi_get_ontologies(), brapi_get_scales_scaleDbId(), brapi_get_scales(), brapi_get_search_variables_searchResultsDbId(), brapi_get_studies_studyDbId_observationvariables(), brapi_get_traits_traitDbId(), brapi_get_traits(), brapi_get_variables_observationVariableDbId(), brapi_get_variables(), brapi_post_methods(), brapi_post_scales(), brapi_post_search_variables(), brapi_post_traits(), brapi_put_methods_methodDbId(), brapi_put_scales_scaleDbId()

Examples

## Not run: 

# Create a connection object
con <- brapi_db()$testserver

# Create an ontologyReference example list object for the traitDbId to be updated
# ontologyDbId should be specified as an existing one (see get /ontologies) or
# left empty (some servers might generate a new ontologyDbId).
ontologyReference <- list(
  documentationLinks = data.frame(URL = "https://Ontology.org/s6",
                                  type = "RDF"),
  ontologyDbId = "MO_123",
  ontologyName = "Ontology.org",
  version = "17")

# Make post /traits call
brapi_put_traits_traitDbId(con = con,
                           traitDbId = "", # retrieve from brapi_get_traits()
                           alternativeAbbreviations = c("clothSizes", "sizesCloth"),
                           attribute = "size",
                           class = "physiological trait",
                           description = "Size designation of clothes",
                           entity = "clothing",
                           mainAbbreviation = "CS",
                           ontologyReference = ontologyReference,
                           status = "legacy",
                           synonyms = c("sizeClothing", "cSizes"),
                           traitName = "clothingSize",
                           xref = "xref")

## End(Not run)

mverouden/brapir documentation built on April 10, 2022, 5:36 p.m.