brapi_put_traits_traitDbId: put /traits/{traitDbId}

In mverouden/brapir-v2: Client to Access BrAPI Compliant Plant Breeding Databases

put /traits/{traitDbId}

Description

Update an existing Trait

Usage

brapi_put_traits_traitDbId(
  con = NULL,
  traitDbId = "",
  additionalInfo = list(),
  alternativeAbbreviations = "",
  attribute = "",
  entity = "",
  externalReferences = "",
  mainAbbreviation = "",
  ontologyReference = list(),
  status = "",
  synonyms = "",
  traitClass = "",
  traitDescription = "",
  traitName = ""
)

Arguments

con	list; required: TRUE; BrAPI connection object
traitDbId	character; required: TRUE; Identifier for the trait to update details of.
additionalInfo	list; required: FALSE; Additional arbitrary information. If provided use the following construct list(additionalProp1 = "string", additionalProp2 = "string", additionalProp3 = "string"). The Examples section shows an example on how to construct the additionalInfo argument as a list.
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".
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".
externalReferences	data.frame; required: FALSE; A data.frame of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI. The externalReferences argument data.frame should contain the following columns: referenceID character; required: TRUE; The external reference ID. Could be a simple string or a URI. referenceSource character; required: TRUE; An identifier for the source system or database of this reference. The Examples section shows an example of how to construct the externalReferences argument as a data.frame.
mainAbbreviation	character; required: FALSE; Main abbreviation for trait name, examples: "Carotenoid content" => "CC").
ontologyReference	list; required: FALSE; MIAPPE V1.1 (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology. (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology). The ontolgyReference list should/can contain the following elements: documentationLinks data.frame; required: FALSE; Links to various ontology documentation. Each row in the documentationLinks data.frame should contain the following columns: URL character; required: FALSE; A uniform resource locator specified as a valid uniform resource identifier (URI), e.g. http://purl.obolibrary.org/obo/ro.owl type character; required: FALSE; one of "OBO"| "RDF"|"WEBPAGE". ontologyDbId character; required: TRUE; Ontology database unique identifier. ontologyName character; required: TRUE; Ontology name, e.g. the Crop Ontology. version character; required: FALSE; Ontology version (no specific format). The Examples section shows an example of how to construct the ontologyReference argument as a list.
status	character; required: FALSE; Trait status (examples: "recommended", "obsolete", "legacy", etc.).
synonyms	vector of type character; required: FALSE; Other trait names; default: "", when using multiple values supply as c( "value1", "value2").
traitClass	character; required: FALSE; Trait class, examples: "morphological", "phenological", "agronomical", "physiological", "abiotic stress", "biotic stress", "biochemical", "quality traits", "fertility", etc.).
traitDescription	character; required: FALSE; The description of a trait.
traitName	character; required: FALSE; The human readable name of a trait. MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation.

Details

Update an existing trait

Value

data.frame

Author(s)

Maikel Verouden

References

BrAPI SwaggerHub

See Also

Other brapi-phenotyping: brapi_get_events(), brapi_get_images_imageDbId(), brapi_get_images(), brapi_get_methods_methodDbId(), brapi_get_methods(), brapi_get_observationlevels(), brapi_get_observations_observationDbId(), brapi_get_observations_table(), brapi_get_observations(), brapi_get_observationunits_observationUnitDbId(), brapi_get_observationunits_table(), brapi_get_observationunits(), brapi_get_ontologies(), brapi_get_scales_scaleDbId(), brapi_get_scales(), brapi_get_search_images_searchResultsDbId(), brapi_get_search_observations_searchResultsDbId(), brapi_get_search_observationunits_searchResultsDbId(), brapi_get_search_variables_searchResultsDbId(), brapi_get_traits_traitDbId(), brapi_get_traits(), brapi_get_variables_observationVariableDbId(), brapi_get_variables(), brapi_post_images(), brapi_post_methods(), brapi_post_observations(), brapi_post_observationunits(), brapi_post_scales(), brapi_post_search_images(), brapi_post_search_observations(), brapi_post_search_observationunits(), brapi_post_search_variables(), brapi_post_traits(), brapi_post_variables(), brapi_put_images_imageDbId_imagecontent(), brapi_put_images_imageDbId(), brapi_put_methods_methodDbId(), brapi_put_observations_observationDbId(), brapi_put_observationunits_observationUnitDbId(), brapi_put_scales_scaleDbId(), brapi_put_variables_observationVariableDbId()

Other Traits: brapi_get_traits_traitDbId(), brapi_get_traits(), brapi_post_traits()

Examples

## Not run: 
con <- brapi_db()$testserver
con[["token"]] <- "YYYY"
additionalInfo <- list(dummyData = "TRUE",
                       example = "post_traits")
alternativeAbbreviations <- c("PHght", "Hght")
attribute <- "heigth"
entity <- "plant"
externalReferences <-
  data.frame(referenceID = c("doi:10.155454/12341234",
                             "http://purl.obolibrary.org/obo/ro.owl",
                             "75a50e76"),
             referenceSource = c("DOI",
                                 "OBO Library",
                                 "Remote Data Collection Upload Tool"))
mainAbbreviation <- "PH"
ontologyReference <- list(
  documentationLinks = data.frame(
    URL = c("http://purl.obolibrary.org/obo/ro.owl",
            "https://www.cropontology.org/terms/CO_323:0000024/"),
    type = c("OBO",
             "WEBPAGE")),
  ontologyDbId = "ontology_variable1",
  ontologyName = "Ontology.org",
  version = "17")
status <- "recommended"
synonyms <- c("Height",
              "Plant Height")
traitClass <- "agrinomically"
traitDescription <- "The height of plant from ground."
traitName <- "Plant heigth"
## Add the new trait
out <- brapi_post_traits(
  con = con,
  additionalInfo = additionalInfo,
  alternativeAbbreviations = alternativeAbbreviations,
  attribute = attribute,
  entity = entity,
  externalReferences = externalReferences,
  mainAbbreviation = mainAbbreviation,
  ontologyReference = ontologyReference,
  status = status,
  synonyms = synonyms,
  traitClass = traitClass,
  traitDescription = traitDescription,
  traitName = traitName)
## Obtain the identifier for the new trait
traitDbId <- unique(out$traitDbId)
## Retrieve the info of the new trait
brapi_get_traits_traitDbId(con = con, traitDbId)
## Update the info of the new trait
brapi_put_traits_traitDbId(
  con = con,
  traitDbId = traitDbId,
  attribute = "Height",
  synonyms = c("Height",
                "Plant Height",
                "Stalk Height",
                "Canopy Height"),
  traitClass = "agronomical",
  traitDescription = "The height of plant from ground to the top part.",
  traitName = "Plant height")

## End(Not run)

mverouden/brapir-v2 documentation built on April 22, 2022, 9:24 a.m.