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

brapi_post_studies

R Documentation

post /studies

Description

Create new Studies.

Usage

brapi_post_studies(
  con = NULL,
  active = NA,
  additionalInfo = list(),
  commonCropName = "",
  contacts = "",
  culturalPractices = "",
  dataLinks = "",
  documentationURL = "",
  endDate = "",
  environmentParameters = "",
  experimentalDesign = list(),
  externalReferences = "",
  growthFacility = list(),
  lastUpdate = list(),
  license = "",
  locationDbId = "",
  locationName = "",
  observationLevels = "",
  observationUnitsDescription = "",
  seasons = "",
  startDate = "",
  studyCode = "",
  studyDescription = "",
  studyName = "",
  studyPUI = "",
  studyType = "",
  trialDbId = "",
  trialName = ""
)

Arguments

`con`	list; required: TRUE; BrAPI connection object
`active`	logical; required: FALSE; Is this study currently active; default: NA, other possible values: TRUE \| FALSE
`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.
`commonCropName`	character; required: FALSE; Common name for the crop associated with this study.
`contacts`	data.frame; required: FALSE; A data.frame of contact entities associated with this study. The `contacts` argument data.frame should or can contain the following columns: `contactDbId` character; required: TRUE; The ID which uniquely identifies this contact. MIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended. `email` character; required: FALSE; The contacts email address. MIAPPE V1.1 (DM-32) Person email - The electronic mail address of the person. `instituteName` character; required: FALSE; The name of the institution which this contact is part of. MIAPPE V1.1 (DM-35) Person affiliation - The institution the person belongs to. `name` character; required: FALSE; The full name of this contact person. MIAPPE V1.1 (DM-31) Person name - The name of the person (either full name or as used in scientific publications). `orcid` character; required: FALSE; The Open Researcher and Contributor ID for this contact person (orcid.org). MIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended. `type` character; required: FALSE; The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.). MIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation. The Examples section shows an example of how to construct the `contacts` argument as a data.frame.
`culturalPractices`	character; required: FALSE; MIAPPE V1.1 (DM-28) Cultural practices - General description of the cultural practices of the study.
`dataLinks`	data.frame; required: FALSE; A data.frame of links to extra data files associated with this study. Extra data could include notes, images, and reference data. The `dataLinks` arguments data.frame can contain the following columns: `dataFormat` character; required: FALSE; The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy). MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. `description` character; required: FALSE; The general description of this data link. MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. `fileFormat` character; required: FALSE; The MIME type of the file (i.e. text/csv, application/excel, application/zip). MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. `name` character; required: FALSE; The name of the external data link. MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. `provenance` character; required: FALSE; The description of the origin or ownership of this linked data. Could be a formal reference to software, method, or workflow. `scientificType` character; required: FALSE; The general type of data. For example- Genotyping, Phenotyping raw data, Phenotyping reduced data, Environmental, etc. `url` character; required: FALSE; URL describing the location of this data file to view or download. MIAPPE V1.1 (DM-37) Data file link - Link to the data file (or digital object) in a public database or in a persistent institutional repository; or identifier of the data file when submitted together with the MIAPPE submission. `version` character; required: FALSE; The version number for this data. MIAPPE V1.1 (DM-39) Data file version - The version of the data set (the actual data). The Examples section shows an example of how to construct the `dataLinks` argument as a data.frame.
`documentationURL`	character; required: FALSE; A URL to the human readable documentation of this object.
`endDate`	character; required: FALSE; The date the study will end or ended. Coded in the ISO 8601 standard extended format, where date, time and time zone information needs to be provided (check for example https://www.w3.org/TR/NOTE-datetime ). MIAPPE V1.1 (DM-15) End date of study - Date and, if relevant, time when the experiment ended.
`environmentParameters`	data.frame; required: FALSE; A data.frame of Environmental parameters that were kept constant throughout the study and did not change between observation units. MIAPPE V1.1 (DM-57) Environment Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below). The `environmentParameters` argument data.frame should or can contain the following columns: `description` character; required: TRUE; Human-readable value of the environment parameter (defined above) constant within the experiment. `parameterName` character; required: TRUE; Name of the environment parameter constant within the experiment. MIAPPE V1.1 (DM-58) Environment parameter - Name of the environment parameter constant within the experiment. `parameterPUI` character; required: FALSE; URI pointing to an ontology class for the parameter. `unit` character; required: FALSE; Unit of the value for this parameter `unitPUI` character; required: FALSE; URI pointing to an ontology class for the unit. `value` character; required: FALSE; Numerical or categorical value. MIAPPE V1.1 (DM-59) Environment parameter value - Value of the environment parameter (defined above) constant within the experiment. `valuePUI` character; required: FALSE; URI pointing to an ontology class for the parameter value. The Examples section shows an example of how to construct the `environmentParameters` argument as a data.frame.
`experimentalDesign`	list; required: FALSE; The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology. The `experimentalDesign` list argument can contain the following elements: `PUI` character; required: FALSE; MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental design of the study, in the form of an accession number from the Crop Ontology. `description` character: required: FALSE; MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be "unknown"/"NA", "aggregated/reduced data", or simply 'none'. The Examples section shows an example of how to construct the `experimentalDesign` argument as a list.
`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.
`growthFacility`	list; required: FALSE; Short description of the facility in which the study was carried out. The `growthFacility` list argument can contain the following elements: `PUI` character; required: FALSE; MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth facility in which the study was carried out, in the form of an accession number from the Crop Ontology. `description` charater; required: FALSE; MIAPPE V1.1 (DM-26) Description of growth facility - Short description of the facility in which the study was carried out. The Examples section shows an example of how to construct the `growthFacility` argument as a list.
`lastUpdate`	list; required: FALSE; The date and time when this study was last modified. The `lastUpdate` list argument can contain the following elements: `timestamp` character; required: FALSE; Coded in the ISO 8601 standard extended format, where date, time and time zone information needs to be provided (check for example https://www.w3.org/TR/NOTE-datetime ). `version` character; required: FALSE; Version number specifying the last update. The Examples section shows an example of how to construct the `lastUpdate` argument as a list.
`license`	character; required: FALSE; The usage license associated with the study data.
`locationDbId`	character; required: FALSE; The unique identifier for a location.
`locationName`	character; required: FALSE; A human readable name for this location. MIAPPE V1.1 (DM-18) Experimental site name - The name of the natural site, experimental field, greenhouse, phenotyping facility, etc. where the experiment took place.
`observationLevels`	data.frame; required: FALSE; A data.frame of Observation levels, which indicate the granularity level at which the measurements are taken. The `observationLevels` argument data.frame can contain the following columns: `levelName` character; required: FALSE; A name for this level. `levelOrder` interger; required: FALSE; `levelOrder` defines, where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers are at the top of the hierarchy (i.e. field -> 1) and higher numbers are at the bottom of the hierarchy (i.e. plant -> 9). The Examples section shows an example of how to construct the `observationLevels` argument as a data.frame.
`observationUnitsDescription`	character; required: FALSE; MIAPPE V1.1 (DM-25) Observation unit description - General description of the observation units in the study.
`seasons`	vector of type character; required: FALSE; seasonDbId value(s) over which this study was performed.; default: "", when using multiple values supply as c("value1", "value2").
`startDate`	character; required: FALSE; The date the study will start or started. Coded in the ISO 8601 standard extended format, where date, time and time zone information needs to be provided (check for example https://www.w3.org/TR/NOTE-datetime ). MIAPPE V1.1 (DM-14) Start date of study - Date and, if relevant, time when the experiment started.
`studyCode`	character; required: FALSE; A short human readable code for a study.
`studyDescription`	character; required: FALSE; The description of this study. MIAPPE V1.1 (DM-13) Study description - Human-readable text describing the study.
`studyName`	character; required: FALSE; The human readable name for a study. MIAPPE V1.1 (DM-12) Study title - Human-readable text summarizing the study.
`studyPUI`	character; required: FALSE; A permanent unique identifier associated with this study data. For example, a URI or DOI.
`studyType`	character; required: FALSE; The type of study being performed. ex. "Yield Trial", etc.
`trialDbId`	character; required: FALSE; The ID which uniquely identifies a trial.
`trialName`	character; required: FALSE; The human readable name of a trial.

Details

Create new studies, where the studDbId is generated by the server.

Value

data.frame

Author(s)

Maikel Verouden

References

BrAPI SwaggerHub

Examples

## Not run: 
con <- brapi_db()$testserver
con[["token"]] <- "YYYY"
active <- TRUE
additionalInfo <- list(additionalProp1 = "string",
                       additionalProp2 = "string",
                       additionalProp3 = "string")
commonCropName <- "Tomatillo"
contacts <- data.frame(contactDbId = "trial_contact_1",
                       email = "a.breeder@brapi.org",
                       instituteName = "Plant Science Institute",
                       name = "A. Breeder",
                       orcid = "http://orcid.org/0000-0002-0607-8728",
                       type = "Breeder")
culturalPractices <- "Irrigation was applied according needs during summer to
                      prevent water stress."
dataLinks <- data.frame(dataFormat = "Image Archive",
                        description = "Raw drone images collected for this study",
                        fileFormat = "application/zip",
                        name = "image-archive.zip",
                        provenance = "Image Processing Pipeline, built at the
                                      University of Antarctica:
                                      https://github.com/antarctica/pipeline",
                        scientificType = "Environmental",
                        url = "https://brapi.org/image-archive.zip",
                        version = "1.0.3")
documentationURL <- "https://wiki.brapi.org"
endDate <- "2021-04-19T12:34:13.494Z"
environmentParameters <- data.frame(description = "the soil type was clay",
                                    parameterName =  "soil type",
                                    parameterPUI = "PECO:0007155",
                                    unit = "pH",
                                    unitPUI = "PECO:0007059",
                                    value = "clay soil",
                                    valuePUI = "ENVO:00002262")
experimentalDesign <- list(PUI = "CO_715:0000145",
                           description = "Lines were repeated twice at each
                                          location using a complete block
                                          design. In order to limit competition
                                          effects, each block was organized into
                                          four sub-blocks corresponding to
                                          earliest groups based on a prior
                                          information.")
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"))
growthFacility <- list(PUI = "CO_715:0000162",
                       description = "field environment condition, greenhouse")
lastUpdate <- list(timestamp = "2021-04-19T12:34:13.494Z",
                   version = "1.2.3")
license <- "MIT License"
locationDbId <- "location_01"
locationName <- "Location 1"
observationLevels <-
  data.frame(levelName = c("field", "block", "plot"),
             levelOrder = c(0, 1, 2))
observationUnitsDescription <- "Observation units consisted in individual
                                plots themselves consisting of a row of 15
                                plants at a density of approximately six
                                plants per square meter."
seasons <- c("spring_2012", "summer_2012")
startDate <- "2021-04-19T12:34:13.494Z"
studyCode <- "Tomatillo_Yield_Spring_2012"
studyDescription <- "This is a yield study for Spring 2012"
studyName <- "INRA's Tomatillo Genetic Resources Observation at Peru"
studyPUI <- "doi:10.155454/12349537312"
studyType <- "Phenotyping"
trialDbId <- "trial1"
trialName <- "Peru Yield Trial 1"

brapi_post_studies(con = con,
                   active = active,
                   additionalInfo = additionalInfo,
                   commonCropName = commonCropName,
                   contacts = contacts,
                   culturalPractices = culturalPractices,
                   dataLinks = dataLinks,
                   documentationURL = documentationURL,
                   endDate = endDate,
                   environmentParameters = environmentParameters,
                   experimentalDesign = experimentalDesign,
                   externalReferences = externalReferences,
                   growthFacility = growthFacility,
                   lastUpdate = lastUpdate,
                   license = license,
                   locationDbId = locationDbId,
                   locationName = locationName,
                   observationLevels = observationLevels,
                   observationUnitsDescription = observationUnitsDescription,
                   seasons = seasons,
                   startDate = startDate,
                   studyCode = studyCode,
                   studyDescription = studyDescription,
                   studyName = studyName,
                   studyPUI = studyPUI,
                   studyType = studyType,
                   trialDbId = trialDbId,
                   trialName = trialName)

## End(Not run)

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