Compose BioCompute Object - Provenance Domain (v1.3.0)

compose_provenance_v1.3.0(
  name = NULL,
  version = NULL,
  review = NULL,
  derived_from = NULL,
  obsolete_after = NULL,
  embargo = NULL,
  created = NULL,
  modified = NULL,
  contributors = NULL,
  license = NULL
)

compose_provenance(
  name = NULL,
  version = NULL,
  review = NULL,
  derived_from = NULL,
  obsolete_after = NULL,
  embargo = NULL,
  created = NULL,
  modified = NULL,
  contributors = NULL,
  license = NULL
)

Arguments

name

Character string. Name for the BCO.

version

Character string. Version of this BCO instance object. Should follow the Semantic Versioning format (MAJOR.MINOR.PATCH).

review

Data frame. Reviewer identifiers and descriptions of the status of an object in the review process.

derived_from

Character string. Inheritance/derivation description.

obsolete_after

Date-time object. Expiration date of the object (optional).

embargo

Vector of date-time objects start_time and end_time. If the object has a period of time that it is not public, that range can be specified with this.

created

Date-time object. Initial creation time of the object.

modified

Date-time object. The most recent modification time of the object.

contributors

Data frame. Contributor identifiers and descriptions of their contribution types.

license

Character string. Licence URL or other licence information (text).

Value

A list of class bco.domain

Examples

name <- "HCV1a ledipasvir resistance SNP detection" version <- "1.0.0" review <- data.frame( "status" = c("approved", "approved"), "reviewer_comment" = c( "Approved by [company name] staff. Waiting for approval from FDA Reviewer", "The revised BCO looks fine" ), "date" = c( as.POSIXct("2017-11-12T12:30:48", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-12-12T12:30:48", format = "%Y-%m-%dT%H:%M:%S", tz = "America/Los_Angeles") ), "reviewer_name" = c("Jane Doe", "John Doe"), "reviewer_affiliation" = c("Seven Bridges Genomics", "U.S. Food and Drug Administration"), "reviewer_email" = c("example@sevenbridges.com", "example@fda.gov"), "reviewer_contribution" = c("curatedBy", "curatedBy"), "reviewer_orcid" = c("https://orcid.org/0000-0000-0000-0000", NA), stringsAsFactors = FALSE ) derived_from <- "https://github.com/biocompute-objects/BCO_Specification/blob/1.2.1-beta/HCV1a.json" obsolete_after <- as.POSIXct("2018-11-12T12:30:48", format = "%Y-%m-%dT%H:%M:%S", tz = "EST") embargo <- c( "start_time" = as.POSIXct("2017-10-12T12:30:48", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), "end_time" = as.POSIXct("2017-11-12T12:30:48", format = "%Y-%m-%dT%H:%M:%S", tz = "EST") ) created <- as.POSIXct("2017-01-20T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST") modified <- as.POSIXct("2019-05-10T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST") contributors <- data.frame( "name" = c("Jane Doe", "John Doe"), "affiliation" = c("Seven Bridges Genomics", "U.S. Food and Drug Administration"), "email" = c("example@sevenbridges.com", "example@fda.gov"), "contribution" = I(list(c("createdBy", "curatedBy"), c("authoredBy"))), "orcid" = c("https://orcid.org/0000-0000-0000-0000", NA), stringsAsFactors = FALSE ) license <- "https://creativecommons.org/licenses/by/4.0/" compose_provenance( name, version, review, derived_from, obsolete_after, embargo, created, modified, contributors, license ) %>% convert_json()
#> { #> "name": "HCV1a ledipasvir resistance SNP detection", #> "version": "1.0.0", #> "review": [ #> { #> "status": "approved", #> "reviewer_comment": "Approved by [company name] staff. Waiting for approval from FDA Reviewer", #> "date": 1510507848, #> "reviewer": [ #> { #> "reviewer_name": "Jane Doe", #> "reviewer_affiliation": "Seven Bridges Genomics", #> "reviewer_email": "example@sevenbridges.com", #> "reviewer_contribution": "curatedBy", #> "reviewer_orcid": "https://orcid.org/0000-0000-0000-0000" #> } #> ] #> }, #> { #> "status": "approved", #> "reviewer_comment": "The revised BCO looks fine", #> "date": 1513110648, #> "reviewer": [ #> { #> "reviewer_name": "John Doe", #> "reviewer_affiliation": "U.S. Food and Drug Administration", #> "reviewer_email": "example@fda.gov", #> "reviewer_contribution": "curatedBy", #> "reviewer_orcid": "NA" #> } #> ] #> } #> ], #> "derived_from": "https://github.com/biocompute-objects/BCO_Specification/blob/1.2.1-beta/HCV1a.json", #> "obsolete_after": "2018-11-12T12:30:48-0500", #> "embargo": ["2017-10-12T13:30:48-0400", "2017-11-12T12:30:48-0500"], #> "created": "2017-01-20T09:40:17-0500", #> "modified": "2019-05-10T09:40:17-0500", #> "contributors": [ #> { #> "name": "Jane Doe", #> "affiliation": "Seven Bridges Genomics", #> "email": "example@sevenbridges.com", #> "contribution": ["createdBy", "curatedBy"], #> "orcid": "https://orcid.org/0000-0000-0000-0000" #> }, #> { #> "name": "John Doe", #> "affiliation": "U.S. Food and Drug Administration", #> "email": "example@fda.gov", #> "contribution": "authoredBy", #> "orcid": "NA" #> } #> ], #> "license": "https://creativecommons.org/licenses/by/4.0/" #> }