Compose BioCompute Object - Description Domain (v1.3.0)

compose_description_v1.3.0(
  keywords = NULL,
  xref = NULL,
  platform = "Seven Bridges Platform",
  pipeline_meta = NULL,
  pipeline_prerequisite = NULL,
  pipeline_input = NULL,
  pipeline_output = NULL
)

compose_description(
  keywords = NULL,
  xref = NULL,
  platform = "Seven Bridges Platform",
  pipeline_meta = NULL,
  pipeline_prerequisite = NULL,
  pipeline_input = NULL,
  pipeline_output = NULL
)

Arguments

keywords

Character vector. A list of keywords to aid in searchability and description of the experiment.

xref

Data frame. A list of the databases and/or ontology IDs that are cross-referenced in the BCO.

platform

Character string. Reference to a particular deployment of an existing platform where this BCO can be reproduced.

pipeline_meta

Data frame. Pipeline metadata. Variables include step_number, name, description, and version.

pipeline_prerequisite

Data frame. Packages or prerequisites for running the tools used. Variables include step_number, name, uri, and access_time.

pipeline_input

Data frame. Input files for the tools. Variables include step_number, uri, and access_time.

pipeline_output

Data frame. Output files for the tools. Variables include step_number, uri, and access_time.

Value

A list of class bco.domain

Examples

keywords <- c("HCV1a", "Ledipasvir", "antiviral resistance", "SNP", "amino acid substitutions") xref <- data.frame( "namespace" = c("pubchem.compound", "pubmed", "so", "taxonomy"), "name" = c("PubChem-compound", "PubMed", "Sequence Ontology", "Taxonomy"), "ids" = I(list( "67505836", "26508693", c("SO:000002", "SO:0000694", "SO:0000667", "SO:0000045"), "31646" )), "access_time" = c( as.POSIXct("2017-01-20T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-01-21T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-01-22T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-01-23T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST") ), stringsAsFactors = FALSE ) platform <- "Seven Bridges Platform" pipeline_meta <- data.frame( "step_number" = c("1"), "name" = c("HIVE-hexagon"), "description" = c("Alignment of reads to a set of references"), "version" = c("1.3"), stringsAsFactors = FALSE ) pipeline_prerequisite <- data.frame( "step_number" = rep("1", 5), "name" = c( "Hepatitis C virus genotype 1", "Hepatitis C virus type 1b complete genome", "Hepatitis C virus (isolate JFH-1) genomic RNA", "Hepatitis C virus clone J8CF, complete genome", "Hepatitis C virus S52 polyprotein gene" ), "uri" = c( "https://www.ncbi.nlm.nih.gov/nuccore/22129792", "https://www.ncbi.nlm.nih.gov/nuccore/5420376", "https://www.ncbi.nlm.nih.gov/nuccore/13122261", "https://www.ncbi.nlm.nih.gov/nuccore/386646758", "https://www.ncbi.nlm.nih.gov/nuccore/295311559" ), "access_time" = c( as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST") ), stringsAsFactors = FALSE ) pipeline_input <- data.frame( "step_number" = rep("1", 2), "uri" = c( "https://example.com/dna.cgi?cmd=objFile&ids=514683", "https://example.com/dna.cgi?cmd=objFile&ids=514682" ), "access_time" = c( as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST") ), stringsAsFactors = FALSE ) pipeline_output <- data.frame( "step_number" = rep("1", 2), "uri" = c( "https://example.com/data/514769/allCount-aligned.csv", "https://example.com/data/514801/SNPProfile*.csv" ), "access_time" = c( as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST"), as.POSIXct("2017-01-24T09:40:17", format = "%Y-%m-%dT%H:%M:%S", tz = "EST") ), stringsAsFactors = FALSE ) compose_description( keywords, xref, platform, pipeline_meta, pipeline_prerequisite, pipeline_input, pipeline_output ) %>% convert_json()
#> { #> "keywords": ["HCV1a", "Ledipasvir", "antiviral resistance", "SNP", "amino acid substitutions"], #> "xref": [ #> { #> "namespace": "pubchem.compound", #> "name": "PubChem-compound", #> "ids": "67505836", #> "access_time": "2017-01-20T09:40:17-0500" #> }, #> { #> "namespace": "pubmed", #> "name": "PubMed", #> "ids": "26508693", #> "access_time": "2017-01-21T09:40:17-0500" #> }, #> { #> "namespace": "so", #> "name": "Sequence Ontology", #> "ids": ["SO:000002", "SO:0000694", "SO:0000667", "SO:0000045"], #> "access_time": "2017-01-22T09:40:17-0500" #> }, #> { #> "namespace": "taxonomy", #> "name": "Taxonomy", #> "ids": "31646", #> "access_time": "2017-01-23T09:40:17-0500" #> } #> ], #> "platform": "Seven Bridges Platform", #> "pipeline_steps": [ #> { #> "step_number": "1", #> "name": "HIVE-hexagon", #> "description": "Alignment of reads to a set of references", #> "version": "1.3", #> "prerequisite": [ #> { #> "name": "Hepatitis C virus genotype 1", #> "uri": { #> "uri": "https://www.ncbi.nlm.nih.gov/nuccore/22129792", #> "access_time": "2017-01-24 09:40:17" #> } #> }, #> { #> "name": "Hepatitis C virus type 1b complete genome", #> "uri": { #> "uri": "https://www.ncbi.nlm.nih.gov/nuccore/5420376", #> "access_time": "2017-01-24 09:40:17" #> } #> }, #> { #> "name": "Hepatitis C virus (isolate JFH-1) genomic RNA", #> "uri": { #> "uri": "https://www.ncbi.nlm.nih.gov/nuccore/13122261", #> "access_time": "2017-01-24 09:40:17" #> } #> }, #> { #> "name": "Hepatitis C virus clone J8CF, complete genome", #> "uri": { #> "uri": "https://www.ncbi.nlm.nih.gov/nuccore/386646758", #> "access_time": "2017-01-24 09:40:17" #> } #> }, #> { #> "name": "Hepatitis C virus S52 polyprotein gene", #> "uri": { #> "uri": "https://www.ncbi.nlm.nih.gov/nuccore/295311559", #> "access_time": "2017-01-24 09:40:17" #> } #> } #> ], #> "input_list": [ #> { #> "uri": "https://example.com/dna.cgi?cmd=objFile&ids=514683", #> "access_time": "2017-01-24 09:40:17" #> }, #> { #> "uri": "https://example.com/dna.cgi?cmd=objFile&ids=514682", #> "access_time": "2017-01-24 09:40:17" #> } #> ], #> "output_list": [ #> { #> "uri": "https://example.com/data/514769/allCount-aligned.csv", #> "access_time": "2017-01-24 09:40:17" #> }, #> { #> "uri": "https://example.com/data/514801/SNPProfile*.csv", #> "access_time": "2017-01-24 09:40:17" #> } #> ] #> } #> ] #> }