Compose BioCompute Object - Description Domain (v1.4.2)

compose_description_v1.4.2(
  keywords = NULL,
  xref = NULL,
  platform = list("Seven Bridges Platform"),
  pipeline_meta = NULL,
  pipeline_prerequisite = NULL,
  pipeline_input = NULL,
  pipeline_output = NULL
)

compose_description(
  keywords = NULL,
  xref = NULL,
  platform = list("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 or list. 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"
#>         }
#>       ]
#>     }
#>   ]
#> }