Retrieve children of a given annotation

Acquires child terms of a given URI based on ontologies loaded into Gemma. Propagated relations are subClassOf and has_part

get_annotation_children(
  uri,
  raw = getOption("gemma.raw", FALSE),
  memoised = getOption("gemma.memoised", FALSE),
  file = getOption("gemma.file", NA_character_),
  overwrite = getOption("gemma.overwrite", FALSE)
)

Arguments

uri

Term URI

raw

TRUE to receive results as-is from Gemma, or FALSE to enable parsing. Raw results usually contain additional fields and flags that are omitted in the parsed results.

memoised

Whether or not to save to cache for future calls with the same inputs and use the result saved in cache if a result is already saved. Doing options(gemma.memoised = TRUE) will ensure that the cache is always used. Use forget_gemma_memoised to clear the cache.

file

The name of a file to save the results to, or NULL to not write results to a file. If raw == TRUE, the output will be the raw endpoint from the API, likely a JSON or a gzip file. Otherwise, it will be a RDS file.

overwrite

Whether or not to overwrite if a file exists at the specified filename.

Value

A data table with annotations (annotation search result value objects) matching the given identifiers. A list if raw = TRUE. A 400 error if required parameters are missing.

The fields of the output data.table are:

• category.name: Category that the annotation belongs to

• category.URI: URI for the category.name

• value.name: Annotation term

• value.URI: URI for the value.name

Examples

get_annotation_children("http://purl.obolibrary.org/obo/MONDO_0000408")
#>    category.name category.URI
#>           <char>       <char>
#> 1:          <NA>         <NA>
#> 2:          <NA>         <NA>
#> 3:          <NA>         <NA>
#> 4:          <NA>         <NA>
#>                                                 value.name
#>                                                     <char>
#> 1: neurobehavioral disorder with prenatal alcohol exposure
#> 2:                            alcohol-related birth defect
#> 3:                                  fetal alcohol syndrome
#> 4:                          partial fetal alcohol syndrome
#>                                       value.URI
#>                                          <char>
#> 1: http://purl.obolibrary.org/obo/MONDO_0850461
#> 2: http://purl.obolibrary.org/obo/MONDO_0000395
#> 3: http://purl.obolibrary.org/obo/MONDO_0016011
#> 4: http://purl.obolibrary.org/obo/MONDO_0000393