get_annotation_parents: Retrieve parents of a given annotation

In jsicherman/GemmAPI: A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

Retrieve parents of a given annotation

Description

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

Usage

get_annotation_parents(
  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_parents("http://purl.obolibrary.org/obo/MONDO_0000408")

jsicherman/GemmAPI documentation built on April 17, 2025, 4:15 p.m.