cedarSearch: Search values in CEDAR

In earnaud/cedarr: Bio Ontology R API Access

Search values in CEDAR

Description

Search for terms, classes or retrieve full ontologies from the CEDAR terminology metadata center. (https://terminology.metadatacenter.org/api/#/).

Usage

cedarSearch(
  api.key,
  query,
  sources = NA_character_,
  scope = "all",
  suggest = FALSE,
  output.mode = "content",
  subtree.root.id = NA_character_,
  subtree.source = NA_character_,
  maxDepth = 1,
  page.index = 1,
  page.size = 50
)

Arguments

api.key	character. An API Key is required to access any API call. It is used within cedarr as a header for http requests. An API key is linked to a CEDAR account (https://cedar.metadatacenter.org/profile)
query	character. Input query as a text.
sources	character. Either value sets collection names or ontologies names in which to get the results of the query.
scope	character. Which search scopes shall be investigated. Accepted values are 1-length vector: "all" (default), "classes", "value_sets", "values".
suggest	logical. Will perform a search specifically geared towards type-ahead suggestions (defaults to FALSE).
output.mode	character. "full" will return the whole response object (from httr) or "content" will fetch the interest values from the response object. Getting the whole object might be interesting to have a look at system metadata, or in case of error to debug the connection. (defaults to "content")
subtree.root.id	character. URL for the class identifier that limits the search to the branch rooted on that class.
subtree.source	character. URL for the ontology for which the subtree search will be performed. Not evaluated if subtree.root.id is not provided.
maxDepth	integer. Subtree depth.Not evaluated if subtree.root.id is not provided.
page.index	integer. Index of the page to be returned (defaults to 1st page).
page.size	integer. Number of results per page, capped at 50. (defaults to 50).

Details

This function matches the following query from the Swagger UI (https://terminology.metadatacenter.org/api/#/):

• /search, for both classes and values

Value

A list or data.frame with detailed information on the queried information and how to access it.

If output.mode = "full", the whole http response object (see httr::response). It is structured as a list with response metadata wrapping the content item which contains the wanted result.

If output.mode = "content", the content item is directly returned, containing database metadata and the interesting information in the collection subitem.

Examples

## Not run: 
my.api.key <- readline()

result <- cedarr::search(
  my.api.key,
  "habitat",
  "ENVO"
)

View(result)

## End(Not run)

earnaud/cedarr documentation built on Oct. 25, 2022, 6:27 a.m.