propertySearch: Search properties in CEDAR

In earnaud/cedarr: Bio Ontology R API Access

Search properties in CEDAR

Description

Function to query properties from ontologies registered in the CEDAR terminology metadata center. (https://terminology.metadatacenter.org/api/#/).

Usage

propertySearch(
  api.key,
  query,
  sources = NA_character_,
  exact.match = FALSE,
  require.definitions = FALSE,
  output.mode = "content",
  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.
exact.match	logical Restricts results only to the exact matches of the query in the property id, label, or the generated label (a label, auto-generated from the id). (defaults to FALSE)
require.definitions	logical. Filter results only to those that include definitions. (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")
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/#/):

• /property_search

Value

A search result with the properties corresponding to the query.

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()

# Search for a property matching "has curation status"

result <- cedarr::propertySearch(
  my.api.key,
  "has curation status",
  "ENVO"
)

View(result)

## End(Not run)

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