api-response: CEDAR API response

In earnaud/cedarr: Bio Ontology R API Access

CEDAR API response

Description

Details about the response obtained after a query.

Details

The cedarr package uses the httr 'GET()' function to retrieve information from the CEDAR API. This API returns a result wrapped within the 'content' part of the http response. This part is structured as follow:

page

which page is returned to you. The default is the first page.

pageCount

how many pages containing results maching your criterion have been found in CEDAR.

pageSize

how many results are present onto the current page (capped at 50).

totalCount

how many results maching your criterion have been found in CEDAR.

prevPage

number of the previous page. You can browse pages with calls to function with the 'page.index' argument.

nextPage

number of the next page. You can browse pages with calls to function with the 'page.index' argument.

collection

this is the core result (which might be organised in a data.frame table or in a list):

id

a litteral identifier given to the result.

@id

a url-format identifier given to the result. This is the one to use if you want to call this result as an argument of functions (e.g. within the 'id' argument.)

@type

a url-format identifier of '@type'.

type

which is the type of the result (class, value, value-set, vs-collection, ontology.)

prefLabel

a human-legible title given to the result.

notation

a short way to note the result.

definition

the definition of the result within its ontology.

source

an url of the original resource in which the result can be found.

CEDAR uses two approaches of the terminology resources: the value sets collections and the ontologies. The first one is structured as value sets collections, parents of value sets, parents of values. The second one is structured as ontologies, which are hierarchies of classes. The "lowest" ontological classes are equivalent to the values.

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