queryup (version 1.0.5)

get_uniprot_data: Retrieve data from UniProt using UniProt's REST API

Description

Retrieve data from UniProt using UniProt's REST API

Usage

get_uniprot_data(
  query = NULL,
  base_url = "https://rest.uniprot.org/uniprotkb/",
  columns = c("accession", "id", "gene_names", "organism_id", "reviewed")
)

Value

a list with the following items :

url

the query url

status

the http status code for the request

messages

messages returned by the REST API

content

a data.frame containing the query results

Arguments

query

list of keys corresponding to UniProt's query fields. For example : list("gene_exact" = c("Pik3r1", "Pik3r2") , "organism" = c("10090", "9606"), "reviewed" = "yes"). See `query_fields` for available query fields.

base_url

The base url for the UniProt REST API

columns

names of UniProt data columns to retrieve. Examples include "accession", "id", "gene_names", "keyword", "sequence". See `return_fields` for available return fields.

Examples

#Getting gene names, keywords and protein sequences for a set of UniProt IDs.
ids <- c("P22682", "P47941")
cols <- c("accession", "id", "gene_names", "keyword", "sequence")
query = list("accession_id" = ids)
df <- get_uniprot_data(query = query, columns = cols)$content
df