fetch_interpro: Fetch domain and residue information from InterPro

In protti: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

Fetch domain and residue information from InterPro

Description

Fetches either domain level information with e.g. gene ontology annotations or residue level information from the InterPro database.

Usage

fetch_interpro(
  uniprot_ids = NULL,
  return_residue_info = FALSE,
  manual_query = NULL,
  page_size = 200,
  max_tries = 3,
  timeout = 20,
  show_progress = TRUE
)

Arguments

uniprot_ids	a character vector of UniProt accession numbers.
return_residue_info	a logical value that specifies if either domain or residue information should be returned by the function. The default is FALSE.
manual_query	optional, a character value that is a custom query to the InterPro database. This query is pastes after "https://www.ebi.ac.uk/interpro/api/" and before "&page_size=200". The raw data of the query is returned as a list.
page_size	a numeric value that specifies the number of entries that should be retrieved per page of a request. The function anyway iterates through all pages, but this parameters allows you to finetune the number of iterations and thus number of requests to the database. Default is 200.
max_tries	a numeric value that specifies the number of times the function tries to download the data in case an error occurs. The default is 3.
timeout	a numeric value that specifies the maximum request time per try. Default is 20 seconds.
show_progress	a logical value that determines if a progress bar will be shown. Default is TRUE.

Value

A data frame that contains either domain or residue level information for the provided UniProt IDs.

Examples

uniprot_ids <- c("P36578", "O43324", "Q00796", "O32583")

domain_info <- fetch_interpro(uniprot_ids = uniprot_ids)

head(domain_info)

residue_info <- fetch_interpro(
  uniprot_ids = uniprot_ids,
  return_residue_info = TRUE
)

head(residue_info)

protti documentation built on Jan. 14, 2026, 9:08 a.m.