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Programmatic access - Downloading data at every UniProt release

Last modified May 11, 2020

The HTTP header Last-Modified: will avoid that you download data more than once per release, if you use a download tool that makes use of this information, e.g. the unix commands lwp-mirror or curl with the -z option. Here are examples of how to do this in Perl:

  • Download all UniProt sequences for a given organism in FASTA format
  • Download the UniProt reference proteomes for all organisms below a given taxonomy node in compressed FASTA format

Release number and date

If you would like to record the UniProt release number and/or date of the data which you retrieve, you can extract this information from the HTTP header of the response (see this Perl example):

use strict;
use warnings;
use LWP::UserAgent;

my $query = $ARGV[0]; # Query URL.

my $contact = ''; # Please set a contact email address here to help us debug in case of problems (see
my $agent = LWP::UserAgent->new(agent => "libwww-perl $contact");
my $response = $agent->get($query);

if ($response->is_success) {
  print 'UniProt release ' . $response->header('X-UniProt-Release') .
  ' of ' . $response->header('Last-Modified') . "\n";
else {
  die 'Failed, got ' . $response->status_line .
    ' for ' . $response->request->uri . "\n";
  • X-UniProt-Release: contains the UniProt release number, e.g. 2010_08
  • Last-Modified: contains the UniProt release date, e.g. Tue, 13 Jul 2010 00:00:00 GMT

See also:
REST API - Access the UniProt website programmatically - batch retrieval, ID mapping, queries, downloads, etc
How can I (programmatically) obtain the number of results returned by my query?

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Main funding by: National Institutes of Health

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