uniprot_sparql_query.pl

use strict;
use LWP::UserAgent;
use URI::Escape;
use feature qw/say/;


my $query = <<'SPARQL';
PREFIX up_core:<http://purl.uniprot.org/core/> 
PREFIX taxon:<http://purl.uniprot.org/taxonomy/>
PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
SELECT ?taxonId ?scitName ?comName
WHERE
{

    ?taxonId a up_core:Taxon .
    ?taxonId rdfs:subClassOf+ taxon:554915 .
    ?taxonId up_core:scientificName ?scitName .
            OPTIONAL {
                    ?taxonId up_core:commonName ?comName .
            }
} LIMIT 2600
SPARQL

my $agent = LWP::UserAgent->new();
my $url = 'http://beta.sparql.uniprot.org';
$query = uri_escape($query);
my $rurl = $url.'?query='.$query;

my $res = $agent->get($rurl, 'Accept' => 'application/sparql-results+xml');
if ($res->is_success) {
    say $res->decoded_content;
}
else {
    say sprintf "%s\t%s\n", $res->code, $res->status_line;
}