{{#sparql:PREFIX xpcv: <http://nextprot.org/rdf/terminology/>
PREFIX xp: <http://nextprot.org/rdf#>

select distinct ?entry where {
  values ?cytoloc {xpcv:SL-0086 xpcv:GO_0005737} # SL and GO values for cytoplasm
  ?entry xp:isoform ?iso.
  ?iso xp:keyword/xp:term xpcv:KW-0597. # Phosphorylated
  ?iso xp:cellularComponent ?loc .
  ?loc xp:term/xp:childOf ?cytoloc.
  filter not exists {?loc  xp:negativeEvidence ?negev} # No negative localization evidence
}
| endpoint = https://sparql.nextprot.org/
| chart=bordercloud.visualization.DataTable
| options=
| log=2
}}

from SPARQLWrapper import SPARQLWrapper, JSON

sparql = SPARQLWrapper("https://sparql.nextprot.org/")
sparql.setQuery("""
    PREFIX xpcv: <http://nextprot.org/rdf/terminology/>
PREFIX xp: <http://nextprot.org/rdf#>

select distinct ?entry where {
  values ?cytoloc {xpcv:SL-0086 xpcv:GO_0005737} # SL and GO values for cytoplasm
  ?entry xp:isoform ?iso.
  ?iso xp:keyword/xp:term xpcv:KW-0597. # Phosphorylated
  ?iso xp:cellularComponent ?loc .
  ?loc xp:term/xp:childOf ?cytoloc.
  filter not exists {?loc  xp:negativeEvidence ?negev} # No negative localization evidence
}""")
sparql.setReturnFormat(JSON)
results = sparql.query().convert()

for result in results["results"]["bindings"]:
    print(result)
    #print(result["label"]["value"])

library(SPARQL) # SPARQL querying package
library(ggplot2)

# Step 1 - Set up preliminaries and define query
# Define the data.gov endpoint
    endpoint <- "https://sparql.nextprot.org/"
# create query statement
    query <- "PREFIX xpcv: <http://nextprot.org/rdf/terminology/>
PREFIX xp: <http://nextprot.org/rdf#>

select distinct ?entry where {
  values ?cytoloc {xpcv:SL-0086 xpcv:GO_0005737} # SL and GO values for cytoplasm
  ?entry xp:isoform ?iso.
  ?iso xp:keyword/xp:term xpcv:KW-0597. # Phosphorylated
  ?iso xp:cellularComponent ?loc .
  ?loc xp:term/xp:childOf ?cytoloc.
  filter not exists {?loc  xp:negativeEvidence ?negev} # No negative localization evidence
}"
# Step 2 - Use SPARQL package to submit query and save results to a data frame
qd <- SPARQL(endpoint,query,curl_args=list(useragent=R.version.string))
df <- qd$results

#!/usr/bin/env ruby
#
# Install sparql for Ruby
#   gem update --system
#   gem install sparql
#
require 'sparql/client'

endpoint = "https://sparql.nextprot.org/"
sparql = <<-EOT
PREFIX xpcv: <http://nextprot.org/rdf/terminology/>
PREFIX xp: <http://nextprot.org/rdf#>

select distinct ?entry where {
  values ?cytoloc {xpcv:SL-0086 xpcv:GO_0005737} # SL and GO values for cytoplasm
  ?entry xp:isoform ?iso.
  ?iso xp:keyword/xp:term xpcv:KW-0597. # Phosphorylated
  ?iso xp:cellularComponent ?loc .
  ?loc xp:term/xp:childOf ?cytoloc.
  filter not exists {?loc  xp:negativeEvidence ?negev} # No negative localization evidence
}
EOT

#For Wikidata, the method get is required
#For other SPARQL endpoints, the method post is prefered
client = SPARQL::Client.new(endpoint, :method => :get)
rows = client.query(sparql)

puts "Number of rows: #{rows.size}"
for row in rows
  for key,val in row do
    # print "#{key.to_s.ljust(10)}: #{val}\t"
    print "#{key}: #{val}\t"
  end
  print "\n"
end

endpoint = 'https://sparql.nextprot.org/';

query = ['PREFIX xpcv: <http://nextprot.org/rdf/terminology/> '...
'PREFIX xp: <http://nextprot.org/rdf#> '...
' '...
'select distinct ?entry where { '...
'  values ?cytoloc {xpcv:SL-0086 xpcv:GO_0005737} # SL and GO values for cytoplasm '...
'  ?entry xp:isoform ?iso. '...
'  ?iso xp:keyword/xp:term xpcv:KW-0597. # Phosphorylated '...
'  ?iso xp:cellularComponent ?loc . '...
'  ?loc xp:term/xp:childOf ?cytoloc. '...
'  filter not exists {?loc  xp:negativeEvidence ?negev} # No negative localization evidence '...
'} '];

url_head = strcat(endpoint,'?query=');
url_query = urlencode(query);
format = 'text/tab-separated-values';
url_tail = strcat('&format=', format);

url = strcat(url_head, url_query, url_tail);

% get the data from the endpoint
query_results = urlread(url);

% write the data to a file so that tdfread can parse it
fid = fopen('query_results.txt','w');
if fid>=0
    fprintf(fid, '%s\n', query_results)
    fclose(fid)
end

% this reads the tsv file into a struct
sparql_data = tdfread('query_results.txt')

<?php
require __DIR__ . '/../vendor/autoload.php';
use BorderCloud\SPARQL\SparqlClient;

$endpoint ="https://sparql.nextprot.org/";
$sp_readonly = new SparqlClient();
$sp_readonly->setEndpointRead($endpoint);
$q = <<<EOD
PREFIX xpcv: <http://nextprot.org/rdf/terminology/>
PREFIX xp: <http://nextprot.org/rdf#>

select distinct ?entry where {
  values ?cytoloc {xpcv:SL-0086 xpcv:GO_0005737} # SL and GO values for cytoplasm
  ?entry xp:isoform ?iso.
  ?iso xp:keyword/xp:term xpcv:KW-0597. # Phosphorylated
  ?iso xp:cellularComponent ?loc .
  ?loc xp:term/xp:childOf ?cytoloc.
  filter not exists {?loc  xp:negativeEvidence ?negev} # No negative localization evidence
}
EOD;
$rows = $sp_readonly->query($q, 'rows');
$err = $sp_readonly->getErrors();
if ($err) {
      print_r($err);
      throw new Exception(print_r($err, true));
}

foreach ($rows["result"]["variables"] as $variable) {
        printf("%-20.20s",$variable);
        echo '|';
 }
 echo "\n";

foreach ($rows["result"]["rows"] as $row) {
        foreach ($rows["result"]["variables"] as $variable) {
            printf("%-20.20s", $row[$variable]);
            echo '|';
        }
        echo "\n";
 }
 ?>

import com.bordercloud.sparql.*;

import java.net.URI;
import java.net.URISyntaxException;
import java.util.HashMap;

public class Main {

    public static void main(String[] args) {
        try {
            URI endpoint = new URI("https://sparql.nextprot.org/");
            String querySelect  = "PREFIX xpcv: <http://nextprot.org/rdf/terminology/> \n"
                    + "PREFIX xp: <http://nextprot.org/rdf#> \n"
                    + " \n"
                    + "select distinct ?entry where { \n"
                    + "  values ?cytoloc {xpcv:SL-0086 xpcv:GO_0005737} # SL and GO values for cytoplasm \n"
                    + "  ?entry xp:isoform ?iso. \n"
                    + "  ?iso xp:keyword/xp:term xpcv:KW-0597. # Phosphorylated \n"
                    + "  ?iso xp:cellularComponent ?loc . \n"
                    + "  ?loc xp:term/xp:childOf ?cytoloc. \n"
                    + "  filter not exists {?loc  xp:negativeEvidence ?negev} # No negative localization evidence \n"
                    + "} \n";
            SparqlClient sc = new SparqlClient(false);
            sc.setEndpointRead(endpoint);
            SparqlResult sr = sc.query(querySelect);
            //sc.printLastQueryAndResult();

            printResult(sr.getModel(),30);
        } catch (URISyntaxException | SparqlClientException e) {
            System.out.println(e);
            e.printStackTrace();
        }
    }

    public static void printResult(SparqlResultModel rs , int size) {
        for (String variable : rs.getVariables()) {
            System.out.print(String.format("%-"+size+"."+size+"s", variable ) + " | ");
        }
        System.out.print("\n");
        for (HashMap row : rs.getRows()) {
            for (String variable : rs.getVariables()) {
                System.out.print(String.format("%-"+size+"."+size+"s", row.get(variable)) + " | ");
            }
            System.out.print("\n");
        }
    }
}

apply plugin: 'java'
apply plugin: 'application'

// This comes out to package + '.' + mainClassName
mainClassName = 'Main'

group 'org.example'
version '1.0-SNAPSHOT'

repositories {
    mavenCentral()
}
dependencies {
    compile "com.bordercloud:SPARQL-JAVA:[1.0,)"
}