{{#sparql:# Show the reaction equation for ATP synthase (reaction 
# *ATPS4m* from BiGG). NB there are two types of protons 
# here, as MetaNetX distinguishes protons used for balancing 
# (MNXM1) from those that are translocated (MNXM01). 

PREFIX mnx: <https://rdf.metanetx.org/schema/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rhea: <http://rdf.rhea-db.org/>
PREFIX biggR: <https://identifiers.org/bigg.reaction:>
SELECT ?chem ?chem_name ?comp ?comp_name $coef
FROM <https://rdf.metanetx.org/>
WHERE{
    ?reaction mnx:reacXref biggR:ATPS4m .
    ?reaction ?side ?part .
    ?part mnx:chem ?chem ;
          mnx:comp ?comp ;
          mnx:coef ?c    .
    ?chem rdfs:comment ?chem_name .
    ?comp rdfs:comment ?comp_name .
    FILTER( ?side IN ( mnx:left , mnx:right ))
    BIND( IF( ?side = mnx:left, - ?c, ?c ) AS ?coef )
}
| endpoint = https://rdf.metanetx.org/sparql
| chart=bordercloud.visualization.DataTable
| options=
| log=2
}}

from SPARQLWrapper import SPARQLWrapper, JSON

sparql = SPARQLWrapper("https://rdf.metanetx.org/sparql")
sparql.setQuery("""
    # Show the reaction equation for ATP synthase (reaction 
# *ATPS4m* from BiGG). NB there are two types of protons 
# here, as MetaNetX distinguishes protons used for balancing 
# (MNXM1) from those that are translocated (MNXM01). 

PREFIX mnx: <https://rdf.metanetx.org/schema/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rhea: <http://rdf.rhea-db.org/>
PREFIX biggR: <https://identifiers.org/bigg.reaction:>
SELECT ?chem ?chem_name ?comp ?comp_name $coef
FROM <https://rdf.metanetx.org/>
WHERE{
    ?reaction mnx:reacXref biggR:ATPS4m .
    ?reaction ?side ?part .
    ?part mnx:chem ?chem ;
          mnx:comp ?comp ;
          mnx:coef ?c    .
    ?chem rdfs:comment ?chem_name .
    ?comp rdfs:comment ?comp_name .
    FILTER( ?side IN ( mnx:left , mnx:right ))
    BIND( IF( ?side = mnx:left, - ?c, ?c ) AS ?coef )
}""")
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://rdf.metanetx.org/sparql"
# create query statement
    query <- "# Show the reaction equation for ATP synthase (reaction 
# *ATPS4m* from BiGG). NB there are two types of protons 
# here, as MetaNetX distinguishes protons used for balancing 
# (MNXM1) from those that are translocated (MNXM01). 

PREFIX mnx: <https://rdf.metanetx.org/schema/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rhea: <http://rdf.rhea-db.org/>
PREFIX biggR: <https://identifiers.org/bigg.reaction:>
SELECT ?chem ?chem_name ?comp ?comp_name $coef
FROM <https://rdf.metanetx.org/>
WHERE{
    ?reaction mnx:reacXref biggR:ATPS4m .
    ?reaction ?side ?part .
    ?part mnx:chem ?chem ;
          mnx:comp ?comp ;
          mnx:coef ?c    .
    ?chem rdfs:comment ?chem_name .
    ?comp rdfs:comment ?comp_name .
    FILTER( ?side IN ( mnx:left , mnx:right ))
    BIND( IF( ?side = mnx:left, - ?c, ?c ) AS ?coef )
}"
# Step 2 - Use SPARQL package to submit query and save results to a data frame
qd <- SPARQL(endpoint,query,curl_args=list(useragent=R.version.string))
df <- qd$results

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

endpoint = "https://rdf.metanetx.org/sparql"
sparql = <<-EOT
# Show the reaction equation for ATP synthase (reaction 
# *ATPS4m* from BiGG). NB there are two types of protons 
# here, as MetaNetX distinguishes protons used for balancing 
# (MNXM1) from those that are translocated (MNXM01). 

PREFIX mnx: <https://rdf.metanetx.org/schema/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rhea: <http://rdf.rhea-db.org/>
PREFIX biggR: <https://identifiers.org/bigg.reaction:>
SELECT ?chem ?chem_name ?comp ?comp_name $coef
FROM <https://rdf.metanetx.org/>
WHERE{
    ?reaction mnx:reacXref biggR:ATPS4m .
    ?reaction ?side ?part .
    ?part mnx:chem ?chem ;
          mnx:comp ?comp ;
          mnx:coef ?c    .
    ?chem rdfs:comment ?chem_name .
    ?comp rdfs:comment ?comp_name .
    FILTER( ?side IN ( mnx:left , mnx:right ))
    BIND( IF( ?side = mnx:left, - ?c, ?c ) AS ?coef )
}
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://rdf.metanetx.org/sparql';

query = ['# Show the reaction equation for ATP synthase (reaction  '...
'# *ATPS4m* from BiGG). NB there are two types of protons  '...
'# here, as MetaNetX distinguishes protons used for balancing  '...
'# (MNXM1) from those that are translocated (MNXM01).  '...
' '...
'PREFIX mnx: <https://rdf.metanetx.org/schema/> '...
'PREFIX owl: <http://www.w3.org/2002/07/owl#> '...
'PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> '...
'PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> '...
'PREFIX rhea: <http://rdf.rhea-db.org/> '...
'PREFIX biggR: <https://identifiers.org/bigg.reaction:> '...
'SELECT ?chem ?chem_name ?comp ?comp_name $coef '...
'FROM <https://rdf.metanetx.org/> '...
'WHERE{ '...
'    ?reaction mnx:reacXref biggR:ATPS4m . '...
'    ?reaction ?side ?part . '...
'    ?part mnx:chem ?chem ; '...
'          mnx:comp ?comp ; '...
'          mnx:coef ?c    . '...
'    ?chem rdfs:comment ?chem_name . '...
'    ?comp rdfs:comment ?comp_name . '...
'    FILTER( ?side IN ( mnx:left , mnx:right )) '...
'    BIND( IF( ?side = mnx:left, - ?c, ?c ) AS ?coef ) '...
'} '];

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://rdf.metanetx.org/sparql";
$sp_readonly = new SparqlClient();
$sp_readonly->setEndpointRead($endpoint);
$q = <<<EOD
# Show the reaction equation for ATP synthase (reaction 
# *ATPS4m* from BiGG). NB there are two types of protons 
# here, as MetaNetX distinguishes protons used for balancing 
# (MNXM1) from those that are translocated (MNXM01). 

PREFIX mnx: <https://rdf.metanetx.org/schema/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rhea: <http://rdf.rhea-db.org/>
PREFIX biggR: <https://identifiers.org/bigg.reaction:>
SELECT ?chem ?chem_name ?comp ?comp_name $coef
FROM <https://rdf.metanetx.org/>
WHERE{
    ?reaction mnx:reacXref biggR:ATPS4m .
    ?reaction ?side ?part .
    ?part mnx:chem ?chem ;
          mnx:comp ?comp ;
          mnx:coef ?c    .
    ?chem rdfs:comment ?chem_name .
    ?comp rdfs:comment ?comp_name .
    FILTER( ?side IN ( mnx:left , mnx:right ))
    BIND( IF( ?side = mnx:left, - ?c, ?c ) AS ?coef )
}
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://rdf.metanetx.org/sparql");
            String querySelect  = "# Show the reaction equation for ATP synthase (reaction  \n"
                    + "# *ATPS4m* from BiGG). NB there are two types of protons  \n"
                    + "# here, as MetaNetX distinguishes protons used for balancing  \n"
                    + "# (MNXM1) from those that are translocated (MNXM01).  \n"
                    + " \n"
                    + "PREFIX mnx: <https://rdf.metanetx.org/schema/> \n"
                    + "PREFIX owl: <http://www.w3.org/2002/07/owl#> \n"
                    + "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n"
                    + "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n"
                    + "PREFIX rhea: <http://rdf.rhea-db.org/> \n"
                    + "PREFIX biggR: <https://identifiers.org/bigg.reaction:> \n"
                    + "SELECT ?chem ?chem_name ?comp ?comp_name $coef \n"
                    + "FROM <https://rdf.metanetx.org/> \n"
                    + "WHERE{ \n"
                    + "    ?reaction mnx:reacXref biggR:ATPS4m . \n"
                    + "    ?reaction ?side ?part . \n"
                    + "    ?part mnx:chem ?chem ; \n"
                    + "          mnx:comp ?comp ; \n"
                    + "          mnx:coef ?c    . \n"
                    + "    ?chem rdfs:comment ?chem_name . \n"
                    + "    ?comp rdfs:comment ?comp_name . \n"
                    + "    FILTER( ?side IN ( mnx:left , mnx:right )) \n"
                    + "    BIND( IF( ?side = mnx:left, - ?c, ?c ) AS ?coef ) \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,)"
}