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Show the reaction equation for ATP synthase
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).
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).

Reuse these data in your code

Query, endpoint and code for reusing the same data
https://rdf.metanetx.org/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 )
}
Howto write a query SPARQL? (in French)
{{#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
}}
Howto install LinkedWiki in my wiki? Howto insert this graph in my wiki?
Test this script in a new tab.
<html>
    <head>
        <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"  async></script>
    </head>
    <body onload="testQuery();">
        <script>
function testQuery(){
    var endpoint = "https://rdf.metanetx.org/sparql";
    var 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 )
}`;

   // $('#bodyContentResearch').append(queryDataset);
    $.ajax({
                url: endpoint,
                dataType: 'json',
                data: {
                    queryLn: 'SPARQL',
                    query: query ,
                    limit: 'none',
                    infer: 'true',
                    Accept: 'application/sparql-results+json'
                },
                success: displayResult,
                error: displayError
        });
}

function displayError(xhr, textStatus, errorThrown) {
    console.log(textStatus);
    console.log(errorThrown);
}

function displayResult(data) {
    $.each(data.results.bindings, function(index, bs) {
        console.log(bs);
        $("body").append(JSON.stringify(bs) + "<hr/>");
    });
}

        </script>
    </body>
</html>
Test this script in a new tab.
<html>
    <head>
        <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"  async></script>
    </head>
    <body onload="testQuery();">
        <script>
function testQuery(){
    var url = new URL("https://rdf.metanetx.org/sparql");
    var params = {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.search = new URLSearchParams(params).toString();

    var myHeaders = new Headers();
    myHeaders.append("Accept", "application/sparql-results+json");

    var requestOptions = {
      method: 'GET',
      headers: myHeaders,
      redirect: 'follow'
    };

    fetch(url, requestOptions)
        .then(response => response.json())
        .then(result => displayResult(result))
        .catch(error => displayError(error));
}

function displayError(error) {
    console.log(error);
}

function displayResult(data) {
    data.results.bindings.forEach(bs => {
            console.log(bs);
            $("body").append(JSON.stringify(bs) + "<hr/>");
    });
}
        </script>
    </body>
</html>
Test this script in a new tab (Careful, several charts need a API key).
Howto insert this graph in my html page?
<html>
    <head>
     <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous">

     <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.9.0/css/all.min.css">

     <script
            src="https://code.jquery.com/jquery-3.4.1.min.js"
            integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="
            crossorigin="anonymous"> </script>
     <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.7/umd/popper.min.js" integrity="sha384-UO2eT0CpHqdSJQ6hJty5KVphtPhzWj9WO1clHTMGa3JDZwrnQq4sF86dIHNDz0W1" crossorigin="anonymous"> </script>
     <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js" integrity="sha384-JjSmVgyd0p3pXB1rRibZUAYoIIy6OrQ6VrjIEaFf/nJGzIxFDsf4x0xIM+B07jRM" crossorigin="anonymous"> </script>

     <script type="text/javascript" src="https://bordercloud.github.io/sgvizler2/sgvizler2/sgvizler2.js" defer> </script>
     <script type="text/javascript" src="https://linkedwiki.com/js/initExampleHTML.js"  defer > </script>
    </head>
<body style="margin:0;">
<div id="sgvzl_example_query"
   data-sgvizler-endpoint="https://rdf.metanetx.org/sparql"
   data-sgvizler-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: &lt;https://rdf.metanetx.org/schema/&gt;
PREFIX owl: &lt;http://www.w3.org/2002/07/owl#&gt;
PREFIX rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt;
PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
PREFIX rhea: &lt;http://rdf.rhea-db.org/&gt;
PREFIX biggR: &lt;https://identifiers.org/bigg.reaction:&gt;
SELECT ?chem ?chem_name ?comp ?comp_name $coef
FROM &lt;https://rdf.metanetx.org/&gt;
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 )
}"
    data-sgvizler-chart='bordercloud.visualization.DataTable'
    data-sgvizler-chart-options=''
    data-sgvizler-endpoint_output_format='json'
    data-sgvizler-log='2'
    style='width:100%; height:auto;'
    lang='en'
   />

<script>
/*$(function() {
   sgvizler2.containerDrawAll({
       // Google Api key
       googleApiKey : "GOOGLE_MAP_API_KEY",
       // OpenStreetMap Access Token
       //  https://www.mapbox.com/api-documentation/#access-tokens
       osmAccessToken : "OSM_MAP_API_KEY"
     });
});*/
</script>

</body>
</html>
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"])
Howto use SPARQL with Python ?
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
SPARQL with R in less than 5 minutes
#!/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
Doc Ruby for SPARQL 1.1
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')
Project Github MatlabSPARQL
<?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";
 }
 ?>
Project Github BorderCloud/SPARQL
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");
        }
    }
}
For example, with Gradle :
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,)"
}
Project Github BorderCloud/SPARQL-JAVA
Other SPARQL client : RDF4J
You can use the SPARQL clients in Java : BorderCloud/SPARQL-JAVA or RDF4J