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  2. MetaNetX / MNXref
  3. Queries
  4. Retrieve the MNXref reaction identifier from a KEGG reaction id
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MetaNetX.org rxn. SPARQL query rxn.
0
Retrieve the MNXref reaction identifier from a KEGG reaction id
Retrieve the MNXref reaction identifier, that corresponds to the KEGG reaction R00703 (lactate dehydrogenase)
Retrieve the MNXref reaction identifier, that corresponds to the KEGG reaction R00703 (lactate dehydrogenase)

Reuse these data in your code

Query, endpoint and code for reusing the same data
https://rdf.metanetx.org/sparql
# Retrieve the MNXref reaction identifier, that corresponds to 
# the KEGG reaction *R00703* (lactate dehydrogenase). 

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 keggR: <https://identifiers.org/kegg.reaction:>
SELECT ?reaction ?reference
FROM <https://rdf.metanetx.org/>
WHERE {
    ?reaction a mnx:REAC .
    ?reaction mnx:reacXref keggR:R00703 .
    ?reaction mnx:reacRefer ?reference
}
Howto write a query SPARQL? (in French) 
{{#sparql:# Retrieve the MNXref reaction identifier, that corresponds to 
# the KEGG reaction *R00703* (lactate dehydrogenase). 

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 keggR: <https://identifiers.org/kegg.reaction:>
SELECT ?reaction ?reference
FROM <https://rdf.metanetx.org/>
WHERE {
    ?reaction a mnx:REAC .
    ?reaction mnx:reacXref keggR:R00703 .
    ?reaction mnx:reacRefer ?reference
}
| 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 = `# Retrieve the MNXref reaction identifier, that corresponds to 
# the KEGG reaction *R00703* (lactate dehydrogenase). 

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 keggR: <https://identifiers.org/kegg.reaction:>
SELECT ?reaction ?reference
FROM <https://rdf.metanetx.org/>
WHERE {
    ?reaction a mnx:REAC .
    ?reaction mnx:reacXref keggR:R00703 .
    ?reaction mnx:reacRefer ?reference
}`;

   // $('#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:`# Retrieve the MNXref reaction identifier, that corresponds to 
# the KEGG reaction *R00703* (lactate dehydrogenase). 

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 keggR: <https://identifiers.org/kegg.reaction:>
SELECT ?reaction ?reference
FROM <https://rdf.metanetx.org/>
WHERE {
    ?reaction a mnx:REAC .
    ?reaction mnx:reacXref keggR:R00703 .
    ?reaction mnx:reacRefer ?reference
}`};

    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="# Retrieve the MNXref reaction identifier, that corresponds to 
# the KEGG reaction *R00703* (lactate dehydrogenase). 

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 keggR: &lt;https://identifiers.org/kegg.reaction:&gt;
SELECT ?reaction ?reference
FROM &lt;https://rdf.metanetx.org/&gt;
WHERE {
    ?reaction a mnx:REAC .
    ?reaction mnx:reacXref keggR:R00703 .
    ?reaction mnx:reacRefer ?reference
}"
    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("""
    # Retrieve the MNXref reaction identifier, that corresponds to 
# the KEGG reaction *R00703* (lactate dehydrogenase). 

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 keggR: <https://identifiers.org/kegg.reaction:>
SELECT ?reaction ?reference
FROM <https://rdf.metanetx.org/>
WHERE {
    ?reaction a mnx:REAC .
    ?reaction mnx:reacXref keggR:R00703 .
    ?reaction mnx:reacRefer ?reference
}""")
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 <- "# Retrieve the MNXref reaction identifier, that corresponds to 
# the KEGG reaction *R00703* (lactate dehydrogenase). 

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 keggR: <https://identifiers.org/kegg.reaction:>
SELECT ?reaction ?reference
FROM <https://rdf.metanetx.org/>
WHERE {
    ?reaction a mnx:REAC .
    ?reaction mnx:reacXref keggR:R00703 .
    ?reaction mnx:reacRefer ?reference
}"
# 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
# Retrieve the MNXref reaction identifier, that corresponds to 
# the KEGG reaction *R00703* (lactate dehydrogenase). 

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 keggR: <https://identifiers.org/kegg.reaction:>
SELECT ?reaction ?reference
FROM <https://rdf.metanetx.org/>
WHERE {
    ?reaction a mnx:REAC .
    ?reaction mnx:reacXref keggR:R00703 .
    ?reaction mnx:reacRefer ?reference
}
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 = ['# Retrieve the MNXref reaction identifier, that corresponds to  '...
'# the KEGG reaction *R00703* (lactate dehydrogenase).  '...
' '...
'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 keggR: <https://identifiers.org/kegg.reaction:> '...
'SELECT ?reaction ?reference '...
'FROM <https://rdf.metanetx.org/> '...
'WHERE { '...
'    ?reaction a mnx:REAC . '...
'    ?reaction mnx:reacXref keggR:R00703 . '...
'    ?reaction mnx:reacRefer ?reference '...
'} '];

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
# Retrieve the MNXref reaction identifier, that corresponds to 
# the KEGG reaction *R00703* (lactate dehydrogenase). 

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 keggR: <https://identifiers.org/kegg.reaction:>
SELECT ?reaction ?reference
FROM <https://rdf.metanetx.org/>
WHERE {
    ?reaction a mnx:REAC .
    ?reaction mnx:reacXref keggR:R00703 .
    ?reaction mnx:reacRefer ?reference
}
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  = "# Retrieve the MNXref reaction identifier, that corresponds to  \n"
                    + "# the KEGG reaction *R00703* (lactate dehydrogenase).  \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 keggR: <https://identifiers.org/kegg.reaction:> \n"
                    + "SELECT ?reaction ?reference \n"
                    + "FROM <https://rdf.metanetx.org/> \n"
                    + "WHERE { \n"
                    + "    ?reaction a mnx:REAC . \n"
                    + "    ?reaction mnx:reacXref keggR:R00703 . \n"
                    + "    ?reaction mnx:reacRefer ?reference \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