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 )
}
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: <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 $coef
FROM <https://rdf.metanetx.org/>
WHERE{
?reaction mnx:reacXref biggR:ATPS4m .
?reaction ?side ?part .
?part mnx:chem ?chem ;
mnx:comp ?comp ;
mnx:coef ?c .
?chem rdfs:comment ?chem_name .
?comp rdfs:comment ?comp_name .
FILTER( ?side IN ( mnx:left , mnx:right ))
BIND( IF( ?side = mnx:left, - ?c, ?c ) AS ?coef )
}"
data-sgvizler-chart='bordercloud.visualization.DataTable'
data-sgvizler-chart-options=''
data-sgvizler-endpoint_output_format='json'
data-sgvizler-log='2'
style='width:100%; height:auto;'
lang='en'
/>
<script>
/*$(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