SPARQL query: List all GEMs currently in the MetaNetX repository

smoretti

MetaNetX.org metabolic network SPARQL query metabolic modeling

List all GEMs currently in the MetaNetX repository

List all GEMs currently in the MetaNetX repository, with their numbers of reactions, chemical, compartments and genes/proteins

Reuse these data in your code

Query, endpoint and code for reusing the same data

Endpoint:

https://rdf.metanetx.org/sparql

Query:

# List all GEMs currently in the MetaNetX repository, with 
# their numbers of reactions, chemical, compartments and 
# genes/proteins. 

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/>
SELECT ?mnet ?taxon
    (COUNT( DISTINCT ?reac) AS ?count_reac)
    (COUNT( DISTINCT ?chem) AS ?count_chem)
    (COUNT( DISTINCT ?comp) AS ?count_comp)
    (COUNT( DISTINCT ?pept) AS ?count_pept)
FROM <https://rdf.metanetx.org/>
WHERE{
    ?mnet a mnx:MNET .
    ?mnet mnx:gpr  ?gpr .
    ?gpr  mnx:reac ?reac .
    ?reac mnx:left|mnx:right ?part .
    ?part mnx:chem ?chem;
          mnx:comp ?comp.
    ?gpr mnx:cata/mnx:pept ?pept .
    OPTIONAL{ ?mnet mnx:taxid ?taxon }
}

Howto write a query SPARQL? (in French)

{{#sparql:# List all GEMs currently in the MetaNetX repository, with 
# their numbers of reactions, chemical, compartments and 
# genes/proteins. 

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/>
SELECT ?mnet ?taxon
    (COUNT( DISTINCT ?reac) AS ?count_reac)
    (COUNT( DISTINCT ?chem) AS ?count_chem)
    (COUNT( DISTINCT ?comp) AS ?count_comp)
    (COUNT( DISTINCT ?pept) AS ?count_pept)
FROM <https://rdf.metanetx.org/>
WHERE{
    ?mnet a mnx:MNET .
    ?mnet mnx:gpr  ?gpr .
    ?gpr  mnx:reac ?reac .
    ?reac mnx:left|mnx:right ?part .
    ?part mnx:chem ?chem;
          mnx:comp ?comp.
    ?gpr mnx:cata/mnx:pept ?pept .
    OPTIONAL{ ?mnet mnx:taxid ?taxon }
}
| endpoint = https://rdf.metanetx.org/sparql
| chart=bordercloud.visualization.DataTable
| options=
| log=2
}}

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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 = `# List all GEMs currently in the MetaNetX repository, with 
# their numbers of reactions, chemical, compartments and 
# genes/proteins. 

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/>
SELECT ?mnet ?taxon
    (COUNT( DISTINCT ?reac) AS ?count_reac)
    (COUNT( DISTINCT ?chem) AS ?count_chem)
    (COUNT( DISTINCT ?comp) AS ?count_comp)
    (COUNT( DISTINCT ?pept) AS ?count_pept)
FROM <https://rdf.metanetx.org/>
WHERE{
    ?mnet a mnx:MNET .
    ?mnet mnx:gpr  ?gpr .
    ?gpr  mnx:reac ?reac .
    ?reac mnx:left|mnx:right ?part .
    ?part mnx:chem ?chem;
          mnx:comp ?comp.
    ?gpr mnx:cata/mnx:pept ?pept .
    OPTIONAL{ ?mnet mnx:taxid ?taxon }
}`;

   // $('#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:`# List all GEMs currently in the MetaNetX repository, with 
# their numbers of reactions, chemical, compartments and 
# genes/proteins. 

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/>
SELECT ?mnet ?taxon
    (COUNT( DISTINCT ?reac) AS ?count_reac)
    (COUNT( DISTINCT ?chem) AS ?count_chem)
    (COUNT( DISTINCT ?comp) AS ?count_comp)
    (COUNT( DISTINCT ?pept) AS ?count_pept)
FROM <https://rdf.metanetx.org/>
WHERE{
    ?mnet a mnx:MNET .
    ?mnet mnx:gpr  ?gpr .
    ?gpr  mnx:reac ?reac .
    ?reac mnx:left|mnx:right ?part .
    ?part mnx:chem ?chem;
          mnx:comp ?comp.
    ?gpr mnx:cata/mnx:pept ?pept .
    OPTIONAL{ ?mnet mnx:taxid ?taxon }
}`};

    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="# List all GEMs currently in the MetaNetX repository, with 
# their numbers of reactions, chemical, compartments and 
# genes/proteins. 

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;
SELECT ?mnet ?taxon
    (COUNT( DISTINCT ?reac) AS ?count_reac)
    (COUNT( DISTINCT ?chem) AS ?count_chem)
    (COUNT( DISTINCT ?comp) AS ?count_comp)
    (COUNT( DISTINCT ?pept) AS ?count_pept)
FROM &lt;https://rdf.metanetx.org/&gt;
WHERE{
    ?mnet a mnx:MNET .
    ?mnet mnx:gpr  ?gpr .
    ?gpr  mnx:reac ?reac .
    ?reac mnx:left|mnx:right ?part .
    ?part mnx:chem ?chem;
          mnx:comp ?comp.
    ?gpr mnx:cata/mnx:pept ?pept .
    OPTIONAL{ ?mnet mnx:taxid ?taxon }
}"
    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("""
    # List all GEMs currently in the MetaNetX repository, with 
# their numbers of reactions, chemical, compartments and 
# genes/proteins. 

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/>
SELECT ?mnet ?taxon
    (COUNT( DISTINCT ?reac) AS ?count_reac)
    (COUNT( DISTINCT ?chem) AS ?count_chem)
    (COUNT( DISTINCT ?comp) AS ?count_comp)
    (COUNT( DISTINCT ?pept) AS ?count_pept)
FROM <https://rdf.metanetx.org/>
WHERE{
    ?mnet a mnx:MNET .
    ?mnet mnx:gpr  ?gpr .
    ?gpr  mnx:reac ?reac .
    ?reac mnx:left|mnx:right ?part .
    ?part mnx:chem ?chem;
          mnx:comp ?comp.
    ?gpr mnx:cata/mnx:pept ?pept .
    OPTIONAL{ ?mnet mnx:taxid ?taxon }
}""")
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 <- "# List all GEMs currently in the MetaNetX repository, with 
# their numbers of reactions, chemical, compartments and 
# genes/proteins. 

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/>
SELECT ?mnet ?taxon
    (COUNT( DISTINCT ?reac) AS ?count_reac)
    (COUNT( DISTINCT ?chem) AS ?count_chem)
    (COUNT( DISTINCT ?comp) AS ?count_comp)
    (COUNT( DISTINCT ?pept) AS ?count_pept)
FROM <https://rdf.metanetx.org/>
WHERE{
    ?mnet a mnx:MNET .
    ?mnet mnx:gpr  ?gpr .
    ?gpr  mnx:reac ?reac .
    ?reac mnx:left|mnx:right ?part .
    ?part mnx:chem ?chem;
          mnx:comp ?comp.
    ?gpr mnx:cata/mnx:pept ?pept .
    OPTIONAL{ ?mnet mnx:taxid ?taxon }
}"
# 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
# List all GEMs currently in the MetaNetX repository, with 
# their numbers of reactions, chemical, compartments and 
# genes/proteins. 

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/>
SELECT ?mnet ?taxon
    (COUNT( DISTINCT ?reac) AS ?count_reac)
    (COUNT( DISTINCT ?chem) AS ?count_chem)
    (COUNT( DISTINCT ?comp) AS ?count_comp)
    (COUNT( DISTINCT ?pept) AS ?count_pept)
FROM <https://rdf.metanetx.org/>
WHERE{
    ?mnet a mnx:MNET .
    ?mnet mnx:gpr  ?gpr .
    ?gpr  mnx:reac ?reac .
    ?reac mnx:left|mnx:right ?part .
    ?part mnx:chem ?chem;
          mnx:comp ?comp.
    ?gpr mnx:cata/mnx:pept ?pept .
    OPTIONAL{ ?mnet mnx:taxid ?taxon }
}
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 = ['# List all GEMs currently in the MetaNetX repository, with  '...
'# their numbers of reactions, chemical, compartments and  '...
'# genes/proteins.  '...
' '...
'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/> '...
'SELECT ?mnet ?taxon '...
'    (COUNT( DISTINCT ?reac) AS ?count_reac) '...
'    (COUNT( DISTINCT ?chem) AS ?count_chem) '...
'    (COUNT( DISTINCT ?comp) AS ?count_comp) '...
'    (COUNT( DISTINCT ?pept) AS ?count_pept) '...
'FROM <https://rdf.metanetx.org/> '...
'WHERE{ '...
'    ?mnet a mnx:MNET . '...
'    ?mnet mnx:gpr  ?gpr . '...
'    ?gpr  mnx:reac ?reac . '...
'    ?reac mnx:left|mnx:right ?part . '...
'    ?part mnx:chem ?chem; '...
'          mnx:comp ?comp. '...
'    ?gpr mnx:cata/mnx:pept ?pept . '...
'    OPTIONAL{ ?mnet mnx:taxid ?taxon } '...
'} '];

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
# List all GEMs currently in the MetaNetX repository, with 
# their numbers of reactions, chemical, compartments and 
# genes/proteins. 

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/>
SELECT ?mnet ?taxon
    (COUNT( DISTINCT ?reac) AS ?count_reac)
    (COUNT( DISTINCT ?chem) AS ?count_chem)
    (COUNT( DISTINCT ?comp) AS ?count_comp)
    (COUNT( DISTINCT ?pept) AS ?count_pept)
FROM <https://rdf.metanetx.org/>
WHERE{
    ?mnet a mnx:MNET .
    ?mnet mnx:gpr  ?gpr .
    ?gpr  mnx:reac ?reac .
    ?reac mnx:left|mnx:right ?part .
    ?part mnx:chem ?chem;
          mnx:comp ?comp.
    ?gpr mnx:cata/mnx:pept ?pept .
    OPTIONAL{ ?mnet mnx:taxid ?taxon }
}
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  = "# List all GEMs currently in the MetaNetX repository, with  \n"
                    + "# their numbers of reactions, chemical, compartments and  \n"
                    + "# genes/proteins.  \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"
                    + "SELECT ?mnet ?taxon \n"
                    + "    (COUNT( DISTINCT ?reac) AS ?count_reac) \n"
                    + "    (COUNT( DISTINCT ?chem) AS ?count_chem) \n"
                    + "    (COUNT( DISTINCT ?comp) AS ?count_comp) \n"
                    + "    (COUNT( DISTINCT ?pept) AS ?count_pept) \n"
                    + "FROM <https://rdf.metanetx.org/> \n"
                    + "WHERE{ \n"
                    + "    ?mnet a mnx:MNET . \n"
                    + "    ?mnet mnx:gpr  ?gpr . \n"
                    + "    ?gpr  mnx:reac ?reac . \n"
                    + "    ?reac mnx:left|mnx:right ?part . \n"
                    + "    ?part mnx:chem ?chem; \n"
                    + "          mnx:comp ?comp. \n"
                    + "    ?gpr mnx:cata/mnx:pept ?pept . \n"
                    + "    OPTIONAL{ ?mnet mnx:taxid ?taxon } \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

Table view

Simple view on the data

Reuse these data in your code

Query, endpoint and code for reusing the same data