requête SPARQL: Retrieve all reactions and models in which a polypeptide appears

smoretti

Réseau métabolique changement chimique enzyme SPARQL query enzyme

Retrieve all reactions and models in which a polypeptide appears

Given the protein with UniProt accession number P42588 (PAT_ECOLI, putrescine aminotransferase, EC 2.6.1.82) retrieve all reactions and models in which this polypeptide appears.

Réutilisez ces données dans votre code

Requête, point d'accès et code permettant de réutiliser les mêmes données

Point d'accès :

https://rdf.metanetx.org/sparql

Requête :

# Given the protein with UniProt accession number *P42588* 
# (PAT_ECOLI, putrescine aminotransferase, EC 2.6.1.82) 
# retrieve all reactions and models in which this polypeptide 
# appears. 

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 up: <http://purl.uniprot.org/uniprot/>
SELECT ?mnet_label ?reac_label ?reac_eq ?MNXR (GROUP_CONCAT( ?cata_label; separator=';' ) AS ?complex )
FROM <https://rdf.metanetx.org/>
WHERE{
    ?pept mnx:peptXref up:P42588 .
    ?cata mnx:pept ?pept ;
          rdfs:label ?cata_label .
    ?gpr mnx:cata ?cata ;
         mnx:reac ?reac .
    ?reac rdfs:label ?reac_label ;
          rdfs:comment ?reac_eq .
    ?mnet mnx:gpr ?gpr ;
          rdfs:label ?mnet_label.
    OPTIONAL{ ?reac mnx:mnxr ?MNXR }
}

Comment écrire une requête SPARQL ?

{{#sparql:# Given the protein with UniProt accession number *P42588* 
# (PAT_ECOLI, putrescine aminotransferase, EC 2.6.1.82) 
# retrieve all reactions and models in which this polypeptide 
# appears. 

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 up: <http://purl.uniprot.org/uniprot/>
SELECT ?mnet_label ?reac_label ?reac_eq ?MNXR (GROUP_CONCAT( ?cata_label; separator=';' ) AS ?complex )
FROM <https://rdf.metanetx.org/>
WHERE{
    ?pept mnx:peptXref up:P42588 .
    ?cata mnx:pept ?pept ;
          rdfs:label ?cata_label .
    ?gpr mnx:cata ?cata ;
         mnx:reac ?reac .
    ?reac rdfs:label ?reac_label ;
          rdfs:comment ?reac_eq .
    ?mnet mnx:gpr ?gpr ;
          rdfs:label ?mnet_label.
    OPTIONAL{ ?reac mnx:mnxr ?MNXR }
}
| endpoint = https://rdf.metanetx.org/sparql
| chart=bordercloud.visualization.DataTable
| options=
| log=2
}}

Comment installer LinkedWiki dans mon wiki ? Comment insérer ce graphique dans mon wiki ?

Tester ce script dans un nouvel onglet.

<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 = `# Given the protein with UniProt accession number *P42588* 
# (PAT_ECOLI, putrescine aminotransferase, EC 2.6.1.82) 
# retrieve all reactions and models in which this polypeptide 
# appears. 

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 up: <http://purl.uniprot.org/uniprot/>
SELECT ?mnet_label ?reac_label ?reac_eq ?MNXR (GROUP_CONCAT( ?cata_label; separator=\';\' ) AS ?complex )
FROM <https://rdf.metanetx.org/>
WHERE{
    ?pept mnx:peptXref up:P42588 .
    ?cata mnx:pept ?pept ;
          rdfs:label ?cata_label .
    ?gpr mnx:cata ?cata ;
         mnx:reac ?reac .
    ?reac rdfs:label ?reac_label ;
          rdfs:comment ?reac_eq .
    ?mnet mnx:gpr ?gpr ;
          rdfs:label ?mnet_label.
    OPTIONAL{ ?reac mnx:mnxr ?MNXR }
}`;

   // $('#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>

Tester ce script dans un nouvel onglet.

<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:`# Given the protein with UniProt accession number *P42588* 
# (PAT_ECOLI, putrescine aminotransferase, EC 2.6.1.82) 
# retrieve all reactions and models in which this polypeptide 
# appears. 

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 up: <http://purl.uniprot.org/uniprot/>
SELECT ?mnet_label ?reac_label ?reac_eq ?MNXR (GROUP_CONCAT( ?cata_label; separator=\';\' ) AS ?complex )
FROM <https://rdf.metanetx.org/>
WHERE{
    ?pept mnx:peptXref up:P42588 .
    ?cata mnx:pept ?pept ;
          rdfs:label ?cata_label .
    ?gpr mnx:cata ?cata ;
         mnx:reac ?reac .
    ?reac rdfs:label ?reac_label ;
          rdfs:comment ?reac_eq .
    ?mnet mnx:gpr ?gpr ;
          rdfs:label ?mnet_label.
    OPTIONAL{ ?reac mnx:mnxr ?MNXR }
}`};

    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>

Tester ce script dans un nouvel onglet (attention, plusieurs graphiques nécessitent une clé API).
Comment insérer ce graphique dans ma page HTML ?

<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>
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     <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="# Given the protein with UniProt accession number *P42588* 
# (PAT_ECOLI, putrescine aminotransferase, EC 2.6.1.82) 
# retrieve all reactions and models in which this polypeptide 
# appears. 

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 up: &lt;http://purl.uniprot.org/uniprot/&gt;
SELECT ?mnet_label ?reac_label ?reac_eq ?MNXR (GROUP_CONCAT( ?cata_label; separator=&#039;;&#039; ) AS ?complex )
FROM &lt;https://rdf.metanetx.org/&gt;
WHERE{
    ?pept mnx:peptXref up:P42588 .
    ?cata mnx:pept ?pept ;
          rdfs:label ?cata_label .
    ?gpr mnx:cata ?cata ;
         mnx:reac ?reac .
    ?reac rdfs:label ?reac_label ;
          rdfs:comment ?reac_eq .
    ?mnet mnx:gpr ?gpr ;
          rdfs:label ?mnet_label.
    OPTIONAL{ ?reac mnx:mnxr ?MNXR }
}"
    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='fr'
   />

<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("""
    # Given the protein with UniProt accession number *P42588* 
# (PAT_ECOLI, putrescine aminotransferase, EC 2.6.1.82) 
# retrieve all reactions and models in which this polypeptide 
# appears. 

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 up: <http://purl.uniprot.org/uniprot/>
SELECT ?mnet_label ?reac_label ?reac_eq ?MNXR (GROUP_CONCAT( ?cata_label; separator=';' ) AS ?complex )
FROM <https://rdf.metanetx.org/>
WHERE{
    ?pept mnx:peptXref up:P42588 .
    ?cata mnx:pept ?pept ;
          rdfs:label ?cata_label .
    ?gpr mnx:cata ?cata ;
         mnx:reac ?reac .
    ?reac rdfs:label ?reac_label ;
          rdfs:comment ?reac_eq .
    ?mnet mnx:gpr ?gpr ;
          rdfs:label ?mnet_label.
    OPTIONAL{ ?reac mnx:mnxr ?MNXR }
}""")
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 <- "# Given the protein with UniProt accession number *P42588* 
# (PAT_ECOLI, putrescine aminotransferase, EC 2.6.1.82) 
# retrieve all reactions and models in which this polypeptide 
# appears. 

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 up: <http://purl.uniprot.org/uniprot/>
SELECT ?mnet_label ?reac_label ?reac_eq ?MNXR (GROUP_CONCAT( ?cata_label; separator=';' ) AS ?complex )
FROM <https://rdf.metanetx.org/>
WHERE{
    ?pept mnx:peptXref up:P42588 .
    ?cata mnx:pept ?pept ;
          rdfs:label ?cata_label .
    ?gpr mnx:cata ?cata ;
         mnx:reac ?reac .
    ?reac rdfs:label ?reac_label ;
          rdfs:comment ?reac_eq .
    ?mnet mnx:gpr ?gpr ;
          rdfs:label ?mnet_label.
    OPTIONAL{ ?reac mnx:mnxr ?MNXR }
}"
# 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
# Given the protein with UniProt accession number *P42588* 
# (PAT_ECOLI, putrescine aminotransferase, EC 2.6.1.82) 
# retrieve all reactions and models in which this polypeptide 
# appears. 

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 up: <http://purl.uniprot.org/uniprot/>
SELECT ?mnet_label ?reac_label ?reac_eq ?MNXR (GROUP_CONCAT( ?cata_label; separator=';' ) AS ?complex )
FROM <https://rdf.metanetx.org/>
WHERE{
    ?pept mnx:peptXref up:P42588 .
    ?cata mnx:pept ?pept ;
          rdfs:label ?cata_label .
    ?gpr mnx:cata ?cata ;
         mnx:reac ?reac .
    ?reac rdfs:label ?reac_label ;
          rdfs:comment ?reac_eq .
    ?mnet mnx:gpr ?gpr ;
          rdfs:label ?mnet_label.
    OPTIONAL{ ?reac mnx:mnxr ?MNXR }
}
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 = ['# Given the protein with UniProt accession number *P42588*  '...
'# (PAT_ECOLI, putrescine aminotransferase, EC 2.6.1.82)  '...
'# retrieve all reactions and models in which this polypeptide  '...
'# appears.  '...
' '...
'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 up: <http://purl.uniprot.org/uniprot/> '...
'SELECT ?mnet_label ?reac_label ?reac_eq ?MNXR (GROUP_CONCAT( ?cata_label; separator=';' ) AS ?complex ) '...
'FROM <https://rdf.metanetx.org/> '...
'WHERE{ '...
'    ?pept mnx:peptXref up:P42588 . '...
'    ?cata mnx:pept ?pept ; '...
'          rdfs:label ?cata_label . '...
'    ?gpr mnx:cata ?cata ; '...
'         mnx:reac ?reac . '...
'    ?reac rdfs:label ?reac_label ; '...
'          rdfs:comment ?reac_eq . '...
'    ?mnet mnx:gpr ?gpr ; '...
'          rdfs:label ?mnet_label. '...
'    OPTIONAL{ ?reac mnx:mnxr ?MNXR } '...
'} '];

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
# Given the protein with UniProt accession number *P42588* 
# (PAT_ECOLI, putrescine aminotransferase, EC 2.6.1.82) 
# retrieve all reactions and models in which this polypeptide 
# appears. 

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 up: <http://purl.uniprot.org/uniprot/>
SELECT ?mnet_label ?reac_label ?reac_eq ?MNXR (GROUP_CONCAT( ?cata_label; separator=';' ) AS ?complex )
FROM <https://rdf.metanetx.org/>
WHERE{
    ?pept mnx:peptXref up:P42588 .
    ?cata mnx:pept ?pept ;
          rdfs:label ?cata_label .
    ?gpr mnx:cata ?cata ;
         mnx:reac ?reac .
    ?reac rdfs:label ?reac_label ;
          rdfs:comment ?reac_eq .
    ?mnet mnx:gpr ?gpr ;
          rdfs:label ?mnet_label.
    OPTIONAL{ ?reac mnx:mnxr ?MNXR }
}
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  = "# Given the protein with UniProt accession number *P42588*  \n"
                    + "# (PAT_ECOLI, putrescine aminotransferase, EC 2.6.1.82)  \n"
                    + "# retrieve all reactions and models in which this polypeptide  \n"
                    + "# appears.  \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 up: <http://purl.uniprot.org/uniprot/> \n"
                    + "SELECT ?mnet_label ?reac_label ?reac_eq ?MNXR (GROUP_CONCAT( ?cata_label; separator=\';\' ) AS ?complex ) \n"
                    + "FROM <https://rdf.metanetx.org/> \n"
                    + "WHERE{ \n"
                    + "    ?pept mnx:peptXref up:P42588 . \n"
                    + "    ?cata mnx:pept ?pept ; \n"
                    + "          rdfs:label ?cata_label . \n"
                    + "    ?gpr mnx:cata ?cata ; \n"
                    + "         mnx:reac ?reac . \n"
                    + "    ?reac rdfs:label ?reac_label ; \n"
                    + "          rdfs:comment ?reac_eq . \n"
                    + "    ?mnet mnx:gpr ?gpr ; \n"
                    + "          rdfs:label ?mnet_label. \n"
                    + "    OPTIONAL{ ?reac mnx:mnxr ?MNXR } \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

Tableau

Liste

Réutilisez ces données dans votre code

Requête, point d'accès et code permettant de réutiliser les mêmes données