requête SPARQL: Human genes updated this week

Karima Rafes

Human genes updated this week

Sample query

Réutilisez ces données dans votre code

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

Point d'accès :

https://query.wikidata.org/sparql

Requête :

PREFIX schema: <http://schema.org/>
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>

SELECT DISTINCT ?item ?ncbi_gene ?date_modified
WHERE
{
	?item wdt:P351 ?ncbi_gene ;
          wdt:P703 wd:Q15978631 ;
          schema:dateModified ?date_modified .
    BIND (now() - ?date_modified as ?date_range)
    FILTER (?date_range < 8)
}

Comment écrire une requête SPARQL ?

{{#sparql:PREFIX schema: <http://schema.org/>
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>

SELECT DISTINCT ?item ?ncbi_gene ?date_modified
WHERE
{
	?item wdt:P351 ?ncbi_gene ;
          wdt:P703 wd:Q15978631 ;
          schema:dateModified ?date_modified .
    BIND (now() - ?date_modified as ?date_range)
    FILTER (?date_range < 8)
}
| endpoint = https://query.wikidata.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://query.wikidata.org/sparql";
    var query = `PREFIX schema: <http://schema.org/>
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>

SELECT DISTINCT ?item ?ncbi_gene ?date_modified
WHERE
{
	?item wdt:P351 ?ncbi_gene ;
          wdt:P703 wd:Q15978631 ;
          schema:dateModified ?date_modified .
    BIND (now() - ?date_modified as ?date_range)
    FILTER (?date_range < 8)
}`;

   // $('#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://query.wikidata.org/sparql");
    var params = {query:`PREFIX schema: <http://schema.org/>
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>

SELECT DISTINCT ?item ?ncbi_gene ?date_modified
WHERE
{
	?item wdt:P351 ?ncbi_gene ;
          wdt:P703 wd:Q15978631 ;
          schema:dateModified ?date_modified .
    BIND (now() - ?date_modified as ?date_range)
    FILTER (?date_range < 8)
}`};

    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>
     <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://query.wikidata.org/sparql"
   data-sgvizler-query="PREFIX schema: &lt;http://schema.org/&gt;
PREFIX wd: &lt;http://www.wikidata.org/entity/&gt;
PREFIX wdt: &lt;http://www.wikidata.org/prop/direct/&gt;

SELECT DISTINCT ?item ?ncbi_gene ?date_modified
WHERE
{
	?item wdt:P351 ?ncbi_gene ;
          wdt:P703 wd:Q15978631 ;
          schema:dateModified ?date_modified .
    BIND (now() - ?date_modified as ?date_range)
    FILTER (?date_range &lt; 8)
}"
    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://query.wikidata.org/sparql")
sparql.setQuery("""
    PREFIX schema: <http://schema.org/>
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>

SELECT DISTINCT ?item ?ncbi_gene ?date_modified
WHERE
{
	?item wdt:P351 ?ncbi_gene ;
          wdt:P703 wd:Q15978631 ;
          schema:dateModified ?date_modified .
    BIND (now() - ?date_modified as ?date_range)
    FILTER (?date_range < 8)
}""")
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://query.wikidata.org/sparql"
# create query statement
    query <- "PREFIX schema: <http://schema.org/>
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>

SELECT DISTINCT ?item ?ncbi_gene ?date_modified
WHERE
{
	?item wdt:P351 ?ncbi_gene ;
          wdt:P703 wd:Q15978631 ;
          schema:dateModified ?date_modified .
    BIND (now() - ?date_modified as ?date_range)
    FILTER (?date_range < 8)
}"
# 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://query.wikidata.org/sparql"
sparql = <<-EOT
PREFIX schema: <http://schema.org/>
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>

SELECT DISTINCT ?item ?ncbi_gene ?date_modified
WHERE
{
	?item wdt:P351 ?ncbi_gene ;
          wdt:P703 wd:Q15978631 ;
          schema:dateModified ?date_modified .
    BIND (now() - ?date_modified as ?date_range)
    FILTER (?date_range < 8)
}
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://query.wikidata.org/sparql';

query = ['PREFIX schema: <http://schema.org/> '...
'PREFIX wd: <http://www.wikidata.org/entity/> '...
'PREFIX wdt: <http://www.wikidata.org/prop/direct/> '...
' '...
'SELECT DISTINCT ?item ?ncbi_gene ?date_modified '...
'WHERE '...
'{ '...
'	?item wdt:P351 ?ncbi_gene ; '...
'          wdt:P703 wd:Q15978631 ; '...
'          schema:dateModified ?date_modified . '...
'    BIND (now() - ?date_modified as ?date_range) '...
'    FILTER (?date_range < 8) '...
'} '];

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://query.wikidata.org/sparql";
$sp_readonly = new SparqlClient();
$sp_readonly->setEndpointRead($endpoint);
$q = <<<EOD
PREFIX schema: <http://schema.org/>
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>

SELECT DISTINCT ?item ?ncbi_gene ?date_modified
WHERE
{
	?item wdt:P351 ?ncbi_gene ;
          wdt:P703 wd:Q15978631 ;
          schema:dateModified ?date_modified .
    BIND (now() - ?date_modified as ?date_range)
    FILTER (?date_range < 8)
}
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://query.wikidata.org/sparql");
            String querySelect  = "PREFIX schema: <http://schema.org/> \n"
                    + "PREFIX wd: <http://www.wikidata.org/entity/> \n"
                    + "PREFIX wdt: <http://www.wikidata.org/prop/direct/> \n"
                    + " \n"
                    + "SELECT DISTINCT ?item ?ncbi_gene ?date_modified \n"
                    + "WHERE \n"
                    + "{ \n"
                    + "	?item wdt:P351 ?ncbi_gene ; \n"
                    + "          wdt:P703 wd:Q15978631 ; \n"
                    + "          schema:dateModified ?date_modified . \n"
                    + "    BIND (now() - ?date_modified as ?date_range) \n"
                    + "    FILTER (?date_range < 8) \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