https://query.wikidata.org/sparql
PREFIX bd: <http://www.bigdata.com/rdf#>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wikibase: <http://wikiba.se/ontology#>
SELECT DISTINCT ?pathway ?pathwayLabel ?reactomeID WHERE {
?pathway wdt:P3937 ?reactomeID .
SERVICE wikibase:label {
bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en".
}
}
LIMIT 100
Howto write a query SPARQL? (in French)
{{#sparql:PREFIX bd: <http://www.bigdata.com/rdf#>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wikibase: <http://wikiba.se/ontology#>
SELECT DISTINCT ?pathway ?pathwayLabel ?reactomeID WHERE {
?pathway wdt:P3937 ?reactomeID .
SERVICE wikibase:label {
bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en".
}
}
LIMIT 100
| endpoint = https://query.wikidata.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://query.wikidata.org/sparql";
var query = "PREFIX bd: <http://www.bigdata.com/rdf#> \n\
PREFIX wdt: <http://www.wikidata.org/prop/direct/> \n\
PREFIX wikibase: <http://wikiba.se/ontology#> \n\
\n\
SELECT DISTINCT ?pathway ?pathwayLabel ?reactomeID WHERE {\n\
?pathway wdt:P3937 ?reactomeID .\n\
\n\
SERVICE wikibase:label { \n\
bd:serviceParam wikibase:language \"[AUTO_LANGUAGE],en\". \n\
}\n\
}\n\
LIMIT 100"
// $('#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);
$("body").append(JSON.stringify(bs) + "<hr/>");
});
}
</script>
</body>
</html>
Test this script in a new tab (Careful, several charts need a API key).
Howto insert this graph in my html page?
<html>
<head>
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.9.0/css/all.min.css">
<script
src="https://code.jquery.com/jquery-3.4.1.min.js"
integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="
crossorigin="anonymous"> </script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.7/umd/popper.min.js" integrity="sha384-UO2eT0CpHqdSJQ6hJty5KVphtPhzWj9WO1clHTMGa3JDZwrnQq4sF86dIHNDz0W1" crossorigin="anonymous"> </script>
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js" integrity="sha384-JjSmVgyd0p3pXB1rRibZUAYoIIy6OrQ6VrjIEaFf/nJGzIxFDsf4x0xIM+B07jRM" crossorigin="anonymous"> </script>
<script type="text/javascript" src="https://bordercloud.github.io/sgvizler2/sgvizler2/sgvizler2.js" defer> </script>
<script type="text/javascript" src="https://io.datascience-paris-saclay.fr/js/initExampleHTML.js" defer > </script>
</head>
<body style="margin:0;">
<div id="sgvzl_example_query"
data-sgvizler-endpoint="https://query.wikidata.org/sparql"
data-sgvizler-query="PREFIX bd: <http://www.bigdata.com/rdf#>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wikibase: <http://wikiba.se/ontology#>
SELECT DISTINCT ?pathway ?pathwayLabel ?reactomeID WHERE {
?pathway wdt:P3937 ?reactomeID .
SERVICE wikibase:label {
bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en".
}
}
LIMIT 100"
data-sgvizler-chart='bordercloud.visualization.DataTable'
data-sgvizler-chart-options=''
data-sgvizler-endpoint_output_format='json'
data-sgvizler-log='2'
style='width:100%; height:auto;' />
<script>
/*$(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 bd: <http://www.bigdata.com/rdf#>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wikibase: <http://wikiba.se/ontology#>
SELECT DISTINCT ?pathway ?pathwayLabel ?reactomeID WHERE {
?pathway wdt:P3937 ?reactomeID .
SERVICE wikibase:label {
bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en".
}
}
LIMIT 100""")
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 bd: <http://www.bigdata.com/rdf#>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wikibase: <http://wikiba.se/ontology#>
SELECT DISTINCT ?pathway ?pathwayLabel ?reactomeID WHERE {
?pathway wdt:P3937 ?reactomeID .
SERVICE wikibase:label {
bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en".
}
}
LIMIT 100"
# Step 2 - Use SPARQL package to submit query and save results to a data frame
qd <- SPARQL(endpoint,query)
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 bd: <http://www.bigdata.com/rdf#>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wikibase: <http://wikiba.se/ontology#>
SELECT DISTINCT ?pathway ?pathwayLabel ?reactomeID WHERE {
?pathway wdt:P3937 ?reactomeID .
SERVICE wikibase:label {
bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en".
}
}
LIMIT 100
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 bd: <http://www.bigdata.com/rdf#> '...
'PREFIX wdt: <http://www.wikidata.org/prop/direct/> '...
'PREFIX wikibase: <http://wikiba.se/ontology#> '...
' '...
'SELECT DISTINCT ?pathway ?pathwayLabel ?reactomeID WHERE { '...
' ?pathway wdt:P3937 ?reactomeID . '...
' '...
' SERVICE wikibase:label { '...
' bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". '...
' } '...
'} '...
'LIMIT 100 '];
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 bd: <http://www.bigdata.com/rdf#>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wikibase: <http://wikiba.se/ontology#>
SELECT DISTINCT ?pathway ?pathwayLabel ?reactomeID WHERE {
?pathway wdt:P3937 ?reactomeID .
SERVICE wikibase:label {
bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en".
}
}
LIMIT 100EOD;
$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.Endpoint;
import java.util.ArrayList;
import java.util.HashMap;
public class Main {
public static void main(String[] args) {
try {
Endpoint sp = new Endpoint("https://query.wikidata.org/sparql";, false);
String querySelect = 'PREFIX bd: <http://www.bigdata.com/rdf#> \n'
+ 'PREFIX wdt: <http://www.wikidata.org/prop/direct/> \n'
+ 'PREFIX wikibase: <http://wikiba.se/ontology#> \n'
+ ' \n'
+ 'SELECT DISTINCT ?pathway ?pathwayLabel ?reactomeID WHERE { \n'
+ ' ?pathway wdt:P3937 ?reactomeID . \n'
+ ' \n'
+ ' SERVICE wikibase:label { \n'
+ ' bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". \n'
+ ' } \n'
+ '} \n'
+ 'LIMIT 100 \n';
HashMap rs = sp.query(querySelect);
printResult(rs,30);
}catch(EndpointException eex) {
System.out.println(eex);
eex.printStackTrace();
}
}
public static void printResult(HashMap rs , int size) {
for (String variable : (ArrayList) rs.get("result").get("variables")) {
System.out.print(String.format("%-"+size+"."+size+"s", variable ) + " | ");
}
System.out.print("\n");
for (HashMap value : (ArrayList>) rs.get("result").get("rows")) {
//System.out.print(value);
/* for (String key : value.keySet()) {
System.out.println(value.get(key));
}*/
for (String variable : (ArrayList) rs.get("result").get("variables")) {
//System.out.println(value.get(variable));
System.out.print(String.format("%-"+size+"."+size+"s", value.get(variable)) + " | ");
}
System.out.print("\n");
}
}
}
Project Github BorderCloud/SPARQL-JAVA
Very soon !