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  1. Datasets
  2. Wikidata
  3. Queries
  4. Variants associated with positive treatment response to anti-cancer drug with provenance information
Variants associated with positive treatment response to anti-cancer drug with provenance information

Reuse these data in your code

Query, endpoint and code for reusing the same data
https://query.wikidata.org/sparql
PREFIX bd: <http://www.bigdata.com/rdf#> 
PREFIX p: <http://www.wikidata.org/prop/> 
PREFIX pq: <http://www.wikidata.org/prop/qualifier/> 
PREFIX pr: <http://www.wikidata.org/prop/reference/> 
PREFIX prov: <http://www.w3.org/ns/prov#> 
PREFIX ps: <http://www.wikidata.org/prop/statement/> 
PREFIX wd: <http://www.wikidata.org/entity/> 
PREFIX wdt: <http://www.wikidata.org/prop/direct/> 
PREFIX wikibase: <http://wikiba.se/ontology#> 

SELECT DISTINCT 
?diseaseLabel ?drugLabel ?variantLabel  ?geneLabel 
?determinationMethodLabel ?ratingLabel 
(CONCAT("https://www.ncbi.nlm.nih.gov/pubmed/?term=",?pubMedID) 
 as ?ArticlePubMed)
WHERE {
  # Find all the disease that are cancers
  ?disease wdt:P31 wd:Q12136 ;
           wdt:P279+ wd:Q12078 .
  
  # Find the drugs treating cancer
  ?drug wdt:P2175 ?disease .
  
  # Find the genetic variants associated with a better response to the treatment
  ?therapeuticPredictor ps:P3354 ?drug ;
          # Find metadata regarding the positive prediction response
                        pq:P4271 ?rating ;
                        pq:P459 ?determinationMethod .
  
  # Find the variant associated with the response predictor
  # Find the associated gene
  ?variant p:P3354 ?therapeuticPredictor ;
           wdt:P3433 ?gene .
  
  # Find the provenance of the predictor
  ?therapeuticPredictor prov:wasDerivedFrom ?wasDerivedFrom .
  ?wasDerivedFrom pr:P248 ?statedIn .
  ?statedIn wdt:P698 ?pubMedID  .   

  SERVICE wikibase:label {
    bd:serviceParam wikibase:language "en,fr" .
  }
} 
limit 10
Howto write a query SPARQL? (in French) 
{{#sparql:PREFIX bd: <http://www.bigdata.com/rdf#> 
PREFIX p: <http://www.wikidata.org/prop/> 
PREFIX pq: <http://www.wikidata.org/prop/qualifier/> 
PREFIX pr: <http://www.wikidata.org/prop/reference/> 
PREFIX prov: <http://www.w3.org/ns/prov#> 
PREFIX ps: <http://www.wikidata.org/prop/statement/> 
PREFIX wd: <http://www.wikidata.org/entity/> 
PREFIX wdt: <http://www.wikidata.org/prop/direct/> 
PREFIX wikibase: <http://wikiba.se/ontology#> 

SELECT DISTINCT 
?diseaseLabel ?drugLabel ?variantLabel  ?geneLabel 
?determinationMethodLabel ?ratingLabel 
(CONCAT("https://www.ncbi.nlm.nih.gov/pubmed/?term=",?pubMedID) 
 as ?ArticlePubMed)
WHERE {
  # Find all the disease that are cancers
  ?disease wdt:P31 wd:Q12136 ;
           wdt:P279+ wd:Q12078 .
  
  # Find the drugs treating cancer
  ?drug wdt:P2175 ?disease .
  
  # Find the genetic variants associated with a better response to the treatment
  ?therapeuticPredictor ps:P3354 ?drug ;
          # Find metadata regarding the positive prediction response
                        pq:P4271 ?rating ;
                        pq:P459 ?determinationMethod .
  
  # Find the variant associated with the response predictor
  # Find the associated gene
  ?variant p:P3354 ?therapeuticPredictor ;
           wdt:P3433 ?gene .
  
  # Find the provenance of the predictor
  ?therapeuticPredictor prov:wasDerivedFrom ?wasDerivedFrom .
  ?wasDerivedFrom pr:P248 ?statedIn .
  ?statedIn wdt:P698 ?pubMedID  .   

  SERVICE wikibase:label {
    bd:serviceParam wikibase:language "en,fr" .
  }
} 
limit 10
| 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#> 
PREFIX p: <http://www.wikidata.org/prop/> 
PREFIX pq: <http://www.wikidata.org/prop/qualifier/> 
PREFIX pr: <http://www.wikidata.org/prop/reference/> 
PREFIX prov: <http://www.w3.org/ns/prov#> 
PREFIX ps: <http://www.wikidata.org/prop/statement/> 
PREFIX wd: <http://www.wikidata.org/entity/> 
PREFIX wdt: <http://www.wikidata.org/prop/direct/> 
PREFIX wikibase: <http://wikiba.se/ontology#> 

SELECT DISTINCT 
?diseaseLabel ?drugLabel ?variantLabel  ?geneLabel 
?determinationMethodLabel ?ratingLabel 
(CONCAT(\"https://www.ncbi.nlm.nih.gov/pubmed/?term=\",?pubMedID) 
 as ?ArticlePubMed)
WHERE {
  # Find all the disease that are cancers
  ?disease wdt:P31 wd:Q12136 ;
           wdt:P279+ wd:Q12078 .
  
  # Find the drugs treating cancer
  ?drug wdt:P2175 ?disease .
  
  # Find the genetic variants associated with a better response to the treatment
  ?therapeuticPredictor ps:P3354 ?drug ;
          # Find metadata regarding the positive prediction response
                        pq:P4271 ?rating ;
                        pq:P459 ?determinationMethod .
  
  # Find the variant associated with the response predictor
  # Find the associated gene
  ?variant p:P3354 ?therapeuticPredictor ;
           wdt:P3433 ?gene .
  
  # Find the provenance of the predictor
  ?therapeuticPredictor prov:wasDerivedFrom ?wasDerivedFrom .
  ?wasDerivedFrom pr:P248 ?statedIn .
  ?statedIn wdt:P698 ?pubMedID  .   

  SERVICE wikibase:label {
    bd:serviceParam wikibase:language \"en,fr\" .
  }
} 
limit 10`;

   // $('#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://query.wikidata.org/sparql");
    var params = {query:`PREFIX bd: <http://www.bigdata.com/rdf#> 
PREFIX p: <http://www.wikidata.org/prop/> 
PREFIX pq: <http://www.wikidata.org/prop/qualifier/> 
PREFIX pr: <http://www.wikidata.org/prop/reference/> 
PREFIX prov: <http://www.w3.org/ns/prov#> 
PREFIX ps: <http://www.wikidata.org/prop/statement/> 
PREFIX wd: <http://www.wikidata.org/entity/> 
PREFIX wdt: <http://www.wikidata.org/prop/direct/> 
PREFIX wikibase: <http://wikiba.se/ontology#> 

SELECT DISTINCT 
?diseaseLabel ?drugLabel ?variantLabel  ?geneLabel 
?determinationMethodLabel ?ratingLabel 
(CONCAT(\"https://www.ncbi.nlm.nih.gov/pubmed/?term=\",?pubMedID) 
 as ?ArticlePubMed)
WHERE {
  # Find all the disease that are cancers
  ?disease wdt:P31 wd:Q12136 ;
           wdt:P279+ wd:Q12078 .
  
  # Find the drugs treating cancer
  ?drug wdt:P2175 ?disease .
  
  # Find the genetic variants associated with a better response to the treatment
  ?therapeuticPredictor ps:P3354 ?drug ;
          # Find metadata regarding the positive prediction response
                        pq:P4271 ?rating ;
                        pq:P459 ?determinationMethod .
  
  # Find the variant associated with the response predictor
  # Find the associated gene
  ?variant p:P3354 ?therapeuticPredictor ;
           wdt:P3433 ?gene .
  
  # Find the provenance of the predictor
  ?therapeuticPredictor prov:wasDerivedFrom ?wasDerivedFrom .
  ?wasDerivedFrom pr:P248 ?statedIn .
  ?statedIn wdt:P698 ?pubMedID  .   

  SERVICE wikibase:label {
    bd:serviceParam wikibase:language \"en,fr\" .
  }
} 
limit 10`};

    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://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: &lt;http://www.bigdata.com/rdf#&gt; 
PREFIX p: &lt;http://www.wikidata.org/prop/&gt; 
PREFIX pq: &lt;http://www.wikidata.org/prop/qualifier/&gt; 
PREFIX pr: &lt;http://www.wikidata.org/prop/reference/&gt; 
PREFIX prov: &lt;http://www.w3.org/ns/prov#&gt; 
PREFIX ps: &lt;http://www.wikidata.org/prop/statement/&gt; 
PREFIX wd: &lt;http://www.wikidata.org/entity/&gt; 
PREFIX wdt: &lt;http://www.wikidata.org/prop/direct/&gt; 
PREFIX wikibase: &lt;http://wikiba.se/ontology#&gt; 

SELECT DISTINCT 
?diseaseLabel ?drugLabel ?variantLabel  ?geneLabel 
?determinationMethodLabel ?ratingLabel 
(CONCAT(&quot;https://www.ncbi.nlm.nih.gov/pubmed/?term=&quot;,?pubMedID) 
 as ?ArticlePubMed)
WHERE {
  # Find all the disease that are cancers
  ?disease wdt:P31 wd:Q12136 ;
           wdt:P279+ wd:Q12078 .
  
  # Find the drugs treating cancer
  ?drug wdt:P2175 ?disease .
  
  # Find the genetic variants associated with a better response to the treatment
  ?therapeuticPredictor ps:P3354 ?drug ;
          # Find metadata regarding the positive prediction response
                        pq:P4271 ?rating ;
                        pq:P459 ?determinationMethod .
  
  # Find the variant associated with the response predictor
  # Find the associated gene
  ?variant p:P3354 ?therapeuticPredictor ;
           wdt:P3433 ?gene .
  
  # Find the provenance of the predictor
  ?therapeuticPredictor prov:wasDerivedFrom ?wasDerivedFrom .
  ?wasDerivedFrom pr:P248 ?statedIn .
  ?statedIn wdt:P698 ?pubMedID  .   

  SERVICE wikibase:label {
    bd:serviceParam wikibase:language &quot;en,fr&quot; .
  }
} 
limit 10"
    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://query.wikidata.org/sparql")
sparql.setQuery("""
    PREFIX bd: <http://www.bigdata.com/rdf#> 
PREFIX p: <http://www.wikidata.org/prop/> 
PREFIX pq: <http://www.wikidata.org/prop/qualifier/> 
PREFIX pr: <http://www.wikidata.org/prop/reference/> 
PREFIX prov: <http://www.w3.org/ns/prov#> 
PREFIX ps: <http://www.wikidata.org/prop/statement/> 
PREFIX wd: <http://www.wikidata.org/entity/> 
PREFIX wdt: <http://www.wikidata.org/prop/direct/> 
PREFIX wikibase: <http://wikiba.se/ontology#> 

SELECT DISTINCT 
?diseaseLabel ?drugLabel ?variantLabel  ?geneLabel 
?determinationMethodLabel ?ratingLabel 
(CONCAT("https://www.ncbi.nlm.nih.gov/pubmed/?term=",?pubMedID) 
 as ?ArticlePubMed)
WHERE {
  # Find all the disease that are cancers
  ?disease wdt:P31 wd:Q12136 ;
           wdt:P279+ wd:Q12078 .
  
  # Find the drugs treating cancer
  ?drug wdt:P2175 ?disease .
  
  # Find the genetic variants associated with a better response to the treatment
  ?therapeuticPredictor ps:P3354 ?drug ;
          # Find metadata regarding the positive prediction response
                        pq:P4271 ?rating ;
                        pq:P459 ?determinationMethod .
  
  # Find the variant associated with the response predictor
  # Find the associated gene
  ?variant p:P3354 ?therapeuticPredictor ;
           wdt:P3433 ?gene .
  
  # Find the provenance of the predictor
  ?therapeuticPredictor prov:wasDerivedFrom ?wasDerivedFrom .
  ?wasDerivedFrom pr:P248 ?statedIn .
  ?statedIn wdt:P698 ?pubMedID  .   

  SERVICE wikibase:label {
    bd:serviceParam wikibase:language "en,fr" .
  }
} 
limit 10""")
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 p: <http://www.wikidata.org/prop/> 
PREFIX pq: <http://www.wikidata.org/prop/qualifier/> 
PREFIX pr: <http://www.wikidata.org/prop/reference/> 
PREFIX prov: <http://www.w3.org/ns/prov#> 
PREFIX ps: <http://www.wikidata.org/prop/statement/> 
PREFIX wd: <http://www.wikidata.org/entity/> 
PREFIX wdt: <http://www.wikidata.org/prop/direct/> 
PREFIX wikibase: <http://wikiba.se/ontology#> 

SELECT DISTINCT 
?diseaseLabel ?drugLabel ?variantLabel  ?geneLabel 
?determinationMethodLabel ?ratingLabel 
(CONCAT("https://www.ncbi.nlm.nih.gov/pubmed/?term=",?pubMedID) 
 as ?ArticlePubMed)
WHERE {
  # Find all the disease that are cancers
  ?disease wdt:P31 wd:Q12136 ;
           wdt:P279+ wd:Q12078 .
  
  # Find the drugs treating cancer
  ?drug wdt:P2175 ?disease .
  
  # Find the genetic variants associated with a better response to the treatment
  ?therapeuticPredictor ps:P3354 ?drug ;
          # Find metadata regarding the positive prediction response
                        pq:P4271 ?rating ;
                        pq:P459 ?determinationMethod .
  
  # Find the variant associated with the response predictor
  # Find the associated gene
  ?variant p:P3354 ?therapeuticPredictor ;
           wdt:P3433 ?gene .
  
  # Find the provenance of the predictor
  ?therapeuticPredictor prov:wasDerivedFrom ?wasDerivedFrom .
  ?wasDerivedFrom pr:P248 ?statedIn .
  ?statedIn wdt:P698 ?pubMedID  .   

  SERVICE wikibase:label {
    bd:serviceParam wikibase:language "en,fr" .
  }
} 
limit 10"
# 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 bd: <http://www.bigdata.com/rdf#> 
PREFIX p: <http://www.wikidata.org/prop/> 
PREFIX pq: <http://www.wikidata.org/prop/qualifier/> 
PREFIX pr: <http://www.wikidata.org/prop/reference/> 
PREFIX prov: <http://www.w3.org/ns/prov#> 
PREFIX ps: <http://www.wikidata.org/prop/statement/> 
PREFIX wd: <http://www.wikidata.org/entity/> 
PREFIX wdt: <http://www.wikidata.org/prop/direct/> 
PREFIX wikibase: <http://wikiba.se/ontology#> 

SELECT DISTINCT 
?diseaseLabel ?drugLabel ?variantLabel  ?geneLabel 
?determinationMethodLabel ?ratingLabel 
(CONCAT("https://www.ncbi.nlm.nih.gov/pubmed/?term=",?pubMedID) 
 as ?ArticlePubMed)
WHERE {
  # Find all the disease that are cancers
  ?disease wdt:P31 wd:Q12136 ;
           wdt:P279+ wd:Q12078 .
  
  # Find the drugs treating cancer
  ?drug wdt:P2175 ?disease .
  
  # Find the genetic variants associated with a better response to the treatment
  ?therapeuticPredictor ps:P3354 ?drug ;
          # Find metadata regarding the positive prediction response
                        pq:P4271 ?rating ;
                        pq:P459 ?determinationMethod .
  
  # Find the variant associated with the response predictor
  # Find the associated gene
  ?variant p:P3354 ?therapeuticPredictor ;
           wdt:P3433 ?gene .
  
  # Find the provenance of the predictor
  ?therapeuticPredictor prov:wasDerivedFrom ?wasDerivedFrom .
  ?wasDerivedFrom pr:P248 ?statedIn .
  ?statedIn wdt:P698 ?pubMedID  .   

  SERVICE wikibase:label {
    bd:serviceParam wikibase:language "en,fr" .
  }
} 
limit 10
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 p: <http://www.wikidata.org/prop/>  '...
'PREFIX pq: <http://www.wikidata.org/prop/qualifier/>  '...
'PREFIX pr: <http://www.wikidata.org/prop/reference/>  '...
'PREFIX prov: <http://www.w3.org/ns/prov#>  '...
'PREFIX ps: <http://www.wikidata.org/prop/statement/>  '...
'PREFIX wd: <http://www.wikidata.org/entity/>  '...
'PREFIX wdt: <http://www.wikidata.org/prop/direct/>  '...
'PREFIX wikibase: <http://wikiba.se/ontology#>  '...
' '...
'SELECT DISTINCT  '...
'?diseaseLabel ?drugLabel ?variantLabel  ?geneLabel  '...
'?determinationMethodLabel ?ratingLabel  '...
'(CONCAT("https://www.ncbi.nlm.nih.gov/pubmed/?term=",?pubMedID)  '...
' as ?ArticlePubMed) '...
'WHERE { '...
'  # Find all the disease that are cancers '...
'  ?disease wdt:P31 wd:Q12136 ; '...
'           wdt:P279+ wd:Q12078 . '...
'   '...
'  # Find the drugs treating cancer '...
'  ?drug wdt:P2175 ?disease . '...
'   '...
'  # Find the genetic variants associated with a better response to the treatment '...
'  ?therapeuticPredictor ps:P3354 ?drug ; '...
'          # Find metadata regarding the positive prediction response '...
'                        pq:P4271 ?rating ; '...
'                        pq:P459 ?determinationMethod . '...
'   '...
'  # Find the variant associated with the response predictor '...
'  # Find the associated gene '...
'  ?variant p:P3354 ?therapeuticPredictor ; '...
'           wdt:P3433 ?gene . '...
'   '...
'  # Find the provenance of the predictor '...
'  ?therapeuticPredictor prov:wasDerivedFrom ?wasDerivedFrom . '...
'  ?wasDerivedFrom pr:P248 ?statedIn . '...
'  ?statedIn wdt:P698 ?pubMedID  .    '...
' '...
'  SERVICE wikibase:label { '...
'    bd:serviceParam wikibase:language "en,fr" . '...
'  } '...
'}  '...
'limit 10 '];

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 p: <http://www.wikidata.org/prop/> 
PREFIX pq: <http://www.wikidata.org/prop/qualifier/> 
PREFIX pr: <http://www.wikidata.org/prop/reference/> 
PREFIX prov: <http://www.w3.org/ns/prov#> 
PREFIX ps: <http://www.wikidata.org/prop/statement/> 
PREFIX wd: <http://www.wikidata.org/entity/> 
PREFIX wdt: <http://www.wikidata.org/prop/direct/> 
PREFIX wikibase: <http://wikiba.se/ontology#> 

SELECT DISTINCT 
?diseaseLabel ?drugLabel ?variantLabel  ?geneLabel 
?determinationMethodLabel ?ratingLabel 
(CONCAT("https://www.ncbi.nlm.nih.gov/pubmed/?term=",?pubMedID) 
 as ?ArticlePubMed)
WHERE {
  # Find all the disease that are cancers
  ?disease wdt:P31 wd:Q12136 ;
           wdt:P279+ wd:Q12078 .
  
  # Find the drugs treating cancer
  ?drug wdt:P2175 ?disease .
  
  # Find the genetic variants associated with a better response to the treatment
  ?therapeuticPredictor ps:P3354 ?drug ;
          # Find metadata regarding the positive prediction response
                        pq:P4271 ?rating ;
                        pq:P459 ?determinationMethod .
  
  # Find the variant associated with the response predictor
  # Find the associated gene
  ?variant p:P3354 ?therapeuticPredictor ;
           wdt:P3433 ?gene .
  
  # Find the provenance of the predictor
  ?therapeuticPredictor prov:wasDerivedFrom ?wasDerivedFrom .
  ?wasDerivedFrom pr:P248 ?statedIn .
  ?statedIn wdt:P698 ?pubMedID  .   

  SERVICE wikibase:label {
    bd:serviceParam wikibase:language "en,fr" .
  }
} 
limit 10
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 bd: <http://www.bigdata.com/rdf#>  \n"
                    + "PREFIX p: <http://www.wikidata.org/prop/>  \n"
                    + "PREFIX pq: <http://www.wikidata.org/prop/qualifier/>  \n"
                    + "PREFIX pr: <http://www.wikidata.org/prop/reference/>  \n"
                    + "PREFIX prov: <http://www.w3.org/ns/prov#>  \n"
                    + "PREFIX ps: <http://www.wikidata.org/prop/statement/>  \n"
                    + "PREFIX wd: <http://www.wikidata.org/entity/>  \n"
                    + "PREFIX wdt: <http://www.wikidata.org/prop/direct/>  \n"
                    + "PREFIX wikibase: <http://wikiba.se/ontology#>  \n"
                    + " \n"
                    + "SELECT DISTINCT  \n"
                    + "?diseaseLabel ?drugLabel ?variantLabel  ?geneLabel  \n"
                    + "?determinationMethodLabel ?ratingLabel  \n"
                    + "(CONCAT(\"https://www.ncbi.nlm.nih.gov/pubmed/?term=\",?pubMedID)  \n"
                    + " as ?ArticlePubMed) \n"
                    + "WHERE { \n"
                    + "  # Find all the disease that are cancers \n"
                    + "  ?disease wdt:P31 wd:Q12136 ; \n"
                    + "           wdt:P279+ wd:Q12078 . \n"
                    + "   \n"
                    + "  # Find the drugs treating cancer \n"
                    + "  ?drug wdt:P2175 ?disease . \n"
                    + "   \n"
                    + "  # Find the genetic variants associated with a better response to the treatment \n"
                    + "  ?therapeuticPredictor ps:P3354 ?drug ; \n"
                    + "          # Find metadata regarding the positive prediction response \n"
                    + "                        pq:P4271 ?rating ; \n"
                    + "                        pq:P459 ?determinationMethod . \n"
                    + "   \n"
                    + "  # Find the variant associated with the response predictor \n"
                    + "  # Find the associated gene \n"
                    + "  ?variant p:P3354 ?therapeuticPredictor ; \n"
                    + "           wdt:P3433 ?gene . \n"
                    + "   \n"
                    + "  # Find the provenance of the predictor \n"
                    + "  ?therapeuticPredictor prov:wasDerivedFrom ?wasDerivedFrom . \n"
                    + "  ?wasDerivedFrom pr:P248 ?statedIn . \n"
                    + "  ?statedIn wdt:P698 ?pubMedID  .    \n"
                    + " \n"
                    + "  SERVICE wikibase:label { \n"
                    + "    bd:serviceParam wikibase:language \"en,fr\" . \n"
                    + "  } \n"
                    + "}  \n"
                    + "limit 10 \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