SPARQL query: Find drugs for cancers that target genes related to cell proliferation

Karima Rafes

pharmacology biology cancer medication gene

Find drugs for cancers that target genes related to cell proliferation

Sample query

Reuse these data in your code

Query, endpoint and code for reusing the same data

Endpoint:

https://query.wikidata.org/sparql

Query:

PREFIX bd: <http://www.bigdata.com/rdf#>
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wikibase: <http://wikiba.se/ontology#>
#added before 2016-10

#cases where a drug physically interacts with the product of gene known to be genetically associated a disease
#these cases may show opportunities to repurpose a drug for a new disease
#See http://database.oxfordjournals.org/content/2016/baw083.long  and
#http://drug-repurposing.nationwidechildrens.org/search
#an example that was recently validated involved a new link between Metformin wd:Q19484 and cancer survival
#https://jamia.oxfordjournals.org/content/22/1/179
#currently set up to find drugs for cancers that target genes related to cell proliferation
#adapt by changing constraints (e.g. to 'heart disease' Q190805) or removing them
SELECT ?biological_process ?drugLabel ?geneLabel ?biological_processLabel ?diseaseLabel
WHERE {
  ?disease wdt:P31 wd:Q12136 .
  ?drug  wdt:P31 wd:Q12140 .
  ?gene wdt:P31 wd:Q7187 .

  ?biological_process wdt:P31 wd:Q2996394 .

  ?drug wdt:P129 ?gene_product .   # drug interacts with a gene_product
  ?gene wdt:P688 ?gene_product .  # gene_product (usually a protein) is a product of a gene (a region of DNA)
  ?disease	wdt:P2293 ?gene .    # genetic association between disease and gene
  ?disease wdt:P279*  wd:Q12078 .  # limit to cancers wd:Q12078 (the * operator runs up a transitive relation..)
  ?gene_product wdt:P682 ?biological_process . #add information about the GO biological processes that the gene is related to
  #limit to genes related to certain biological processes (and their sub-processes):
  		#apoptosis wd:Q14599311
  		#cell proliferation wd:Q14818032
   ?biological_process (wdt:P361|wdt:P279)* wd:Q14818032  # chain down subclass/part-of

    #uncomment the next line to find a subset of the known true positives (there are not a lot of them in here yet)
  #?disease wdt:P2176 ?drug . 	# disease is treated by a drug
  	SERVICE wikibase:label {
        bd:serviceParam wikibase:language "en" .
	}
}
LIMIT 1000

Howto write a query SPARQL? (in French)

{{#sparql:PREFIX bd: <http://www.bigdata.com/rdf#>
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wikibase: <http://wikiba.se/ontology#>
#added before 2016-10

#cases where a drug physically interacts with the product of gene known to be genetically associated a disease
#these cases may show opportunities to repurpose a drug for a new disease
#See http://database.oxfordjournals.org/content/2016/baw083.long  and
#http://drug-repurposing.nationwidechildrens.org/search
#an example that was recently validated involved a new link between Metformin wd:Q19484 and cancer survival
#https://jamia.oxfordjournals.org/content/22/1/179
#currently set up to find drugs for cancers that target genes related to cell proliferation
#adapt by changing constraints (e.g. to 'heart disease' Q190805) or removing them
SELECT ?biological_process ?drugLabel ?geneLabel ?biological_processLabel ?diseaseLabel
WHERE {
  ?disease wdt:P31 wd:Q12136 .
  ?drug  wdt:P31 wd:Q12140 .
  ?gene wdt:P31 wd:Q7187 .

  ?biological_process wdt:P31 wd:Q2996394 .

  ?drug wdt:P129 ?gene_product .   # drug interacts with a gene_product
  ?gene wdt:P688 ?gene_product .  # gene_product (usually a protein) is a product of a gene (a region of DNA)
  ?disease	wdt:P2293 ?gene .    # genetic association between disease and gene
  ?disease wdt:P279*  wd:Q12078 .  # limit to cancers wd:Q12078 (the * operator runs up a transitive relation..)
  ?gene_product wdt:P682 ?biological_process . #add information about the GO biological processes that the gene is related to
  #limit to genes related to certain biological processes (and their sub-processes):
  		#apoptosis wd:Q14599311
  		#cell proliferation wd:Q14818032
   ?biological_process (wdt:P361|wdt:P279)* wd:Q14818032  # chain down subclass/part-of

    #uncomment the next line to find a subset of the known true positives (there are not a lot of them in here yet)
  #?disease wdt:P2176 ?drug . 	# disease is treated by a drug
  	SERVICE wikibase:label {
        bd:serviceParam wikibase:language "en" .
	}
}
LIMIT 1000
| 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 wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wikibase: <http://wikiba.se/ontology#>
#added before 2016-10

#cases where a drug physically interacts with the product of gene known to be genetically associated a disease
#these cases may show opportunities to repurpose a drug for a new disease
#See http://database.oxfordjournals.org/content/2016/baw083.long  and
#http://drug-repurposing.nationwidechildrens.org/search
#an example that was recently validated involved a new link between Metformin wd:Q19484 and cancer survival
#https://jamia.oxfordjournals.org/content/22/1/179
#currently set up to find drugs for cancers that target genes related to cell proliferation
#adapt by changing constraints (e.g. to \'heart disease\' Q190805) or removing them
SELECT ?biological_process ?drugLabel ?geneLabel ?biological_processLabel ?diseaseLabel
WHERE {
  ?disease wdt:P31 wd:Q12136 .
  ?drug  wdt:P31 wd:Q12140 .
  ?gene wdt:P31 wd:Q7187 .

  ?biological_process wdt:P31 wd:Q2996394 .

  ?drug wdt:P129 ?gene_product .   # drug interacts with a gene_product
  ?gene wdt:P688 ?gene_product .  # gene_product (usually a protein) is a product of a gene (a region of DNA)
  ?disease	wdt:P2293 ?gene .    # genetic association between disease and gene
  ?disease wdt:P279*  wd:Q12078 .  # limit to cancers wd:Q12078 (the * operator runs up a transitive relation..)
  ?gene_product wdt:P682 ?biological_process . #add information about the GO biological processes that the gene is related to
  #limit to genes related to certain biological processes (and their sub-processes):
  		#apoptosis wd:Q14599311
  		#cell proliferation wd:Q14818032
   ?biological_process (wdt:P361|wdt:P279)* wd:Q14818032  # chain down subclass/part-of

    #uncomment the next line to find a subset of the known true positives (there are not a lot of them in here yet)
  #?disease wdt:P2176 ?drug . 	# disease is treated by a drug
  	SERVICE wikibase:label {
        bd:serviceParam wikibase:language \"en\" .
	}
}
LIMIT 1000`;

   // $('#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 wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wikibase: <http://wikiba.se/ontology#>
#added before 2016-10

#cases where a drug physically interacts with the product of gene known to be genetically associated a disease
#these cases may show opportunities to repurpose a drug for a new disease
#See http://database.oxfordjournals.org/content/2016/baw083.long  and
#http://drug-repurposing.nationwidechildrens.org/search
#an example that was recently validated involved a new link between Metformin wd:Q19484 and cancer survival
#https://jamia.oxfordjournals.org/content/22/1/179
#currently set up to find drugs for cancers that target genes related to cell proliferation
#adapt by changing constraints (e.g. to \'heart disease\' Q190805) or removing them
SELECT ?biological_process ?drugLabel ?geneLabel ?biological_processLabel ?diseaseLabel
WHERE {
  ?disease wdt:P31 wd:Q12136 .
  ?drug  wdt:P31 wd:Q12140 .
  ?gene wdt:P31 wd:Q7187 .

  ?biological_process wdt:P31 wd:Q2996394 .

  ?drug wdt:P129 ?gene_product .   # drug interacts with a gene_product
  ?gene wdt:P688 ?gene_product .  # gene_product (usually a protein) is a product of a gene (a region of DNA)
  ?disease	wdt:P2293 ?gene .    # genetic association between disease and gene
  ?disease wdt:P279*  wd:Q12078 .  # limit to cancers wd:Q12078 (the * operator runs up a transitive relation..)
  ?gene_product wdt:P682 ?biological_process . #add information about the GO biological processes that the gene is related to
  #limit to genes related to certain biological processes (and their sub-processes):
  		#apoptosis wd:Q14599311
  		#cell proliferation wd:Q14818032
   ?biological_process (wdt:P361|wdt:P279)* wd:Q14818032  # chain down subclass/part-of

    #uncomment the next line to find a subset of the known true positives (there are not a lot of them in here yet)
  #?disease wdt:P2176 ?drug . 	# disease is treated by a drug
  	SERVICE wikibase:label {
        bd:serviceParam wikibase:language \"en\" .
	}
}
LIMIT 1000`};

    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://query.wikidata.org/sparql"
   data-sgvizler-query="PREFIX bd: &lt;http://www.bigdata.com/rdf#&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;
#added before 2016-10

#cases where a drug physically interacts with the product of gene known to be genetically associated a disease
#these cases may show opportunities to repurpose a drug for a new disease
#See http://database.oxfordjournals.org/content/2016/baw083.long  and
#http://drug-repurposing.nationwidechildrens.org/search
#an example that was recently validated involved a new link between Metformin wd:Q19484 and cancer survival
#https://jamia.oxfordjournals.org/content/22/1/179
#currently set up to find drugs for cancers that target genes related to cell proliferation
#adapt by changing constraints (e.g. to &#039;heart disease&#039; Q190805) or removing them
SELECT ?biological_process ?drugLabel ?geneLabel ?biological_processLabel ?diseaseLabel
WHERE {
  ?disease wdt:P31 wd:Q12136 .
  ?drug  wdt:P31 wd:Q12140 .
  ?gene wdt:P31 wd:Q7187 .

  ?biological_process wdt:P31 wd:Q2996394 .

  ?drug wdt:P129 ?gene_product .   # drug interacts with a gene_product
  ?gene wdt:P688 ?gene_product .  # gene_product (usually a protein) is a product of a gene (a region of DNA)
  ?disease	wdt:P2293 ?gene .    # genetic association between disease and gene
  ?disease wdt:P279*  wd:Q12078 .  # limit to cancers wd:Q12078 (the * operator runs up a transitive relation..)
  ?gene_product wdt:P682 ?biological_process . #add information about the GO biological processes that the gene is related to
  #limit to genes related to certain biological processes (and their sub-processes):
  		#apoptosis wd:Q14599311
  		#cell proliferation wd:Q14818032
   ?biological_process (wdt:P361|wdt:P279)* wd:Q14818032  # chain down subclass/part-of

    #uncomment the next line to find a subset of the known true positives (there are not a lot of them in here yet)
  #?disease wdt:P2176 ?drug . 	# disease is treated by a drug
  	SERVICE wikibase:label {
        bd:serviceParam wikibase:language &quot;en&quot; .
	}
}
LIMIT 1000"
    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 wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wikibase: <http://wikiba.se/ontology#>
#added before 2016-10

#cases where a drug physically interacts with the product of gene known to be genetically associated a disease
#these cases may show opportunities to repurpose a drug for a new disease
#See http://database.oxfordjournals.org/content/2016/baw083.long  and
#http://drug-repurposing.nationwidechildrens.org/search
#an example that was recently validated involved a new link between Metformin wd:Q19484 and cancer survival
#https://jamia.oxfordjournals.org/content/22/1/179
#currently set up to find drugs for cancers that target genes related to cell proliferation
#adapt by changing constraints (e.g. to 'heart disease' Q190805) or removing them
SELECT ?biological_process ?drugLabel ?geneLabel ?biological_processLabel ?diseaseLabel
WHERE {
  ?disease wdt:P31 wd:Q12136 .
  ?drug  wdt:P31 wd:Q12140 .
  ?gene wdt:P31 wd:Q7187 .

  ?biological_process wdt:P31 wd:Q2996394 .

  ?drug wdt:P129 ?gene_product .   # drug interacts with a gene_product
  ?gene wdt:P688 ?gene_product .  # gene_product (usually a protein) is a product of a gene (a region of DNA)
  ?disease	wdt:P2293 ?gene .    # genetic association between disease and gene
  ?disease wdt:P279*  wd:Q12078 .  # limit to cancers wd:Q12078 (the * operator runs up a transitive relation..)
  ?gene_product wdt:P682 ?biological_process . #add information about the GO biological processes that the gene is related to
  #limit to genes related to certain biological processes (and their sub-processes):
  		#apoptosis wd:Q14599311
  		#cell proliferation wd:Q14818032
   ?biological_process (wdt:P361|wdt:P279)* wd:Q14818032  # chain down subclass/part-of

    #uncomment the next line to find a subset of the known true positives (there are not a lot of them in here yet)
  #?disease wdt:P2176 ?drug . 	# disease is treated by a drug
  	SERVICE wikibase:label {
        bd:serviceParam wikibase:language "en" .
	}
}
LIMIT 1000""")
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 wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wikibase: <http://wikiba.se/ontology#>
#added before 2016-10

#cases where a drug physically interacts with the product of gene known to be genetically associated a disease
#these cases may show opportunities to repurpose a drug for a new disease
#See http://database.oxfordjournals.org/content/2016/baw083.long  and
#http://drug-repurposing.nationwidechildrens.org/search
#an example that was recently validated involved a new link between Metformin wd:Q19484 and cancer survival
#https://jamia.oxfordjournals.org/content/22/1/179
#currently set up to find drugs for cancers that target genes related to cell proliferation
#adapt by changing constraints (e.g. to 'heart disease' Q190805) or removing them
SELECT ?biological_process ?drugLabel ?geneLabel ?biological_processLabel ?diseaseLabel
WHERE {
  ?disease wdt:P31 wd:Q12136 .
  ?drug  wdt:P31 wd:Q12140 .
  ?gene wdt:P31 wd:Q7187 .

  ?biological_process wdt:P31 wd:Q2996394 .

  ?drug wdt:P129 ?gene_product .   # drug interacts with a gene_product
  ?gene wdt:P688 ?gene_product .  # gene_product (usually a protein) is a product of a gene (a region of DNA)
  ?disease	wdt:P2293 ?gene .    # genetic association between disease and gene
  ?disease wdt:P279*  wd:Q12078 .  # limit to cancers wd:Q12078 (the * operator runs up a transitive relation..)
  ?gene_product wdt:P682 ?biological_process . #add information about the GO biological processes that the gene is related to
  #limit to genes related to certain biological processes (and their sub-processes):
  		#apoptosis wd:Q14599311
  		#cell proliferation wd:Q14818032
   ?biological_process (wdt:P361|wdt:P279)* wd:Q14818032  # chain down subclass/part-of

    #uncomment the next line to find a subset of the known true positives (there are not a lot of them in here yet)
  #?disease wdt:P2176 ?drug . 	# disease is treated by a drug
  	SERVICE wikibase:label {
        bd:serviceParam wikibase:language "en" .
	}
}
LIMIT 1000"
# 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 wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wikibase: <http://wikiba.se/ontology#>
#added before 2016-10

#cases where a drug physically interacts with the product of gene known to be genetically associated a disease
#these cases may show opportunities to repurpose a drug for a new disease
#See http://database.oxfordjournals.org/content/2016/baw083.long  and
#http://drug-repurposing.nationwidechildrens.org/search
#an example that was recently validated involved a new link between Metformin wd:Q19484 and cancer survival
#https://jamia.oxfordjournals.org/content/22/1/179
#currently set up to find drugs for cancers that target genes related to cell proliferation
#adapt by changing constraints (e.g. to 'heart disease' Q190805) or removing them
SELECT ?biological_process ?drugLabel ?geneLabel ?biological_processLabel ?diseaseLabel
WHERE {
  ?disease wdt:P31 wd:Q12136 .
  ?drug  wdt:P31 wd:Q12140 .
  ?gene wdt:P31 wd:Q7187 .

  ?biological_process wdt:P31 wd:Q2996394 .

  ?drug wdt:P129 ?gene_product .   # drug interacts with a gene_product
  ?gene wdt:P688 ?gene_product .  # gene_product (usually a protein) is a product of a gene (a region of DNA)
  ?disease	wdt:P2293 ?gene .    # genetic association between disease and gene
  ?disease wdt:P279*  wd:Q12078 .  # limit to cancers wd:Q12078 (the * operator runs up a transitive relation..)
  ?gene_product wdt:P682 ?biological_process . #add information about the GO biological processes that the gene is related to
  #limit to genes related to certain biological processes (and their sub-processes):
  		#apoptosis wd:Q14599311
  		#cell proliferation wd:Q14818032
   ?biological_process (wdt:P361|wdt:P279)* wd:Q14818032  # chain down subclass/part-of

    #uncomment the next line to find a subset of the known true positives (there are not a lot of them in here yet)
  #?disease wdt:P2176 ?drug . 	# disease is treated by a drug
  	SERVICE wikibase:label {
        bd:serviceParam wikibase:language "en" .
	}
}
LIMIT 1000
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 wd: <http://www.wikidata.org/entity/> '...
'PREFIX wdt: <http://www.wikidata.org/prop/direct/> '...
'PREFIX wikibase: <http://wikiba.se/ontology#> '...
'#added before 2016-10 '...
' '...
'#cases where a drug physically interacts with the product of gene known to be genetically associated a disease '...
'#these cases may show opportunities to repurpose a drug for a new disease '...
'#See http://database.oxfordjournals.org/content/2016/baw083.long  and '...
'#http://drug-repurposing.nationwidechildrens.org/search '...
'#an example that was recently validated involved a new link between Metformin wd:Q19484 and cancer survival '...
'#https://jamia.oxfordjournals.org/content/22/1/179 '...
'#currently set up to find drugs for cancers that target genes related to cell proliferation '...
'#adapt by changing constraints (e.g. to 'heart disease' Q190805) or removing them '...
'SELECT ?biological_process ?drugLabel ?geneLabel ?biological_processLabel ?diseaseLabel '...
'WHERE { '...
'  ?disease wdt:P31 wd:Q12136 . '...
'  ?drug  wdt:P31 wd:Q12140 . '...
'  ?gene wdt:P31 wd:Q7187 . '...
' '...
'  ?biological_process wdt:P31 wd:Q2996394 . '...
' '...
'  ?drug wdt:P129 ?gene_product .   # drug interacts with a gene_product '...
'  ?gene wdt:P688 ?gene_product .  # gene_product (usually a protein) is a product of a gene (a region of DNA) '...
'  ?disease	wdt:P2293 ?gene .    # genetic association between disease and gene '...
'  ?disease wdt:P279*  wd:Q12078 .  # limit to cancers wd:Q12078 (the * operator runs up a transitive relation..) '...
'  ?gene_product wdt:P682 ?biological_process . #add information about the GO biological processes that the gene is related to '...
'  #limit to genes related to certain biological processes (and their sub-processes): '...
'  		#apoptosis wd:Q14599311 '...
'  		#cell proliferation wd:Q14818032 '...
'   ?biological_process (wdt:P361|wdt:P279)* wd:Q14818032  # chain down subclass/part-of '...
' '...
'    #uncomment the next line to find a subset of the known true positives (there are not a lot of them in here yet) '...
'  #?disease wdt:P2176 ?drug . 	# disease is treated by a drug '...
'  	SERVICE wikibase:label { '...
'        bd:serviceParam wikibase:language "en" . '...
'	} '...
'} '...
'LIMIT 1000 '];

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 wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wikibase: <http://wikiba.se/ontology#>
#added before 2016-10

#cases where a drug physically interacts with the product of gene known to be genetically associated a disease
#these cases may show opportunities to repurpose a drug for a new disease
#See http://database.oxfordjournals.org/content/2016/baw083.long  and
#http://drug-repurposing.nationwidechildrens.org/search
#an example that was recently validated involved a new link between Metformin wd:Q19484 and cancer survival
#https://jamia.oxfordjournals.org/content/22/1/179
#currently set up to find drugs for cancers that target genes related to cell proliferation
#adapt by changing constraints (e.g. to 'heart disease' Q190805) or removing them
SELECT ?biological_process ?drugLabel ?geneLabel ?biological_processLabel ?diseaseLabel
WHERE {
  ?disease wdt:P31 wd:Q12136 .
  ?drug  wdt:P31 wd:Q12140 .
  ?gene wdt:P31 wd:Q7187 .

  ?biological_process wdt:P31 wd:Q2996394 .

  ?drug wdt:P129 ?gene_product .   # drug interacts with a gene_product
  ?gene wdt:P688 ?gene_product .  # gene_product (usually a protein) is a product of a gene (a region of DNA)
  ?disease	wdt:P2293 ?gene .    # genetic association between disease and gene
  ?disease wdt:P279*  wd:Q12078 .  # limit to cancers wd:Q12078 (the * operator runs up a transitive relation..)
  ?gene_product wdt:P682 ?biological_process . #add information about the GO biological processes that the gene is related to
  #limit to genes related to certain biological processes (and their sub-processes):
  		#apoptosis wd:Q14599311
  		#cell proliferation wd:Q14818032
   ?biological_process (wdt:P361|wdt:P279)* wd:Q14818032  # chain down subclass/part-of

    #uncomment the next line to find a subset of the known true positives (there are not a lot of them in here yet)
  #?disease wdt:P2176 ?drug . 	# disease is treated by a drug
  	SERVICE wikibase:label {
        bd:serviceParam wikibase:language "en" .
	}
}
LIMIT 1000
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 wd: <http://www.wikidata.org/entity/> \n"
                    + "PREFIX wdt: <http://www.wikidata.org/prop/direct/> \n"
                    + "PREFIX wikibase: <http://wikiba.se/ontology#> \n"
                    + "#added before 2016-10 \n"
                    + " \n"
                    + "#cases where a drug physically interacts with the product of gene known to be genetically associated a disease \n"
                    + "#these cases may show opportunities to repurpose a drug for a new disease \n"
                    + "#See http://database.oxfordjournals.org/content/2016/baw083.long  and \n"
                    + "#http://drug-repurposing.nationwidechildrens.org/search \n"
                    + "#an example that was recently validated involved a new link between Metformin wd:Q19484 and cancer survival \n"
                    + "#https://jamia.oxfordjournals.org/content/22/1/179 \n"
                    + "#currently set up to find drugs for cancers that target genes related to cell proliferation \n"
                    + "#adapt by changing constraints (e.g. to \'heart disease\' Q190805) or removing them \n"
                    + "SELECT ?biological_process ?drugLabel ?geneLabel ?biological_processLabel ?diseaseLabel \n"
                    + "WHERE { \n"
                    + "  ?disease wdt:P31 wd:Q12136 . \n"
                    + "  ?drug  wdt:P31 wd:Q12140 . \n"
                    + "  ?gene wdt:P31 wd:Q7187 . \n"
                    + " \n"
                    + "  ?biological_process wdt:P31 wd:Q2996394 . \n"
                    + " \n"
                    + "  ?drug wdt:P129 ?gene_product .   # drug interacts with a gene_product \n"
                    + "  ?gene wdt:P688 ?gene_product .  # gene_product (usually a protein) is a product of a gene (a region of DNA) \n"
                    + "  ?disease	wdt:P2293 ?gene .    # genetic association between disease and gene \n"
                    + "  ?disease wdt:P279*  wd:Q12078 .  # limit to cancers wd:Q12078 (the * operator runs up a transitive relation..) \n"
                    + "  ?gene_product wdt:P682 ?biological_process . #add information about the GO biological processes that the gene is related to \n"
                    + "  #limit to genes related to certain biological processes (and their sub-processes): \n"
                    + "  		#apoptosis wd:Q14599311 \n"
                    + "  		#cell proliferation wd:Q14818032 \n"
                    + "   ?biological_process (wdt:P361|wdt:P279)* wd:Q14818032  # chain down subclass/part-of \n"
                    + " \n"
                    + "    #uncomment the next line to find a subset of the known true positives (there are not a lot of them in here yet) \n"
                    + "  #?disease wdt:P2176 ?drug . 	# disease is treated by a drug \n"
                    + "  	SERVICE wikibase:label { \n"
                    + "        bd:serviceParam wikibase:language \"en\" . \n"
                    + "	} \n"
                    + "} \n"
                    + "LIMIT 1000 \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