SPARQL query: Samples from homo sapiens and their provenance

Karima Rafes

biology Homo sapiens

Samples from homo sapiens and their provenance

Shows how to get and filter sample attributes. It also shows how the web pages on the provenance databases are linked.

Reuse these data in your code

Query, endpoint and code for reusing the same data

Endpoint:

https://www.ebi.ac.uk/rdf/services/sparql

Query:

PREFIX dc: <http://purl.org/dc/elements/1.1/> 
PREFIX dcterms: <http://purl.org/dc/terms/> 
PREFIX foaf: <http://xmlns.com/foaf/0.1/> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 

PREFIX biosd-terms: <http://rdf.ebi.ac.uk/terms/biosd/>
PREFIX pav: <http://purl.org/pav/2.0/>
PREFIX atlas: <http://rdf.ebi.ac.uk/terms/atlas/>
# 
## Samples with a given property value and type, and external links
## This version doesn't exploit any ontology for sample properties.
#
SELECT DISTINCT ?smp ?pvLabel ?propTypeLabel ?repoName ?repoAcc ?repoUrl
WHERE
{
  ?smp a biosd-terms:Sample;
       biosd-terms:has-sample-attribute ?pv;
       pav:derivedFrom ?webRec.
# atlas:propertyValue, atlas:propertyType, 
# dcterms:title are available too, data integration purposes.
  ?pv  rdfs:label ?pvLabel;
# this is used even when no specific type is present
       dc:type ?propTypeLabel. 
  
  FILTER ( LCASE ( STR ( ?propTypeLabel ) ) = 'organism' ).
  FILTER ( LCASE ( STR ( ?pvLabel ) ) = 'homo sapiens' ).
  
  ?webRec dcterms:identifier ?repoAcc;
          dcterms:source ?repoName;
          foaf:page ?repoUrl.
}
LIMIT 10

Howto write a query SPARQL? (in French)

{{#sparql:PREFIX dc: <http://purl.org/dc/elements/1.1/> 
PREFIX dcterms: <http://purl.org/dc/terms/> 
PREFIX foaf: <http://xmlns.com/foaf/0.1/> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 

PREFIX biosd-terms: <http://rdf.ebi.ac.uk/terms/biosd/>
PREFIX pav: <http://purl.org/pav/2.0/>
PREFIX atlas: <http://rdf.ebi.ac.uk/terms/atlas/>
# 
## Samples with a given property value and type, and external links
## This version doesn't exploit any ontology for sample properties.
#
SELECT DISTINCT ?smp ?pvLabel ?propTypeLabel ?repoName ?repoAcc ?repoUrl
WHERE
{
  ?smp a biosd-terms:Sample;
       biosd-terms:has-sample-attribute ?pv;
       pav:derivedFrom ?webRec.
# atlas:propertyValue, atlas:propertyType, 
# dcterms:title are available too, data integration purposes.
  ?pv  rdfs:label ?pvLabel;
# this is used even when no specific type is present
       dc:type ?propTypeLabel. 
  
  FILTER ( LCASE ( STR ( ?propTypeLabel ) ) = 'organism' ).
  FILTER ( LCASE ( STR ( ?pvLabel ) ) = 'homo sapiens' ).
  
  ?webRec dcterms:identifier ?repoAcc;
          dcterms:source ?repoName;
          foaf:page ?repoUrl.
}
LIMIT 10
| endpoint = https://www.ebi.ac.uk/rdf/services/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://www.ebi.ac.uk/rdf/services/sparql";
    var query = `PREFIX dc: <http://purl.org/dc/elements/1.1/> 
PREFIX dcterms: <http://purl.org/dc/terms/> 
PREFIX foaf: <http://xmlns.com/foaf/0.1/> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 

PREFIX biosd-terms: <http://rdf.ebi.ac.uk/terms/biosd/>
PREFIX pav: <http://purl.org/pav/2.0/>
PREFIX atlas: <http://rdf.ebi.ac.uk/terms/atlas/>
# 
## Samples with a given property value and type, and external links
## This version doesn\'t exploit any ontology for sample properties.
#
SELECT DISTINCT ?smp ?pvLabel ?propTypeLabel ?repoName ?repoAcc ?repoUrl
WHERE
{
  ?smp a biosd-terms:Sample;
       biosd-terms:has-sample-attribute ?pv;
       pav:derivedFrom ?webRec.
# atlas:propertyValue, atlas:propertyType, 
# dcterms:title are available too, data integration purposes.
  ?pv  rdfs:label ?pvLabel;
# this is used even when no specific type is present
       dc:type ?propTypeLabel. 
  
  FILTER ( LCASE ( STR ( ?propTypeLabel ) ) = \'organism\' ).
  FILTER ( LCASE ( STR ( ?pvLabel ) ) = \'homo sapiens\' ).
  
  ?webRec dcterms:identifier ?repoAcc;
          dcterms:source ?repoName;
          foaf:page ?repoUrl.
}
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://www.ebi.ac.uk/rdf/services/sparql");
    var params = {query:`PREFIX dc: <http://purl.org/dc/elements/1.1/> 
PREFIX dcterms: <http://purl.org/dc/terms/> 
PREFIX foaf: <http://xmlns.com/foaf/0.1/> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 

PREFIX biosd-terms: <http://rdf.ebi.ac.uk/terms/biosd/>
PREFIX pav: <http://purl.org/pav/2.0/>
PREFIX atlas: <http://rdf.ebi.ac.uk/terms/atlas/>
# 
## Samples with a given property value and type, and external links
## This version doesn\'t exploit any ontology for sample properties.
#
SELECT DISTINCT ?smp ?pvLabel ?propTypeLabel ?repoName ?repoAcc ?repoUrl
WHERE
{
  ?smp a biosd-terms:Sample;
       biosd-terms:has-sample-attribute ?pv;
       pav:derivedFrom ?webRec.
# atlas:propertyValue, atlas:propertyType, 
# dcterms:title are available too, data integration purposes.
  ?pv  rdfs:label ?pvLabel;
# this is used even when no specific type is present
       dc:type ?propTypeLabel. 
  
  FILTER ( LCASE ( STR ( ?propTypeLabel ) ) = \'organism\' ).
  FILTER ( LCASE ( STR ( ?pvLabel ) ) = \'homo sapiens\' ).
  
  ?webRec dcterms:identifier ?repoAcc;
          dcterms:source ?repoName;
          foaf:page ?repoUrl.
}
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://www.ebi.ac.uk/rdf/services/sparql"
   data-sgvizler-query="PREFIX dc: &lt;http://purl.org/dc/elements/1.1/&gt; 
PREFIX dcterms: &lt;http://purl.org/dc/terms/&gt; 
PREFIX foaf: &lt;http://xmlns.com/foaf/0.1/&gt; 
PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; 

PREFIX biosd-terms: &lt;http://rdf.ebi.ac.uk/terms/biosd/&gt;
PREFIX pav: &lt;http://purl.org/pav/2.0/&gt;
PREFIX atlas: &lt;http://rdf.ebi.ac.uk/terms/atlas/&gt;
# 
## Samples with a given property value and type, and external links
## This version doesn&#039;t exploit any ontology for sample properties.
#
SELECT DISTINCT ?smp ?pvLabel ?propTypeLabel ?repoName ?repoAcc ?repoUrl
WHERE
{
  ?smp a biosd-terms:Sample;
       biosd-terms:has-sample-attribute ?pv;
       pav:derivedFrom ?webRec.
# atlas:propertyValue, atlas:propertyType, 
# dcterms:title are available too, data integration purposes.
  ?pv  rdfs:label ?pvLabel;
# this is used even when no specific type is present
       dc:type ?propTypeLabel. 
  
  FILTER ( LCASE ( STR ( ?propTypeLabel ) ) = &#039;organism&#039; ).
  FILTER ( LCASE ( STR ( ?pvLabel ) ) = &#039;homo sapiens&#039; ).
  
  ?webRec dcterms:identifier ?repoAcc;
          dcterms:source ?repoName;
          foaf:page ?repoUrl.
}
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://www.ebi.ac.uk/rdf/services/sparql")
sparql.setQuery("""
    PREFIX dc: <http://purl.org/dc/elements/1.1/> 
PREFIX dcterms: <http://purl.org/dc/terms/> 
PREFIX foaf: <http://xmlns.com/foaf/0.1/> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 

PREFIX biosd-terms: <http://rdf.ebi.ac.uk/terms/biosd/>
PREFIX pav: <http://purl.org/pav/2.0/>
PREFIX atlas: <http://rdf.ebi.ac.uk/terms/atlas/>
# 
## Samples with a given property value and type, and external links
## This version doesn't exploit any ontology for sample properties.
#
SELECT DISTINCT ?smp ?pvLabel ?propTypeLabel ?repoName ?repoAcc ?repoUrl
WHERE
{
  ?smp a biosd-terms:Sample;
       biosd-terms:has-sample-attribute ?pv;
       pav:derivedFrom ?webRec.
# atlas:propertyValue, atlas:propertyType, 
# dcterms:title are available too, data integration purposes.
  ?pv  rdfs:label ?pvLabel;
# this is used even when no specific type is present
       dc:type ?propTypeLabel. 
  
  FILTER ( LCASE ( STR ( ?propTypeLabel ) ) = 'organism' ).
  FILTER ( LCASE ( STR ( ?pvLabel ) ) = 'homo sapiens' ).
  
  ?webRec dcterms:identifier ?repoAcc;
          dcterms:source ?repoName;
          foaf:page ?repoUrl.
}
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://www.ebi.ac.uk/rdf/services/sparql"
# create query statement
    query <- "PREFIX dc: <http://purl.org/dc/elements/1.1/> 
PREFIX dcterms: <http://purl.org/dc/terms/> 
PREFIX foaf: <http://xmlns.com/foaf/0.1/> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 

PREFIX biosd-terms: <http://rdf.ebi.ac.uk/terms/biosd/>
PREFIX pav: <http://purl.org/pav/2.0/>
PREFIX atlas: <http://rdf.ebi.ac.uk/terms/atlas/>
# 
## Samples with a given property value and type, and external links
## This version doesn't exploit any ontology for sample properties.
#
SELECT DISTINCT ?smp ?pvLabel ?propTypeLabel ?repoName ?repoAcc ?repoUrl
WHERE
{
  ?smp a biosd-terms:Sample;
       biosd-terms:has-sample-attribute ?pv;
       pav:derivedFrom ?webRec.
# atlas:propertyValue, atlas:propertyType, 
# dcterms:title are available too, data integration purposes.
  ?pv  rdfs:label ?pvLabel;
# this is used even when no specific type is present
       dc:type ?propTypeLabel. 
  
  FILTER ( LCASE ( STR ( ?propTypeLabel ) ) = 'organism' ).
  FILTER ( LCASE ( STR ( ?pvLabel ) ) = 'homo sapiens' ).
  
  ?webRec dcterms:identifier ?repoAcc;
          dcterms:source ?repoName;
          foaf:page ?repoUrl.
}
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://www.ebi.ac.uk/rdf/services/sparql"
sparql = <<-EOT
PREFIX dc: <http://purl.org/dc/elements/1.1/> 
PREFIX dcterms: <http://purl.org/dc/terms/> 
PREFIX foaf: <http://xmlns.com/foaf/0.1/> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 

PREFIX biosd-terms: <http://rdf.ebi.ac.uk/terms/biosd/>
PREFIX pav: <http://purl.org/pav/2.0/>
PREFIX atlas: <http://rdf.ebi.ac.uk/terms/atlas/>
# 
## Samples with a given property value and type, and external links
## This version doesn't exploit any ontology for sample properties.
#
SELECT DISTINCT ?smp ?pvLabel ?propTypeLabel ?repoName ?repoAcc ?repoUrl
WHERE
{
  ?smp a biosd-terms:Sample;
       biosd-terms:has-sample-attribute ?pv;
       pav:derivedFrom ?webRec.
# atlas:propertyValue, atlas:propertyType, 
# dcterms:title are available too, data integration purposes.
  ?pv  rdfs:label ?pvLabel;
# this is used even when no specific type is present
       dc:type ?propTypeLabel. 
  
  FILTER ( LCASE ( STR ( ?propTypeLabel ) ) = 'organism' ).
  FILTER ( LCASE ( STR ( ?pvLabel ) ) = 'homo sapiens' ).
  
  ?webRec dcterms:identifier ?repoAcc;
          dcterms:source ?repoName;
          foaf:page ?repoUrl.
}
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://www.ebi.ac.uk/rdf/services/sparql';

query = ['PREFIX dc: <http://purl.org/dc/elements/1.1/>  '...
'PREFIX dcterms: <http://purl.org/dc/terms/>  '...
'PREFIX foaf: <http://xmlns.com/foaf/0.1/>  '...
'PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>  '...
' '...
'PREFIX biosd-terms: <http://rdf.ebi.ac.uk/terms/biosd/> '...
'PREFIX pav: <http://purl.org/pav/2.0/> '...
'PREFIX atlas: <http://rdf.ebi.ac.uk/terms/atlas/> '...
'#  '...
'## Samples with a given property value and type, and external links '...
'## This version doesn't exploit any ontology for sample properties. '...
'# '...
'SELECT DISTINCT ?smp ?pvLabel ?propTypeLabel ?repoName ?repoAcc ?repoUrl '...
'WHERE '...
'{ '...
'  ?smp a biosd-terms:Sample; '...
'       biosd-terms:has-sample-attribute ?pv; '...
'       pav:derivedFrom ?webRec. '...
'# atlas:propertyValue, atlas:propertyType,  '...
'# dcterms:title are available too, data integration purposes. '...
'  ?pv  rdfs:label ?pvLabel; '...
'# this is used even when no specific type is present '...
'       dc:type ?propTypeLabel.  '...
'   '...
'  FILTER ( LCASE ( STR ( ?propTypeLabel ) ) = 'organism' ). '...
'  FILTER ( LCASE ( STR ( ?pvLabel ) ) = 'homo sapiens' ). '...
'   '...
'  ?webRec dcterms:identifier ?repoAcc; '...
'          dcterms:source ?repoName; '...
'          foaf:page ?repoUrl. '...
'} '...
'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://www.ebi.ac.uk/rdf/services/sparql";
$sp_readonly = new SparqlClient();
$sp_readonly->setEndpointRead($endpoint);
$q = <<<EOD
PREFIX dc: <http://purl.org/dc/elements/1.1/> 
PREFIX dcterms: <http://purl.org/dc/terms/> 
PREFIX foaf: <http://xmlns.com/foaf/0.1/> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 

PREFIX biosd-terms: <http://rdf.ebi.ac.uk/terms/biosd/>
PREFIX pav: <http://purl.org/pav/2.0/>
PREFIX atlas: <http://rdf.ebi.ac.uk/terms/atlas/>
# 
## Samples with a given property value and type, and external links
## This version doesn't exploit any ontology for sample properties.
#
SELECT DISTINCT ?smp ?pvLabel ?propTypeLabel ?repoName ?repoAcc ?repoUrl
WHERE
{
  ?smp a biosd-terms:Sample;
       biosd-terms:has-sample-attribute ?pv;
       pav:derivedFrom ?webRec.
# atlas:propertyValue, atlas:propertyType, 
# dcterms:title are available too, data integration purposes.
  ?pv  rdfs:label ?pvLabel;
# this is used even when no specific type is present
       dc:type ?propTypeLabel. 
  
  FILTER ( LCASE ( STR ( ?propTypeLabel ) ) = 'organism' ).
  FILTER ( LCASE ( STR ( ?pvLabel ) ) = 'homo sapiens' ).
  
  ?webRec dcterms:identifier ?repoAcc;
          dcterms:source ?repoName;
          foaf:page ?repoUrl.
}
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://www.ebi.ac.uk/rdf/services/sparql");
            String querySelect  = "PREFIX dc: <http://purl.org/dc/elements/1.1/>  \n"
                    + "PREFIX dcterms: <http://purl.org/dc/terms/>  \n"
                    + "PREFIX foaf: <http://xmlns.com/foaf/0.1/>  \n"
                    + "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>  \n"
                    + " \n"
                    + "PREFIX biosd-terms: <http://rdf.ebi.ac.uk/terms/biosd/> \n"
                    + "PREFIX pav: <http://purl.org/pav/2.0/> \n"
                    + "PREFIX atlas: <http://rdf.ebi.ac.uk/terms/atlas/> \n"
                    + "#  \n"
                    + "## Samples with a given property value and type, and external links \n"
                    + "## This version doesn\'t exploit any ontology for sample properties. \n"
                    + "# \n"
                    + "SELECT DISTINCT ?smp ?pvLabel ?propTypeLabel ?repoName ?repoAcc ?repoUrl \n"
                    + "WHERE \n"
                    + "{ \n"
                    + "  ?smp a biosd-terms:Sample; \n"
                    + "       biosd-terms:has-sample-attribute ?pv; \n"
                    + "       pav:derivedFrom ?webRec. \n"
                    + "# atlas:propertyValue, atlas:propertyType,  \n"
                    + "# dcterms:title are available too, data integration purposes. \n"
                    + "  ?pv  rdfs:label ?pvLabel; \n"
                    + "# this is used even when no specific type is present \n"
                    + "       dc:type ?propTypeLabel.  \n"
                    + "   \n"
                    + "  FILTER ( LCASE ( STR ( ?propTypeLabel ) ) = \'organism\' ). \n"
                    + "  FILTER ( LCASE ( STR ( ?pvLabel ) ) = \'homo sapiens\' ). \n"
                    + "   \n"
                    + "  ?webRec dcterms:identifier ?repoAcc; \n"
                    + "          dcterms:source ?repoName; \n"
                    + "          foaf:page ?repoUrl. \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

Table view

Simple view on the data

Reuse these data in your code

Query, endpoint and code for reusing the same data