Feedback

Creating synergies and interactions among the analysts and the “producers” of data. See details.

Reuse these data in your code

Query, endpoint and code for reusing the same data
https://www.ebi.ac.uk/rdf/services/sparql
PREFIX dc: <http://purl.org/dc/elements/1.1/> 
PREFIX ensembl: <http://rdf.ebi.ac.uk/resource/ensembl/> 
PREFIX faldo: <http://biohackathon.org/resource/faldo#> 
PREFIX obo: <http://purl.obolibrary.org/obo/> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 

SELECT DISTINCT ?transcript ?id ?typeLabel ?reference ?begin ?end ?location 
WHERE {
	?transcript obo:SO_transcribed_from ensembl:ENSG00000139618 ;
				a ?type;
				dc:identifier ?id .
    OPTIONAL {
      ?transcript faldo:location ?location .
      ?location faldo:begin [faldo:position ?begin] .
      ?location faldo:end [faldo:position ?end ] .
      ?location faldo:reference ?reference .
    }
    OPTIONAL {?type rdfs:label ?typeLabel}
}
Howto write a query SPARQL? (in French)
{{#sparql:PREFIX dc: <http://purl.org/dc/elements/1.1/> 
PREFIX ensembl: <http://rdf.ebi.ac.uk/resource/ensembl/> 
PREFIX faldo: <http://biohackathon.org/resource/faldo#> 
PREFIX obo: <http://purl.obolibrary.org/obo/> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 

SELECT DISTINCT ?transcript ?id ?typeLabel ?reference ?begin ?end ?location 
WHERE {
	?transcript obo:SO_transcribed_from ensembl:ENSG00000139618 ;
				a ?type;
				dc:identifier ?id .
    OPTIONAL {
      ?transcript faldo:location ?location .
      ?location faldo:begin [faldo:position ?begin] .
      ?location faldo:end [faldo:position ?end ] .
      ?location faldo:reference ?reference .
    }
    OPTIONAL {?type rdfs:label ?typeLabel}
}
| 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/> \n\
PREFIX ensembl: <http://rdf.ebi.ac.uk/resource/ensembl/> \n\
PREFIX faldo: <http://biohackathon.org/resource/faldo#> \n\
PREFIX obo: <http://purl.obolibrary.org/obo/> \n\
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n\
\n\
SELECT DISTINCT ?transcript ?id ?typeLabel ?reference ?begin ?end ?location \n\
WHERE {\n\
	?transcript obo:SO_transcribed_from ensembl:ENSG00000139618 ;\n\
				a ?type;\n\
				dc:identifier ?id .\n\
    OPTIONAL {\n\
      ?transcript faldo:location ?location .\n\
      ?location faldo:begin [faldo:position ?begin] .\n\
      ?location faldo:end [faldo:position ?end ] .\n\
      ?location faldo:reference ?reference .\n\
    }\n\
    OPTIONAL {?type rdfs:label ?typeLabel}\n\
}"

   // $('#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://www.ebi.ac.uk/rdf/services/sparql"
   data-sgvizler-query="PREFIX dc: &lt;http://purl.org/dc/elements/1.1/&gt; 
PREFIX ensembl: &lt;http://rdf.ebi.ac.uk/resource/ensembl/&gt; 
PREFIX faldo: &lt;http://biohackathon.org/resource/faldo#&gt; 
PREFIX obo: &lt;http://purl.obolibrary.org/obo/&gt; 
PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; 

SELECT DISTINCT ?transcript ?id ?typeLabel ?reference ?begin ?end ?location 
WHERE {
	?transcript obo:SO_transcribed_from ensembl:ENSG00000139618 ;
				a ?type;
				dc:identifier ?id .
    OPTIONAL {
      ?transcript faldo:location ?location .
      ?location faldo:begin [faldo:position ?begin] .
      ?location faldo:end [faldo:position ?end ] .
      ?location faldo:reference ?reference .
    }
    OPTIONAL {?type rdfs:label ?typeLabel}
}"
    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://www.ebi.ac.uk/rdf/services/sparql")
sparql.setQuery("""
    PREFIX dc: <http://purl.org/dc/elements/1.1/> 
PREFIX ensembl: <http://rdf.ebi.ac.uk/resource/ensembl/> 
PREFIX faldo: <http://biohackathon.org/resource/faldo#> 
PREFIX obo: <http://purl.obolibrary.org/obo/> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 

SELECT DISTINCT ?transcript ?id ?typeLabel ?reference ?begin ?end ?location 
WHERE {
	?transcript obo:SO_transcribed_from ensembl:ENSG00000139618 ;
				a ?type;
				dc:identifier ?id .
    OPTIONAL {
      ?transcript faldo:location ?location .
      ?location faldo:begin [faldo:position ?begin] .
      ?location faldo:end [faldo:position ?end ] .
      ?location faldo:reference ?reference .
    }
    OPTIONAL {?type rdfs:label ?typeLabel}
}""")
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 ensembl: <http://rdf.ebi.ac.uk/resource/ensembl/> 
PREFIX faldo: <http://biohackathon.org/resource/faldo#> 
PREFIX obo: <http://purl.obolibrary.org/obo/> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 

SELECT DISTINCT ?transcript ?id ?typeLabel ?reference ?begin ?end ?location 
WHERE {
	?transcript obo:SO_transcribed_from ensembl:ENSG00000139618 ;
				a ?type;
				dc:identifier ?id .
    OPTIONAL {
      ?transcript faldo:location ?location .
      ?location faldo:begin [faldo:position ?begin] .
      ?location faldo:end [faldo:position ?end ] .
      ?location faldo:reference ?reference .
    }
    OPTIONAL {?type rdfs:label ?typeLabel}
}"
# 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://www.ebi.ac.uk/rdf/services/sparql"
sparql = <<-EOT
PREFIX dc: <http://purl.org/dc/elements/1.1/> 
PREFIX ensembl: <http://rdf.ebi.ac.uk/resource/ensembl/> 
PREFIX faldo: <http://biohackathon.org/resource/faldo#> 
PREFIX obo: <http://purl.obolibrary.org/obo/> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 

SELECT DISTINCT ?transcript ?id ?typeLabel ?reference ?begin ?end ?location 
WHERE {
	?transcript obo:SO_transcribed_from ensembl:ENSG00000139618 ;
				a ?type;
				dc:identifier ?id .
    OPTIONAL {
      ?transcript faldo:location ?location .
      ?location faldo:begin [faldo:position ?begin] .
      ?location faldo:end [faldo:position ?end ] .
      ?location faldo:reference ?reference .
    }
    OPTIONAL {?type rdfs:label ?typeLabel}
}
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 ensembl: <http://rdf.ebi.ac.uk/resource/ensembl/>  '...
'PREFIX faldo: <http://biohackathon.org/resource/faldo#>  '...
'PREFIX obo: <http://purl.obolibrary.org/obo/>  '...
'PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>  '...
' '...
'SELECT DISTINCT ?transcript ?id ?typeLabel ?reference ?begin ?end ?location  '...
'WHERE { '...
'	?transcript obo:SO_transcribed_from ensembl:ENSG00000139618 ; '...
'				a ?type; '...
'				dc:identifier ?id . '...
'    OPTIONAL { '...
'      ?transcript faldo:location ?location . '...
'      ?location faldo:begin [faldo:position ?begin] . '...
'      ?location faldo:end [faldo:position ?end ] . '...
'      ?location faldo:reference ?reference . '...
'    } '...
'    OPTIONAL {?type rdfs:label ?typeLabel} '...
'} '];

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 ensembl: <http://rdf.ebi.ac.uk/resource/ensembl/> 
PREFIX faldo: <http://biohackathon.org/resource/faldo#> 
PREFIX obo: <http://purl.obolibrary.org/obo/> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 

SELECT DISTINCT ?transcript ?id ?typeLabel ?reference ?begin ?end ?location 
WHERE {
	?transcript obo:SO_transcribed_from ensembl:ENSG00000139618 ;
				a ?type;
				dc:identifier ?id .
    OPTIONAL {
      ?transcript faldo:location ?location .
      ?location faldo:begin [faldo:position ?begin] .
      ?location faldo:end [faldo:position ?end ] .
      ?location faldo:reference ?reference .
    }
    OPTIONAL {?type rdfs:label ?typeLabel}
}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.Endpoint;
import java.util.ArrayList;
import java.util.HashMap;

public class Main {

    public static void main(String[] args) {
        try {
            Endpoint sp = new Endpoint("https://www.ebi.ac.uk/rdf/services/sparql";, false);

            String querySelect = 'PREFIX dc: <http://purl.org/dc/elements/1.1/>  \n'
                    + 'PREFIX ensembl: <http://rdf.ebi.ac.uk/resource/ensembl/>  \n'
                    + 'PREFIX faldo: <http://biohackathon.org/resource/faldo#>  \n'
                    + 'PREFIX obo: <http://purl.obolibrary.org/obo/>  \n'
                    + 'PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>  \n'
                    + ' \n'
                    + 'SELECT DISTINCT ?transcript ?id ?typeLabel ?reference ?begin ?end ?location  \n'
                    + 'WHERE { \n'
                    + '	?transcript obo:SO_transcribed_from ensembl:ENSG00000139618 ; \n'
                    + '				a ?type; \n'
                    + '				dc:identifier ?id . \n'
                    + '    OPTIONAL { \n'
                    + '      ?transcript faldo:location ?location . \n'
                    + '      ?location faldo:begin [faldo:position ?begin] . \n'
                    + '      ?location faldo:end [faldo:position ?end ] . \n'
                    + '      ?location faldo:reference ?reference . \n'
                    + '    } \n'
                    + '    OPTIONAL {?type rdfs:label ?typeLabel} \n'
                    + '} \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 !
TODO