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All anatomic entities in Rattus norvegicus where the APOC1 gene is expresse
For example, to retrieve all anatomic entities in Rattus norvegicus where the APOC1 gene is expresse
For example, to retrieve all anatomic entities in Rattus norvegicus where the APOC1 gene is expresse

Reuse these data in your code

Query, endpoint and code for reusing the same data
https://bgee.org/sparql
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
PREFIX orth: <http://purl.org/net/orth#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX genex: <http://purl.org/genex#>
PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT DISTINCT ?anatEntity ?anatName {
    ?seq a orth:Gene .
    ?seq rdfs:label ?geneName .
    ?seq genex:isExpressedIn ?cond .
    ?cond genex:hasAnatomicalEntity ?anatEntity .
    ?anatEntity rdfs:label ?anatName .
    ?cond obo:RO_0002162 <http://purl.uniprot.org/taxonomy/10116> . 
    FILTER (LCASE(?geneName) = LCASE('APOC1'))
}
Howto write a query SPARQL? (in French)
{{#sparql:PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
PREFIX orth: <http://purl.org/net/orth#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX genex: <http://purl.org/genex#>
PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT DISTINCT ?anatEntity ?anatName {
    ?seq a orth:Gene .
    ?seq rdfs:label ?geneName .
    ?seq genex:isExpressedIn ?cond .
    ?cond genex:hasAnatomicalEntity ?anatEntity .
    ?anatEntity rdfs:label ?anatName .
    ?cond obo:RO_0002162 <http://purl.uniprot.org/taxonomy/10116> . 
    FILTER (LCASE(?geneName) = LCASE('APOC1'))
}
| endpoint = https://bgee.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://bgee.org/sparql";
    var query = `PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
PREFIX orth: <http://purl.org/net/orth#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX genex: <http://purl.org/genex#>
PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT DISTINCT ?anatEntity ?anatName {
    ?seq a orth:Gene .
    ?seq rdfs:label ?geneName .
    ?seq genex:isExpressedIn ?cond .
    ?cond genex:hasAnatomicalEntity ?anatEntity .
    ?anatEntity rdfs:label ?anatName .
    ?cond obo:RO_0002162 <http://purl.uniprot.org/taxonomy/10116> . 
    FILTER (LCASE(?geneName) = LCASE(\'APOC1\'))
}`;

   // $('#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://bgee.org/sparql");
    var params = {query:`PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
PREFIX orth: <http://purl.org/net/orth#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX genex: <http://purl.org/genex#>
PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT DISTINCT ?anatEntity ?anatName {
    ?seq a orth:Gene .
    ?seq rdfs:label ?geneName .
    ?seq genex:isExpressedIn ?cond .
    ?cond genex:hasAnatomicalEntity ?anatEntity .
    ?anatEntity rdfs:label ?anatName .
    ?cond obo:RO_0002162 <http://purl.uniprot.org/taxonomy/10116> . 
    FILTER (LCASE(?geneName) = LCASE(\'APOC1\'))
}`};

    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://bgee.org/sparql"
   data-sgvizler-query="PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; 
PREFIX orth: &lt;http://purl.org/net/orth#&gt;
PREFIX up: &lt;http://purl.uniprot.org/core/&gt;
PREFIX genex: &lt;http://purl.org/genex#&gt;
PREFIX obo: &lt;http://purl.obolibrary.org/obo/&gt;

SELECT DISTINCT ?anatEntity ?anatName {
    ?seq a orth:Gene .
    ?seq rdfs:label ?geneName .
    ?seq genex:isExpressedIn ?cond .
    ?cond genex:hasAnatomicalEntity ?anatEntity .
    ?anatEntity rdfs:label ?anatName .
    ?cond obo:RO_0002162 &lt;http://purl.uniprot.org/taxonomy/10116&gt; . 
    FILTER (LCASE(?geneName) = LCASE(&#039;APOC1&#039;))
}"
    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://bgee.org/sparql")
sparql.setQuery("""
    PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
PREFIX orth: <http://purl.org/net/orth#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX genex: <http://purl.org/genex#>
PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT DISTINCT ?anatEntity ?anatName {
    ?seq a orth:Gene .
    ?seq rdfs:label ?geneName .
    ?seq genex:isExpressedIn ?cond .
    ?cond genex:hasAnatomicalEntity ?anatEntity .
    ?anatEntity rdfs:label ?anatName .
    ?cond obo:RO_0002162 <http://purl.uniprot.org/taxonomy/10116> . 
    FILTER (LCASE(?geneName) = LCASE('APOC1'))
}""")
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://bgee.org/sparql"
# create query statement
    query <- "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
PREFIX orth: <http://purl.org/net/orth#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX genex: <http://purl.org/genex#>
PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT DISTINCT ?anatEntity ?anatName {
    ?seq a orth:Gene .
    ?seq rdfs:label ?geneName .
    ?seq genex:isExpressedIn ?cond .
    ?cond genex:hasAnatomicalEntity ?anatEntity .
    ?anatEntity rdfs:label ?anatName .
    ?cond obo:RO_0002162 <http://purl.uniprot.org/taxonomy/10116> . 
    FILTER (LCASE(?geneName) = LCASE('APOC1'))
}"
# 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://bgee.org/sparql"
sparql = <<-EOT
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
PREFIX orth: <http://purl.org/net/orth#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX genex: <http://purl.org/genex#>
PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT DISTINCT ?anatEntity ?anatName {
    ?seq a orth:Gene .
    ?seq rdfs:label ?geneName .
    ?seq genex:isExpressedIn ?cond .
    ?cond genex:hasAnatomicalEntity ?anatEntity .
    ?anatEntity rdfs:label ?anatName .
    ?cond obo:RO_0002162 <http://purl.uniprot.org/taxonomy/10116> . 
    FILTER (LCASE(?geneName) = LCASE('APOC1'))
}
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://bgee.org/sparql';

query = ['PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>  '...
'PREFIX orth: <http://purl.org/net/orth#> '...
'PREFIX up: <http://purl.uniprot.org/core/> '...
'PREFIX genex: <http://purl.org/genex#> '...
'PREFIX obo: <http://purl.obolibrary.org/obo/> '...
' '...
'SELECT DISTINCT ?anatEntity ?anatName { '...
'    ?seq a orth:Gene . '...
'    ?seq rdfs:label ?geneName . '...
'    ?seq genex:isExpressedIn ?cond . '...
'    ?cond genex:hasAnatomicalEntity ?anatEntity . '...
'    ?anatEntity rdfs:label ?anatName . '...
'    ?cond obo:RO_0002162 <http://purl.uniprot.org/taxonomy/10116> .  '...
'    FILTER (LCASE(?geneName) = LCASE('APOC1')) '...
'} '];

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://bgee.org/sparql";
$sp_readonly = new SparqlClient();
$sp_readonly->setEndpointRead($endpoint);
$q = <<<EOD
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
PREFIX orth: <http://purl.org/net/orth#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX genex: <http://purl.org/genex#>
PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT DISTINCT ?anatEntity ?anatName {
    ?seq a orth:Gene .
    ?seq rdfs:label ?geneName .
    ?seq genex:isExpressedIn ?cond .
    ?cond genex:hasAnatomicalEntity ?anatEntity .
    ?anatEntity rdfs:label ?anatName .
    ?cond obo:RO_0002162 <http://purl.uniprot.org/taxonomy/10116> . 
    FILTER (LCASE(?geneName) = LCASE('APOC1'))
}
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://bgee.org/sparql");
            String querySelect  = "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>  \n"
                    + "PREFIX orth: <http://purl.org/net/orth#> \n"
                    + "PREFIX up: <http://purl.uniprot.org/core/> \n"
                    + "PREFIX genex: <http://purl.org/genex#> \n"
                    + "PREFIX obo: <http://purl.obolibrary.org/obo/> \n"
                    + " \n"
                    + "SELECT DISTINCT ?anatEntity ?anatName { \n"
                    + "    ?seq a orth:Gene . \n"
                    + "    ?seq rdfs:label ?geneName . \n"
                    + "    ?seq genex:isExpressedIn ?cond . \n"
                    + "    ?cond genex:hasAnatomicalEntity ?anatEntity . \n"
                    + "    ?anatEntity rdfs:label ?anatName . \n"
                    + "    ?cond obo:RO_0002162 <http://purl.uniprot.org/taxonomy/10116> .  \n"
                    + "    FILTER (LCASE(?geneName) = LCASE(\'APOC1\')) \n"
                    + "} \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