SPARQL query: Retrieve all PRO terms that represent a specified protein modification form

Karima Rafes

Retrieve all PRO terms that represent a specified protein modification form

The following query will retrieve all PRO terms that represent acetylated proteins. More precisely, the results will be terms and that contain the word "acetylated" that are also categorized as modified. To search for other types of modifications, substitute a modification of interest on the VALUES line (first indented line within the WHERE block).

Please note: the quotes are required.

Examples: phosphorylated methylated ubiquitinated sumoylated glycosylated

Reuse these data in your code

Query, endpoint and code for reusing the same data

Endpoint:

https://sparql.proconsortium.org/virtuoso/sparql

Query:

PREFIX owl: <http://www.w3.org/2002/07/owl#> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
 
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX pr: <http://purl.obolibrary.org/obo/pr#>
SELECT DISTINCT ?PRO_term ?Label ?Category ?PRO_short_label ?PRO_proteoform_std
FROM <http://purl.obolibrary.org/obo/pr>
WHERE
{
   VALUES ?mod { "acetylated" }
   ?PRO_term rdfs:label ?_Label .
   ?PRO_term rdfs:comment ?_Category .
   OPTIONAL {
     ?x a owl:Axiom .
     ?x oboInOwl:hasSynonymType pr:PRO-short-label .
     ?x owl:annotatedSource ?PRO_term .
     ?x owl:annotatedTarget ?_PRO_short_label
   } . 
   OPTIONAL {
     ?y a owl:Axiom .
     ?y oboInOwl:hasSynonymType pr:PRO-proteoform-std .
     ?y owl:annotatedSource ?PRO_term .
     ?y owl:annotatedTarget ?_PRO_proteoform_std
  } . 
   FILTER (regex(?_Category,"Category=.*modification")
     && regex(?Label, CONCAT(" ", ?mod))) .
   BIND(str(?_Label) as ?Label) .
   BIND(strafter(strbefore(str(?_Category), "."), "=") as ?Category) .
   BIND(str(?_PRO_short_label) as ?PRO_short_label)
   BIND(str(?_PRO_proteoform_std) as ?PRO_proteoform_std)
}
ORDER BY ASC(?_PRO_short_label)
LIMIT 100

Howto write a query SPARQL? (in French)

{{#sparql:PREFIX owl: <http://www.w3.org/2002/07/owl#> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
 
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX pr: <http://purl.obolibrary.org/obo/pr#>
SELECT DISTINCT ?PRO_term ?Label ?Category ?PRO_short_label ?PRO_proteoform_std
FROM <http://purl.obolibrary.org/obo/pr>
WHERE
{
   VALUES ?mod { "acetylated" }
   ?PRO_term rdfs:label ?_Label .
   ?PRO_term rdfs:comment ?_Category .
   OPTIONAL {
     ?x a owl:Axiom .
     ?x oboInOwl:hasSynonymType pr:PRO-short-label .
     ?x owl:annotatedSource ?PRO_term .
     ?x owl:annotatedTarget ?_PRO_short_label
   } . 
   OPTIONAL {
     ?y a owl:Axiom .
     ?y oboInOwl:hasSynonymType pr:PRO-proteoform-std .
     ?y owl:annotatedSource ?PRO_term .
     ?y owl:annotatedTarget ?_PRO_proteoform_std
  } . 
   FILTER (regex(?_Category,"Category=.*modification")
     && regex(?Label, CONCAT(" ", ?mod))) .
   BIND(str(?_Label) as ?Label) .
   BIND(strafter(strbefore(str(?_Category), "."), "=") as ?Category) .
   BIND(str(?_PRO_short_label) as ?PRO_short_label)
   BIND(str(?_PRO_proteoform_std) as ?PRO_proteoform_std)
}
ORDER BY ASC(?_PRO_short_label)
LIMIT 100
| endpoint = https://sparql.proconsortium.org/virtuoso/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://sparql.proconsortium.org/virtuoso/sparql";
    var query = `PREFIX owl: <http://www.w3.org/2002/07/owl#> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
 
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX pr: <http://purl.obolibrary.org/obo/pr#>
SELECT DISTINCT ?PRO_term ?Label ?Category ?PRO_short_label ?PRO_proteoform_std
FROM <http://purl.obolibrary.org/obo/pr>
WHERE
{
   VALUES ?mod { \"acetylated\" }
   ?PRO_term rdfs:label ?_Label .
   ?PRO_term rdfs:comment ?_Category .
   OPTIONAL {
     ?x a owl:Axiom .
     ?x oboInOwl:hasSynonymType pr:PRO-short-label .
     ?x owl:annotatedSource ?PRO_term .
     ?x owl:annotatedTarget ?_PRO_short_label
   } . 
   OPTIONAL {
     ?y a owl:Axiom .
     ?y oboInOwl:hasSynonymType pr:PRO-proteoform-std .
     ?y owl:annotatedSource ?PRO_term .
     ?y owl:annotatedTarget ?_PRO_proteoform_std
  } . 
   FILTER (regex(?_Category,\"Category=.*modification\")
     && regex(?Label, CONCAT(\" \", ?mod))) .
   BIND(str(?_Label) as ?Label) .
   BIND(strafter(strbefore(str(?_Category), \".\"), \"=\") as ?Category) .
   BIND(str(?_PRO_short_label) as ?PRO_short_label)
   BIND(str(?_PRO_proteoform_std) as ?PRO_proteoform_std)
}
ORDER BY ASC(?_PRO_short_label)
LIMIT 100`;

   // $('#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://sparql.proconsortium.org/virtuoso/sparql");
    var params = {query:`PREFIX owl: <http://www.w3.org/2002/07/owl#> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
 
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX pr: <http://purl.obolibrary.org/obo/pr#>
SELECT DISTINCT ?PRO_term ?Label ?Category ?PRO_short_label ?PRO_proteoform_std
FROM <http://purl.obolibrary.org/obo/pr>
WHERE
{
   VALUES ?mod { \"acetylated\" }
   ?PRO_term rdfs:label ?_Label .
   ?PRO_term rdfs:comment ?_Category .
   OPTIONAL {
     ?x a owl:Axiom .
     ?x oboInOwl:hasSynonymType pr:PRO-short-label .
     ?x owl:annotatedSource ?PRO_term .
     ?x owl:annotatedTarget ?_PRO_short_label
   } . 
   OPTIONAL {
     ?y a owl:Axiom .
     ?y oboInOwl:hasSynonymType pr:PRO-proteoform-std .
     ?y owl:annotatedSource ?PRO_term .
     ?y owl:annotatedTarget ?_PRO_proteoform_std
  } . 
   FILTER (regex(?_Category,\"Category=.*modification\")
     && regex(?Label, CONCAT(\" \", ?mod))) .
   BIND(str(?_Label) as ?Label) .
   BIND(strafter(strbefore(str(?_Category), \".\"), \"=\") as ?Category) .
   BIND(str(?_PRO_short_label) as ?PRO_short_label)
   BIND(str(?_PRO_proteoform_std) as ?PRO_proteoform_std)
}
ORDER BY ASC(?_PRO_short_label)
LIMIT 100`};

    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://sparql.proconsortium.org/virtuoso/sparql"
   data-sgvizler-query="PREFIX owl: &lt;http://www.w3.org/2002/07/owl#&gt; 
PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; 
 
PREFIX oboInOwl: &lt;http://www.geneontology.org/formats/oboInOwl#&gt;
PREFIX pr: &lt;http://purl.obolibrary.org/obo/pr#&gt;
SELECT DISTINCT ?PRO_term ?Label ?Category ?PRO_short_label ?PRO_proteoform_std
FROM &lt;http://purl.obolibrary.org/obo/pr&gt;
WHERE
{
   VALUES ?mod { &quot;acetylated&quot; }
   ?PRO_term rdfs:label ?_Label .
   ?PRO_term rdfs:comment ?_Category .
   OPTIONAL {
     ?x a owl:Axiom .
     ?x oboInOwl:hasSynonymType pr:PRO-short-label .
     ?x owl:annotatedSource ?PRO_term .
     ?x owl:annotatedTarget ?_PRO_short_label
   } . 
   OPTIONAL {
     ?y a owl:Axiom .
     ?y oboInOwl:hasSynonymType pr:PRO-proteoform-std .
     ?y owl:annotatedSource ?PRO_term .
     ?y owl:annotatedTarget ?_PRO_proteoform_std
  } . 
   FILTER (regex(?_Category,&quot;Category=.*modification&quot;)
     &amp;&amp; regex(?Label, CONCAT(&quot; &quot;, ?mod))) .
   BIND(str(?_Label) as ?Label) .
   BIND(strafter(strbefore(str(?_Category), &quot;.&quot;), &quot;=&quot;) as ?Category) .
   BIND(str(?_PRO_short_label) as ?PRO_short_label)
   BIND(str(?_PRO_proteoform_std) as ?PRO_proteoform_std)
}
ORDER BY ASC(?_PRO_short_label)
LIMIT 100"
    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://sparql.proconsortium.org/virtuoso/sparql")
sparql.setQuery("""
    PREFIX owl: <http://www.w3.org/2002/07/owl#> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
 
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX pr: <http://purl.obolibrary.org/obo/pr#>
SELECT DISTINCT ?PRO_term ?Label ?Category ?PRO_short_label ?PRO_proteoform_std
FROM <http://purl.obolibrary.org/obo/pr>
WHERE
{
   VALUES ?mod { "acetylated" }
   ?PRO_term rdfs:label ?_Label .
   ?PRO_term rdfs:comment ?_Category .
   OPTIONAL {
     ?x a owl:Axiom .
     ?x oboInOwl:hasSynonymType pr:PRO-short-label .
     ?x owl:annotatedSource ?PRO_term .
     ?x owl:annotatedTarget ?_PRO_short_label
   } . 
   OPTIONAL {
     ?y a owl:Axiom .
     ?y oboInOwl:hasSynonymType pr:PRO-proteoform-std .
     ?y owl:annotatedSource ?PRO_term .
     ?y owl:annotatedTarget ?_PRO_proteoform_std
  } . 
   FILTER (regex(?_Category,"Category=.*modification")
     && regex(?Label, CONCAT(" ", ?mod))) .
   BIND(str(?_Label) as ?Label) .
   BIND(strafter(strbefore(str(?_Category), "."), "=") as ?Category) .
   BIND(str(?_PRO_short_label) as ?PRO_short_label)
   BIND(str(?_PRO_proteoform_std) as ?PRO_proteoform_std)
}
ORDER BY ASC(?_PRO_short_label)
LIMIT 100""")
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://sparql.proconsortium.org/virtuoso/sparql"
# create query statement
    query <- "PREFIX owl: <http://www.w3.org/2002/07/owl#> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
 
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX pr: <http://purl.obolibrary.org/obo/pr#>
SELECT DISTINCT ?PRO_term ?Label ?Category ?PRO_short_label ?PRO_proteoform_std
FROM <http://purl.obolibrary.org/obo/pr>
WHERE
{
   VALUES ?mod { "acetylated" }
   ?PRO_term rdfs:label ?_Label .
   ?PRO_term rdfs:comment ?_Category .
   OPTIONAL {
     ?x a owl:Axiom .
     ?x oboInOwl:hasSynonymType pr:PRO-short-label .
     ?x owl:annotatedSource ?PRO_term .
     ?x owl:annotatedTarget ?_PRO_short_label
   } . 
   OPTIONAL {
     ?y a owl:Axiom .
     ?y oboInOwl:hasSynonymType pr:PRO-proteoform-std .
     ?y owl:annotatedSource ?PRO_term .
     ?y owl:annotatedTarget ?_PRO_proteoform_std
  } . 
   FILTER (regex(?_Category,"Category=.*modification")
     && regex(?Label, CONCAT(" ", ?mod))) .
   BIND(str(?_Label) as ?Label) .
   BIND(strafter(strbefore(str(?_Category), "."), "=") as ?Category) .
   BIND(str(?_PRO_short_label) as ?PRO_short_label)
   BIND(str(?_PRO_proteoform_std) as ?PRO_proteoform_std)
}
ORDER BY ASC(?_PRO_short_label)
LIMIT 100"
# 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://sparql.proconsortium.org/virtuoso/sparql"
sparql = <<-EOT
PREFIX owl: <http://www.w3.org/2002/07/owl#> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
 
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX pr: <http://purl.obolibrary.org/obo/pr#>
SELECT DISTINCT ?PRO_term ?Label ?Category ?PRO_short_label ?PRO_proteoform_std
FROM <http://purl.obolibrary.org/obo/pr>
WHERE
{
   VALUES ?mod { "acetylated" }
   ?PRO_term rdfs:label ?_Label .
   ?PRO_term rdfs:comment ?_Category .
   OPTIONAL {
     ?x a owl:Axiom .
     ?x oboInOwl:hasSynonymType pr:PRO-short-label .
     ?x owl:annotatedSource ?PRO_term .
     ?x owl:annotatedTarget ?_PRO_short_label
   } . 
   OPTIONAL {
     ?y a owl:Axiom .
     ?y oboInOwl:hasSynonymType pr:PRO-proteoform-std .
     ?y owl:annotatedSource ?PRO_term .
     ?y owl:annotatedTarget ?_PRO_proteoform_std
  } . 
   FILTER (regex(?_Category,"Category=.*modification")
     && regex(?Label, CONCAT(" ", ?mod))) .
   BIND(str(?_Label) as ?Label) .
   BIND(strafter(strbefore(str(?_Category), "."), "=") as ?Category) .
   BIND(str(?_PRO_short_label) as ?PRO_short_label)
   BIND(str(?_PRO_proteoform_std) as ?PRO_proteoform_std)
}
ORDER BY ASC(?_PRO_short_label)
LIMIT 100
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://sparql.proconsortium.org/virtuoso/sparql';

query = ['PREFIX owl: <http://www.w3.org/2002/07/owl#>  '...
'PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>  '...
'  '...
'PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#> '...
'PREFIX pr: <http://purl.obolibrary.org/obo/pr#> '...
'SELECT DISTINCT ?PRO_term ?Label ?Category ?PRO_short_label ?PRO_proteoform_std '...
'FROM <http://purl.obolibrary.org/obo/pr> '...
'WHERE '...
'{ '...
'   VALUES ?mod { "acetylated" } '...
'   ?PRO_term rdfs:label ?_Label . '...
'   ?PRO_term rdfs:comment ?_Category . '...
'   OPTIONAL { '...
'     ?x a owl:Axiom . '...
'     ?x oboInOwl:hasSynonymType pr:PRO-short-label . '...
'     ?x owl:annotatedSource ?PRO_term . '...
'     ?x owl:annotatedTarget ?_PRO_short_label '...
'   } .  '...
'   OPTIONAL { '...
'     ?y a owl:Axiom . '...
'     ?y oboInOwl:hasSynonymType pr:PRO-proteoform-std . '...
'     ?y owl:annotatedSource ?PRO_term . '...
'     ?y owl:annotatedTarget ?_PRO_proteoform_std '...
'  } .  '...
'   FILTER (regex(?_Category,"Category=.*modification") '...
'     && regex(?Label, CONCAT(" ", ?mod))) . '...
'   BIND(str(?_Label) as ?Label) . '...
'   BIND(strafter(strbefore(str(?_Category), "."), "=") as ?Category) . '...
'   BIND(str(?_PRO_short_label) as ?PRO_short_label) '...
'   BIND(str(?_PRO_proteoform_std) as ?PRO_proteoform_std) '...
'} '...
'ORDER BY ASC(?_PRO_short_label) '...
'LIMIT 100 '];

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://sparql.proconsortium.org/virtuoso/sparql";
$sp_readonly = new SparqlClient();
$sp_readonly->setEndpointRead($endpoint);
$q = <<<EOD
PREFIX owl: <http://www.w3.org/2002/07/owl#> 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
 
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX pr: <http://purl.obolibrary.org/obo/pr#>
SELECT DISTINCT ?PRO_term ?Label ?Category ?PRO_short_label ?PRO_proteoform_std
FROM <http://purl.obolibrary.org/obo/pr>
WHERE
{
   VALUES ?mod { "acetylated" }
   ?PRO_term rdfs:label ?_Label .
   ?PRO_term rdfs:comment ?_Category .
   OPTIONAL {
     ?x a owl:Axiom .
     ?x oboInOwl:hasSynonymType pr:PRO-short-label .
     ?x owl:annotatedSource ?PRO_term .
     ?x owl:annotatedTarget ?_PRO_short_label
   } . 
   OPTIONAL {
     ?y a owl:Axiom .
     ?y oboInOwl:hasSynonymType pr:PRO-proteoform-std .
     ?y owl:annotatedSource ?PRO_term .
     ?y owl:annotatedTarget ?_PRO_proteoform_std
  } . 
   FILTER (regex(?_Category,"Category=.*modification")
     && regex(?Label, CONCAT(" ", ?mod))) .
   BIND(str(?_Label) as ?Label) .
   BIND(strafter(strbefore(str(?_Category), "."), "=") as ?Category) .
   BIND(str(?_PRO_short_label) as ?PRO_short_label)
   BIND(str(?_PRO_proteoform_std) as ?PRO_proteoform_std)
}
ORDER BY ASC(?_PRO_short_label)
LIMIT 100
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://sparql.proconsortium.org/virtuoso/sparql");
            String querySelect  = "PREFIX owl: <http://www.w3.org/2002/07/owl#>  \n"
                    + "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>  \n"
                    + "  \n"
                    + "PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#> \n"
                    + "PREFIX pr: <http://purl.obolibrary.org/obo/pr#> \n"
                    + "SELECT DISTINCT ?PRO_term ?Label ?Category ?PRO_short_label ?PRO_proteoform_std \n"
                    + "FROM <http://purl.obolibrary.org/obo/pr> \n"
                    + "WHERE \n"
                    + "{ \n"
                    + "   VALUES ?mod { \"acetylated\" } \n"
                    + "   ?PRO_term rdfs:label ?_Label . \n"
                    + "   ?PRO_term rdfs:comment ?_Category . \n"
                    + "   OPTIONAL { \n"
                    + "     ?x a owl:Axiom . \n"
                    + "     ?x oboInOwl:hasSynonymType pr:PRO-short-label . \n"
                    + "     ?x owl:annotatedSource ?PRO_term . \n"
                    + "     ?x owl:annotatedTarget ?_PRO_short_label \n"
                    + "   } .  \n"
                    + "   OPTIONAL { \n"
                    + "     ?y a owl:Axiom . \n"
                    + "     ?y oboInOwl:hasSynonymType pr:PRO-proteoform-std . \n"
                    + "     ?y owl:annotatedSource ?PRO_term . \n"
                    + "     ?y owl:annotatedTarget ?_PRO_proteoform_std \n"
                    + "  } .  \n"
                    + "   FILTER (regex(?_Category,\"Category=.*modification\") \n"
                    + "     && regex(?Label, CONCAT(\" \", ?mod))) . \n"
                    + "   BIND(str(?_Label) as ?Label) . \n"
                    + "   BIND(strafter(strbefore(str(?_Category), \".\"), \"=\") as ?Category) . \n"
                    + "   BIND(str(?_PRO_short_label) as ?PRO_short_label) \n"
                    + "   BIND(str(?_PRO_proteoform_std) as ?PRO_proteoform_std) \n"
                    + "} \n"
                    + "ORDER BY ASC(?_PRO_short_label) \n"
                    + "LIMIT 100 \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