SPARQL query: Retrieve all PRO terms that pertain to products of a specified gene

Karima Rafes

Retrieve all PRO terms that pertain to products of a specified gene

The following query finds all PRO terms that pertain to products of the mouse Ctnnb1 gene, denoted by MGI:88276. To retrieve the analogous list for a different gene of interest, please substitute MGI:88276 with the relevant database prefix (selected from the first PREFIX block below), along with a precise identifier. For example, to get all PRO terms relevant to human NCOA3, replace MGI:88276 with HGNC:7670 on the VALUES line (first indented line within the WHERE block), or to get those relevant to fission yeast hht3, replace with PomBase:SPBC1105.11c.

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 HGNC: <http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=>
PREFIX CGNC: <http://birdgenenames.org/cgnc/GeneReport?id=>
PREFIX MGI: <http://www.informatics.jax.org/marker/MGI:>
PREFIX EcoGene: <http://www.ecogene.org/gene/>
PREFIX SGD: <http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=>
PREFIX PomBase: <http://www.pombase.org/spombe/result/>
PREFIX dictyBase: <http://dictybase.org/gene/>
PREFIX FlyBase: <http://flybase.org/reports/>
PREFIX RGD: <http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=>
PREFIX TAIR: <http://www.arabidopsis.org/servlets/TairObject?type=locus&name=>
PREFIX Araport: <https://www.araport.org/locus/>
PREFIX WormBase: <http://www.wormbase.org/species/c_elegans/gene/>
PREFIX ZFIN: <http://zfin.org/action/marker/view/>
 
PREFIX has_gene_template: <http://purl.obolibrary.org/obo/pr#has_gene_template>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX pr: <http://purl.obolibrary.org/obo/pr#>

SELECT DISTINCT ?PRO_term ?Label ?Gene ?PRO_short_label ?PRO_proteoform_std
FROM <http://purl.obolibrary.org/obo/pr>
WHERE
{
   VALUES ?gn_id { MGI:88276 }
   ?PRO_term rdfs:subClassOf+ ?r . 
   ?r owl:onProperty has_gene_template: . 
   ?r owl:someValuesFrom ?gn_id . 
   ?PRO_term rdfs:label ?_Label .
   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
   } . 
   OPTIONAL {
     ?gn_id rdfs:label ?g
   } .
   bind(str(?_Label) as ?Label)
   bind(str(?_PRO_short_label) as ?PRO_short_label)
   bind(str(?_PRO_proteoform_std) as ?PRO_proteoform_std)
   bind(str(?g) as ?Gene)
}
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 HGNC: <http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=>
PREFIX CGNC: <http://birdgenenames.org/cgnc/GeneReport?id=>
PREFIX MGI: <http://www.informatics.jax.org/marker/MGI:>
PREFIX EcoGene: <http://www.ecogene.org/gene/>
PREFIX SGD: <http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=>
PREFIX PomBase: <http://www.pombase.org/spombe/result/>
PREFIX dictyBase: <http://dictybase.org/gene/>
PREFIX FlyBase: <http://flybase.org/reports/>
PREFIX RGD: <http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=>
PREFIX TAIR: <http://www.arabidopsis.org/servlets/TairObject?type=locus&name=>
PREFIX Araport: <https://www.araport.org/locus/>
PREFIX WormBase: <http://www.wormbase.org/species/c_elegans/gene/>
PREFIX ZFIN: <http://zfin.org/action/marker/view/>
 
PREFIX has_gene_template: <http://purl.obolibrary.org/obo/pr#has_gene_template>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX pr: <http://purl.obolibrary.org/obo/pr#>

SELECT DISTINCT ?PRO_term ?Label ?Gene ?PRO_short_label ?PRO_proteoform_std
FROM <http://purl.obolibrary.org/obo/pr>
WHERE
{
   VALUES ?gn_id { MGI:88276 }
   ?PRO_term rdfs:subClassOf+ ?r . 
   ?r owl:onProperty has_gene_template: . 
   ?r owl:someValuesFrom ?gn_id . 
   ?PRO_term rdfs:label ?_Label .
   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
   } . 
   OPTIONAL {
     ?gn_id rdfs:label ?g
   } .
   bind(str(?_Label) as ?Label)
   bind(str(?_PRO_short_label) as ?PRO_short_label)
   bind(str(?_PRO_proteoform_std) as ?PRO_proteoform_std)
   bind(str(?g) as ?Gene)
}
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 HGNC: <http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=>
PREFIX CGNC: <http://birdgenenames.org/cgnc/GeneReport?id=>
PREFIX MGI: <http://www.informatics.jax.org/marker/MGI:>
PREFIX EcoGene: <http://www.ecogene.org/gene/>
PREFIX SGD: <http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=>
PREFIX PomBase: <http://www.pombase.org/spombe/result/>
PREFIX dictyBase: <http://dictybase.org/gene/>
PREFIX FlyBase: <http://flybase.org/reports/>
PREFIX RGD: <http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=>
PREFIX TAIR: <http://www.arabidopsis.org/servlets/TairObject?type=locus&name=>
PREFIX Araport: <https://www.araport.org/locus/>
PREFIX WormBase: <http://www.wormbase.org/species/c_elegans/gene/>
PREFIX ZFIN: <http://zfin.org/action/marker/view/>
 
PREFIX has_gene_template: <http://purl.obolibrary.org/obo/pr#has_gene_template>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX pr: <http://purl.obolibrary.org/obo/pr#>

SELECT DISTINCT ?PRO_term ?Label ?Gene ?PRO_short_label ?PRO_proteoform_std
FROM <http://purl.obolibrary.org/obo/pr>
WHERE
{
   VALUES ?gn_id { MGI:88276 }
   ?PRO_term rdfs:subClassOf+ ?r . 
   ?r owl:onProperty has_gene_template: . 
   ?r owl:someValuesFrom ?gn_id . 
   ?PRO_term rdfs:label ?_Label .
   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
   } . 
   OPTIONAL {
     ?gn_id rdfs:label ?g
   } .
   bind(str(?_Label) as ?Label)
   bind(str(?_PRO_short_label) as ?PRO_short_label)
   bind(str(?_PRO_proteoform_std) as ?PRO_proteoform_std)
   bind(str(?g) as ?Gene)
}
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 HGNC: <http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=>
PREFIX CGNC: <http://birdgenenames.org/cgnc/GeneReport?id=>
PREFIX MGI: <http://www.informatics.jax.org/marker/MGI:>
PREFIX EcoGene: <http://www.ecogene.org/gene/>
PREFIX SGD: <http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=>
PREFIX PomBase: <http://www.pombase.org/spombe/result/>
PREFIX dictyBase: <http://dictybase.org/gene/>
PREFIX FlyBase: <http://flybase.org/reports/>
PREFIX RGD: <http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=>
PREFIX TAIR: <http://www.arabidopsis.org/servlets/TairObject?type=locus&name=>
PREFIX Araport: <https://www.araport.org/locus/>
PREFIX WormBase: <http://www.wormbase.org/species/c_elegans/gene/>
PREFIX ZFIN: <http://zfin.org/action/marker/view/>
 
PREFIX has_gene_template: <http://purl.obolibrary.org/obo/pr#has_gene_template>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX pr: <http://purl.obolibrary.org/obo/pr#>

SELECT DISTINCT ?PRO_term ?Label ?Gene ?PRO_short_label ?PRO_proteoform_std
FROM <http://purl.obolibrary.org/obo/pr>
WHERE
{
   VALUES ?gn_id { MGI:88276 }
   ?PRO_term rdfs:subClassOf+ ?r . 
   ?r owl:onProperty has_gene_template: . 
   ?r owl:someValuesFrom ?gn_id . 
   ?PRO_term rdfs:label ?_Label .
   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
   } . 
   OPTIONAL {
     ?gn_id rdfs:label ?g
   } .
   bind(str(?_Label) as ?Label)
   bind(str(?_PRO_short_label) as ?PRO_short_label)
   bind(str(?_PRO_proteoform_std) as ?PRO_proteoform_std)
   bind(str(?g) as ?Gene)
}
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 HGNC: &lt;http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=&gt;
PREFIX CGNC: &lt;http://birdgenenames.org/cgnc/GeneReport?id=&gt;
PREFIX MGI: &lt;http://www.informatics.jax.org/marker/MGI:&gt;
PREFIX EcoGene: &lt;http://www.ecogene.org/gene/&gt;
PREFIX SGD: &lt;http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=&gt;
PREFIX PomBase: &lt;http://www.pombase.org/spombe/result/&gt;
PREFIX dictyBase: &lt;http://dictybase.org/gene/&gt;
PREFIX FlyBase: &lt;http://flybase.org/reports/&gt;
PREFIX RGD: &lt;http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=&gt;
PREFIX TAIR: &lt;http://www.arabidopsis.org/servlets/TairObject?type=locus&amp;name=&gt;
PREFIX Araport: &lt;https://www.araport.org/locus/&gt;
PREFIX WormBase: &lt;http://www.wormbase.org/species/c_elegans/gene/&gt;
PREFIX ZFIN: &lt;http://zfin.org/action/marker/view/&gt;
 
PREFIX has_gene_template: &lt;http://purl.obolibrary.org/obo/pr#has_gene_template&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 ?Gene ?PRO_short_label ?PRO_proteoform_std
FROM &lt;http://purl.obolibrary.org/obo/pr&gt;
WHERE
{
   VALUES ?gn_id { MGI:88276 }
   ?PRO_term rdfs:subClassOf+ ?r . 
   ?r owl:onProperty has_gene_template: . 
   ?r owl:someValuesFrom ?gn_id . 
   ?PRO_term rdfs:label ?_Label .
   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
   } . 
   OPTIONAL {
     ?gn_id rdfs:label ?g
   } .
   bind(str(?_Label) as ?Label)
   bind(str(?_PRO_short_label) as ?PRO_short_label)
   bind(str(?_PRO_proteoform_std) as ?PRO_proteoform_std)
   bind(str(?g) as ?Gene)
}
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 HGNC: <http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=>
PREFIX CGNC: <http://birdgenenames.org/cgnc/GeneReport?id=>
PREFIX MGI: <http://www.informatics.jax.org/marker/MGI:>
PREFIX EcoGene: <http://www.ecogene.org/gene/>
PREFIX SGD: <http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=>
PREFIX PomBase: <http://www.pombase.org/spombe/result/>
PREFIX dictyBase: <http://dictybase.org/gene/>
PREFIX FlyBase: <http://flybase.org/reports/>
PREFIX RGD: <http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=>
PREFIX TAIR: <http://www.arabidopsis.org/servlets/TairObject?type=locus&name=>
PREFIX Araport: <https://www.araport.org/locus/>
PREFIX WormBase: <http://www.wormbase.org/species/c_elegans/gene/>
PREFIX ZFIN: <http://zfin.org/action/marker/view/>
 
PREFIX has_gene_template: <http://purl.obolibrary.org/obo/pr#has_gene_template>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX pr: <http://purl.obolibrary.org/obo/pr#>

SELECT DISTINCT ?PRO_term ?Label ?Gene ?PRO_short_label ?PRO_proteoform_std
FROM <http://purl.obolibrary.org/obo/pr>
WHERE
{
   VALUES ?gn_id { MGI:88276 }
   ?PRO_term rdfs:subClassOf+ ?r . 
   ?r owl:onProperty has_gene_template: . 
   ?r owl:someValuesFrom ?gn_id . 
   ?PRO_term rdfs:label ?_Label .
   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
   } . 
   OPTIONAL {
     ?gn_id rdfs:label ?g
   } .
   bind(str(?_Label) as ?Label)
   bind(str(?_PRO_short_label) as ?PRO_short_label)
   bind(str(?_PRO_proteoform_std) as ?PRO_proteoform_std)
   bind(str(?g) as ?Gene)
}
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 HGNC: <http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=>
PREFIX CGNC: <http://birdgenenames.org/cgnc/GeneReport?id=>
PREFIX MGI: <http://www.informatics.jax.org/marker/MGI:>
PREFIX EcoGene: <http://www.ecogene.org/gene/>
PREFIX SGD: <http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=>
PREFIX PomBase: <http://www.pombase.org/spombe/result/>
PREFIX dictyBase: <http://dictybase.org/gene/>
PREFIX FlyBase: <http://flybase.org/reports/>
PREFIX RGD: <http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=>
PREFIX TAIR: <http://www.arabidopsis.org/servlets/TairObject?type=locus&name=>
PREFIX Araport: <https://www.araport.org/locus/>
PREFIX WormBase: <http://www.wormbase.org/species/c_elegans/gene/>
PREFIX ZFIN: <http://zfin.org/action/marker/view/>
 
PREFIX has_gene_template: <http://purl.obolibrary.org/obo/pr#has_gene_template>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX pr: <http://purl.obolibrary.org/obo/pr#>

SELECT DISTINCT ?PRO_term ?Label ?Gene ?PRO_short_label ?PRO_proteoform_std
FROM <http://purl.obolibrary.org/obo/pr>
WHERE
{
   VALUES ?gn_id { MGI:88276 }
   ?PRO_term rdfs:subClassOf+ ?r . 
   ?r owl:onProperty has_gene_template: . 
   ?r owl:someValuesFrom ?gn_id . 
   ?PRO_term rdfs:label ?_Label .
   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
   } . 
   OPTIONAL {
     ?gn_id rdfs:label ?g
   } .
   bind(str(?_Label) as ?Label)
   bind(str(?_PRO_short_label) as ?PRO_short_label)
   bind(str(?_PRO_proteoform_std) as ?PRO_proteoform_std)
   bind(str(?g) as ?Gene)
}
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 HGNC: <http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=>
PREFIX CGNC: <http://birdgenenames.org/cgnc/GeneReport?id=>
PREFIX MGI: <http://www.informatics.jax.org/marker/MGI:>
PREFIX EcoGene: <http://www.ecogene.org/gene/>
PREFIX SGD: <http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=>
PREFIX PomBase: <http://www.pombase.org/spombe/result/>
PREFIX dictyBase: <http://dictybase.org/gene/>
PREFIX FlyBase: <http://flybase.org/reports/>
PREFIX RGD: <http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=>
PREFIX TAIR: <http://www.arabidopsis.org/servlets/TairObject?type=locus&name=>
PREFIX Araport: <https://www.araport.org/locus/>
PREFIX WormBase: <http://www.wormbase.org/species/c_elegans/gene/>
PREFIX ZFIN: <http://zfin.org/action/marker/view/>
 
PREFIX has_gene_template: <http://purl.obolibrary.org/obo/pr#has_gene_template>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX pr: <http://purl.obolibrary.org/obo/pr#>

SELECT DISTINCT ?PRO_term ?Label ?Gene ?PRO_short_label ?PRO_proteoform_std
FROM <http://purl.obolibrary.org/obo/pr>
WHERE
{
   VALUES ?gn_id { MGI:88276 }
   ?PRO_term rdfs:subClassOf+ ?r . 
   ?r owl:onProperty has_gene_template: . 
   ?r owl:someValuesFrom ?gn_id . 
   ?PRO_term rdfs:label ?_Label .
   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
   } . 
   OPTIONAL {
     ?gn_id rdfs:label ?g
   } .
   bind(str(?_Label) as ?Label)
   bind(str(?_PRO_short_label) as ?PRO_short_label)
   bind(str(?_PRO_proteoform_std) as ?PRO_proteoform_std)
   bind(str(?g) as ?Gene)
}
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 HGNC: <http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=> '...
'PREFIX CGNC: <http://birdgenenames.org/cgnc/GeneReport?id=> '...
'PREFIX MGI: <http://www.informatics.jax.org/marker/MGI:> '...
'PREFIX EcoGene: <http://www.ecogene.org/gene/> '...
'PREFIX SGD: <http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=> '...
'PREFIX PomBase: <http://www.pombase.org/spombe/result/> '...
'PREFIX dictyBase: <http://dictybase.org/gene/> '...
'PREFIX FlyBase: <http://flybase.org/reports/> '...
'PREFIX RGD: <http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=> '...
'PREFIX TAIR: <http://www.arabidopsis.org/servlets/TairObject?type=locus&name=> '...
'PREFIX Araport: <https://www.araport.org/locus/> '...
'PREFIX WormBase: <http://www.wormbase.org/species/c_elegans/gene/> '...
'PREFIX ZFIN: <http://zfin.org/action/marker/view/> '...
'  '...
'PREFIX has_gene_template: <http://purl.obolibrary.org/obo/pr#has_gene_template> '...
'PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#> '...
'PREFIX pr: <http://purl.obolibrary.org/obo/pr#> '...
' '...
'SELECT DISTINCT ?PRO_term ?Label ?Gene ?PRO_short_label ?PRO_proteoform_std '...
'FROM <http://purl.obolibrary.org/obo/pr> '...
'WHERE '...
'{ '...
'   VALUES ?gn_id { MGI:88276 } '...
'   ?PRO_term rdfs:subClassOf+ ?r .  '...
'   ?r owl:onProperty has_gene_template: .  '...
'   ?r owl:someValuesFrom ?gn_id .  '...
'   ?PRO_term rdfs:label ?_Label . '...
'   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 '...
'   } .  '...
'   OPTIONAL { '...
'     ?gn_id rdfs:label ?g '...
'   } . '...
'   bind(str(?_Label) as ?Label) '...
'   bind(str(?_PRO_short_label) as ?PRO_short_label) '...
'   bind(str(?_PRO_proteoform_std) as ?PRO_proteoform_std) '...
'   bind(str(?g) as ?Gene) '...
'} '...
'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 HGNC: <http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=>
PREFIX CGNC: <http://birdgenenames.org/cgnc/GeneReport?id=>
PREFIX MGI: <http://www.informatics.jax.org/marker/MGI:>
PREFIX EcoGene: <http://www.ecogene.org/gene/>
PREFIX SGD: <http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=>
PREFIX PomBase: <http://www.pombase.org/spombe/result/>
PREFIX dictyBase: <http://dictybase.org/gene/>
PREFIX FlyBase: <http://flybase.org/reports/>
PREFIX RGD: <http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=>
PREFIX TAIR: <http://www.arabidopsis.org/servlets/TairObject?type=locus&name=>
PREFIX Araport: <https://www.araport.org/locus/>
PREFIX WormBase: <http://www.wormbase.org/species/c_elegans/gene/>
PREFIX ZFIN: <http://zfin.org/action/marker/view/>
 
PREFIX has_gene_template: <http://purl.obolibrary.org/obo/pr#has_gene_template>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX pr: <http://purl.obolibrary.org/obo/pr#>

SELECT DISTINCT ?PRO_term ?Label ?Gene ?PRO_short_label ?PRO_proteoform_std
FROM <http://purl.obolibrary.org/obo/pr>
WHERE
{
   VALUES ?gn_id { MGI:88276 }
   ?PRO_term rdfs:subClassOf+ ?r . 
   ?r owl:onProperty has_gene_template: . 
   ?r owl:someValuesFrom ?gn_id . 
   ?PRO_term rdfs:label ?_Label .
   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
   } . 
   OPTIONAL {
     ?gn_id rdfs:label ?g
   } .
   bind(str(?_Label) as ?Label)
   bind(str(?_PRO_short_label) as ?PRO_short_label)
   bind(str(?_PRO_proteoform_std) as ?PRO_proteoform_std)
   bind(str(?g) as ?Gene)
}
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"
                    + "PREFIX HGNC: <http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=> \n"
                    + "PREFIX CGNC: <http://birdgenenames.org/cgnc/GeneReport?id=> \n"
                    + "PREFIX MGI: <http://www.informatics.jax.org/marker/MGI:> \n"
                    + "PREFIX EcoGene: <http://www.ecogene.org/gene/> \n"
                    + "PREFIX SGD: <http://www.yeastgenome.org/cgi-bin/locus.fpl?dbid=> \n"
                    + "PREFIX PomBase: <http://www.pombase.org/spombe/result/> \n"
                    + "PREFIX dictyBase: <http://dictybase.org/gene/> \n"
                    + "PREFIX FlyBase: <http://flybase.org/reports/> \n"
                    + "PREFIX RGD: <http://rgd.mcw.edu/rgdweb/report/gene/main.html?id=> \n"
                    + "PREFIX TAIR: <http://www.arabidopsis.org/servlets/TairObject?type=locus&name=> \n"
                    + "PREFIX Araport: <https://www.araport.org/locus/> \n"
                    + "PREFIX WormBase: <http://www.wormbase.org/species/c_elegans/gene/> \n"
                    + "PREFIX ZFIN: <http://zfin.org/action/marker/view/> \n"
                    + "  \n"
                    + "PREFIX has_gene_template: <http://purl.obolibrary.org/obo/pr#has_gene_template> \n"
                    + "PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#> \n"
                    + "PREFIX pr: <http://purl.obolibrary.org/obo/pr#> \n"
                    + " \n"
                    + "SELECT DISTINCT ?PRO_term ?Label ?Gene ?PRO_short_label ?PRO_proteoform_std \n"
                    + "FROM <http://purl.obolibrary.org/obo/pr> \n"
                    + "WHERE \n"
                    + "{ \n"
                    + "   VALUES ?gn_id { MGI:88276 } \n"
                    + "   ?PRO_term rdfs:subClassOf+ ?r .  \n"
                    + "   ?r owl:onProperty has_gene_template: .  \n"
                    + "   ?r owl:someValuesFrom ?gn_id .  \n"
                    + "   ?PRO_term rdfs:label ?_Label . \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"
                    + "   OPTIONAL { \n"
                    + "     ?gn_id rdfs:label ?g \n"
                    + "   } . \n"
                    + "   bind(str(?_Label) as ?Label) \n"
                    + "   bind(str(?_PRO_short_label) as ?PRO_short_label) \n"
                    + "   bind(str(?_PRO_proteoform_std) as ?PRO_proteoform_std) \n"
                    + "   bind(str(?g) as ?Gene) \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