LSDB Archive @ NBDC

Operation / Service Description

Started at: 2025-03-25 12:44:13 UTC
Finished at: 2025-03-25 12:44:13 UTC

The endpoint does not provide Service Description.

Elapsed time2.579 [s]
RequestMethod
GET
URL
https://dba-rdf.biosciencedbc.jp/sparql
Headers
User-Agent: Umaka-Crawler/1.0.0 by DBCLS (umakadata@dbcls.jp)
Accept: text/turtle, text/n3, application/n-triples, application/n-quads, application/rdf+xml, application/rdf+json, application/ld+json, application/trig, application/trix
Body
ResponseURL
https://dba-rdf.biosciencedbc.jp/sparql
Status
200
Headers
Date: Tue, 25 Mar 2025 12:44:05 GMT
X-Frame-Options: SAMEORIGIN, SAMEORIGIN, SAMEORIGIN, SAMEORIGIN
X-Content-Type-Options: nosniff
X-Xss-Protection: 1; mode=block
Content-Type: text/html;charset=UTF-8
Access-Control-Allow-Origin: *
X-Download-Options: noopen
Keep-Alive: timeout=5, max=99
Connection: Keep-Alive
Transfer-Encoding: chunked
Body
<!DOCTYPE html>
<html lang="ja">
  <head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="description" content="">
<meta name="author" content="">

<title>Home - LSDB Archive SPARQL Endpoint</title>

<!-- Bootstrap core CSS -->
<link href="./sparql/css/bootstrap.css" rel="stylesheet">
<link href="./sparql/css/bootstrap-select.css" rel="stylesheet">

<!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
<!--[if lt IE 9]>
  <script src="./sparql/js/html5shiv.js"></script>
  <script src="./sparql/js/respond.min.js"></script>
<![endif]-->

</head>
<body>

<div class="container">
  
  <div style="float:right;">
    <a href="?nsdecl">Namespace Prefixes</a> | <a href="?rdfinf">Inference Rules</a>
  </div>

  <div class="page-header">
    <h1>SPARQL Query Interface</h1>
  </div>

  <form role="form" action="sparql" method="get">
    <div class="form-group">
      <label class="control-label">Default Data Set Name (Graph IRI):</label>
      <input type="text" class="form-control" rows="10" name="default-graph-uri">
    </div>

    <div class="form-group">
      <label class="control-label">Query:</label>
      <textarea class="form-control" rows="10" name="query">SELECT DISTINCT ?Concept WHERE {[] a ?Concept} LIMIT 100</textarea>
    </div>

    <div class="form-group">

      <div class="form-group">
        <label class="control-label">Results Format:</label>
        <div class="controls">
          <select name="format">
            <option selected="selected" value="default">HTML</option>
            <option value="text/html">HTML (Table Only)</option>
            <!-- option value="application/vnd.ms-excel">Spreadsheet</option -->
            <option value="application/sparql-results+xml">XML</option>
            <option value="application/sparql-results+json">JSON</option>
            <option value="application/javascript">Javascript</option>
            <option value="text/turtle">Turtle</option>
            <option value="application/rdf+xml">RDF/XML</option>
            <option value="text/plain">NTriples</option>
            <option value="text/csv">CSV</option>
            <option value="text/tab-separated-values">TSV</option>
          </select>
        </div>
      </div>
    </div>

    <div class="form-group">
      <button type="submit" class="btn btn-primary">Run Query</button>
    </div>
  </form>

  <hr>

  <div class="page-header">
    <h2>Examples</h2>
  </div>

      <div>
      <p>What DBs target mammals? (哺乳類を対象にしたDBを知りたい)</p>
      <pre><a href="?query=DEFINE+input%3Ainference+%22subClassOf_NCBITaxon%22%0APREFIX+dbc%3A+%3Chttp%3A%2F%2Fintegbio.jp%2Fdbcatalog%2Fmeta%23%3E%0ASELECT+DISTINCT+%3Fdb_name+%3Fdb_id+%3Forganism%0AWHERE+%7B%0A++%3Ftaxon+rdfs%3Alabel+%22Mammalia%22%5E%5Exsd%3Astring+.%0A++%3Fsub+rdfs%3AsubClassOf+%3Ftaxon+.%0A++%3Fdb_id+dbc%3Adbcat_taxonomy_id+%3Fsub+.%0A++%3Fdb_id+dbc%3Adbcat_db_name+%3Fdb_name+.%0A++%3Fdb_id+dbc%3Adbcat_organism+%3Forganism+.%0A%7D%0AORDER+BY+%3Fdb_name&format=default">DEFINE input:inference &quot;subClassOf_NCBITaxon&quot;
PREFIX dbc: &lt;http://integbio.jp/dbcatalog/meta#&gt;
SELECT DISTINCT ?db_name ?db_id ?organism
WHERE {
  ?taxon rdfs:label &quot;Mammalia&quot;^^xsd:string .
  ?sub rdfs:subClassOf ?taxon .
  ?db_id dbc:dbcat_taxonomy_id ?sub .
  ?db_id dbc:dbcat_db_name ?db_name .
  ?db_id dbc:dbcat_organism ?organism .
}
ORDER BY ?db_name</a></pre>
    </div>
    <hr>
      <div>
      <p>What taxa cover organisms containing alpha-Thujene? (α-ツジェンを生体内に含む生物の分類群は？)</p>
      <pre><a href="?query=DEFINE+input%3Ainference+%22subClassOf_NCBITaxon%22%0APREFIX+rdfs%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0APREFIX+kc%3A+%3Chttp%3A%2F%2Ftogodb.biosciencedbc.jp%2Fontology%2Fknapsack_core%23%3E%0ASELECT+%28STR%28%3Flabel%29+AS+%3Fname%29+%3Ftotal_super%0A%7B%0A++%7B%0A++++SELECT+%3Fsuper+%28COUNT%28%3Fsuper%29+AS+%3Ftotal_super%29+WHERE+%7B%0A++++++%3Fknapsackcore+kc%3Ametabolite+%22alpha-Thujene%22+.%0A++++++%3Fknapsackcore+kc%3Aorganism_uri+%3Forganism+.%0A++++++%3Forganism+rdfs%3AsubClassOf+%3Fsuper+.%0A++++%7D%0A++++GROUP+BY+%3Fsuper%0A++%7D%0A++%3Fsuper+rdfs%3Alabel+%3Flabel+.%0A%7D%0AORDER+BY+DESC%28%3Ftotal_super%29+%3Flabel&format=default">DEFINE input:inference &quot;subClassOf_NCBITaxon&quot;
PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt;
PREFIX kc: &lt;http://togodb.biosciencedbc.jp/ontology/knapsack_core#&gt;
SELECT (STR(?label) AS ?name) ?total_super
{
  {
    SELECT ?super (COUNT(?super) AS ?total_super) WHERE {
      ?knapsackcore kc:metabolite &quot;alpha-Thujene&quot; .
      ?knapsackcore kc:organism_uri ?organism .
      ?organism rdfs:subClassOf ?super .
    }
    GROUP BY ?super
  }
  ?super rdfs:label ?label .
}
ORDER BY DESC(?total_super) ?label</a></pre>
    </div>
    <hr>
      <div>
      <p>What plants contain compounds that cause hypertrophy in rat livers? (ラットを肝細胞肥大させた化合物を含む植物は？)</p>
      <pre><a href="?query=PREFIX+otp%3A+%3Chttp%3A%2F%2Ftogodb.biosciencedbc.jp%2Fontology%2Fopen_tggates_pathology%23%3E%0APREFIX+otm%3A+%3Chttp%3A%2F%2Ftogodb.biosciencedbc.jp%2Fontology%2Fopen_tggates_main%23%3E%0APREFIX+kc%3A+%3Chttp%3A%2F%2Ftogodb.biosciencedbc.jp%2Fontology%2Fknapsack_core%23%3E%0ASELECT+DISTINCT+%3Forganism+%3Fcompound_name+%3Fchebi%0AWHERE+%7B%0A++%3Ftggatespatho+otp%3Afind_type+%22Hypertrophy%22+.%0A++%3Ftggatespatho+otp%3Acompound_name+%3Fcompound_name+.%0A++%3Ftggatesmain+otm%3Acompound_name+%3Fcompound_name+.%0A++%3Ftggatesmain+otm%3Achebi+%3Fchebi+.%0A++%3Fknapsackcore+kc%3Achebi+%3Fchebi+.%0A++%3Fknapsackcore+kc%3Aorganism+%3Forganism%0A%7D%0AORDER+BY+%3Forganism&format=default">PREFIX otp: &lt;http://togodb.biosciencedbc.jp/ontology/open_tggates_pathology#&gt;
PREFIX otm: &lt;http://togodb.biosciencedbc.jp/ontology/open_tggates_main#&gt;
PREFIX kc: &lt;http://togodb.biosciencedbc.jp/ontology/knapsack_core#&gt;
SELECT DISTINCT ?organism ?compound_name ?chebi
WHERE {
  ?tggatespatho otp:find_type &quot;Hypertrophy&quot; .
  ?tggatespatho otp:compound_name ?compound_name .
  ?tggatesmain otm:compound_name ?compound_name .
  ?tggatesmain otm:chebi ?chebi .
  ?knapsackcore kc:chebi ?chebi .
  ?knapsackcore kc:organism ?organism
}
ORDER BY ?organism</a></pre>
    </div>
    <hr>
      <div>
      <p>List up gene pairs on the photosynthesis pathway whose mutants show similar fluorescence time-course in Synechocystis sp. PCC 6803. (Synechocystis sp. PCC 6803 の Photosynthesis のパスウェイ上の遺伝子について，蛍光時系列が似ているもののリストが欲しい)</p>
      <pre><a href="?query=PREFIX+fl%3A+%3Chttp%3A%2F%2Ftogodb.biosciencedbc.jp%2Fontology%2Ffluorome_sim%23%3E%0ASELECT+%3Fsimid+%3Forf1+%3Forf2+%3Fproduct1+%3Fproduct2+%3Fdist_h+%3Fdist_l%0AWHERE+%7B%0A+++%3Chttp%3A%2F%2Fwww.kegg.jp%2Fentry%2Fsyn00195%3E+%3Chttp%3A%2F%2Fwww.genome.jp%2Flinkdb%2Freverse%3E+%3Fgene1+.%0A+++BIND%28+IRI%28CONCAT%28%22http%3A%2F%2Fidentifiers.org%2Fkegg.genes%2Fsyn%3A%22%2C+SUBSTR%28STR%28%3Fgene1%29%2C+30%29%29%29+AS+%3Forf1+%29%0A+++%3Fsimid+fl%3Abox1_orf+%3Forf1+.%0A+++%3Fsimid+fl%3Abox2_orf+%3Forf2+.%0A+++%3Fsimid+fl%3Abox1_product+%3Fproduct1+.%0A+++%3Fsimid+fl%3Abox2_product+%3Fproduct2+.%0A+++OPTIONAL%7B+%3Fsimid+fl%3Adistance_a_high+%3Fdist_h+.+%7D%0A+++%3Fsimid+fl%3Adistance_a_low+%3Fdist_l+.%0A+++BIND%28+IRI%28CONCAT%28%22http%3A%2F%2Fwww.kegg.jp%2Fentry%2Fsyn%3A%22%2C+SUBSTR%28STR%28%3Forf2%29%2C+39%29%29%29+AS+%3Fgene2+%29%0A+++FILTER+%28+%3Forf1+%21%3D+%3Forf2+%26%26+%3Fdist_l+%3C+0.2+%29%0A+++%3Chttp%3A%2F%2Fwww.kegg.jp%2Fentry%2Fsyn00195%3E+%3Chttp%3A%2F%2Fwww.genome.jp%2Flinkdb%2Freverse%3E+%3Fgene2+.%0A%7D&format=default">PREFIX fl: &lt;http://togodb.biosciencedbc.jp/ontology/fluorome_sim#&gt;
SELECT ?simid ?orf1 ?orf2 ?product1 ?product2 ?dist_h ?dist_l
WHERE {
   &lt;http://www.kegg.jp/entry/syn00195&gt; &lt;http://www.genome.jp/linkdb/reverse&gt; ?gene1 .
   BIND( IRI(CONCAT(&quot;http://identifiers.org/kegg.genes/syn:&quot;, SUBSTR(STR(?gene1), 30))) AS ?orf1 )
   ?simid fl:box1_orf ?orf1 .
   ?simid fl:box2_orf ?orf2 .
   ?simid fl:box1_product ?product1 .
   ?simid fl:box2_product ?product2 .
   OPTIONAL{ ?simid fl:distance_a_high ?dist_h . }
   ?simid fl:distance_a_low ?dist_l .
   BIND( IRI(CONCAT(&quot;http://www.kegg.jp/entry/syn:&quot;, SUBSTR(STR(?orf2), 39))) AS ?gene2 )
   FILTER ( ?orf1 != ?orf2 &amp;&amp; ?dist_l &lt; 0.2 )
   &lt;http://www.kegg.jp/entry/syn00195&gt; &lt;http://www.genome.jp/linkdb/reverse&gt; ?gene2 .
}</a></pre>
    </div>
    <hr>
      <div>
      <p>What proteins are targeted by compounds from Vigna unguiculata? (ササゲに含まれる化合物のターゲットタンパク質を知りたい)</p>
      <pre><a href="?query=PREFIX+kc%3A+%3Chttp%3A%2F%2Ftogodb.biosciencedbc.jp%2Fontology%2Fknapsack_core%23%3E%0APREFIX+sio%3A+%3Chttp%3A%2F%2Fsemanticscience.org%2Fresource%2F%3E%0APREFIX+chbl%3A+%3Chttp%3A%2F%2Frdf.ebi.ac.uk%2Fterms%2Fchembl%23%3E%0ASELECT+DISTINCT+%3Fcompound_name+%3Ftarget_name+%3Ftarget%0AWHERE+%7B%0A++%3Fkc_id+kc%3Aorganism+%22Vigna+unguiculata%22.%0A++%3Fkc_id+kc%3Ainchi+%3Finchi+.%0A++%3Fkc_id+kc%3Ametabolite+%3Fcompound_name+.%0A%0A++SERVICE+%3Chttps%3A%2F%2Fwww.ebi.ac.uk%2Frdf%2Fservices%2Fchembl%2Fsparql%3E+%7B%0A++++%3Fmolecule+sio%3ASIO_000008+%3Fattribute+.%0A++++FILTER+regex%28%3Fattribute%2C+%22standard_inchi%24%22%29+.%0A++++%3Fattribute+sio%3ASIO_000300+%3Finchi+.%0A++++%3Factivity+chbl%3AhasMolecule+%3Fmolecule+.%0A++++%3Factivity+chbl%3AhasAssay+%3Fassay+.%0A++++%3Fassay+chbl%3AhasTarget+%3Ftarget+.%0A++++%3Ftarget+rdfs%3Alabel+%3Ftarget_name+.%0A++%7D%0A%7D%0AORDER+BY+%3Fcompound_name+%3Ftarget_name+%3Ftarget&format=default">PREFIX kc: &lt;http://togodb.biosciencedbc.jp/ontology/knapsack_core#&gt;
PREFIX sio: &lt;http://semanticscience.org/resource/&gt;
PREFIX chbl: &lt;http://rdf.ebi.ac.uk/terms/chembl#&gt;
SELECT DISTINCT ?compound_name ?target_name ?target
WHERE {
  ?kc_id kc:organism &quot;Vigna unguiculata&quot;.
  ?kc_id kc:inchi ?inchi .
  ?kc_id kc:metabolite ?compound_name .

  SERVIC…
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