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UniProt

<!DOCTYPE html SYSTEM "about:legacy-compat"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head><title>UniProt</title><meta content="text/html; charset=UTF-8" http-equiv="Content-Type"/><link href="/" rel="home"/><link href="/base.css" type="text/css" rel="stylesheet"/><link type="image/vnd.microsoft.icon" href="/uniprot-favicon.ico" rel="shortcut icon"/><link href="/uniprot-sparql.css" type="text/css" rel="stylesheet"/><link href="http://creativecommons.org/licenses/by/4.0/" rel="license"/><script src="https://cdn.jsdelivr.net/npm/yasgui-yasqe@2.11.22/dist/yasqe.bundled.min.js"></script><link type="text/css" rel="stylesheet" href="https://cdn.jsdelivr.net/yasqe/2.2/yasqe.min.css"/><meta content="width=device-width, initial-scale=1" name="viewport"/><meta content="no-referrer" name="referrer"/></head><body typeof="schema:WebPage"><nav id="nav-header"><a accesskey="1" href="https://www.uniprot.org/" id="www"><img alt="" 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" title="UniProt home"/></a><a href="/sparql">SPARQL</a><a href="https://www.uniprot.org/downloads" id="download">Downloads</a><a accesskey="9" href="https://www.uniprot.org/contact" id="contact"><img alt="Contact" src="data:image/svg+xml;base64,PHN2ZyB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciIHZpZXdCb3g9IjAgMCAxMyAxMCIgZmlsbD0iI2ZmZiIgd2lkdGg9IjEuNGVtIj48cGF0aCBmaWxsLXJ1bGU9ImV2ZW5vZGQiIGQ9Ik0xMiAxLjI1QzEyIC41NiAxMS40NiAwIDEwLjggMEgxLjJDLjU0IDAgMCAuNTYgMCAxLjI1djcuNUMwIDkuNDQuNTQgMTAgMS4yIDEwaDkuNmMuNjYgMCAxLjItLjU2IDEuMi0xLjI1di03LjV6bS0xLjIgMEw2IDQuMzggMS4yIDEuMjVoOS42ek02IDUuNjNMMS4yIDIuNXY2LjI1aDkuNlYyLjVMNiA1LjYzeiI+PC9wYXRoPjwvc3ZnPgo="/></a><a rel="help" href="https://www.uniprot.org/help/" id="help">Documentation/Help</a></nav><a accesskey="2" href="#content" hidden="hidden">Skip Header</a><main class="sparql homepage" id="content"><section id="examples"><h3>Examples</h3><ol><li>Select all taxa from the <a href="https://www.uniprot.org/taxonomy/">UniProt taxonomy</a><a href="/sparql/?queryPREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?taxon FROM &lt;http://sparql.uniprot.org/taxonomy&gt; WHERE { ?taxon a up:Taxon . }" class="exampleQuery">PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?taxon FROM &lt;http://sparql.uniprot.org/taxonomy&gt; WHERE { ?taxon a up:Taxon . }</a></li><li>Select all bacterial taxa and their scientific name from the <a href="https://www.uniprot.org/taxonomy/">UniProt taxonomy</a><a href="/sparql/?queryPREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; PREFIX taxon: &lt;http://purl.uniprot.org/taxonomy/&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?taxon ?name WHERE { ?taxon a up:Taxon . ?taxon up:scientificName ?name . # Taxon subclasses are materialized, do not use rdfs:subClassOf+ ?taxon rdfs:subClassOf taxon:2 . }" class="exampleQuery">PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; PREFIX taxon: &lt;http://purl.uniprot.org/taxonomy/&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?taxon ?name WHERE { ?taxon a up:Taxon . ?taxon up:scientificName ?name . # Taxon subclasses are materialized, do not use rdfs:subClassOf+ ?taxon rdfs:subClassOf taxon:2 . }</a></li><li>Select all UniProtKB entries, and their organism and amino acid sequences (including isoforms), for <a href="http://purl.uniprot.org/taxonomy/83333"><i>E. coli K12</i> and all its strains</a><a href="/sparql/?queryPREFIX rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt; PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; PREFIX taxon: &lt;http://purl.uniprot.org/taxonomy/&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?protein ?organism ?isoform ?sequence WHERE { ?protein a up:Protein . ?protein up:organism ?organism . # Taxon subclasses are materialized, do not use rdfs:subClassOf+ ?organism rdfs:subClassOf taxon:83333 . ?protein up:sequence ?isoform . ?isoform rdf:value ?sequence . }" class="exampleQuery">PREFIX rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt; PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; PREFIX taxon: &lt;http://purl.uniprot.org/taxonomy/&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?protein ?organism ?isoform ?sequence WHERE { ?protein a up:Protein . ?protein up:organism ?organism . # Taxon subclasses are materialized, do not use rdfs:subClassOf+ ?organism rdfs:subClassOf taxon:83333 . ?protein up:sequence ?isoform . ?isoform rdf:value ?sequence . }</a></li><li>Select the UniProtKB entry with the <a href="https://www.uniprot.org/manual/entry_name">mnemonic</a> 'A4_HUMAN'<a href="/sparql/?queryPREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?protein WHERE { ?protein a up:Protein . ?protein up:mnemonic 'A4_HUMAN' }" class="exampleQuery">PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?protein WHERE { ?protein a up:Protein . ?protein up:mnemonic &#039;A4_HUMAN&#039; }</a></li><li>Select a mapping of UniProtKB to PDB entries using the UniProtKB cross-references to the <a href="https://www.uniprot.org/database/DB-0070">PDB</a> database<a href="/sparql/?queryPREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?protein ?db WHERE { ?protein a up:Protein . ?protein rdfs:seeAlso ?db . ?db up:database &lt;http://purl.uniprot.org/database/PDB&gt; }" class="exampleQuery">PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?protein ?db WHERE { ?protein a up:Protein . ?protein rdfs:seeAlso ?db . ?db up:database &lt;http://purl.uniprot.org/database/PDB&gt; }</a></li><li>Select all cross-references to external databases of the category <a href="https://www.uniprot.org/database?query=category_exact%3A%223D%20structure%20databases%22">'3D structure databases'</a> of UniProtKB entries that are classified with the keyword <a href="https://www.uniprot.org/keywords/5">'Acetoin biosynthesis (KW-0005)'</a><a href="/sparql/?queryPREFIX keywords: &lt;http://purl.uniprot.org/keywords/&gt; PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT DISTINCT ?link WHERE { ?protein a up:Protein . ?protein up:classifiedWith keywords:5 . ?protein rdfs:seeAlso ?link . ?link up:database ?db . ?db up:category '3D structure databases' }" class="exampleQuery">PREFIX keywords: &lt;http://purl.uniprot.org/keywords/&gt; PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT DISTINCT ?link WHERE { ?protein a up:Protein . ?protein up:classifiedWith keywords:5 . ?protein rdfs:seeAlso ?link . ?link up:database ?db . ?db up:category &#039;3D structure databases&#039; }</a></li><li>Select reviewed UniProtKB entries (Swiss-Prot), and their recommended protein name, that have a preferred gene name that contains the text 'DNA'<a href="/sparql/?queryPREFIX skos: &lt;http://www.w3.org/2004/02/skos/core#&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?protein ?name WHERE { ?protein a up:Protein . ?protein up:reviewed true . ?protein up:recommendedName ?recommended . ?recommended up:fullName ?name . ?protein up:encodedBy ?gene . ?gene skos:prefLabel ?text . FILTER CONTAINS(?text, 'DNA') }" class="exampleQuery">PREFIX skos: &lt;http://www.w3.org/2004/02/skos/core#&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?protein ?name WHERE { ?protein a up:Protein . ?protein up:reviewed true . ?protein up:recommendedName ?recommended . ?recommended up:fullName ?name . ?protein up:encodedBy ?gene . ?gene skos:prefLabel ?text . FILTER CONTAINS(?text, &#039;DNA&#039;) }</a></li><li>Select the preferred gene name and disease annotation of all human UniProtKB entries that are known to be involved in a disease<a href="/sparql/?queryPREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; PREFIX skos: &lt;http://www.w3.org/2004/02/skos/core#&gt; PREFIX taxon: &lt;http://purl.uniprot.org/taxonomy/&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?name ?text WHERE { ?protein a up:Protein . ?protein up:organism taxon:9606 . ?protein up:encodedBy ?gene . ?gene skos:prefLabel ?name . ?protein up:annotation ?annotation . ?annotation a up:Disease_Annotation . ?annotation rdfs:comment ?text }" class="exampleQuery">PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; PREFIX skos: &lt;http://www.w3.org/2004/02/skos/core#&gt; PREFIX taxon: &lt;http://purl.uniprot.org/taxonomy/&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?name ?text WHERE { ?protein a up:Protein . ?protein up:organism taxon:9606 . ?protein up:encodedBy ?gene . ?gene skos:prefLabel ?name . ?protein up:annotation ?annotation . ?annotation a up:Disease_Annotation . ?annotation rdfs:comment ?text }</a></li><li>Select all human UniProtKB entries with a sequence variant that leads to a 'loss of function'<a href="/sparql/?queryPREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; PREFIX taxon: &lt;http://purl.uniprot.org/taxonomy/&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?protein ?text WHERE { ?protein a up:Protein . ?protein up:organism taxon:9606 . ?protein up:annotation ?annotation . ?annotation a up:Natural_Variant_Annotation . ?annotation rdfs:comment ?text . FILTER (CONTAINS(?text, 'loss of function')) }" class="exampleQuery">PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; PREFIX taxon: &lt;http://purl.uniprot.org/taxonomy/&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?protein ?text WHERE { ?protein a up:Protein . ?protein up:organism taxon:9606 . ?protein up:annotation ?annotation . ?annotation a up:Natural_Variant_Annotation . ?annotation rdfs:comment ?text . FILTER (CONTAINS(?text, &#039;loss of function&#039;)) }</a></li><li>Select all human UniProtKB entries with a sequence variant that leads to a tyrosine to phenylalanine substitution<a href="/sparql/?queryPREFIX faldo: &lt;http://biohackathon.org/resource/faldo#&gt; PREFIX rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt; PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; PREFIX taxon: &lt;http://purl.uniprot.org/taxonomy/&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?protein ?annotation ?begin ?text WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:annotation ?annotation . ?annotation a up:Natural_Variant_Annotation ; rdfs:comment ?text ; up:substitution ?substitution ; up:range/faldo:begin [ faldo:position ?begin ; faldo:reference ?sequence ] . ?sequence rdf:value ?value . BIND (substr(?value, ?begin, 1) as ?original) . FILTER(?original = 'Y' &amp;&amp; ?substitution = 'F') . }" class="exampleQuery">PREFIX faldo: &lt;http://biohackathon.org/resource/faldo#&gt; PREFIX rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt; PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; PREFIX taxon: &lt;http://purl.uniprot.org/taxonomy/&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?protein ?annotation ?begin ?text WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:annotation ?annotation . ?annotation a up:Natural_Variant_Annotation ; rdfs:comment ?text ; up:substitution ?substitution ; up:range/faldo:begin [ faldo:position ?begin ; faldo:reference ?sequence ] . ?sequence rdf:value ?value . BIND (substr(?value, ?begin, 1) as ?original) . FILTER(?original = &#039;Y&#039; &amp;&amp; ?substitution = &#039;F&#039;) . }</a></li><li>Select all UniProtKB entries with annotated transmembrane regions and the regions' begin and end coordinates on the canonical sequence<a href="/sparql/?queryPREFIX faldo: &lt;http://biohackathon.org/resource/faldo#&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?protein ?begin ?end WHERE { ?protein a up:Protein . ?protein up:annotation ?annotation . ?annotation a up:Transmembrane_Annotation . ?annotation up:range ?range . ?range faldo:begin/faldo:position ?begin . ?range faldo:end/faldo:position ?end }" class="exampleQuery">PREFIX faldo: &lt;http://biohackathon.org/resource/faldo#&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT ?protein ?begin ?end WHERE { ?protein a up:Protein . ?protein up:annotation ?annotation . ?annotation a up:Transmembrane_Annotation . ?annotation up:range ?range . ?range faldo:begin/faldo:position ?begin . ?range faldo:end/faldo:position ?end }</a></li><li>Select all UniProtKB entries that were integrated on the 30th of November 2010<a href="/sparql/?queryPREFIX up: &lt;http://purl.uniprot.org/core/&gt; PREFIX xsd: &lt;http://www.w3.org/2001/XMLSchema#&gt; SELECT ?protein WHERE { ?protein a up:Protein . ?protein up:created '2010-11-30'^^xsd:date }" class="exampleQuery">PREFIX up: &lt;http://purl.uniprot.org/core/&gt; PREFIX xsd: &lt;http://www.w3.org/2001/XMLSchema#&gt; SELECT ?protein WHERE { ?protein a up:Protein . ?protein up:created &#039;2010-11-30&#039;^^xsd:date }</a></li><li>Was any UniProtKB entry integrated on the 9th of January 2013<a href="/sparql/?queryPREFIX up: &lt;http://purl.uniprot.org/core/&gt; PREFIX xsd: &lt;http://www.w3.org/2001/XMLSchema#&gt; ASK WHERE { ?protein a up:Protein . ?protein up:created '2013-01-09'^^xsd:date }" class="exampleQuery">PREFIX up: &lt;http://purl.uniprot.org/core/&gt; PREFIX xsd: &lt;http://www.w3.org/2001/XMLSchema#&gt; ASK WHERE { ?protein a up:Protein . ?protein up:created &#039;2013-01-09&#039;^^xsd:date }</a></li><li>Construct new triples of the type 'HumanProtein' from all human UniProtKB entries<a href="/sparql/?queryPREFIX taxon: &lt;http://purl.uniprot.org/taxonomy/&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; CONSTRUCT { ?protein a up:HumanProtein . } WHERE { ?protein a up:Protein . ?protein up:organism taxon:9606 }" class="exampleQuery">PREFIX taxon: &lt;http://purl.uniprot.org/taxonomy/&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; CONSTRUCT { ?protein a up:HumanProtein . } WHERE { ?protein a up:Protein . ?protein up:organism taxon:9606 }</a></li><li>Select the average number of cross-references to the <a href="${uniprot}database/DB-0070">PDB</a> database of UniProtKB entries that have at least one cross-reference to the PDB database<a href="/sparql/?queryPREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT (AVG(?linksToPdbPerEntry) AS ?avgLinksToPdbPerEntry) WHERE { SELECT ?protein (COUNT(DISTINCT ?db) AS ?linksToPdbPerEntry) WHERE { ?protein a up:Protein . ?protein rdfs:seeAlso ?db . ?db up:database &lt;http://purl.uniprot.org/database/PDB&gt; . } GROUP BY ?protein ORDER BY DESC(?linksToPdbPerEntry) }" class="exampleQuery">PREFIX rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; PREFIX up: &lt;http://purl.uniprot.org/core/&gt; SELECT (AVG(?linksToPdbPerEntry) AS ?avgLinksToPdbPerEntry) WHERE { SELECT ?protein (COUNT(DISTINCT ?db) AS ?linksToPdbPerEntry) WHERE { ?protein a up:Protein . ?protein rdfs:seeAlso ?db . ?db up:database &lt;http://purl.uniprot.org/database/PDB&gt; . } GROUP BY ?protein ORDER BY DESC(?linksToPdbPerEntry) }</a></li><li><a href="/.well-known/sparql-examples/?offset=15">More examples</a></li></ol></section><section id="sparql-area"><h3><label for="query">Your SPARQL query</label></h3><form method="get" action="/sparql/" name="sparql-form" id="sparql-form"><button id="addPrefix" type="button">Add common prefixes</button><textarea accesskey="1" rows="10" cols="80" name="query" id="query"></textarea><input type="hidden" name="format" value="html"><button id="sparqlFormSubmitter" type="submit">Submit Query</button></form></section><section class="shortcuts transparent" id="news-container"><div id="news"> <script> fetch('https://rest.uniprot.org/release-notes/search/?query=*&sort=release_date%20desc&size=5', { method: 'GET', mode: 'cors' }) .then(response => { return response.json(); }).then(r => { for (i in r.results) { const item = r.results[i]; var newLink = "<li><a id='news"+item.id+"' href='https://www.uniprot.org/help/"+item.id+"'>"+item.title+"</a></li>"; document.getElementById('newsectionlist').insertAdjacentHTML("beforeend", newLink); fetch('https://rest.uniprot.org/release-notes/'+item.id, { method: 'GET', mode: 'cors' }) .then(response => { return response.json(); }).then(r => { const re = /^[^#]{0,120} /gm; const match=r.content.match(re); if (match !== null) { const des=match[0].replace(/[\[]{1}([^\]]+)[\]]{1}[\(]{1}([^\)\"]+)(\"(.+)\")?[\)]{1}/g, '<a href="$2" title="$4"<$1</a>'); document.getElementById('news'+item.id).insertAdjacentHTML("afterend", '<p>'+des+'...</p>'); } }); }}); </script> <h3 class="pane-title"><a href="https://www.uniprot.org/news/&amp;sort=created">News</a><a title="Facebook logo" target="_blank" class="icon-right socialmedia icon_facebook" href="https://www.facebook.com/uniprot.org">聽</a><a title="Twitter Logo" target="_blank" class="icon-right socialmedia icon_twitter" href="https://twitter.com/uniprot">聽</a></h3><div id="newsection"><ul id="newsectionlist"></ul></div><a href="https://www.uniprot.org/news/?sort=release_date%20desc" data-icon=";" class="icon icon-generic newsArchiveLink">News archive</a></div></section><section id="about-area"><h4>About</h4><p> This SPARQL endpoint contains all UniProt data. It is free to access and supports the <a href="http://www.w3.org/TR/sparql11-query/">SPARQL 1.1 Standard</a>. </p><p> There are 210,122,358,019 triples in this release (2025_01). The query timeout is 45 minutes. All triples are available in the default graph. There are 22 named graphs. </p><h4>Documentation</h4><ol><li><a href="http://purl.uniprot.org/core/">Classes and predicates defined by the UniProt consortium</a></li><li><a href="https://github.com/sib-swiss/sparql-training/tree/master/uniprot">Tutorial on using SPARQL with UniProt</a></li><li><a href="/.well-known/void">Statistics and diagrams</a></li><li><a href="/.well-known/sparql-examples/">Example queries</a></li></ol></section></main><footer id="page-footer"><section class="small" id="copyright"> &copy; 2002&ndash; <span property="schema:copyrightYear">2025</span> <a accesskey="9" href="https://www.uniprot.org/help/about">UniProt Consortium</a> | <a href="https://www.uniprot.org/help/license" property="schema:license">License &amp; Disclaimer</a> | <a href="https://www.uniprot.org/help/privacy">Privacy Notice</a></section><section><div resource="/help/about#UniProt" id="logos" typeof="NGO" property="creator"><span resource="/help/about#EBI" typeof="Organization" class="ebi" property="member"><span hidden="hidden" property="name">European Bioinformatics Institute</span><a href="https://www.ebi.ac.uk/" property="url"></a></span><span resource="/help/about#PIR" typeof="Organization" class="pir" property="member"><span hidden="hidden" property="name">Protein Information Resource</span><a href="http://pir.georgetown.edu/" property="url"></a></span><span resource="/help/about#SIB" typeof="Organization" class="sib" property="member"><span hidden="hidden" property="name">SIB Swiss Institute of Bioinformatics</span><a href="https://www.sib.swiss/" property="url"></a></span></div></section><section id="poweredby"><h3>Powered by</h3><span class="vitalit" resource="https://www.sib.swiss/alan-bridge-group/" typeof="schema:NGO" property="schema:sponsor"><h4>Hardware</h4><a href="https://www.sib.swiss/alan-bridge-group" property="schema:url"><img alt="Swiss-Prot" src="https://www.sib.swiss//templates/sib/images/SIB_LogoQ_GBv.svg"/><h5 property="schema:name">Swiss-Prot</h5></a></span><span class="openlinksw" resource="http://www.openlinksw.com/#this" typeof="schema:Corporation" property="schema:sponsor"><h4>Software</h4><a href="http://virtuoso.openlinksw.com/" property="schema:url"><img alt="Virtuoso" src="/images/logos/virtuoso.png"/><h5 property="schema:name">Virtuoso</h5></a></span></section></footer><script src="/sparql.js" type="text/javascript"> </script></body></html>

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