Examples

  1. Select all taxa from the UniProt taxonomySELECT ?taxon FROM <http://sparql.uniprot.org/taxonomy> WHERE { ?taxon a up:Taxon . }
  2. Select all bacterial taxa and their scientific name from the UniProt taxonomySELECT ?taxon ?name WHERE { ?taxon a up:Taxon . ?taxon up:scientificName ?name . ?taxon rdfs:subClassOf taxon:2 . }
  3. Select all UniProt entries, and their organism and amino acid sequences (including isoforms), for _E. coli K12_ and all its strainsSELECT ?protein ?organism ?isoform ?aa_sequence WHERE { ?protein a up:Protein . ?protein up:organism ?organism . ?organism rdfs:subClassOf taxon:83333 . ?protein up:sequence ?isoform . ?isoform rdf:value ?aa_sequence . }
  4. Select the UniProt entry with the mnemonic 'A4_HUMAN'SELECT ?protein WHERE { ?protein a up:Protein . ?protein up:mnemonic 'A4_HUMAN' }
  5. Select all cross-references to external databases of the category '3D structure databases' of UniProt entries that are classified with the keyword 'Acetoin biosynthesis (KW-0005)'SELECT ?protein ?db WHERE { ?protein a up:Protein ; up:classifiedWith keywords:5 ; rdfs:seeAlso ?db . ?db up:database <http://purl.uniprot.org/database/PDB> }
  6. Select all cross-references to external databases of the category '3D structure databases' of UniProt entries that are classified with the keyword 'Acetoin biosynthesis (KW-0005)'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' }
  7. Select all UniProt entries, and their recommended protein name, that have a preferred gene name that contains the text 'DNA'SELECT ?protein ?name WHERE { ?protein a up:Protein . ?protein up:recommendedName ?recommended . ?recommended up:fullName ?name . ?protein up:encodedBy ?gene . ?gene skos:prefLabel ?text . FILTER CONTAINS(?text, 'DNA') }
  8. Select the preferred gene name and disease annotation of all human UniProt entries that are known to be involved in a diseaseSELECT ?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 }
  9. Select all human UniProt entries with a sequence variant that leads to a 'loss of function'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')) }
  10. Select all UniProt entries with annotated transmembrane regions and the regions' begin and end coordinates on the canonical sequenceSELECT ?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 }
  11. Select all UniProt entries that were integrated on the 30th of November 2010SELECT ?protein WHERE { ?protein a up:Protein . ?protein up:created '2010-11-30'^^xsd:date }
  12. Was any UniProt entry integrated on the 9th of January 2013ASK WHERE { ?protein a up:Protein . ?protein up:created '2013-01-09'^^xsd:date }
  13. Construct new triples of the type 'HumanProtein' from all human UniProt entriesCONSTRUCT { ?protein a up:HumanProtein . } WHERE { ?protein a up:Protein . ?protein up:organism taxon:9606 }
  14. Select all triples that relate to the EMBL CDS entry AA089367.1: DESCRIBE <http://purl.uniprot.org/embl-cds/AAO89367.1>
  15. Select all triples that relate to the taxon that describes Homo sapiens in the named graph for taxonomyDESCRIBE taxon:9606 FROM <http://sparql.uniprot.org/taxonomy>
  16. Select the average number of cross-references to the PDB database of UniProt entries that have at least one cross-reference to the PDB databaseSELECT (AVG(?linksToPdbPerEntry) AS ?avgLinksToPdbPerEntry) WHERE { SELECT ?protein (COUNT(DISTINCT ?db) AS ?linksToPdbPerEntry) WHERE { ?protein a up:Protein . ?protein rdfs:seeAlso ?db . ?db up:database &amp;lt;http://purl.uniprot.org/database/PDB&amp;gt; } GROUP BY ?protein ORDER BY DESC(?linksToPdbPerEntry) }
  17. Select the number of UniProt entries for each of the EC (Enzyme Commission) second level categoriesSELECT ?enzyme (COUNT(?protein) as ?size) WHERE { VALUES (?ecClass) {(ec:1.-.-.-) (ec:2.-.-.-) (ec:3.-.-.-) (ec:4.-.-.-) (ec:5.-.-.-) (ec:6.-.-.-) (ec:7.-.-.-) } ?protein up:enzyme ?enzyme . ?enzyme rdfs:subClassOf ?ecClass . } GROUP BY ?enzyme ORDER BY ?enzyme
  18. Find all Natural Variant Annotations if associated via an evidence tag to an article with a pubmed identifierSELECT ?accession ?annotation_acc ?pubmed WHERE { ?protein a up:Protein ; up:annotation ?annotation . ?annotation a up:Natural_Variant_Annotation . ?linkToEvidence rdf:object ?annotation ; up:attribution ?attribution . ?attribution up:source ?source . ?source a up:Journal_Citation . BIND(SUBSTR(STR(?protein),33) AS ?accession) BIND(IF(CONTAINS(STR(?annotation), "#SIP"), SUBSTR(STR(?annotation),33), SUBSTR(STR(?annotation),36))AS?annotation_acc) BIND(SUBSTR(STR(?source),35) AS ?pubmed) }

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About

This SPARQL endpoint contains all UniProt data. It is free to access and supports the SPARQL 1.1 Standard.

There are 59,284,525,352 triples is this release (2019_10). The query timeout is 45 minutes. All triples are available in the default graph. There are 19 named graphs.

Documentation

  1. Classes and predicates defined by the UniProt consortium
  2. Statistics and diagrams
  3. Example queries