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

There are 15,134,824,394 triples is this release. All triples are available in the default graph. There are 16 named graphs. Click on the links per graph to find out what is inside.

nametriples
http://beta.sparql.uniprot.org/uniprot11,203,817,151
http://beta.sparql.uniprot.org/uniparc2,693,251,840
http://beta.sparql.uniprot.org/uniref1,092,835,948
http://beta.sparql.uniprot.org/citationmapping120,361,501
http://beta.sparql.uniprot.org/citations15,017,939
http://beta.sparql.uniprot.org/taxonomy8,934,621
http://beta.sparql.uniprot.org/go416,326
http://beta.sparql.uniprot.org/enzymes73,250
http://beta.sparql.uniprot.org/diseases37,769
http://beta.sparql.uniprot.org/journals35,533
http://beta.sparql.uniprot.org/keywords12,049
http://beta.sparql.uniprot.org/pathways11,567
http://beta.sparql.uniprot.org/tissues6,113
http://beta.sparql.uniprot.org/locations5,079
http://purl.uniprot.org/core2,103
http://beta.sparql.uniprot.org/databases1,787

UniProt News

UniProt release 2014_07
July 2014

Lark or owl? PER3 is the answer | Cross-references to CCDS and GeneReviews | UniParc cross-references with protein and gene names

Examples

  1. Select all taxa from the UniProt taxonomy: SELECT ?taxon FROM <http://beta.sparql.uniprot.org/taxonomy/> WHERE { ?taxon a up:Taxon . }
  2. Select all bacterial taxa, and their scientific name, from the UniProt taxonomy: SELECT ?taxon ?name WHERE { ?taxon a up:Taxon . ?taxon up:scientificName ?name . ?taxon rdfs:subClassOf* taxon:2 . }
  3. Select all E-Coli K12 (including strains) UniProt entries and their amino acid sequence: SELECT ?protein ?aa WHERE { ?protein a up:Protein . ?protein up:organism ?organism . { ?protein up:organism taxon:83333 . } UNION { ?protein up:organism ?organism . ?organism rdfs:subClassOf+ taxon:83333 . } ?protein up:sequence ?s . ?s rdf:value ?aa }
  4. Select the UniProt entry with the mnemonic 'A4_HUMAN': SELECT ?protein WHERE { ?protein a up:Protein . ?protein up:mnemonic 'A4_HUMAN' }
  5. Select a mapping of UniProt to PDB entries using the UniProt cross-references to the PDB database: SELECT ?protein ?db WHERE { ?protein a up:Protein . ?protein 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 '3Fe-4S': SELECT DISTINCT ?link WHERE { ?protein a up:Protein . ?protein up:classifiedWith keywords:3 . ?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 disease: 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 }
  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 human UniProt entries with a sequence variant that leads to a tyrosine to phenylalanine substitution: SELECT ?protein ?annotation ?begin ?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 . ?annotation up:substitution ?substitution . ?annotation up:range/faldo:begin/faldo:position ?begin . ?protein up:sequence ?sequence . ?sequence rdf:value ?value . BIND (substr(?value, ?begin, 1) as ?original) . FILTER(?original = 'Y' && ?substitution = 'F') . }
  11. Select all UniProt entries with annotated transmembrane regions and the regions' begin and end coordinates on the canonical sequence: 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 }
  12. Select all UniProt entries that were integrated on the 30th of November 2010: SELECT ?protein WHERE { ?protein a up:Protein . ?protein up:created '2010-11-30'^^xsd:date }
  13. Was any UniProt entry integrated on the 9th of January 2013? ASK WHERE { ?protein a up:Protein . ?protein up:created '2013-01-09'^^xsd:date }
  14. Construct new triples of the type 'HumanProtein' from all human UniProt entries: CONSTRUCT { ?protein a up:HumanProtein . } WHERE { ?protein a up:Protein . ?protein up:organism taxon:9606 }
  15. Select all triples that relate to the EMBL CDS entry AA089367.1: DESCRIBE <http://purl.uniprot.org/embl-cds/AAO89367.1>
  16. Select all triples that relate to the taxon that describes Homo sapiens: DESCRIBE taxon:9606 FROM <http://beta.sparql.uniprot.org/taxonomy/>
  17. Select the average number of cross-references to the PDB database of UniProt entries that have at least one cross-reference to the PDB database: 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 <http://purl.uniprot.org/database/PDB> } GROUP BY ?protein ORDER BY DESC(?linksToPdbPerEntry) }
  18. Select the number of UniProt entries for each of the EC (Enzyme Commission) second level categories: SELECT ?enzyme (COUNT(?protein) as ?size) WHERE { VALUES (?ecClass) {(ec:1.-.-.-) (ec:2.-.-.-) (ec:3.-.-.-) (ec:4.-.-.-) (ec:5.-.-.-) (ec:6.-.-.-) } ?protein up:enzyme ?enzyme. ?enzyme rdfs:subClassOf ?ecClass } GROUP BY ?enzyme ORDER BY ?enzyme