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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 13,081,788,247 triples is this release. All triples are available in the default graph. There are 16 named graphs.

nametriples
http://beta.sparql.uniprot.org/uniprot8,439,331,521
http://beta.sparql.uniprot.org/uniparc3,578,871,450
http://beta.sparql.uniprot.org/uniref910,028,635
http://beta.sparql.uniprot.org/citationmapping115,025,035
http://beta.sparql.uniprot.org/taxonomy23,170,499
http://beta.sparql.uniprot.org/citations14,141,735
http://beta.sparql.uniprot.org/go1,037,071
http://beta.sparql.uniprot.org/enzymes72,139
http://beta.sparql.uniprot.org/diseases37,371
http://beta.sparql.uniprot.org/journals35,346
http://beta.sparql.uniprot.org/pathways11,543
http://beta.sparql.uniprot.org/keywords11,251
http://beta.sparql.uniprot.org/tissues6,113
http://beta.sparql.uniprot.org/locations4,669
http://purl.uniprot.org/core2,103
http://beta.sparql.uniprot.org/databases1,766

UniProt News

UniProt release 2014_04
April 2014

An old unwanted guest being shown the door | Cross-references for isoform sequences: Ensembl Genomes

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 ?orig) . 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