SPARQL example query

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82_rhea_reactions_associated_with_ec_in_uniprotkb: List Rhea reactions associated with an EC (enzyme classification).

 
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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT
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  ?rhea
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  ?EC
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WHERE {
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  ?CatalyticActivity  up:catalyzedReaction   ?rhea ;
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    up:enzymeClass         ?EC .
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}
Use

83_rhea_reactions_not_associated_with_ec_in_uniprotkb: List Rhea reactions that are not associated with an EC (enzyme classification).

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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT
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  ?rhea
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  ?EC
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WHERE {
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  ?CatalyticActivity up:catalyzedReaction ?rhea .
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  MINUS {
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    ?CatalyticActivity up:enzymeClass ?EC .
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  }
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}
Use

84_taxonomy_hierarchy: Find all taxonomic records that describe species of the genus Homo.

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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT
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  ?species
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  ?genus
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WHERE {
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  BIND(taxon:9605 AS ?genus)
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  ?species a up:Taxon ;
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           up:rank up:Species ;
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           rdfs:subClassOf ?genus .
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  ?genus a up:Taxon ;
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         up:rank up:Genus .
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}
Use

85_taxonomy_host: Find taxon records that are known to have part of their life cycle in other organisms (e.g. parasite, symbiont, infection)

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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT
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  ?virus
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  ?host
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WHERE {
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    ?virus up:host ?host .
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}
Use

86_taxonomy_rank_and_scientific_name: Retrieve the rank and the scientific name of an taxonomic record. Not all taxonomic records have a rank associated with them.

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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT
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  ?taxon
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  ?scientificName
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  ?rank
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WHERE {
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  ?taxon a up:Taxon ;
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         up:scientificName ?scientificName .
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  OPTIONAL {
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    ?taxon up:rank ?rank
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  }
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}
Use

87_taxonomy_with_at_least_one_swissprot: Find taxon records for which one reviewed UniProtKB/Swiss-Prot entry exists. We might expect species, strains, subspecies and isolates in the taxon list.

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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT
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    DISTINCT
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         ?taxid
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         ?scientificName
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         ?domain
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         ?domainName
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WHERE {
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  ?uniprot a up:Protein .
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  # reviewed entries
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  ?uniprot up:reviewed true .
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  ?uniprot up:organism ?taxid .
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  ?taxid up:scientificName ?scientificName .
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  VALUES ?domain { taxon:2 # bacteria
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                   taxon:2157 # archaea
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                   taxon:2759 # eukaryota
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                   taxon:10239 #viruses
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                 } .
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  ?taxid rdfs:subClassOf ?domain .
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}
Use

88_uniparc_linked_to_active_uniprot: Show for a given UniParc accessions which active UniProtKB entries have the same amino acid sequence

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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT
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  ?uniparc
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  ?uniprot
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WHERE {
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  GRAPH <http://sparql.uniprot.org/uniparc>{
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    BIND(<http://purl.uniprot.org/uniparc/UPI000002DB1C> AS ?uniparc)
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    ?uniparc up:sequenceFor ?uniprot .
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  }
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  GRAPH <http://sparql.uniprot.org/uniprot> {
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    ?uniprot a up:Protein .
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  }
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}
Use

89_uniparc_triples_directly_associated: Predicates and objects, for a given UniParc accession as a subject

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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT
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  ?predicate
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  ?object
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WHERE {
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  <http://purl.uniprot.org/uniparc/UPI000012A0AD> ?predicate ?object
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}
Use

90_uniprot_affected_by_metabolic_diseases_using_MeSH: Proteins involved in metabolic diseases in UniProtKB. Using the MeSH concept as a root to find metabolic diseases in UniProt.

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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT
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 ?disease ?protein
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WHERE {
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  SERVICE<https://id.nlm.nih.gov/mesh/sparql> {
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    GRAPH <http://id.nlm.nih.gov/mesh> {
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      # Mesh M0013493 is a meaningless gathering about the concept 'Metabolic Diseases'
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      ?mesh <http://id.nlm.nih.gov/mesh/vocab#broaderDescriptor>* ?broader .
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      ?broader <http://id.nlm.nih.gov/mesh/vocab#preferredConcept> <http://id.nlm.nih.gov/mesh/M0013493> .
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    }
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  }
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  GRAPH <http://sparql.uniprot.org/diseases>{
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    ?disease a up:Disease ;
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        rdfs:seeAlso ?mesh .
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    ?mesh up:database <http://purl.uniprot.org/database/MeSH> .
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  }
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  GRAPH <http://sparql.uniprot.org/uniprot> {
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     ?protein up:annotation/up:disease ?disease .
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  }
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}
Use

91_uniprot_alternative_protein_full_name: Alternative protein full names for UniProtKB entries

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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT ?protein
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  ?fullName
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WHERE {
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  ?protein a up:Protein ;
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           up:alternativeName ?recommendedName .
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  ?recommendedName up:fullName ?fullName .
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}
Use

92_uniprot_bioregistry_iri_translation: Translate the global unique identifier for a UniProtKB record into other options using the bioregistry translating endpoint.

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PREFIX owl: <http://www.w3.org/2002/07/owl#>
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PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/>
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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT
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    ?protein
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    ?otherIdentifier
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WHERE {
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    BIND(uniprotkb:P00750 AS ?protein)
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    ?protein a up:Protein .
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    SERVICE <https://bioregistry.io/sparql> {
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        ?protein owl:sameAs ?otherIdentifier .
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    }
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}
Use

93_uniprot_created_modified_updated: List the created, last modified, and last sequence update dates for UniProtKB proteins.

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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT
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  ?protein
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  ?created
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  ?modified
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  ?version
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WHERE {
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  ?protein a up:Protein ;
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           up:created ?created ;
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           up:modified ?modified ;
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           up:version ?version .
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}
Use

94_uniprot_encoding_gene: List UniProtKB proteins with their associated named gene

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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT ?protein
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  ?gene
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WHERE {
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  ?protein a up:Protein ;
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           up:encodedBy ?gene .
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}
Use

96_uniprot_encoding_gene_name: List UniProtKB proteins with their associated gene and the gene's preffered name

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PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT ?protein
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  ?gene
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WHERE {
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  ?protein a up:Protein ;
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           up:encodedBy ?gene .
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  ?gene skos:prefLabel ?recommendedGeneName .
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}
Use

97_uniprot_encoding_gene_org_name: List UniProtKB proteins with their associated gene and the gene's ORF label

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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT
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  ?gene
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  ?orfName
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WHERE {
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  ?protein a up:Protein ;
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           up:encodedBy ?gene .
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  ?gene up:orfName ?orfName .
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}
Use

98_uniprot_entries_with_more_than_two_geneid_crossrefences: Find GeneID's crosslinked to more than one human or mouse UniProtKB entry

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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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PREFIX up: <http://purl.uniprot.org/core/>
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PREFIX taxon:<http://purl.uniprot.org/taxon/>
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SELECT
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  ?geneid
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  ?organism
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  (GROUP_CONCAT(?protein; separator=', ') AS ?entries)
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WHERE
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{
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  VALUES ?organism {taxon:9606 taxon:10090}
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  ?geneid up:database <http://purl.uniprot.org/database/GeneID> .
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  ?protein rdfs:seeAlso ?geneid ;
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           up:organism ?organism
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} GROUP BY ?geneid ?organism HAVING (COUNT(?protein) > 1) ORDER BY ?organism ?geneid
Use

99_uniprot_identifiers_org_translation: Translate a selection of UniProtKB accession numbers into other options using the identifiers.org translating endpoint.

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PREFIX owl: <http://www.w3.org/2002/07/owl#>
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PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/>
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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT
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    ?protein
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    ?otherIdentifier
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WHERE {
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    VALUES (?protein) {(uniprotkb:P00750) (uniprotkb:P05067)}
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    ?protein a up:Protein .
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    SERVICE <https://sparql.api.identifiers.org/sparql> {
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        ?protein owl:sameAs ?otherIdentifier .
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    }
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}
Use

drosophila_enzymes_derived_from_at_least_two_mRNAs: Find Drosophila proteins, that depend on more than one transcript (requires cross-references to Ensembl family of resources).

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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT
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  ?protein
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WHERE {
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  ?protein up:organism taxon:7227 ;
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    a up:Protein ;
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    up:reviewed true ;
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    rdfs:seeAlso ?transcript .
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  ?transcript  a up:Transcript_Resource .
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} GROUP BY ?protein HAVING(COUNT(?transcript) >= 2)
Use

drosophila_proteins_derived_from_at_least_two_mRNAs: Find Drosophila enzymes, that depend on more than one transcript (requires cross-references to Ensembl family of resources).

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PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
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PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT
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  ?protein
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WHERE {
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  ?protein up:organism taxon:7227 ;
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    a up:Protein ;
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    up:reviewed true ;
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    rdfs:seeAlso ?transcript .
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  {
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    ?protein up:annotation/a up:Catalytic_Activity_Annotation ;
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  } UNION {
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    ?protein up:enzyme ?enzyme .
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  }
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  ?transcript  a up:Transcript_Resource .
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} GROUP BY ?protein HAVING(COUNT(?transcript) >= 2)
Use

enzyme_with_threonine_as_active_site: Find enzymes with a Tyrosine (Y) as an active site

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PREFIX faldo: <http://biohackathon.org/resource/faldo#>
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PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT
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  ?protein
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WHERE {
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  ?protein up:annotation ?activeSiteAnnotation .
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  ?activeSiteAnnotation a up:Active_Site_Annotation ;
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    up:range ?range .
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  ?range faldo:begin ?begin .
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  ?begin faldo:position ?beginPosition ;
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    faldo:reference ?sequence .
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  ?sequence rdf:value ?sequenceVal .
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  FILTER(SUBSTR(?sequenceVal, ?beginPosition, 1) = 'Y')
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}
Use

uniprot_encoding_gene_name_alternative_name: List UniProtKB proteins with their associated gene and the gene's names that are used in the field, but not recommended for use by UniProtKB

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PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
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PREFIX up: <http://purl.uniprot.org/core/>
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SELECT ?protein
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  ?gene ?altGeneName
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WHERE {
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  ?protein a up:Protein ;
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           up:encodedBy ?gene .
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  ?gene skos:altLabel ?altGeneName .
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}
Use
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