SPARQL example query

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

SELECT ?virus ?host WHERE { ?virus up:host ?host . }Use

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

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

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.

SELECT ?taxon ?scientificName ?rank WHERE { ?taxon a up:Taxon ; up:scientificName ?scientificName . OPTIONAL { ?taxon up:rank ?rank } }Use

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.

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

taxonomy_with_at_least_one_swissprot: Find taxon records for which one reviewed UniProtKB (Swiss-Prot) entry exists

SELECT DISTINCT ?taxid ?scientificName ?domain ?domainName WHERE { ?uniprot a up:Protein . # reviewed entries ?uniprot up:reviewed true . ?uniprot up:organism ?taxid . ?taxid up:scientificName ?scientificName . VALUES ?domain { taxon:2 # bacteria taxon:2157 # archaea taxon:2759 # eukaryota taxon:10239 #viruses } . ?taxid rdfs:subClassOf ?domain . }Use

taxonomy_with_at_least_one_swissprot: Find taxon records for which one reviewed UniProtKB (Swiss-Prot) entry exists

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

uniparc_linked_to_active_uniprot: Show for a given UniParc accessions which active UniProt entries have the same amino acid sequence

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

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

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

uniprot_affected_by_metabolic_diseases_using_MeSH: Proteins annotated in UniProtKB to be affected by metabolic diseases. Using the MeSH concept as a root to find metabolic diseases in UniProt.

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

uniprot_alternative_protein_full_name: Alternative protein full names for UniProtKB entries

SELECT ?protein ?fullName WHERE { ?protein a up:Protein ; up:alternativeName ?recommendedName . ?recommendedName up:fullName ?fullName . }Use

uniprot_alternative_protein_full_name: Alternative protein full names for UniProtKB entries

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

uniprot_bioregistry_iri_translation: Translate the global unique identifier for a UniProt record into other options using the bioregistry translating endpoint.

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

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

SELECT ?protein ?created ?modified ?version WHERE { ?protein a up:Protein ; up:created ?created ; up:modified ?modified ; up:version ?version . }Use

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

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

uniprot_encoding_gene: List UniProt proteins with their associated named gene

SELECT ?protein ?gene WHERE { ?protein a up:Protein ; up:encodedBy ?gene . }Use

uniprot_encoding_gene: List UniProt proteins with their associated named gene

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

uniprot_encoding_gene_name: List UniProt proteins with their associated gene and the gene's preffered name

SELECT ?protein ?gene WHERE { ?protein a up:Protein ; up:encodedBy ?gene . ?gene skos:prefLabel ?recommendedGeneName . }Use

uniprot_encoding_gene_name: List UniProt proteins with their associated gene and the gene's preffered name

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

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

SELECT ?protein ?gene ?altGeneName WHERE { ?protein a up:Protein ; up:encodedBy ?gene . ?gene skos:altLabel ?altGeneName . }Use

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

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

uniprot_encoding_gene_org_name: List UniProt proteins with their associated gene and the gene's ORF label

SELECT ?gene ?orfName WHERE { ?protein a up:Protein ; up:encodedBy ?gene . ?gene up:orfName ?orfName . }Use

uniprot_encoding_gene_org_name: List UniProt proteins with their associated gene and the gene's ORF label

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

uniprot_identifiers_org_translation: Translate the global unique identifier for a UniProt record into other options using the identifiers.org translating endpoint.

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

uniprot_organelles_or_plasmids: If a gene is located in an organelle other than the nucleus, or/and on a plasmid rather than a chromosome, the gene location is stored in encodedIn properties. Note that if a plasmid has several names, they are listed as multiple rdfs:label properties.

SELECT ?protein ?plasmidOrOrganelle ?label WHERE { ?protein a up:Protein ; up:encodedIn ?plasmidOrOrganelle . OPTIONAL { ?plasmidOrOrganelle rdfs:label ?label . } }Use

uniprot_organelles_or_plasmids: If a gene is located in an organelle other than the nucleus, or/and on a plasmid rather than a chromosome, the gene location is stored in encodedIn properties. Note that if a plasmid has several names, they are listed as multiple rdfs:label properties.

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?plasmidOrOrganelle ?label WHERE { ?protein a up:Protein ; up:encodedIn ?plasmidOrOrganelle . OPTIONAL { ?plasmidOrOrganelle rdfs:label ?label . } }Use

uniprot_potential_isoforms: List all Human UniProt entries and their computationaly potential isoforms..

PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?entry ?sequence ?isCanonical WHERE { # We don't want to look into the UniParc graph which will # confuse matters GRAPH <http://sparql.uniprot.org/uniprot> { # we need the UniProt entries that are human ?entry a up:Protein ; up:organism taxon:9606 ; # and we select the computationally mapped sequences up:potentialSequence ?sequence . } }Use
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