SPARQL example query
2: Select all bacterial taxa and their scientific name from the UniProt taxonomy
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 ?taxon ?name WHERE { ?taxon a up:Taxon . ?taxon up:scientificName ?name . # Taxon subclasses are materialized, do not use rdfs:subClassOf+ ?taxon rdfs:subClassOf taxon:2 . }Use3: Select all UniProt entries, and their organism and amino acid sequences (including isoforms), for E. coli K12 and all its strains
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 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 ?protein ?organism ?isoform ?sequence WHERE { ?protein a up:Protein . ?protein up:organism ?organism . # Taxon subclasses are materialized, do not use rdfs:subClassOf+ ?organism rdfs:subClassOf taxon:83333 . ?protein up:sequence ?isoform . ?isoform rdf:value ?sequence . }Use3: Select all UniProt entries, and their organism and amino acid sequences (including isoforms), for E. coli K12 and all its strains
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 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 ?protein ?organism ?isoform ?sequence WHERE { ?protein a up:Protein . ?protein up:organism ?organism . # Taxon subclasses are materialized, do not use rdfs:subClassOf+ ?organism rdfs:subClassOf taxon:83333 . ?protein up:sequence ?isoform . ?isoform rdf:value ?sequence . }Use4: Select the UniProt entry with the mnemonic 'A4_HUMAN'
PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein WHERE { ?protein a up:Protein . ?protein up:mnemonic 'A4_HUMAN' }Use5: Select a mapping of UniProt to PDB entries using the UniProt cross-references to the PDB database
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?db WHERE { ?protein a up:Protein . ?protein rdfs:seeAlso ?db . ?db up:database <http://purl.uniprot.org/database/PDB> }Use6: 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)'
PREFIX keywords: <http://purl.uniprot.org/keywords/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> 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' }Use7: Select reviewed UniProt entries (Swiss-Prot), and their recommended protein name, that have a preferred gene name that contains the text 'DNA'
PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?name WHERE { ?protein a up:Protein . ?protein up:reviewed true . ?protein up:recommendedName ?recommended . ?recommended up:fullName ?name . ?protein up:encodedBy ?gene . ?gene skos:prefLabel ?text . FILTER CONTAINS(?text, 'DNA') }Use8: Select the preferred gene name and disease annotation of all human UniProt entries that are known to be involved in a disease
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> 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 }Use9: Select all human UniProt entries with a sequence variant that leads to a 'loss of function'
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 ?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')) }Use10: Select all human UniProt entries with a sequence variant that leads to a tyrosine to phenylalanine substitution
PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 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 ?protein ?annotation ?begin ?text WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:annotation ?annotation . ?annotation a up:Natural_Variant_Annotation ; rdfs:comment ?text ; up:substitution ?substitution ; up:range/faldo:begin [ faldo:position ?begin ; faldo:reference ?sequence ] . ?sequence rdf:value ?value . BIND (substr(?value, ?begin, 1) as ?original) . FILTER(?original = 'Y' && ?substitution = 'F') . }Use11: Select all UniProt entries with annotated transmembrane regions and the regions' begin and end coordinates on the canonical sequence
PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX up: <http://purl.uniprot.org/core/> 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 }Use12: Select all UniProt entries that were integrated on the 30th of November 2010
PREFIX up: <http://purl.uniprot.org/core/> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> SELECT ?protein WHERE { ?protein a up:Protein . ?protein up:created '2010-11-30'^^xsd:date }Use13: Was any UniProt entry integrated on the 9th of January 2013
PREFIX up: <http://purl.uniprot.org/core/> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> ASK WHERE { ?protein a up:Protein . ?protein up:created '2013-01-09'^^xsd:date }Use14: Construct new triples of the type 'HumanProtein' from all human UniProt entries
PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> CONSTRUCT { ?protein a up:HumanProtein . } WHERE { ?protein a up:Protein . ?protein up:organism taxon:9606 }Use15: Select all triples that relate to the EMBL CDS entry AA089367.1:
DESCRIBE <http://purl.uniprot.org/embl-cds/AAO89367.1>Use16: Select all triples that relate to the taxon that describes Homo sapiens in the named graph for taxonomy
PREFIX taxon: <http://purl.uniprot.org/taxonomy/> DESCRIBE taxon:9606 FROM <http://sparql.uniprot.org/taxonomy>Use17: 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
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> 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) }Use18: Select the number of UniProt entries for each of the EC (Enzyme Commission) top level categories
PREFIX ec: <http://purl.uniprot.org/enzyme/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?ecClass (COUNT(?protein) as ?size) WHERE { VALUES (?ecClass) {(ec:1.-.-.-) (ec:2.-.-.-) (ec:3.-.-.-) (ec:4.-.-.-) (ec:5.-.-.-) (ec:6.-.-.-) (ec:7.-.-.-)} . ?protein ( up:enzyme | up:domain/up:enzyme | up:component/up:enzyme ) ?enzyme . # Enzyme subclasses are materialized, do not use rdfs:subClassOf+ ?enzyme rdfs:subClassOf ?ecClass . } GROUP BY ?ecClass ORDER BY ?ecClassUse19: Find all Natural Variant Annotations if associated via an evidence tag to an article with a pubmed identifier
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?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) }Use20: Find how often an article in pubmed was used in an evidence tag in a human protein (ordered by most used to least)
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?source (COUNT(?attribution) AS ?attribitions) WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:annotation ?annotation . ?linkToEvidence rdf:object ?annotation ; up:attribution ?attribution . ?attribution up:source ?source . ?source a up:Journal_Citation . } GROUP BY ?source ORDER BY DESC(COUNT(?attribution))Use21: Find where disease related proteins are known to be located in the cell
PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?disease ?location_inside_cell ?cellcmpt WHERE { ?protein up:annotation ?diseaseAnnotation , ?subcellAnnotation . ?diseaseAnnotation up:disease/skos:prefLabel ?disease . ?subcellAnnotation up:locatedIn/up:cellularComponent ?cellcmpt . ?cellcmpt skos:prefLabel ?location_inside_cell . }Use22: For two accessions find the GO term labels and group them into GO process,function and component
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> PREFIX GO:<http://purl.obolibrary.org/obo/GO_> SELECT (CONCAT(SUBSTR(STR(?protein), 33)) AS ?uniprot) (GROUP_CONCAT(?celtype; separator=";") AS ?celtypes) (GROUP_CONCAT(?biotype; separator=";") AS ?biotypes) (GROUP_CONCAT(?moltype; separator=";") AS ?moltypes) WHERE { VALUES (?ac) {("Q6GZX4") ("Q96375")} BIND (IRI(CONCAT("http://purl.uniprot.org/uniprot/",?ac)) AS ?protein) ?protein a up:Protein . ?protein up:classifiedWith ?goTerm . #Determine if the type is biological_process OPTIONAL { ?goTerm rdfs:subClassOf GO:0008150 . ?goTerm rdfs:label ?biotype . } #Determine if the type is cellular_component OPTIONAL { ?goTerm rdfs:subClassOf GO:0005575 . ?goTerm rdfs:label ?celtype . } #Determine if the type is molecular_function OPTIONAL { ?goTerm rdfs:subClassOf GO:0003674 . ?goTerm rdfs:label ?moltype . } #Filter out the uniprot keywords FILTER(bound(?biotype) || bound(?celtype) || bound(?moltype)) } GROUP BY ?proteinUse23: Number of reviewed entries (Swiss-Prot) that are related to kinase activity
PREFIX GO: <http://purl.obolibrary.org/obo/GO_> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 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 (COUNT(DISTINCT(?protein)) AS ?pc) WHERE { ?protein rdf:type up:Protein ; up:reviewed true ; up:organism taxon:9606 ; up:classifiedWith|(up:classifiedWith/rdfs:subClassOf) GO:0016301 . }Use24: Find the release number of the uniprot data that is currently being queried
SELECT ?version FROM <https://sparql.uniprot.org/.well-known/void> WHERE { [] <http://purl.org/pav/version> ?version }Use25: Find any uniprot entry which has a name 'HLA class I histocompatibility antigen, B-73 alpha chain'
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?anyKindOfName WHERE { ?protein a up:Protein . ?protein (up:recommendedName|up:alternativeName) ?structuredName . ?structuredName ?anyKindOfName "HLA class I histocompatibility antigen, B alpha chain" . ?anyKindOfName rdfs:subPropertyOf up:structuredNameType . }Use26: Find any uniprot entry, or an uniprot entries domain or component which has a name 'HLA class I histocompatibility antigen, B-73 alpha chain'
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?anyKindOfName WHERE { ?protein a up:Protein . ?protein (up:recommendedName|up:alternativeName)|((up:domain|up:component)/(up:recommendedName|up:alternativeName)) ?structuredName . ?structuredName ?anyKindOfName "HLA class I histocompatibility antigen, B-73 alpha chain" . ?anyKindOfName rdfs:subPropertyOf up:structuredNameType . }Use