SPARQL example query

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  1. Find how often an article in pubmed was used in an evidence tag (ordered by most used to least)

    SELECT ?source (COUNT(?attribution) AS ?attribitions) WHERE { ?protein a up:Protein ; 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))Use

  2. Find where disease related proteins are known to be located in the cell

    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 . }Use

  3. For two accessions find the GO term labels and group them into GO process,function and component

    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 <http://purl.obolibrary.org/obo/GO_0008150>. ?goTerm rdfs:label ?biotype . } #Determine if the type is cellular_component OPTIONAL { ?goTerm rdfs:subClassOf <http://purl.obolibrary.org/obo/GO_0005575>. ?goTerm rdfs:label ?celtype . } #Determine if the type is molecular_function OPTIONAL { ?goTerm rdfs:subClassOf <http://purl.obolibrary.org/obo/GO_0003674> . ?goTerm rdfs:label ?moltype . } #Filter out the uniprot keywords FILTER(bound(?biotype) || bound(?celtype) || bound(?moltype)) } GROUP BY ?proteinUse

  4. Number of reviewed entries (Swiss-Prot) that are related to kinase activity

    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 . }Use

  5. Find the release number of the uniprot data that is currently being queried

    SELECT ?version FROM <http://sparql.uniprot.org/.well-known/void> WHERE { [] <http://purl.org/pav/2.0/version> ?version }Use

  6. Find any uniprot entry which has a name 'HLA class I histocompatibility antigen, B-73 alpha chain'

    SELECT ?protein ?anyKindOfName WHERE { ?protein a up:Protein . ?protein (up:recommendedName|up:alternativeName) ?structuredName . ?structuredName ?anyKindOfName "HLA class I histocompatibility antigen, B-73 alpha chain" . ?anyKindOfName rdfs:subPropertyOf up:structuredNameType . }Use

  7. Find any uniprot entry, or an uniprot entries domain or component which has a name 'HLA class I histocompatibility antigen, B-73 alpha chain'

    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

  8. Find all names associated with uniprot entry P05067, and if the name is associated with the entry it's domains or its components

    SELECT ?protein ?anyKindOfName ?names ?partType WHERE { BIND(<http://purl.uniprot.org/uniprot/P05067> AS ?protein) ?protein a up:Protein . { ?protein (up:recommendedName|up:alternativeName) ?structuredName . } UNION { VALUES(?partType){(up:domain) (up:component)} ?protein ?partType ?part . ?part (up:recommendedName|up:alternativeName) ?structuredName . } ?structuredName ?anyKindOfName ?names . ?anyKindOfName rdfs:subPropertyOf up:structuredNameType . }Use

  9. Get the list of uniprot entries for the chromosome of proteome UP000000625

    SELECT ?protein ?proteome WHERE { ?protein a up:Protein ; up:reviewed true ; up:proteome ?proteome . VALUES (?proteome) {(<http://purl.uniprot.org/proteomes/UP000000625#Chromosome>)} }Use

  10. Use ALLIE a service for Abbreviation / Long Form in Japanese and English to search in UniProt using Japanese.

    SELECT ?protein ?englishLabelStr WHERE { SERVICE<http://data.allie.dbcls.jp/sparql>{ ?x rdfs:label "アミロイド前駆体タンパク質"@ja ; rdfs:label ?englishLabel . FILTER(lang(?englishLabel) = "en") } BIND (STR(?englishLabel) AS ?englishLabelStr) ?protein a up:Protein . { ?protein (up:recommendedName|up:alternativeName) ?structuredName . } UNION { VALUES(?partType){(up:domain) (up:component)} ?protein ?partType ?part . ?part (up:recommendedName|up:alternativeName) ?structuredName . } ?structuredName ?anyKindOfName ?englishLabelStr . ?anyKindOfName rdfs:subPropertyOf up:structuredNameType . }Use

  11. Find UniProt entries with merged loci in Bordetella avium

    SELECT ?protein (GROUP_CONCAT(?locusName; separator=',') AS ?locusNames) WHERE { ?protein a up:Protein ; up:organism taxon:360910 ; up:encodedBy ?gene . ?gene up:locusName ?locusName . } GROUP BY ?protein HAVING (COUNT(?locusName) > 1)Use

  12. Find UniParc records whose sequence point to the most database entries

    SELECT ?sequence ?entries WHERE { SELECT ?sequence (COUNT(?entry) AS ?entries) WHERE { GRAPH <http://sparql.uniprot.org/uniparc> { ?sequence up:sequenceFor ?entry . } } GROUP BY ?sequence } ORDER BY DESC(?entries)Use

  13. Find UniProtKB entries with more than 1 Topological domain annotation

    SELECT ?protein (GROUP_CONCAT(?comment; separator=", ") AS ?comments) WHERE { ?protein a up:Protein ; up:annotation ?annotation . ?annotation rdf:type up:Topological_Domain_Annotation ; rdfs:comment ?comment . } GROUP BY ?protein HAVING (COUNT(?annotation) > 1)Use

  14. Find longest comment text associated with a UniProtKB Natural Variant Annotation

    SELECT ?annotation ?comment WHERE { ?annotation a up:Natural_Variant_Annotation ; rdfs:comment ?comment . } ORDER BY DESC(STRLEN(?comment))Use

  15. Find the co-occurence count of Topological Domain comment text in UniProtKB entries

    SELECT ?comment1 ?comment2 (COUNT(?comment1) AS ?count1) WHERE { ?protein a up:Protein ; up:annotation ?annotation1 , ?annotation2 . ?annotation1 rdf:type up:Topological_Domain_Annotation ; rdfs:comment ?rawComment1 . ?annotation2 rdf:type up:Topological_Domain_Annotation ; rdfs:comment ?rawComment2 . BIND(IF(contains(?rawComment1, ';'), STRBEFORE(?rawComment1,';'), ?rawComment1) AS ?comment1) BIND(IF(contains(?rawComment2, ';'), STRBEFORE(?rawComment2,';'), ?rawComment2) AS ?comment2) FILTER(?annotation1 != ?annotation2) } GROUP BY ?comment1 ?comment2 ORDER BY DESC(COUNT(?comment1))Use

  16. Find the similar proteins for UniProtKB entry P05067 sorted by UniRef cluser identity

    SELECT ?similar ?identity FROM <http://sparql.uniprot.org/uniref> FROM <http://sparql.uniprot.org/uniprot> WHERE { BIND (uniprotkb:P05607 AS ?protein) ?cluster up:member ?member ; up:member/up:sequenceFor ?protein; up:identity ?identity . ?member up:sequenceFor ?similar . FILTER(!sameTerm(?similar, ?protein)) } ORDER BY DESC(?identity)Use

  17. Find the orthologous proteins for UniProtKB entry P05067 using the OrthoDB database

    SELECT ?protein ?orthoGroup ?scientificName ?functionComment ?prefferedGeneName ((STRLEN(?value) - ?medianLength) as ?deviationFromMedianLength) WHERE { uniprotkb:P05067 a up:Protein ; up:organism/up:scientificName ?scientificName ; rdfs:seeAlso ?orthoGroup ; up:encodedBy/skos:prefLabel ?prefferedGeneName ; up:sequence/rdf:value ?value . OPTIONAL { ?protein up:annotation ?functionAnnotation . ?functionAnnotation a up:Function_Annotation ; rdfs:comment ?functionComment . } SERVICE<http://sparql.orthodb.org/sparql>{ ?orthoGroup orthodb:ogMedianProteinLength ?medianLength . ?orthoGroup orthodb:hasMember ?xref . ?xref orthodb:xref/orthodb:xrefResource uniprotkb:P05067 . } }Use

  18. Find the human protein which contains an Epitope VSTQ, where T is a phosporylated threonine

    SELECT ?protein ?comment ?begin ?end WHERE { ?protein a up:Protein ; up:organism taxon:9606 ; up:sequence ?sequence ; up:annotation ?annotation . ?annotation a up:Modified_Residue_Annotation ; rdfs:comment ?comment ; up:range ?range . ?range faldo:begin [ faldo:position ?begin ; faldo:reference ?sequence ] ; faldo:end [ faldo:position ?end ; faldo:reference ?sequence ] . ?sequence rdf:value ?aaSequence . FILTER (SUBSTR(?aaSequence, ?begin -2 , 4) = "VSTQ") FILTER (CONTAINS(?comment, "Phosphothreonine")) }Use

  19. For the human entry P05067 (Amyloid-beta precursor protein) find the trascript start ends in Ensembl

    SELECT ?protein ?transcript ?begin ?end WHERE { BIND(uniprotkb:P05067 AS ?protein) SERVICE <https://www.ebi.ac.uk/rdf/services/sparql> { ?ensemblGene ensemblterms:DEPENDENT ?protein. ?transcript faldo:location ?location ; obo:SO_transcribed_from ?ensemblGene . ?location faldo:begin [faldo:position ?begin] ; faldo:end [faldo:position ?end ] . } }Use

  20. Retrieve entries and Catalytic activities in the reviewed (Swiss-Prot) section that have experimental evidences,

    SELECT ?protein ?rhea WHERE { # ECO 269 is experimental evidence BIND (<http://purl.obolibrary.org/obo/ECO_0000269> as ?evidence) ?protein up:reviewed true ; up:organism taxon:9606 ; up:classifiedWith keywords:1185 ; up:annotation ?a ; up:attribution ?attribution . ?a a up:Catalytic_Activity_Annotation ; up:catalyticActivity ?ca . ?ca up:catalyzedReaction ?rhea . [] rdf:subject ?a ; rdf:predicate up:catalyticActivity ; rdf:object ?ca ; up:attribution ?attribution . ?attribution up:evidence ?evidence . }Use

  21. Retrieve human enzymes that targets that metabolize sphingolipids with all drugs having an assay. Considering only drugs with highestDevelopmentPhase 4, and uniprot entries in a reference proteome (KW:1185)

    SELECT DISTINCT ?protein ?activityType ?standardActivityValue ?standardActivityUnit ?chemblMolecule ?chemlbMoleculePrefLabel WHERE { SERVICE <https://sparql.rhea-db.org/sparql> { ?rhea rdfs:subClassOf rh:Reaction ; rh:status rh:Approved ; rh:side/rh:contains/rh:compound/rh:chebi/rdfs:subClassOf+ CHEBI:26739 . } ?ca up:catalyzedReaction ?rhea . ?protein up:annotation/up:catalyticActivity ?ca ; up:organism taxon:9606 ; up:classifiedWith keywords:1185 . # ChEMBL: retrieve the corresponding targets and with drugs in clinical phase 4 SERVICE <https://www.ebi.ac.uk/rdf/services/sparql> { ?activity a cco:Activity ; cco:hasMolecule ?chemblMolecule ; cco:hasAssay ?assay ; cco:standardType ?activityType ; cco:standardValue ?standardActivityValue ; cco:standardUnits ?standardActivityUnit . ?chemblMolecule cco:highestDevelopmentPhase 4 ; rdfs:label ?chemblMoleculeLabel ; skos:prefLabel ?chemlbMoleculePrefLabel . ?assay cco:hasTarget ?target . ?target cco:hasTargetComponent/cco:targetCmptXref ?protein . ?protein a cco:UniprotRef . } }Use

  22. Retrieve entries with sequences that are composed of fragments

    SELECT DISTINCT ?protein WHERE { ?protein a up:Protein ; up:sequence ?sequence ; MINUS { ?sequence up:fragment [] } }Use

  23. Connect patents cited in UniProtKB with those in the patent database at EPO via publication number.

    SELECT ?citation ?patent ?application ?applicationNo WHERE { ?citation a up:Patent_Citation ; skos:exactMatch ?patent . FILTER(CONTAINS(STR(?patent), 'EP')) BIND(SUBSTR(STR(?patent), 35) AS ?applicationNo) SERVICE<https://data.epo.org/linked-data/query>{ ?application patent:publicationNumber ?applicationNo } }Use

  24. Connect patents cited in UniProtKB with those in the patent database at EPO via publication number, whose grant date is more than twenty years in the past.

    PREFIX rdf:<http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#> PREFIX skos:<http://www.w3.org/2004/02/skos/core#> PREFIX up:<http://purl.uniprot.org/core/> prefix patent: <http://data.epo.org/linked-data/def/patent/> SELECT ?grantDate ?patent ?application ?applicationNo WHERE { ?citation a up:Patent_Citation ; skos:exactMatch ?patent . BIND(SUBSTR(STR(?patent), 35) AS ?applicationNo) BIND(SUBSTR(STR(?patent), 33, 2) AS ?countryCode) SERVICE<https://data.epo.org/linked-data/query>{ ?publication patent:publicationNumber ?applicationNo ; patent:application ?application . ?application patent:grantDate ?grantDate . } BIND((year(now()) - 20) AS ?thisYearMinusTwenty) BIND(year(?grantDate) AS ?grantYear) FILTER(?grantYear < ?thisYearMinusTwenty) } ORDER BY ?grantYearUse

  25. Find the Rhea and Interpro combinations in UniProtKB entries.

    SELECT ?interpro ?rhea FROM <http://sparql.uniprot.org/uniprot> WHERE { ?protein up:reviewed true . ?protein up:annotation ?annotation . ?annotation up:catalyticActivity ?rhea . ?protein rdfs:seeAlso ?interpro . ?interpro up:database <http://purl.uniprot.org/database/InterPro> . } ORDER BY ?rheaUse
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