SPARQL example query

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19: Find all Natural Variant Annotations if associated via an evidence tag to an article with a pubmed identifier

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) }Use

20: Find how often an article in pubmed was used in an evidence tag in a human protein (ordered by most used to least)

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))Use

21: 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

22: 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

23: 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

24: 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/version> ?version }Use

25: 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

26: 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

27: 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

28: 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

29: 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

30: 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

31: 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

32: 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

33: 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

34: 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

35: 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

36: 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

37: 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

38: For the human entry P05067 (Amyloid-beta precursor protein) find the gene start ends in WikiData

SELECT ?protein ?begin ?end ?chromosome ?assembly WHERE { { BIND(uniprotkb:P05067 AS ?proteinIRI) BIND (SUBSTR(STR(?proteinIRI), STRLEN(STR(uniprotkb:))+1) AS ?protein) } SERVICE <https://query.wikidata.org/sparql> { ?wp wdt:P352 ?protein ; wdt:P702 ?wg . ?wg p:P644 ?wgss . ?wgss ps:P644 ?begin ; pq:P1057/wdt:P1813 ?chromosome ; pq:P659/rdfs:label ?assembly . ?wg p:P645 ?wgse . ?wgse ps:P645 ?end ; pq:P1057/wdt:P1813 ?chromosome ; pq:P659/rdfs:label ?assembly . FILTER(lang(?assembly) = "en") } }Use

39: 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) GRAPH <http://sparql.uniprot.org/uniprot> { ?protein up:reviewed true ; 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

40: Retrieve human enzymes that metabolize sphingolipids and are annotated in ChEMBL

SELECT DISTINCT ?protein ?chemblEntry WHERE { SERVICE <https://sparql.rhea-db.org/sparql> { ?rhea rdfs:subClassOf rh:Reaction ; 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 ; rdfs:seeAlso ?chemblEntry . ?chemblEntry up:database <http://purl.uniprot.org/database/ChEMBL> . }Use

41: 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

42: 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

43: 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

44: 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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