25: 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 . }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'

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

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

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> 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

PREFIX up: <http://purl.uniprot.org/core/> 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.

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> 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

PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> 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

PREFIX up: <http://purl.uniprot.org/core/> 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

33: Find longest comment text associated with a UniProtKB Natural Variant Annotation

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> 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

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> 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 cluster identity

PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/> PREFIX up: <http://purl.uniprot.org/core/> 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

PREFIX orthodb: <http://purl.orthodb.org/> 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 uniprotkb: <http://purl.uniprot.org/uniprot/> PREFIX up: <http://purl.uniprot.org/core/> 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 <https://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

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 ?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

PREFIX p: <http://www.wikidata.org/prop/> PREFIX pq: <http://www.wikidata.org/prop/qualifier/> PREFIX ps: <http://www.wikidata.org/prop/statement/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/> PREFIX wdt: <http://www.wikidata.org/prop/direct/> 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,

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX up: <http://purl.uniprot.org/core/> 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

PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> 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

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

41: Retrieve entries with sequences that are composed of fragments

PREFIX up: <http://purl.uniprot.org/core/> 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.

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 patent: <http://data.epo.org/linked-data/def/patent/> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX up: <http://purl.uniprot.org/core/> 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.

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX up: <http://purl.uniprot.org/core/> 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

45: Retrieve drugs that target human enzymes involved in sterol metabolism (federated query with WikiData and Rhea).

PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_> PREFIX chebihash: <http://purl.obolibrary.org/obo/chebi#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/> PREFIX up: <http://purl.uniprot.org/core/> PREFIX wdt: <http://www.wikidata.org/prop/direct/> SELECT DISTINCT ?protein ?proteinFullName ?wikiChemical ?wikiChemicalLabel ?medicalConditionTreatedLabel WHERE { # ChEBI: retrieve members of the ChEBI class ChEBI:15889 (sterol) # Rhea: retrieve the reactions involving these ChEBI as participants SERVICE <https://sparql.rhea-db.org/sparql> { ?reaction rdfs:subClassOf rh:Reaction ; rh:status rh:Approved ; rh:side ?reactionSide . ?reactionSide rh:contains ?participant . ?participant rh:compound ?compound { ?compound rh:chebi ?chebi . ?chebi (rdfs:subClassOf)+ CHEBI:15889 } UNION { ?compound rh:chebi ?chebi . ?chebi2 rdfs:subClassOf ?chebiRestriction . ?chebiRestriction a owl:Restriction ; owl:onProperty chebihash:has_major_microspecies_at_pH_7_3 ; owl:someValuesFrom ?chebi . ?chebi2 (rdfs:subClassOf)+ CHEBI:15889 } } # UniProt: retrieve the human (taxid:9606) enzymes catalyzing these Rhea reactions ?ca up:catalyzedReaction ?reaction . ?a up:catalyticActivity ?ca . ?proteinIRI up:annotation ?a ; up:organism taxon:9606 ; up:recommendedName ?proteinRecName . ?proteinRecName up:fullName ?proteinFullName . # Find drugs in wikidata that interact with the UniProt Proteins BIND (SUBSTR(STR(?proteinIRI), STRLEN(STR(uniprotkb:))+1) AS ?protein) SERVICE <https://query.wikidata.org/sparql> { ?wp wdt:P352 ?protein . ?wikiChemical wdt:P129 ?wp . # Physically interacts with ?wikiChemical rdfs:label ?wikiChemicalLabel . ?wikiChemical wdt:P2175 ?wmc . # Medical conndition treated ?wmc rdfs:label ?medicalConditionTreatedLabel . FILTER(lang(?medicalConditionTreatedLabel) = 'en') FILTER(lang(?wikiChemicalLabel) = 'en') } }Use

46: Retrieve images of 'Anas' (Ducks) from the European Environmental Agency databases (federated query).

PREFIX eunisSpecies: <http://eunis.eea.europa.eu/rdf/species-schema.rdf#> 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 ?ncbiTaxid ?eunisTaxon ?eunisName ?image WHERE { GRAPH <http://sparql.uniprot.org/taxonomy> { ?taxon a up:Taxon . # Taxon subclasses are materialized, do not use rdfs:subClassOf+ ?taxon rdfs:subClassOf taxon:8835 . BIND(strafter(str(?taxon), 'onomy/') AS ?ncbiTaxid) } SERVICE <https://semantic.eea.europa.eu/sparql> { ?eunisTaxon a eunisSpecies:SpeciesSynonym ; eunisSpecies:binomialName ?eunisName ; eunisSpecies:sameSpeciesNCBI ?ncbiTaxid ; <http://xmlns.com/foaf/0.1/depiction> ?image . } }Use

47: Find UniProt entries with a transmembrane region, with an Alanine in the 15 Aminoacid region preceding the transmembrane

PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX up: <http://purl.uniprot.org/core/> SELECT ?protein ?from ?interestingRegion WHERE { ?protein up:annotation ?annotation . ?annotation a up:Transmembrane_Annotation . # Get the coordinates of the Transmembrane ?annotation up:range ?range . ?range faldo:begin ?beginI . ?beginI faldo:position ?begin . ?beginI faldo:reference ?sequence . # The aas will have the specific IUPAC aminoacids ?sequence rdf:value ?aas . # We calculate the start by substracting 10 BIND(?begin - 10 AS ?tenBeforeBegin) # Can't start before the sequence starts or we might miss some results BIND(IF(?tenBeforeBegin < 1, 0, ?tenBeforeBegin) AS ?from) # Substring the IUPAC aminoacids BIND(SUBSTR(?aas, ?from, 15) AS ?interestingRegion) # The interestingRegion needds to contain an Alanine FILTER(CONTAINS(?interestingRegion, 'A')) }Use

48: Retrieve glycosylation sites and glycans on human enzymes (federated with glyconnect)

PREFIX faldo: <http://biohackathon.org/resource/faldo#> PREFIX foaf: <http://xmlns.com/foaf/0.1/> PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT DISTINCT ?protein ?glycosite ?glycostructure ?glycoimage WHERE{ ?protein up:annotation ?annotation . ?protein up:organism taxon:9606 . ?annotation a up:Catalytic_Activity_Annotation . ?protein up:sequence ?isoform . SERVICE <https://glyconnect.expasy.org/sparql> { ?glycosite faldo:reference ?isoform . ?glycosite faldo:position ?position . ?specificglycosite faldo:location ?glycosite . ?glycoprotein glycan:glycosylated_at ?specificglycosite . ?glycostructure glycan:glycosylates_at ?specificglycosite . ?glycostructure foaf:depiction ?glycoimage . } }Use

49: Retrieve the UniProt proteins, their catalyzed Rhea reactions, their encoding genes (Ensembl) and the anatomic entities where the genes are expressed (UBERON anatomic entites from Bgee expression data resource).

PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_> PREFIX genex: <http://purl.org/genex#> PREFIX lscr: <http://purl.org/lscr#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX rh: <http://rdf.rhea-db.org/> PREFIX taxon: <http://purl.uniprot.org/taxonomy/> PREFIX up: <http://purl.uniprot.org/core/> SELECT DISTINCT ?protein ?ensemblGene ?reaction ?anatomicEntityLabel ?anatomicEntity WHERE { # federated query to Rhea enadpoint { SELECT DISTINCT ?reaction WHERE { SERVICE <https://sparql.rhea-db.org/sparql> { ?reaction rdfs:subClassOf rh:Reaction ; rh:equation ?reactionEquation ; rh:side ?reactionSide . ?reactionSide rh:contains ?participant . ?participant rh:compound ?compound . # compound constraint (CHEBI:16113 == cholesterol) ?compound rh:chebi CHEBI:16113 . } } } # taxonomy constraint (taxon:9606 == Homo sapiens) ?protein up:organism taxon:9606 ; up:annotation ?a ; rdfs:seeAlso / up:transcribedFrom ?ensemblGene . ?a a up:Catalytic_Activity_Annotation ; up:catalyticActivity ?ca . ?ca up:catalyzedReaction ?reaction . # federated query to Bgee (expression data) BIND(IRI(REPLACE(STR(?ensemblGene), "\\.[0-9]+$", "")) AS ?ensemblGeneNoVersion) SERVICE <https://www.bgee.org/sparql/> { ?gene lscr:xrefEnsemblGene ?ensemblGeneNoVersion ; genex:isExpressedIn ?anatomicEntity . ?anatomicEntity rdfs:label ?anatomicEntityLabel . } }Use

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SPARQL example query