1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. Retrieve drugs that target human enzymes involved in sterol metabolism (federated query).

    SELECT DISTINCT ?protein ?proteinFullName ?activityType ?standardActivityValue ?standardActivityUnit ?chemblMolecule ?chemlbMoleculePrefLabel 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, KW-1185) enzymes catalyzing these Rhea reactions ?ca up:catalyzedReaction ?reaction . ?a up:catalyticActivity ?ca . ?protein up:annotation ?a ; up:organism taxon:9606 ; up:classifiedWith keywords:1185 ; up:recommendedName ?proteinRecName . ?proteinRecName up:fullName ?proteinFullName # 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
  20. Retrieve images of 'Anas' (Ducks) in the European Environmental Agency databases (federated query).

    SELECT ?taxon ?ncbiTaxid ?eunisTaxon ?eunisname ?image WHERE { GRAPH<http://sparql.uniprot.org/taxonomy>{ ?taxon a up:Taxon . ?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
  21. 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).

    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 . ?reaction rh:equation ?reactionEquation . ?reaction rh:side ?reactionSide . ?reactionSide rh:contains ?participant . ?participant rh:compound ?compound . # compound constraint (ch:CHEBI_16113 == cholesterol) ?compound rh:chebi ch:CHEBI_16113 . } } } # taxonomy constraint (taxon:9606 == Homo sapiens) ?protein up:organism taxon:9606 . ?protein up:annotation ?a . ?a a up:Catalytic_Activity_Annotation . ?a up:catalyticActivity ?ca . ?ca up:catalyzedReaction ?reaction . ?protein rdfs:seeAlso / up:transcribedFrom ?ensemblGene . # federated query to Bgee (expression data) SERVICE <http://biosoda.expasy.org/rdf4j-server/repositories/bgeelight> { ?gene genex:isExpressedIn ?anatomicEntity . ?gene lscr:xrefEnsemblGene ?ensemblGene . ?anatomicEntity rdfs:label ?anatomicEntityLabel . } }Use