1. 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
  2. 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
  3. 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
  4. 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
  5. Retrieve drugs that target human enzymes involved in sterol metabolism (federated query with WikiData and Rhea).

    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
  6. 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
  7. 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 (CHEBI:16113 == cholesterol) ?compound rh:chebi 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
  8. Retrieve drugs that target human enzymes involved in sterol metabolism (federated query with Rhea and ChEMBL via IDSM/Elixir czech republic).

    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) enzymes catalyzing these Rhea reactions ?ca up:catalyzedReaction ?reaction . ?a up:catalyticActivity ?ca . ?protein up:annotation ?a ; up:organism taxon:9606 ; up:recommendedName ?proteinRecName . ?proteinRecName up:fullName ?proteinFullName . # Find drugs in wikidata that interact with the UniProt Proteins # ChEMBL: retrieve the corresponding targets and with drugs in clinical phase 4 # Via https://idsm.elixir-czech.cz/sparql/ SERVICE <https://idsm.elixir-czech.cz/sparql/endpoint/idsm> { ?activity a cco:Activity ; cco:hasMolecule ?chemblMolecule ; cco:hasAssay ?assay ; cco:standardType ?activityType ; cco:standardValue ?standardActivityValue ; cco:standardUnits ?standardActivityUnit . ?chemblMolecule cco:highestDevelopmentPhase ?highestDevelopmentPhase ; rdfs:label ?chemblMoleculeLabel ; skos:prefLabel ?chemlbMoleculePrefLabel . FILTER (?highestDevelopmentPhase > 3) ?assay cco:hasTarget ?target . ?target cco:hasTargetComponent/cco:targetCmptXref ?protein . ?protein a cco:UniprotRef . } }Use