CommentQuery
Find all names associated with uniprot entry P05067, and if the name is associated with the entry it's domains or its componentsSELECT ?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 . }
Get the list of uniprot entries for the chromosome of proteome UP000000625SELECT ?protein ?proteome WHERE { ?protein a up:Protein ; up:reviewed true ; up:proteome ?proteome . VALUES (?proteome) {(<http://purl.uniprot.org/proteomes/UP000000625#Chromosome>)} }
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 . }
Find UniProt entries with merged loci in Bordetella aviumSELECT ?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)
Find UniParc records whose sequence point to the most database entriesSELECT ?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)
Find UniProtKB entries with more than 1 Topological domain annotationSELECT ?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)
Find longest comment text associated with a UniProtKB Natural Variant AnnotationSELECT ?annotation ?comment WHERE { ?annotation a up:Natural_Variant_Annotation ; rdfs:comment ?comment . } ORDER BY DESC(STRLEN(?comment))
Find the co-occurence count of Topological Domain comment text in UniProtKB entriesSELECT ?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))
Find the similar proteins for UniProtKB entry P05067 sorted by UniRef cluser identitySELECT ?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)
Find the orthologous proteins for UniProtKB entry P05067 using the OrthoDB databaseSELECT ?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 . } }
Find the human protein which contains an Epitope VSTQ, where T is a phosporylated threonineSELECT ?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")) }
For the human entry P05067 (Amyloid-beta precursor protein) find the trascript start ends in EnsemblSELECT ?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 ] . } }
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 . }
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 . 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 . } }
Retrieve entries with sequences that are composed of fragmentsSELECT DISTINCT ?protein WHERE { ?protein a up:Protein ; up:sequence ?sequence ; MINUS { ?sequence up:fragment [] } }