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VirtSPARQLGeneExamplesCollecton

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%META:TOPICPARENT{name="VirtTipsAndTricksGuide"}% ---+LinkedData SPARQL Reference Collection Using the Gene Ontology %TOC% The following guide presents collection of LinkedData SPARQL Query Examples Using the Gene Ontology: ---++Example Find Genes and their links to Gene Ontology terms <verbatim> PREFIX psys: <http://proton.semanticweb.org/2006/05/protons#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX gene: <http://linkedlifedata.com/resource/entrezgene/> SELECT * WHERE { ?gene rdf:type gene:Gene . ?gene gene:goTerm ?go . } LIMIT 10 </verbatim> * [[http://bit.ly/14PKiJh][View the SPARQL Query Definition via SPARQL Protocol URL]] * [[http://bit.ly/YnSgE5][View the SPARQL Query Results via SPARQL Protocol URL]] ---++Example Find interacting partners for specified protein <verbatim> PREFIX biopax2: <http://www.biopax.org/release/biopax-level2.owl#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> SELECT DISTINCT ?protein ?interactor_uri ?interactor_name WHERE { ?i rdf:type biopax2:interaction . ?i biopax2:PARTICIPANTS ?p . ?p biopax2:PHYSICAL-ENTITY ?protein . ?protein biopax2:NAME "Phytochrome A" . ?i biopax2:PARTICIPANTS ?p1 . ?p1 biopax2:PHYSICAL-ENTITY ?interactor_uri . ?interactor_uri rdf:type biopax2:protein . ?interactor_uri biopax2:NAME ?interactor_name . } </verbatim> * [[http://bit.ly/X4Hnqw][View the SPARQL Query Definition via SPARQL Protocol URL]] * [[http://bit.ly/12IxrtU][View the SPARQL Query Results via SPARQL Protocol URL]] ---++Example Find Interactions where Participates Specified Protein <verbatim> PREFIX biopax2: <http://www.biopax.org/release/biopax-level2.owl#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> SELECT ?interaction ?protein WHERE { ?interaction rdf:type biopax2:interaction . ?interaction biopax2:PARTICIPANTS ?p . ?p biopax2:PHYSICAL-ENTITY ?protein . ?protein biopax2:NAME "Phytochrome A" . } </verbatim> * [[http://bit.ly/14PKp7H][View the SPARQL Query Definition via SPARQL Protocol URL]] * [[http://bit.ly/Vd7n5N][View the SPARQL Query Results via SPARQL Protocol URL]] ---++Example Find All Proteins That are Linked to a Curated Interaction from the Literature and to Inflammatory Response <verbatim> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX biopax2: <http://www.biopax.org/release/biopax-level2.owl#> PREFIX uniprot: <http://purl.uniprot.org/core/> SELECT distinct ?fullname WHERE { ?interaction rdf:type biopax2:physicalInteraction . ?interaction biopax2:PARTICIPANTS ?participant . ?participant biopax2:PHYSICAL-ENTITY ?physicalEntity . ?physicalEntity skos:exactMatch ?protein . ?protein uniprot:classifiedWith <http://purl.uniprot.org/go/0006954>. ?protein uniprot:recommendedName ?name . ?name uniprot:fullName ?fullname . } </verbatim> * [[http://bit.ly/WGnABt][View the SPARQL Query Definition via SPARQL Protocol URL]] * [[http://bit.ly/WXFRbP][View the SPARQL Query Results via SPARQL Protocol URL]] ---++Example Find All Proteins that are Linked to a Curated Molecular Interaction, to Inflammatory Response and to a Target of Existing Drug <verbatim> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX biopax2: <http://www.biopax.org/release/biopax-level2.owl#> PREFIX uniprot: <http://purl.uniprot.org/core/> PREFIX drugbank: <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/> SELECT distinct ?fullname WHERE { ?interaction rdf:type biopax2:physicalInteraction . ?interaction biopax2:PARTICIPANTS ?participant . ?participant biopax2:PHYSICAL-ENTITY ?physicalEntity . ?physicalEntity skos:exactMatch ?protein . ?protein uniprot:classifiedWith <http://purl.uniprot.org/go/0006954>. ?protein uniprot:recommendedName ?name. ?name uniprot:fullName ?fullname . ?protein uniprot:mnemonic ?mnemonic . ?target drugbank:swissprotName ?mnemonic . } </verbatim> * [[http://bit.ly/12aOyoe][View the SPARQL Query Definition via SPARQL Protocol URL]] * [[http://bit.ly/YnSo6C][View the SPARQL Query Results via SPARQL Protocol URL]] ---++Example Fund Drugs Related to Asthma that are Linked to a Molecular Interaction <verbatim> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX biopax2: <http://www.biopax.org/release/biopax-level2.owl#> PREFIX uniprot: <http://purl.uniprot.org/core/> PREFIX drugbank: <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/> SELECT distinct ?fullname ?drugname ?indication WHERE { ?participant biopax2:PHYSICAL-ENTITY ?physicalEntity . ?physicalEntity skos:semanticRelation ?protein . ?protein uniprot:recommendedName ?name. ?name uniprot:fullName ?fullname . ?target skos:exactMatch ?protein . ?drug drugbank:target ?target. ?drug drugbank:genericName ?drugname. ?drug drugbank:indication ?indication. filter(regex(?indication, "asthma", "i")) } </verbatim> * [[http://bit.ly/Z7o8Tq][View the SPARQL Query Definition via SPARQL Protocol URL]] * [[http://bit.ly/Y9idZe][View the SPARQL Query Results via SPARQL Protocol URL]] ---++Example Find Drugs Related to Asthma that are Linked to a Curated Molecular Interaction in the Literature where the Protein is Known to cause Inflammatory Response <verbatim> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX biopax2: <http://www.biopax.org/release/biopax-level2.owl#> PREFIX uniprot: <http://purl.uniprot.org/core/> PREFIX drugbank: <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/> SELECT DISTINCT ?fullname ?drugname WHERE { ?interaction rdf:type biopax2:physicalInteraction . ?interaction biopax2:PARTICIPANTS ?participant . ?participant biopax2:PHYSICAL-ENTITY ?physicalEntity . ?physicalEntity skos:exactMatch ?protein . ?protein uniprot:classifiedWith <http://purl.uniprot.org/go/0006954>. ?protein uniprot:recommendedName ?name. ?name uniprot:fullName ?fullname . ?target skos:exactMatch ?protein . ?drug drugbank:target ?target . ?drug drugbank:genericName ?drugname . ?drug drugbank:indication ?indication . } </verbatim> * [[http://bit.ly/X1PrLQ][View the SPARQL Query Definition via SPARQL Protocol URL]] * [[http://bit.ly/XFR7c9][View the SPARQL Query Results via SPARQL Protocol URL]] ---++Example Find All Located in Y-chromosome Human Genes <verbatim> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX gene: <http://linkedlifedata.com/resource/entrezgene/> PREFIX uniprot: <http://purl.uniprot.org/uniprot/core/> PREFIX core: <http://purl.uniprot.org/core/> SELECT ?genedescription ?taxonomy WHERE { ?geneid gene:description ?genedescription . ?geneid gene:uniprotAccession ?uniprotaccession . ?geneid gene:chromosome 'Y' . ?uniprotaccession core:organism ?taxonomy . ?taxonomy core:scientificName 'Homo sapiens' . } </verbatim> * [[http://bit.ly/WXGlP3][View the SPARQL Query Definition via SPARQL Protocol URL]] * [[http://bit.ly/Xyl5Nc][View the SPARQL Query Results via SPARQL Protocol URL]] ---++Example Find All Located in Y-chromosome Human Genes with Known Molecular Interactions <verbatim> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX gene: <http://linkedlifedata.com/resource/entrezgene/> PREFIX core: <http://purl.uniprot.org/core/> PREFIX biopax2: <http://www.biopax.org/release/biopax-level2.owl#> SELECT ?genedescription ?taxonomy ?interactionname WHERE { ?interaction rdf:type biopax2:interaction . ?interaction biopax2:PARTICIPANTS ?p . ?interaction biopax2:NAME ?interactionname . ?p biopax2:PHYSICAL-ENTITY ?protein . ?protein skos:exactMatch ?uniprotaccession . ?uniprotaccession core:organism ?taxonomy . ?taxonomy core:scientificName 'Homo sapiens' . ?geneid gene:uniprotAccession ?uniprotaccession . ?geneid gene:description ?genedescription . ?geneid gene:chromosome 'Y' . } </verbatim> * [[http://bit.ly/V2Q6hS][View the SPARQL Query Definition via SPARQL Protocol URL]] * [[http://bit.ly/12aOQLR][View the SPARQL Query Results via SPARQL Protocol URL]] ---++Example Find All Located in Y-chromosome, Human Genes with Known Molecular Interactions, which are analyzed with Molecular Techniques <verbatim> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX gene: <http://linkedlifedata.com/resource/entrezgene/> PREFIX core: <http://purl.uniprot.org/core/> PREFIX biopax2: <http://www.biopax.org/release/biopax-level2.owl#> PREFIX lifeskim: <http://linkedlifedata.com/resource/lifeskim/> PREFIX umls: <http://linkedlifedata.com/resource/umls/> PREFIX pubmed: <http://linkedlifedata.com/resource/pubmed/> SELECT distinct ?genedescription ?prefLabel WHERE { ?interaction rdf:type biopax2:interaction . ?interaction biopax2:PARTICIPANTS ?p . ?p biopax2:PHYSICAL-ENTITY ?protein . ?protein skos:exactMatch ?uniprotaccession . ?uniprotaccession core:organism <http://purl.uniprot.org/taxonomy/9606> . ?geneid gene:uniprotAccession ?uniprotaccession . ?geneid gene:description ?genedescription . ?geneid gene:pubmed ?pmid . ?geneid gene:chromosome 'Y' . ?pmid lifeskim:mentions ?umlsid . ?umlsid skos:prefLabel ?prefLabel . ?umlsid rdf:type <http://linkedlifedata.com/resource/semanticnetwork/id/T063> . } </verbatim> * [[http://bit.ly/WXGPEP][View the SPARQL Query Definition via SPARQL Protocol URL]] * [[http://bit.ly/XylbVb][View the SPARQL Query Results via SPARQL Protocol URL]] ---++Example Find All Located in Y-chromosome, Human Genes with Known Molecular Interactions, which are analyzed with 'Transfection' <verbatim> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX gene: <http://linkedlifedata.com/resource/entrezgene/> PREFIX core: <http://purl.uniprot.org/core/> PREFIX biopax2: <http://www.biopax.org/release/biopax-level2.owl#> PREFIX lifeskim: <http://linkedlifedata.com/resource/lifeskim/> PREFIX umls: <http://linkedlifedata.com/resource/umls/> PREFIX pubmed: <http://linkedlifedata.com/resource/pubmed/> SELECT distinct ?genedescription ?prefLabel WHERE { ?interaction rdf:type biopax2:interaction . ?interaction biopax2:PARTICIPANTS ?p . ?p biopax2:PHYSICAL-ENTITY ?protein . ?protein skos:exactMatch ?uniprotaccession . ?uniprotaccession core:organism <http://purl.uniprot.org/taxonomy/9606> . ?geneid gene:uniprotAccession ?uniprotaccession . ?geneid gene:description ?genedescription . ?geneid gene:pubmed ?pmid . ?geneid gene:chromosome 'Y' . ?pmid lifeskim:mentions ?umlsid . ?umlsid skos:prefLabel 'Transfection' . ?umlsid skos:prefLabel ?prefLabel . } </verbatim> * [[http://bit.ly/X4HVgd][View the SPARQL Query Definition via SPARQL Protocol URL]] * [[http://bit.ly/Vd7GO2][View the SPARQL Query Results via SPARQL Protocol URL]] ---++Example Show All White blood Cell Types <verbatim> PREFIX umls-concept: <http://linkedlifedata.com/resource/umls/id/> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX lld: <http://linkedlifedata.com/resource/> SELECT ?concept ?prefLabel WHERE { { ?concept skos:prefLabel "Leukocytes" . ?concept skos:inScheme lld:umls . ?concept skos:prefLabel ?prefLabel } UNION { ?concept1 skos:prefLabel "Leukocytes" . ?concept1 skos:inScheme lld:umls . ?concept skos:broaderTransitive ?concept1 . ?concept skos:inScheme lld:umls . ?concept skos:prefLabel ?prefLabel } } </verbatim> * [[http://bit.ly/11DxdF9][View the SPARQL Query Definition via SPARQL Protocol URL]] * [[http://bit.ly/VQHXxa][View the SPARQL Query Results via SPARQL Protocol URL]] ---++Example Show Respirations Disorder Types <verbatim> PREFIX umls-concept: <http://linkedlifedata.com/resource/umls/id/> PREFIX skos: <http://www.w3.org/2004/02/skos/core#> PREFIX lld: <http://linkedlifedata.com/resource/> SELECT ?concept ?prefLabel WHERE { { ?concept skos:prefLabel "Respiration Disorders" . ?concept skos:inScheme lld:umls . ?concept skos:prefLabel ?prefLabel } UNION { ?concept1 skos:prefLabel "Respiration Disorders" . ?concept1 skos:inScheme lld:umls . ?concept skos:broaderTransitive ?concept1 . ?concept skos:inScheme lld:umls . ?concept skos:prefLabel ?prefLabel } } </verbatim> * [[http://bit.ly/WXKUJ2][View the SPARQL Query Definition via SPARQL Protocol URL]] * [[http://bit.ly/VQI0ZR][View the SPARQL Query Results via SPARQL Protocol URL]] ---++Related * [[http://linkedlifedata.com/sparql][The Linked Life Data SPARQL Endpoint]] * [[VirtTipsAndTricksGuide][Virtuoso Tips and Tricks Collection]] * [[http://docs.openlinksw.com/virtuoso/rdfsparql.html][Virtuoso Documentation]]

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