LinkedData SPARQL Reference Collection Using the Gene Ontology The following guide presents collection of LinkedData SPARQL Query Examples Using the Gene Ontology: Example Find Genes and their links to Gene Ontology terms 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 View the SPARQL Query Definition via SPARQL Protocol URL View the SPARQL Query Results via SPARQL Protocol URL Example Find interacting partners for specified protein 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 . } View the SPARQL Query Definition via SPARQL Protocol URL View the SPARQL Query Results via SPARQL Protocol URL Example Find Interactions where Participates Specified Protein 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" . } View the SPARQL Query Definition via SPARQL Protocol URL 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 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 . } View the SPARQL Query Definition via SPARQL Protocol URL 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 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 . } View the SPARQL Query Definition via SPARQL Protocol URL View the SPARQL Query Results via SPARQL Protocol URL Example Fund Drugs Related to Asthma that are Linked to a Molecular Interaction 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")) } View the SPARQL Query Definition via SPARQL Protocol URL 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 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 . } View the SPARQL Query Definition via SPARQL Protocol URL View the SPARQL Query Results via SPARQL Protocol URL Example Find All Located in Y-chromosome Human Genes 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' . } View the SPARQL Query Definition via SPARQL Protocol URL View the SPARQL Query Results via SPARQL Protocol URL Example Find All Located in Y-chromosome Human Genes with Known Molecular Interactions 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' . } View the SPARQL Query Definition via SPARQL Protocol URL 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 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> . } View the SPARQL Query Definition via SPARQL Protocol URL 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' 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 . } View the SPARQL Query Definition via SPARQL Protocol URL View the SPARQL Query Results via SPARQL Protocol URL Example Show All White blood Cell Types 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 } } View the SPARQL Query Definition via SPARQL Protocol URL View the SPARQL Query Results via SPARQL Protocol URL Example Show Respirations Disorder Types 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 } } View the SPARQL Query Definition via SPARQL Protocol URL View the SPARQL Query Results via SPARQL Protocol URL Related The Linked Life Data SPARQL Endpoint Virtuoso Tips and Tricks Collection Virtuoso Documentation