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

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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 .
  }

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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" .
  }

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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 .
  }

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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 .
  }

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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"))
  }

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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 .
  }

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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' .
  }

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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' .
  }

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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> . 
  }

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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 .
  }

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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 }
  }

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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 }
  }

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Related

• The Linked Life Data SPARQL Endpoint
• Virtuoso Tips and Tricks Collection
• Virtuoso Documentation