RdfRdbMappingExamples

Mapping Examples

Find me papers about alzheimer's disease gene association studies looking at polymorphisms in gene products involved in synapse organization and biogenesis (go:GO_0050808 GO schema Neurocommons Demo):

prefix go: <http://purl.org/obo/owl/GO#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix owl: <http://www.w3.org/2002/07/owl#>
prefix mesh: <http://purl.org/commons/record/mesh/>
prefix sc: <http://purl.org/science/owl/sciencecommons/>
prefix ro: <http://www.obofoundry.org/ro/ro.owl#>
 
select distinct ?gene ?genename
 
where
{   graph <http://purl.org/commons/hcls/goa>
    { ?protein rdfs:subClassOf ?res.
      ?res owl:onProperty ro:has_function.
      ?res owl:someValuesFrom ?res2.
      ?res2 owl:onProperty ro:realized_as.
      ?res2 owl:someValuesFrom ?process.

      # Gene
      graph <http://purl.org/commons/hcls/20070416/classrelations>
        {{?process <http://purl.org/obo/owl/obo#part_of> go:GO_0050808}
         union
        {?process rdfs:subClassOf go:GO_0050808 }}
      ?protein rdfs:subClassOf ?parent.
      ?parent owl:equivalentClass ?res3.
      ?res3 owl:hasValue ?gene.
     }
  graph <http://purl.org/commons/hcls/gene>
    { ?gene rdfs:label ?genename.
      ?gene sc:from_species_described_by <http://purl.org/commons/record/taxon/9606> }
  graph <http://purl.org/commons/hcls/20070416>
    { ?process rdfs:label ?processname}
}

The AlzGene portion of this query translates to:

SELECT g.GeneID, g.LocusID, pa.ProteinAlias, pa.ProteinAlias, ed.EthnicDataID, s.StudyID, s.StudyName, s.PubMedID, e.Ethnicity, r.ResultDesc
  FROM "GeneAlias" AS ga
       INNER JOIN "Gene" AS g ON ga.GeneID=g.GeneID
       INNER JOIN "Protein" AS p ON g.GeneID=p.GeneID
       INNER JOIN "ProteinAlias" AS pa ON p.ProteinID=pa.ProteinID
       INNER JOIN "EthnicData" AS ed ON g.GeneID=ed.GeneID
       INNER JOIN "Study" AS s ON ed.StudyID=s.StudyID
       INNER JOIN "Ethnicity" AS e ON ed.EthnicityID=e.EthnicityID
       INNER JOIN "Result" AS r ON ed.ResultID=r.ResultID
 WHERE ga.GeneAlias='CTSD';

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