Federating Patient Data From RPPA Data

query.sparql

PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
PREFIX tcga:<http://purl.org/tcga/core#>
PREFIX tcgameta:<http://purl.org/tcga/metadata#>
PREFIX tcgaclin:<http://purl.org/tcga/clin#>
PREFIX tcgaclinProp:<http://purl.org/tcga/clin#property/>
SELECT ?patientId ?tumorTissueSite ?ageAtInitialDiagnosis ?gender ?race ?vitalStatus
WHERE {
  SERVICE <http://agalpha.mathbiol.org:10035/repositories/tcga> {
    ?file tcga:platform ?platform .
    ?platform rdfs:label "mda_rppa_core" .
    ?file tcga:diseaseStudy ?diseaseStudy .
    ?diseaseStudy rdfs:label "gbm" .
    ?file rdfs:label ?name .
    FILTER contains(?name, "Level_3")
    MINUS {
        ?file rdfs:label ?name .
        filter contains(?name, "Control")
    }
    BIND(STRBEFORE(?name, ".txt") AS ?nameWithoutExtension)
    BIND(STRAFTER(?nameWithoutExtension, "mdanderson.org_GBM.MDA_RPPA_Core.protein_expression.Level_3.") AS ?sampleId)
  }
  SERVICE <http://agalpha.mathbiol.org:10035/repositories/tcga-metadata> {
    ?sample rdfs:label ?sampleId .
    ?sample tcgameta:barcode ?barcode .
    BIND(SUBSTR(?barcode, 1, 12) AS ?patientId)
  }
  SERVICE <http://agalpha.mathbiol.org:10035/repositories/tcga-patient> {
    ?patient tcgaclinProp:bcr_patient_barcode ?patientId .
    ?patient tcgaclinProp:tumor_tissue_site ?tumorTissueSite .
    ?patient tcgaclinProp:age_at_initial_pathologic_diagnosis ?ageAtInitialDiagnosis .
    ?patient tcgaclinProp:gender ?gender .
    ?patient tcgaclinProp:race ?race .
    ?patient tcgaclinProp:vital_status ?vitalStatus .
  }
}