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@@ -0,0 +1,1481 @@
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+@prefix rr: <http://www.w3.org/ns/r2rml#> .
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+@prefix fvc: <http://ontologies.adaptcentre.ie/fairvasc#> .
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+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
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+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
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+@prefix sno: <http://purl.bioontology.org/ontology/SNOMEDCT#> .
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+@prefix prov: <http://www.w3.org/ns/prov#> .
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+@prefix ordo:<http://www.orpha.net/ORDO/> .
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+@prefix dcterms: <http://purl.org/dc/terms/> .
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+@prefix foaf: <http://xmlns.com/foaf/0.1/> .
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+
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+<#patient>
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+
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+ rr:logicalTable [ rr:sqlQuery """SELECT
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+ RECORD_ID,
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+ YEAR_OF_BIRTH,
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+ DATE_OF_EVENT_COMP,
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+ FORMATDATETIME(PARSEDATETIME(DATE_OF_VISIT, 'dd/MM/yyyy'), 'yyyy-MM-dd')||'T00:00:00' AS ENCOUNTER_DATE,
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+ REDCAP_REPEAT_INSTANCE,
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+ GENDER,
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+ CASE
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+ WHEN GENDER = 1 THEN 'C20197'
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+ WHEN GENDER = 2 THEN 'C16576'
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+ WHEN GENDER = 3 THEN 'C41438'
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+ END AS GENDER_
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+ FROM RKD""" ];
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+
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+ rr:subjectMap [
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+ rr:template "http://data.fairvasc.ie/resource/rkd/patient/{RECORD_ID}" ;
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+ rr:class fvc:Patient;
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+ ] ;
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:patientID ;
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+ rr:objectMap [
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+ rr:column "RECORD_ID" ;
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+ rr:datatype xsd:string;
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+ ] ;
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+ ] ;
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:yearOfBirth ;
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+ rr:objectMap [
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+ rr:column "YEAR_OF_BIRTH" ;
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+ rr:datatype xsd:gYear;
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+ ] ;
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+ ] ;
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:gender ;
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+ rr:objectMap [
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+ rr:template "https://identifiers.org/ncit:{GENDER_}" ;
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+ rr:datatype xsd:anyURI;
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+ ];
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+ ] ;
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+
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:hasPatientOverview;
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+ rr:objectMap [
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+ rr:parentTriplesMap <#patient_overview> ;
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+ rr:joinCondition [
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+ rr:child "RECORD_ID" ;
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+ rr:parent "RECORD_ID" ;
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+ ] ;
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+ ] ;
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+ ];
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+
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+
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+
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+.
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+
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+<#patient_overview>
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+
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+ rr:logicalTable [ rr:sqlQuery """SELECT
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+ RECORD_ID,
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+ FORMATDATETIME(PARSEDATETIME(DATE_OF_DIAGNOSIS, 'dd/MM/yyyy'), 'yyyy-MM-dd')||'T00:00:00' AS DIAGNOSIS_DATE,
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+ HEIGHT_CMS_KNOWN,
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+ WEIGHT_KG,
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+ BMI
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+ FROM RKD""" ];
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+
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+ rr:subjectMap [
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+ rr:template "http://data.fairvasc.ie/resource/rkd/patient/patientoverview/{RECORD_ID}" ;
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+ rr:class fvc:PatientOverview;
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+ ] ;
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+
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:height ;
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+ rr:objectMap [
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+ rr:column "HEIGHT_CMS_KNOWN" ;
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+ rr:datatype xsd:double;
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+ ] ;
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+ ] ;
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:weight ;
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+ rr:objectMap [
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+ rr:column "WEIGHT_KG" ;
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+ rr:datatype xsd:double;
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+ ] ;
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+ ] ;
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:BMI ;
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+ rr:objectMap [
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+ rr:column "BMI" ;
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+ rr:datatype xsd:double;
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+ ] ;
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+ ] ;
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:hasDiagnosis;
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+ rr:objectMap [
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+ rr:parentTriplesMap <#diagnosis> ;
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+ rr:joinCondition [
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+ rr:child "RECORD_ID" ;
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+ rr:parent "RECORD_ID" ;
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+ ] ;
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+ rr:joinCondition [
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+ rr:child "DIAGNOSIS_DATE" ;
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+ rr:parent "DIAGNOSIS_DATE" ;
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+ ] ;
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+ ] ;
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+ ];
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:hasANCA;
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+ rr:objectMap [
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+ rr:parentTriplesMap <#anca> ;
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+ rr:joinCondition [
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+ rr:child "RECORD_ID" ;
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+ rr:parent "RECORD_ID" ;
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+ ] ;
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+ ] ;
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+ ];
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:hasOrganPattern;
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+ rr:objectMap [
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+ rr:parentTriplesMap <#organ_pattern_generic> ;
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+ rr:joinCondition [
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+ rr:child "RECORD_ID" ;
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+ rr:parent "RECORD_ID" ;
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+ ] ;
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+ ] ;
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+ ];
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:hasOrganPattern;
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+ rr:objectMap [
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+ rr:parentTriplesMap <#organ_pattern_specific> ;
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+ rr:joinCondition [
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+ rr:child "RECORD_ID" ;
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+ rr:parent "RECORD_ID" ;
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+ ] ;
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+ ] ;
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+ ];
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+
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:hasTreatment;
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+ rr:objectMap [
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+ rr:parentTriplesMap <#treatment> ;
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+ rr:joinCondition [
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+ rr:child "RECORD_ID" ;
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+ rr:parent "RECORD_ID" ;
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+ ] ;
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+ ] ;
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+ ];
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+
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:hasTreatment;
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+ rr:objectMap [
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+ rr:parentTriplesMap <#treatment_induction> ;
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+ rr:joinCondition [
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+ rr:child "RECORD_ID" ;
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+ rr:parent "RECORD_ID" ;
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+ ] ;
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+ ] ;
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+ ];
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:hasTreatment;
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+ rr:objectMap [
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+ rr:parentTriplesMap <#treatment_maintenance> ;
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+ rr:joinCondition [
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+ rr:child "RECORD_ID" ;
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+ rr:parent "RECORD_ID" ;
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+ ] ;
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+ ] ;
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+ ];
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:hasComorbidities;
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+ rr:objectMap [
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+ rr:parentTriplesMap <#comorbidities> ;
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+ rr:joinCondition [
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+ rr:child "RECORD_ID" ;
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+ rr:parent "RECORD_ID" ;
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+ ] ;
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+ ] ;
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+ ];
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:hasConsent;
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+ rr:objectMap [
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+ rr:parentTriplesMap <#consent> ;
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+ rr:joinCondition [
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+ rr:child "RECORD_ID" ;
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+ rr:parent "RECORD_ID" ;
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+ ] ;
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+ ] ;
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+ ];
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+
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+.
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+
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+<#treatment_induction>
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+ rr:logicalTable [ rr:sqlQuery """
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+ SELECT
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+ RECORD_ID,
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+ DRUG_SELECTED_CHOICES,
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+ IV_THERAPY,
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+ CASE
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+ WHEN INDUCTION_TREATMENT___1 = 1 THEN 'C769'
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+ END AS INDUCTION_ENCODING___1,
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+ CASE
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+ WHEN INDUCTION_TREATMENT___2 = 1 THEN 'C647'
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+ END AS INDUCTION_ENCODING___2,
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+ CASE
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+ WHEN INDUCTION_TREATMENT___3 = 1 THEN 'C405'
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+ END AS INDUCTION_ENCODING___3,
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+ CASE
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+ WHEN INDUCTION_TREATMENT___4 = 1 THEN 'C15304'
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+ END AS INDUCTION_ENCODING___4,
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+ CASE
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+ WHEN INDUCTION_TREATMENT___5 = 1 THEN 'C1702'
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+ END AS INDUCTION_ENCODING___5,
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+ CASE
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+ WHEN INDUCTION_TREATMENT___6 = 1 THEN 'C1468'
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+ END AS INDUCTION_ENCODING___6,
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+ CASE
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+ WHEN INDUCTION_TREATMENT___7 = 1 THEN 'C290'
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+ END AS INDUCTION_ENCODING___7,
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+ CASE
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+ WHEN INDUCTION_TREATMENT___8 = 1 THEN 'C642'
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+ END AS INDUCTION_ENCODING___8,
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+ CASE
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+ WHEN INDUCTION_TREATMENT___9 = 1 THEN 'C1128'
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+ END AS INDUCTION_ENCODING___9,
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+ CASE
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+ WHEN INDUCTION_TREATMENT___11 = 1 THEN 'C405'
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+ END AS INDUCTION_ENCODING___11,
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+ FORMATDATETIME(PARSEDATETIME(DATE_OF_DIAGNOSIS, 'dd/MM/yyyy'), 'yyyy-MM-dd')||'T00:00:00' AS DIAGNOSIS_DATE,
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+ FORMATDATETIME(PARSEDATETIME(START_DATE, 'dd/MM/yyyy'), 'yyyy-MM-dd')||'T00:00:00' AS DRUG_START_DATE,
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+ FORMATDATETIME(PARSEDATETIME(DATE_OF_IV_THERAPY, 'dd/MM/yyyy'), 'yyyy-MM-dd')||'T00:00:00' AS IV_DATE
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+ FROM RKD
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+ WHERE INDUCTION NOT IN(0)
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+ """ ];
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+
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+ rr:subjectMap [
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+ rr:template "http://data.fairvasc.ie/resource/rkd/overview/treatment/induction/{RECORD_ID}" ;
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+ rr:class fvc:TreatmentInduction;
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+ ] ;
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:treatmentType;
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+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___1}";
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+ rr:datatype xsd:anyURI; ];
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+ ];
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:treatmentType;
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+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___2}";
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+ rr:datatype xsd:anyURI; ];
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+ ];
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:treatmentType;
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+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___3}";
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+ rr:datatype xsd:anyURI; ];
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+ ];
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:treatmentType;
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+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___4}";
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+ rr:datatype xsd:anyURI; ];
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+ ];
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:treatmentType;
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+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___5}";
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+ rr:datatype xsd:anyURI; ];
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+ ];
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:treatmentType;
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+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___6}";
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+ rr:datatype xsd:anyURI; ];
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+ ];
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:treatmentType;
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+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___7}";
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+ rr:datatype xsd:anyURI; ];
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+ ];
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:treatmentType;
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+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___8}";
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+ rr:datatype xsd:anyURI; ];
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+ ];
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:treatmentType;
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+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___9}";
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+ rr:datatype xsd:anyURI; ];
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+ ];
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:treatmentType;
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+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___11}";
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+ rr:datatype xsd:anyURI; ];
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+ ];
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+
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+.
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+
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+<#consent>
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+ rr:logicalTable [ rr:sqlQuery """
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+ SELECT
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+ RECORD_ID,
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+ CASE
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+ WHEN consent_obtained_for_regis___1 = 1 THEN 'Registry_Consent'
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+ END AS CONSENT_ENCODING___1,
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+ CASE
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+ WHEN consent_obtained_for_regis___2 = 1 THEN 'Biobanking_Consent'
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+ END AS CONSENT_ENCODING___2,
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+ CASE
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+ WHEN consent_obtained_for_regis___3 = 1 THEN 'Future_Contact_Consent'
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+ END AS CONSENT_ENCODING___3,
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+ CASE
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+ WHEN consent_obtained_for_regis___4 = 1 THEN 'All'
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+ END AS CONSENT_ENCODING___1, CONSENT_ENCODING___2, CONSENT_ENCODING___4,
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+ CASE
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+ WHEN consent_obtained_for_regis___5 = 1 THEN 'No'
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+ END AS CONSENT_ENCODING___5,
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+ FROM RKD
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+ """ ];
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+
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+ rr:subjectMap [
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+ rr:template "http://data.fairvasc.ie/resource/rkd/overview/consent/{RECORD_ID}" ;
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+ rr:class fvc:Consent;
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+ ] ;
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:consentType;
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+ rr:objectMap [ rr:template "http://data.fairvasc.ie/resource/rkd/overview/consent/{CONSENT_ENCODING___1}";
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+ rr:datatype xsd:anyURI; ];
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+ ];
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:consentType;
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+ rr:objectMap [ rr:template "http://data.fairvasc.ie/resource/rkd/overview/consent/CONSENT_ENCODING___2}";
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+ rr:datatype xsd:anyURI; ];
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+ ];
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:consentType;
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+ rr:objectMap [ rr:template "http://data.fairvasc.ie/resource/rkd/overview/consent/CONSENT_ENCODING___3}";
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+ rr:datatype xsd:anyURI; ];
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+ ];
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:hasConsentForDataUseInRegistry;
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+ rr:objectMap [
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+ rr:template "true";
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+ rr:datatype xsd:boolean;
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+ ];
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+ ];
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:hasConsentForBiobanking;
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+ rr:objectMap [
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+ rr:template "true";
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+ rr:datatype xsd:boolean;
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+ ];
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+ ];
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+
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+
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+ rr:predicateObjectMap [
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+ rr:predicate fvc:hasConsentForFutureContact;
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+ rr:objectMap [
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+ rr:template "true";
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+ rr:datatype xsd:boolean;
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+ ];
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+ ];
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+
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+ rr:predicateObjectMap [
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|
|
+ rr:predicate fvc:hasBiobankLink;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "consent_version_number";
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:consentDate;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "Date_of_Initial_Consent";
|
|
|
+ rr:datatype xsd:dateTime;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+.
|
|
|
+
|
|
|
+
|
|
|
+<#comorbidities>
|
|
|
+ rr:logicalTable [ rr:sqlQuery """
|
|
|
+ SELECT
|
|
|
+ RECORD_ID,
|
|
|
+ CASE
|
|
|
+ WHEN COMORBID_EVENTS___1 = 1 THEN 'C3149'
|
|
|
+ END AS COMORBID_ENCODING___1,
|
|
|
+ CASE
|
|
|
+ WHEN COMORBID_EVENTS___2 = 1 THEN 'C26732'
|
|
|
+ END AS COMORBID_ENCODING___2,
|
|
|
+ CASE
|
|
|
+ WHEN COMORBID_EVENTS___3 = 1 THEN 'C35136'
|
|
|
+ END AS COMORBID_ENCODING___3,
|
|
|
+ CASE
|
|
|
+ WHEN COMORBID_EVENTS___4 = 1 THEN 'C3117'
|
|
|
+ END AS COMORBID_ENCODING___4,
|
|
|
+ CASE
|
|
|
+ WHEN COMORBID_EVENTS___5 = 1 THEN 'C3199'
|
|
|
+ END AS COMORBID_ENCODING___5,
|
|
|
+ CASE
|
|
|
+ WHEN COMORBID_EVENTS___6 = 1 THEN 'C28195'
|
|
|
+ END AS COMORBID_ENCODING___6,
|
|
|
+ CASE
|
|
|
+ WHEN COMORBID_EVENTS___7 = 1 THEN 'C9305'
|
|
|
+ END AS COMORBID_ENCODING___7,
|
|
|
+ CASE
|
|
|
+ WHEN COMORBID_EVENTS___8 = 1 THEN 'C80097'
|
|
|
+ END AS COMORBID_ENCODING___8,
|
|
|
+ CASE
|
|
|
+ WHEN COMORBID_EVENTS___9 = 1 THEN 'C2985'
|
|
|
+ END AS COMORBID_ENCODING___9,
|
|
|
+ CASE
|
|
|
+ WHEN COMORBID_EVENTS___10 = 1 THEN 'C3390'
|
|
|
+ END AS COMORBID_ENCODING___10,
|
|
|
+ CASE
|
|
|
+ WHEN COMORBID_EVENTS___13 = 1 THEN 'C28397'
|
|
|
+ END AS COMORBID_ENCODING___13,
|
|
|
+ CASE
|
|
|
+ WHEN COMORBID_EVENTS___14 = 1 THEN 'C50466'
|
|
|
+ END AS COMORBID_ENCODING___14,
|
|
|
+ CASE
|
|
|
+ WHEN COMORBID_EVENTS___15 = 1 THEN 'C80385'
|
|
|
+ END AS COMORBID_ENCODING___15,
|
|
|
+ CASE
|
|
|
+ WHEN COMORBID_EVENTS___16 = 1 THEN 'C26800'
|
|
|
+ END AS COMORBID_ENCODING___16,
|
|
|
+ FORMATDATETIME(PARSEDATETIME(DATE_OF_DIAGNOSIS, 'dd/MM/yyyy'), 'yyyy-MM-dd')||'T00:00:00' AS DIAGNOSIS_DATE,
|
|
|
+ FROM RKD
|
|
|
+ """ ];
|
|
|
+
|
|
|
+ rr:subjectMap [
|
|
|
+ rr:template "http://data.fairvasc.ie/resource/rkd/overview/comorbidity/{RECORD_ID}" ;
|
|
|
+ rr:class fvc:Comorbidities;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:comorbidity;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{COMORBID_ENCODING___1}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:comorbidity;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{COMORBID_ENCODING___2}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:comorbidity;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{COMORBID_ENCODING___3}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:comorbidity;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{COMORBID_ENCODING___4}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:comorbidity;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{COMORBID_ENCODING___5}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:comorbidity;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{COMORBID_ENCODING___6}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:comorbidity;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{COMORBID_ENCODING___7}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:comorbidity;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{COMORBID_ENCODING___10}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:comorbidity;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{COMORBID_ENCODING___14}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:comorbidity;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{COMORBID_ENCODING___15}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:comorbidity;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{COMORBID_ENCODING___16}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+.
|
|
|
+
|
|
|
+
|
|
|
+<#treatment>
|
|
|
+ rr:logicalTable [ rr:sqlQuery """
|
|
|
+ SELECT
|
|
|
+ RECORD_ID,
|
|
|
+ DRUG_SELECTED_CHOICES,
|
|
|
+ IV_THERAPY,
|
|
|
+ FORMATDATETIME(PARSEDATETIME(START_DATE, 'dd/MM/yyyy'), 'yyyy-MM-dd')||'T00:00:00' AS DRUG_START_DATE,
|
|
|
+ FORMATDATETIME(PARSEDATETIME(DATE_OF_IV_THERAPY, 'dd/MM/yyyy'), 'yyyy-MM-dd')||'T00:00:00' AS IV_DATE
|
|
|
+ FROM RKD
|
|
|
+ """ ];
|
|
|
+
|
|
|
+ rr:subjectMap [
|
|
|
+ rr:template "http://data.fairvasc.ie/resource/rkd/overview/treatment/{RECORD_ID}" ;
|
|
|
+ rr:class fvc:Treatment;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:hasMedication;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:parentTriplesMap <#treatment_medication> ;
|
|
|
+ rr:joinCondition [
|
|
|
+ rr:child "RECORD_ID" ;
|
|
|
+ rr:parent "RECORD_ID" ;
|
|
|
+ ] ;
|
|
|
+ rr:joinCondition [
|
|
|
+ rr:child "DRUG_SELECTED_CHOICES" ;
|
|
|
+ rr:parent "DRUG_SELECTED_CHOICES" ;
|
|
|
+ ] ;
|
|
|
+ rr:joinCondition [
|
|
|
+ rr:child "DRUG_START_DATE" ;
|
|
|
+ rr:parent "DRUG_START_DATE" ;
|
|
|
+ ] ;
|
|
|
+ ] ;
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:hasIVTherapy;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:parentTriplesMap <#treatment_iv> ;
|
|
|
+ rr:joinCondition [
|
|
|
+ rr:child "RECORD_ID" ;
|
|
|
+ rr:parent "RECORD_ID" ;
|
|
|
+ ] ;
|
|
|
+ rr:joinCondition [
|
|
|
+ rr:child "IV_THERAPY" ;
|
|
|
+ rr:parent "IV_THERAPY" ;
|
|
|
+ ] ;
|
|
|
+ rr:joinCondition [
|
|
|
+ rr:child "IV_DATE" ;
|
|
|
+ rr:parent "IV_DATE" ;
|
|
|
+ ] ;
|
|
|
+ ] ;
|
|
|
+ ];
|
|
|
+.
|
|
|
+
|
|
|
+<#treatment_induction>
|
|
|
+ rr:logicalTable [ rr:sqlQuery """
|
|
|
+ SELECT
|
|
|
+ RECORD_ID,
|
|
|
+ DRUG_SELECTED_CHOICES,
|
|
|
+ IV_THERAPY,
|
|
|
+ CASE
|
|
|
+ WHEN INDUCTION_TREATMENT___1 = 1 THEN 'C769'
|
|
|
+ END AS INDUCTION_ENCODING___1,
|
|
|
+ CASE
|
|
|
+ WHEN INDUCTION_TREATMENT___2 = 1 THEN 'C647'
|
|
|
+ END AS INDUCTION_ENCODING___2,
|
|
|
+ CASE
|
|
|
+ WHEN INDUCTION_TREATMENT___3 = 1 THEN 'C405'
|
|
|
+ END AS INDUCTION_ENCODING___3,
|
|
|
+ CASE
|
|
|
+ WHEN INDUCTION_TREATMENT___4 = 1 THEN 'C15304'
|
|
|
+ END AS INDUCTION_ENCODING___4,
|
|
|
+ CASE
|
|
|
+ WHEN INDUCTION_TREATMENT___5 = 1 THEN 'C1702'
|
|
|
+ END AS INDUCTION_ENCODING___5,
|
|
|
+ CASE
|
|
|
+ WHEN INDUCTION_TREATMENT___6 = 1 THEN 'C1468'
|
|
|
+ END AS INDUCTION_ENCODING___6,
|
|
|
+ CASE
|
|
|
+ WHEN INDUCTION_TREATMENT___7 = 1 THEN 'C290'
|
|
|
+ END AS INDUCTION_ENCODING___7,
|
|
|
+ CASE
|
|
|
+ WHEN INDUCTION_TREATMENT___8 = 1 THEN 'C642'
|
|
|
+ END AS INDUCTION_ENCODING___8,
|
|
|
+ CASE
|
|
|
+ WHEN INDUCTION_TREATMENT___9 = 1 THEN 'C1128'
|
|
|
+ END AS INDUCTION_ENCODING___9,
|
|
|
+ CASE
|
|
|
+ WHEN INDUCTION_TREATMENT___11 = 1 THEN 'C405'
|
|
|
+ END AS INDUCTION_ENCODING___11,
|
|
|
+ FORMATDATETIME(PARSEDATETIME(DATE_OF_DIAGNOSIS, 'dd/MM/yyyy'), 'yyyy-MM-dd')||'T00:00:00' AS DIAGNOSIS_DATE,
|
|
|
+ FORMATDATETIME(PARSEDATETIME(START_DATE, 'dd/MM/yyyy'), 'yyyy-MM-dd')||'T00:00:00' AS DRUG_START_DATE,
|
|
|
+ FORMATDATETIME(PARSEDATETIME(DATE_OF_IV_THERAPY, 'dd/MM/yyyy'), 'yyyy-MM-dd')||'T00:00:00' AS IV_DATE
|
|
|
+ FROM RKD
|
|
|
+ WHERE INDUCTION NOT IN(0)
|
|
|
+ """ ];
|
|
|
+
|
|
|
+ rr:subjectMap [
|
|
|
+ rr:template "http://data.fairvasc.ie/resource/rkd/overview/treatment/induction/{RECORD_ID}" ;
|
|
|
+ rr:class fvc:TreatmentInduction;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:treatmentType;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___1}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:treatmentType;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___2}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:treatmentType;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___3}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:treatmentType;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___4}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:treatmentType;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___5}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:treatmentType;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___6}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:treatmentType;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___7}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:treatmentType;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___8}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:treatmentType;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___9}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:treatmentType;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{INDUCTION_ENCODING___11}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+
|
|
|
+.
|
|
|
+
|
|
|
+<#treatment_maintenance>
|
|
|
+ rr:logicalTable [ rr:sqlQuery """
|
|
|
+ SELECT
|
|
|
+ RECORD_ID,
|
|
|
+ CASE
|
|
|
+ WHEN MAINTENANCE_TREATMENT___1 = 1 THEN 'C769'
|
|
|
+ END AS MAINTENANCE_ENCODING___1,
|
|
|
+ CASE
|
|
|
+ WHEN MAINTENANCE_TREATMENT___2 = 1 THEN 'C405'
|
|
|
+ END AS MAINTENANCE_ENCODING___2,
|
|
|
+ CASE
|
|
|
+ WHEN MAINTENANCE_TREATMENT___3 = 1 THEN 'C1702'
|
|
|
+ END AS MAINTENANCE_ENCODING___3,
|
|
|
+ CASE
|
|
|
+ WHEN MAINTENANCE_TREATMENT___4 = 1 THEN 'C1468'
|
|
|
+ END AS MAINTENANCE_ENCODING___4,
|
|
|
+ CASE
|
|
|
+ WHEN MAINTENANCE_TREATMENT___5 = 1 THEN 'C290'
|
|
|
+ END AS MAINTENANCE_ENCODING___5,
|
|
|
+ CASE
|
|
|
+ WHEN MAINTENANCE_TREATMENT___6 = 1 THEN 'C642'
|
|
|
+ END AS MAINTENANCE_ENCODING___6,
|
|
|
+ CASE
|
|
|
+ WHEN MAINTENANCE_TREATMENT___7 = 1 THEN 'C1128'
|
|
|
+ END AS MAINTENANCE_ENCODING___7,
|
|
|
+ CASE
|
|
|
+ WHEN MAINTENANCE_TREATMENT___8 = 1 THEN 'Other'
|
|
|
+ END AS MAINTENANCE_ENCODING___8,
|
|
|
+ FROM RKD
|
|
|
+ """ ];
|
|
|
+
|
|
|
+ rr:subjectMap [
|
|
|
+ rr:template "http://data.fairvasc.ie/resource/rkd/overview/treatment/maintenance/{RECORD_ID}" ;
|
|
|
+ rr:class fvc:TreatmentMaintenance;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:treatmentType;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{MAINTENANCE_ENCODING___1}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:treatmentType;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{MAINTENANCE_ENCODING___2}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:treatmentType;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{MAINTENANCE_ENCODING___3}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:treatmentType;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{MAINTENANCE_ENCODING___4}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:treatmentType;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{MAINTENANCE_ENCODING___5}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:treatmentType;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{MAINTENANCE_ENCODING___6}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:treatmentType;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{MAINTENANCE_ENCODING___7}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:treatmentType;
|
|
|
+ rr:objectMap [ rr:template "https://identifiers.org/ncit:{MAINTENANCE_ENCODING___8}";
|
|
|
+ rr:datatype xsd:anyURI; ];
|
|
|
+ ];
|
|
|
+
|
|
|
+
|
|
|
+.
|
|
|
+
|
|
|
+
|
|
|
+<#treatment_medication>
|
|
|
+ rr:logicalTable [ rr:sqlQuery """
|
|
|
+ SELECT
|
|
|
+ RECORD_ID,
|
|
|
+ DRUG_SELECTED_CHOICES,
|
|
|
+ CASE
|
|
|
+ WHEN DRUG_SELECTED_CHOICES = 1 THEN 'C769'
|
|
|
+ WHEN DRUG_SELECTED_CHOICES = 2 THEN 'C405'
|
|
|
+ WHEN DRUG_SELECTED_CHOICES = 3 THEN 'C290'
|
|
|
+ WHEN DRUG_SELECTED_CHOICES = 4 THEN 'C1468'
|
|
|
+ WHEN DRUG_SELECTED_CHOICES = 5 THEN 'C642'
|
|
|
+ WHEN DRUG_SELECTED_CHOICES = 6 THEN 'Other'
|
|
|
+ END AS DRUG_ENCODING,
|
|
|
+ CASE
|
|
|
+ WHEN UNIT_OF_DOSES = 1 THEN 'Other'
|
|
|
+ WHEN UNIT_OF_DOSES = 2 THEN 'C28254'
|
|
|
+ WHEN UNIT_OF_DOSES = 3 THEN 'C48579'
|
|
|
+ WHEN UNIT_OF_DOSES = 4 THEN 'C48152'
|
|
|
+ WHEN UNIT_OF_DOSES = 5 THEN 'C48155'
|
|
|
+ WHEN UNIT_OF_DOSES = 6 THEN 'C28253'
|
|
|
+ WHEN UNIT_OF_DOSES = 7 THEN 'T'
|
|
|
+ END AS UNIT_DRUG_DOSE,
|
|
|
+ DOSE,
|
|
|
+ CASE
|
|
|
+ WHEN FREQUENCY = 1 THEN 'Annually'
|
|
|
+ WHEN FREQUENCY = 2 THEN 'Other'
|
|
|
+ WHEN FREQUENCY = 3 THEN 'Once every 6 months'
|
|
|
+ WHEN FREQUENCY = 4 THEN 'Once monthly'
|
|
|
+ WHEN FREQUENCY = 5 THEN 'Twice monthly'
|
|
|
+ WHEN FREQUENCY = 6 THEN 'Three times weekly'
|
|
|
+ WHEN FREQUENCY = 7 THEN 'Twice weekly'
|
|
|
+ WHEN FREQUENCY = 8 THEN 'Once weekly'
|
|
|
+ WHEN FREQUENCY = 9 THEN 'Five times daily'
|
|
|
+ WHEN FREQUENCY = 10 THEN 'Four times daily'
|
|
|
+ WHEN FREQUENCY = 11 THEN 'Once daily'
|
|
|
+ WHEN FREQUENCY = 12 THEN 'Twice daily'
|
|
|
+ WHEN FREQUENCY = 13 THEN 'Three times daily'
|
|
|
+ WHEN FREQUENCY = 14 THEN 'Daily'
|
|
|
+ END AS DRUG_FREQUENCY,
|
|
|
+ CASE
|
|
|
+ WHEN ON_GOING = 0 THEN 'false'
|
|
|
+ WHEN ON_GOING = 1 THEN 'true'
|
|
|
+ END AS ONGOING,
|
|
|
+ FORMATDATETIME(PARSEDATETIME(START_DATE, 'dd/MM/yyyy'), 'yyyy-MM-dd')||'T00:00:00' AS DRUG_START_DATE,
|
|
|
+ FORMATDATETIME(PARSEDATETIME(STOP_DATE, 'dd/MM/yyyy'), 'yyyy-MM-dd')||'T00:00:00' AS DRUG_STOP_DATE
|
|
|
+ FROM RKD
|
|
|
+ """ ];
|
|
|
+
|
|
|
+ rr:subjectMap [
|
|
|
+ rr:template "http://data.fairvasc.ie/resource/rkd/overview/treatment/medication/{RECORD_ID}_{DRUG_SELECTED_CHOICES}_{DRUG_START_DATE}" ;
|
|
|
+ rr:class fvc:TreatmentMaintenance;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:medicationType;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:template "https://identifiers.org/ncit:{DRUG_ENCODING}";
|
|
|
+ rr:datatype xsd:anyURI;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:medicationDose;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "DOSE";
|
|
|
+ rr:datatype xsd:double;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:medicationUnitOfDose;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:template "https://identifiers.org/ncit:{UNIT_DRUG_DOSE}";
|
|
|
+ rr:datatype xsd:anyURI;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:medicationFrequency;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "DRUG_FREQUENCY";
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:medicationOngoing;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "ONGOING";
|
|
|
+ rr:datatype xsd:boolean;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:medicationStartDate;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "DRUG_START_DATE";
|
|
|
+ rr:datatype xsd:dateTime;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:medicationStopDate;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "DRUG_STOP_DATE";
|
|
|
+ rr:datatype xsd:dateTime;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+.
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+<#treatment_iv>
|
|
|
+ rr:logicalTable [ rr:sqlQuery """
|
|
|
+ SELECT
|
|
|
+ RECORD_ID,
|
|
|
+ IV_THERAPY,
|
|
|
+ CASE
|
|
|
+ WHEN IV_THERAPY = 1 THEN 'C405'
|
|
|
+ WHEN IV_THERAPY = 2 THEN 'C1702'
|
|
|
+ WHEN IV_THERAPY = 3 THEN 'C647'
|
|
|
+ WHEN IV_THERAPY = 4 THEN 'C572'
|
|
|
+ WHEN IV_THERAPY = 5 THEN 'C1702'
|
|
|
+ WHEN IV_THERAPY = 6 THEN 'Other'
|
|
|
+ WHEN IV_THERAPY = 7 THEN 'C157376'
|
|
|
+ END AS IV_THERAPY_ENCODING,
|
|
|
+ CASE
|
|
|
+ WHEN UNIT_OF_DOSE = 1 THEN 'C28253'
|
|
|
+ WHEN UNIT_OF_DOSE = 2 THEN 'C48155'
|
|
|
+ WHEN UNIT_OF_DOSE = 3 THEN 'C48152'
|
|
|
+ WHEN UNIT_OF_DOSE = 4 THEN 'C48579'
|
|
|
+ WHEN UNIT_OF_DOSE = 5 THEN 'C28254'
|
|
|
+ WHEN UNIT_OF_DOSE = 6 THEN 'Other'
|
|
|
+ END AS UNIT_IV_DOSE,
|
|
|
+ DOSE_OF_IV_THERAPY,
|
|
|
+ CASE
|
|
|
+ WHEN TREATMENT_INTERMITTENT_PULSE_ADMINISTRATIONS_COMPLETE = 1 THEN 'false'
|
|
|
+ WHEN TREATMENT_INTERMITTENT_PULSE_ADMINISTRATIONS_COMPLETE = 2 THEN 'true'
|
|
|
+ END AS IV_COMPLETE,
|
|
|
+ FORMATDATETIME(PARSEDATETIME(DATE_OF_IV_THERAPY, 'dd/MM/yyyy'), 'yyyy-MM-dd')||'T00:00:00' AS IV_DATE
|
|
|
+ FROM RKD
|
|
|
+ """ ];
|
|
|
+
|
|
|
+ rr:subjectMap [
|
|
|
+ rr:template "http://data.fairvasc.ie/resource/rkd/overview/treatment/ivtherapy/{RECORD_ID}_{IV_THERAPY}_{IV_DATE}" ;
|
|
|
+ rr:class fvc:IntravenousTherapy;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:ivTherapyType;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:template "https://identifiers.org/ncit:{IV_THERAPY_ENCODING}";
|
|
|
+ rr:datatype xsd:anyURI;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:ivDose;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "DOSE_OF_IV_THERAPY";
|
|
|
+ rr:datatype xsd:double;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:ivUnitOfDose;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:template "http://qudt.org/vocab/unit/{UNIT_IV_DOSE}";
|
|
|
+ rr:datatype xsd:anyURI;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:ivComplete;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "IV_COMPLETE";
|
|
|
+ rr:datatype xsd:boolean;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:ivDate;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "IV_DATE";
|
|
|
+ rr:datatype xsd:dateTime;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+
|
|
|
+
|
|
|
+.
|
|
|
+
|
|
|
+
|
|
|
+<#anca>
|
|
|
+
|
|
|
+ rr:logicalTable [ rr:sqlQuery """
|
|
|
+ SELECT RECORD_ID,
|
|
|
+ CASE
|
|
|
+ WHEN ANCA_SPEC = 1 THEN 'MPO positive'
|
|
|
+ WHEN ANCA_SPEC = 2 THEN 'ELISA negative'
|
|
|
+ WHEN ANCA_SPEC = 3 THEN 'PR3 positive'
|
|
|
+ WHEN ANCA_SPEC = 4 THEN 'Other'
|
|
|
+ WHEN ANCA_SPEC = 5 THEN 'No ELISA performed'
|
|
|
+ WHEN ANCA_SPEC = 6 THEN 'MPO and PR3 positive'
|
|
|
+ END AS ANCASPEC,
|
|
|
+ CASE
|
|
|
+ WHEN ANCA_IF = 1 THEN 'cANCA positive'
|
|
|
+ WHEN ANCA_IF = 2 THEN 'pANCA positive'
|
|
|
+ WHEN ANCA_IF = 3 THEN 'Atypical'
|
|
|
+ WHEN ANCA_IF = 4 THEN 'Negative'
|
|
|
+ WHEN ANCA_IF = 5 THEN 'Not tested'
|
|
|
+ END AS ANCAIF,
|
|
|
+
|
|
|
+ FROM RKD"""];
|
|
|
+
|
|
|
+ rr:subjectMap [
|
|
|
+ rr:template "http://data.fairvasc.ie/resource/rkd/anca/{RECORD_ID}" ;
|
|
|
+ rr:class fvc:ANCA;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:ancaIF;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "ANCAIF" ;
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ] ;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:ancaSpec ;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "ANCASPEC" ;
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ] ;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+.
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+<#diagnosis>
|
|
|
+ rr:logicalTable [ rr:sqlQuery """
|
|
|
+ SELECT RECORD_ID, AGE_ONSET, AGE_AT_DIAGNOSIS, DATE_OF_SYMPTONS,
|
|
|
+ FORMATDATETIME(PARSEDATETIME(DATE_OF_DIAGNOSIS, 'dd/MM/yyyy'), 'yyyy-MM-dd')||'T00:00:00' AS DIAGNOSIS_DATE,
|
|
|
+ CASE
|
|
|
+ WHEN SMALL_VESSEL_VAS_ANCA = 1 THEN '156152'
|
|
|
+ WHEN SMALL_VESSEL_VAS_ANCA = 2 THEN '183'
|
|
|
+ WHEN SMALL_VESSEL_VAS_ANCA = 3 THEN '900'
|
|
|
+ WHEN SMALL_VESSEL_VAS_ANCA = 4 THEN '727'
|
|
|
+ END AS DIAGNOSIS,
|
|
|
+ CASE
|
|
|
+ WHEN DIAGNOSIS_CONFIDENCE_INIT = 1 THEN 'Possible'
|
|
|
+ WHEN DIAGNOSIS_CONFIDENCE_INIT = 2 THEN 'Probable'
|
|
|
+ WHEN DIAGNOSIS_CONFIDENCE_INIT = 3 THEN 'Definite'
|
|
|
+ END AS DIAGNOSIS_CONFIDENCE,
|
|
|
+ CASE
|
|
|
+ WHEN DATEDIFF(day, FORMATDATETIME(PARSEDATETIME(DATE_OF_DIAGNOSIS, 'dd/MM/yyyy'), 'yyyy-MM-dd'), FORMATDATETIME(PARSEDATETIME(DATE_OF_CONSENT, 'dd/MM/yyyy'), 'yyyy-MM-dd')) < 180 THEN 'Retrospective'
|
|
|
+ WHEN DATEDIFF(day, FORMATDATETIME(PARSEDATETIME(DATE_OF_DIAGNOSIS, 'dd/MM/yyyy'), 'yyyy-MM-dd'), FORMATDATETIME(PARSEDATETIME(DATE_OF_CONSENT, 'dd/MM/yyyy'), 'yyyy-MM-dd')) >= 180 THEN 'Prospective'
|
|
|
+ END AS INCLUSION_TYPE
|
|
|
+ FROM RKD""" ];
|
|
|
+
|
|
|
+ rr:subjectMap [
|
|
|
+ rr:template "http://data.fairvasc.ie/resource/rkd/diagnosis/{RECORD_ID}{DIAGNOSIS_DATE}" ;
|
|
|
+ rr:class fvc:Diagnosis;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:mainDiagnosis ;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:template "https://identifiers.org/orphanet:{DIAGNOSIS}" ;
|
|
|
+ rr:datatype xsd:anyURI;
|
|
|
+ ];
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:inclusionType ;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "INCLUSION_TYPE" ;
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ] ;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:diagnosisClassification ;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:template "EMA algorithm";
|
|
|
+ rr:datatype xsd:string
|
|
|
+ ];
|
|
|
+ ] ;
|
|
|
+
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:diagnosisConfidence ;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "DIAGNOSIS_CONFIDENCE" ;
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ] ;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:dateOfDiagnosis ;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "DIAGNOSIS_DATE" ;
|
|
|
+ rr:datatype xsd:dateTime;
|
|
|
+ ] ;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:hasFirstClinicalContact ;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "date_of_diagnosis" ;
|
|
|
+ rr:datatype xsd:dateTime;
|
|
|
+ ] ;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:hasAgeAtOnset ;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "age_onset" ;
|
|
|
+ rr:datatype xsd:integer;
|
|
|
+ ] ;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:hasAgeAtDiagnosis ;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "age_at_diagnosis" ;
|
|
|
+ rr:datatype xsd:integer;
|
|
|
+ ] ;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:hasDateAtOnset ;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "date_of_symptons" ;
|
|
|
+ rr:datatype xsd:dateTime;
|
|
|
+ ] ;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:hasDateAtDiagnosis ;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "date_of_diagnosis" ;
|
|
|
+ rr:datatype xsd:dateTime;
|
|
|
+ ] ;
|
|
|
+ ] ;
|
|
|
+.
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+<#organ_pattern_specific>
|
|
|
+ rr:logicalTable [ rr:sqlQuery """
|
|
|
+ SELECT RECORD_ID,
|
|
|
+ DATE_OF_VISIT,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___1 = 1 OR EXISTS(SELECT RENAL FROM RKD) THEN 'Kidney'
|
|
|
+ END AS ORGAN_PATTERN___1,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___2 = 1 OR EXISTS(SELECT CHEST FROM RKD) THEN 'Lung'
|
|
|
+ END AS ORGAN_PATTERN___2,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___2 = 1 THEN 'Pulmonary granuloma'
|
|
|
+ END AS ORGAN_PATTERN_DISEASE___2,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___3 = 1 OR EXISTS(SELECT CHEST FROM RKD) THEN 'Lung'
|
|
|
+ END AS ORGAN_PATTERN___3,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___3 = 1 THEN 'Pulmonary hemorrhage'
|
|
|
+ END AS ORGAN_PATTERN_DISEASE___3,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___4 = 1 OR EXISTS(SELECT ENT FROM RKD) THEN 'Ear/Nose/Throat'
|
|
|
+ END AS ORGAN_PATTERN___4,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___5 = 1 OR EXISTS(SELECT ENT FROM RKD) THEN 'Tracheal'
|
|
|
+ END AS ORGAN_PATTERN___5,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___6 = 1 OR EXISTS(SELECT CUTANEOUS FROM RKD) THEN 'Mucocutaneous'
|
|
|
+ END AS ORGAN_PATTERN___6,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___7 = 1 THEN 'Musculoskeletal'
|
|
|
+ END AS ORGAN_PATTERN___7,
|
|
|
+ CASE
|
|
|
+ WHEN EXISTS(SELECT NERVOUS_SYSTEM FROM RKD) THEN 'Nervous system'
|
|
|
+ END AS ORGAN_PATTERN___88,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___8 = 1 OR EXISTS(SELECT NERVOUS_SYSTEM FROM RKD) THEN 'Central Nervous system'
|
|
|
+ END AS ORGAN_PATTERN___8,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___9 = 1 OR EXISTS(SELECT NERVOUS_SYSTEM FROM RKD) THEN 'Peripheral Nervous system'
|
|
|
+ END AS ORGAN_PATTERN___9,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___10 = 1 OR EXISTS(SELECT ABDOMINAL FROM RKD) THEN 'Abdominal'
|
|
|
+ END AS ORGAN_PATTERN___10,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___11 = 1 OR EXISTS(SELECT MUCOUS_MEMBRANES_EYES FROM RKD) THEN 'Eye'
|
|
|
+ END AS ORGAN_PATTERN___11,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___12 = 1 OR EXISTS(SELECT CARDIOVASCULAR FROM RKD) THEN 'Cardiovascular'
|
|
|
+ END AS ORGAN_PATTERN___12
|
|
|
+ FROM RKD
|
|
|
+ """ ];
|
|
|
+
|
|
|
+ rr:subjectMap [
|
|
|
+ rr:template "http://data.fairvasc.ie/resource/rkd/organ_pattern/organ_pattern_specific/{RECORD_ID}" ;
|
|
|
+ rr:class fvc:OrganPattern;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:genericTerm ;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:template "false" ;
|
|
|
+ rr:datatype xsd:boolean;
|
|
|
+ ] ;
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "ORGAN_PATTERN___1";
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "ORGAN_PATTERN___2";
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:organDiseasePatternLung;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "ORGAN_PATTERN_DISEASE___2";
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "ORGAN_PATTERN___3";
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:organDiseasePatternLung;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "ORGAN_PATTERN_DISEASE___3";
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "ORGAN_PATTERN___4";
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "ORGAN_PATTERN___5";
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "ORGAN_PATTERN___6";
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "ORGAN_PATTERN___7";
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "ORGAN_PATTERN___88";
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "ORGAN_PATTERN___8";
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "ORGAN_PATTERN___9";
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "ORGAN_PATTERN___10";
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "ORGAN_PATTERN___11";
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "ORGAN_PATTERN___12";
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+
|
|
|
+.
|
|
|
+
|
|
|
+
|
|
|
+<#organ_pattern_generic>
|
|
|
+ rr:logicalTable [ rr:sqlQuery """
|
|
|
+ SELECT RECORD_ID,
|
|
|
+ DATE_OF_VISIT,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___1 = 1 OR EXISTS(SELECT RENAL FROM RKD) THEN 'Kidney'
|
|
|
+ END AS ORGAN_PATTERN___1,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___2 = 1 OR EXISTS(SELECT CHEST FROM RKD) THEN 'Lung'
|
|
|
+ END AS ORGAN_PATTERN___2,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___2 = 1 THEN 'Pulmonary granuloma'
|
|
|
+ END AS ORGAN_PATTERN_DISEASE___2,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___3 = 1 OR EXISTS(SELECT CHEST FROM RKD) THEN 'Lung'
|
|
|
+ END AS ORGAN_PATTERN___3,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___3 = 1 THEN 'Pulmonary hemorrhage'
|
|
|
+ END AS ORGAN_PATTERN_DISEASE___3,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___4 = 1 OR EXISTS(SELECT ENT FROM RKD) THEN 'Ear/Nose/Throat'
|
|
|
+ END AS ORGAN_PATTERN___4,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___5 = 1 OR EXISTS(SELECT ENT FROM RKD) THEN 'Ear/Nose/Throat'
|
|
|
+ END AS ORGAN_PATTERN___5,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___6 = 1 OR EXISTS(SELECT CUTANEOUS FROM RKD) THEN 'Mucocutaneous/Eye'
|
|
|
+ END AS ORGAN_PATTERN___6,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___7 = 1 THEN 'Musculoskeletal'
|
|
|
+ END AS ORGAN_PATTERN___7,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___8 = 1 OR EXISTS(SELECT NERVOUS_SYSTEM FROM RKD) THEN 'Nervous system'
|
|
|
+ END AS ORGAN_PATTERN___8,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___9 = 1 OR EXISTS(SELECT NERVOUS_SYSTEM FROM RKD) THEN 'Nervous system'
|
|
|
+ END AS ORGAN_PATTERN___9,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___10 = 1 OR EXISTS(SELECT ABDOMINAL FROM RKD) THEN 'Abdominal'
|
|
|
+ END AS ORGAN_PATTERN___10,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___11 = 1 OR EXISTS(SELECT MUCOUS_MEMBRANES_EYES FROM RKD) THEN 'Mucocutaneous/Eye'
|
|
|
+ END AS ORGAN_PATTERN___11,
|
|
|
+ CASE
|
|
|
+ WHEN SYSTEMS_INVOLVED___12 = 1 OR EXISTS(SELECT CARDIOVASCULAR FROM RKD) THEN 'Cardiovascular'
|
|
|
+ END AS ORGAN_PATTERN___12,
|
|
|
+ FROM RKD""" ];
|
|
|
+
|
|
|
+ rr:subjectMap [
|
|
|
+ rr:template "http://data.fairvasc.ie/resource/rkd/organ_pattern/organ_pattern_generic/{RECORD_ID}" ;
|
|
|
+ rr:class fvc:OrganPattern;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:genericTerm ;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:template "true" ;
|
|
|
+ rr:datatype xsd:boolean;
|
|
|
+ ] ;
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "ORGAN_PATTERN___1";
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ];
|
|
|
+ ];
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [ rr:column "ORGAN_PATTERN___2";
|
|
|
+ rr:datatype xsd:string; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:organDiseasePatternLung;
|
|
|
+ rr:objectMap [ rr:column "ORGAN_PATTERN_DISEASE___2";
|
|
|
+ rr:datatype xsd:string; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [ rr:column "ORGAN_PATTERN___3";
|
|
|
+ rr:datatype xsd:string; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:organDiseasePatternLung;
|
|
|
+ rr:objectMap [ rr:column "ORGAN_PATTERN_DISEASE___3";
|
|
|
+ rr:datatype xsd:string; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [ rr:column "ORGAN_PATTERN___4";
|
|
|
+ rr:datatype xsd:string; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [ rr:column "ORGAN_PATTERN___5";
|
|
|
+ rr:datatype xsd:string; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [ rr:column "ORGAN_PATTERN___6";
|
|
|
+ rr:datatype xsd:string; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [ rr:column "ORGAN_PATTERN___7";
|
|
|
+ rr:datatype xsd:string; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [ rr:column "ORGAN_PATTERN___8";
|
|
|
+ rr:datatype xsd:string; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [ rr:column "ORGAN_PATTERN___9";
|
|
|
+ rr:datatype xsd:string; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [ rr:column "ORGAN_PATTERN___10";
|
|
|
+ rr:datatype xsd:string; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [ rr:column "ORGAN_PATTERN___11";
|
|
|
+ rr:datatype xsd:string; ];
|
|
|
+ ];
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:affectedOrgan;
|
|
|
+ rr:objectMap [ rr:column "ORGAN_PATTERN___12";
|
|
|
+ rr:datatype xsd:string; ];
|
|
|
+ ];
|
|
|
+
|
|
|
+.
|
|
|
+
|
|
|
+<#creatinine>
|
|
|
+ rr:logicalTable [ rr:sqlQuery """
|
|
|
+ SELECT RECORD_ID,
|
|
|
+ DATE_OF_VISIT,
|
|
|
+ FORMATDATETIME(PARSEDATETIME(DATE_OF_VISIT, 'dd/MM/yyyy'), 'yyyy-MM-dd')||'T00:00:00' AS DATE,
|
|
|
+ CREATININE,
|
|
|
+ CREATININE_RELATION_TO_LAB,
|
|
|
+ CASE
|
|
|
+ WHEN CREATININE_RELATION_TO_LAB = 1 THEN 'Below'
|
|
|
+ WHEN CREATININE_RELATION_TO_LAB = 2 THEN 'Normal'
|
|
|
+ WHEN CREATININE_RELATION_TO_LAB = 3 THEN 'Above'
|
|
|
+ WHEN CREATININE_RELATION_TO_LAB = 3 THEN 'Not performed'
|
|
|
+ WHEN CREATININE_RELATION_TO_LAB = 3 THEN 'Pending'
|
|
|
+ END AS CREATININE_LAB
|
|
|
+ FROM RKD
|
|
|
+ """ ];
|
|
|
+
|
|
|
+ rr:subjectMap [
|
|
|
+ rr:template "http://data.fairvasc.ie/resource/rkd/creatinine/{RECORD_ID}{DATE_OF_VISIT}" ;
|
|
|
+ rr:class fvc:Creatinine;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:dateOfEncounter ;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "DATE" ;
|
|
|
+ rr:datatype xsd:dateTime;
|
|
|
+ ] ;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:creatinineValue ;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "CREATININE" ;
|
|
|
+ rr:datatype xsd:integer;
|
|
|
+ ] ;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+ rr:predicateObjectMap [
|
|
|
+ rr:predicate fvc:creatinineRelationToLab ;
|
|
|
+ rr:objectMap [
|
|
|
+ rr:column "CREATININE_LAB" ;
|
|
|
+ rr:datatype xsd:string;
|
|
|
+ ] ;
|
|
|
+ ] ;
|
|
|
+
|
|
|
+.
|
beyza.yaman
2 years ago