PARADISE/fairvasc_rkd_mapping.ttl

@prefix rr: <http://www.w3.org/ns/r2rml#> .
@prefix fvc: <http://ontologies.adaptcentre.ie/fairvasc#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix sno: <http://purl.bioontology.org/ontology/SNOMEDCT#> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix ordo:<http://www.orpha.net/ORDO/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .

<#patient>

	rr:logicalTable [ rr:sqlQuery """SELECT 
		RECORD_ID, 
		YEAR_OF_BIRTH,   
		DATE_OF_EVENT_COMP,
		FORMATDATETIME(PARSEDATETIME(DATE_OF_VISIT, 'dd/MM/yyyy'), 'yyyy-MM-dd')||'T00:00:00' AS ENCOUNTER_DATE,
		REDCAP_REPEAT_INSTANCE,
		GENDER,
			CASE 
			WHEN GENDER = 1 THEN 'C20197' 
			WHEN GENDER = 2 THEN 'C16576' 
			WHEN GENDER = 3 THEN 'C41438' 
		END AS GENDER_
	FROM RKD""" ];
	
	rr:subjectMap [
		rr:template "http://data.fairvasc.ie/resource/rkd/patient/{RECORD_ID}" ;
		rr:class fvc:Patient;
	] ;
		
	rr:predicateObjectMap [
		rr:predicate fvc:patientID ;
		rr:objectMap [			
			rr:column "RECORD_ID" ;
			rr:datatype xsd:string;
		] ;
	] ;
	
	rr:predicateObjectMap [
		rr:predicate fvc:yearOfBirth ;
		rr:objectMap [			
			rr:column "YEAR_OF_BIRTH" ;
			rr:datatype xsd:gYear;
		] ;
	] ;

	rr:predicateObjectMap [
		rr:predicate fvc:gender ;
		rr:objectMap [ 
			rr:template "https://identifiers.org/ncit:{GENDER_}" ;
			rr:datatype xsd:anyURI;
			];
	] ;
	

	rr:predicateObjectMap [
		rr:predicate fvc:hasPatientOverview;
		rr:objectMap [
		rr:parentTriplesMap <#patient_overview> ;
		rr:joinCondition [
			rr:child "RECORD_ID" ;
			rr:parent "RECORD_ID" ;
		] ;
		] ;
	];


	
.

<#patient_overview>

	rr:logicalTable [ rr:sqlQuery """SELECT 
		RECORD_ID,
		FORMATDATETIME(PARSEDATETIME(DATE_OF_DIAGNOSIS, 'dd/MM/yyyy'), 'yyyy-MM-dd')||'T00:00:00' AS DIAGNOSIS_DATE,
		HEIGHT_CMS_KNOWN,
		WEIGHT_KG,
		BMI
	FROM RKD""" ];
	
	rr:subjectMap [
		rr:template "http://data.fairvasc.ie/resource/rkd/patient/patientoverview/{RECORD_ID}" ;
		rr:class fvc:PatientOverview;
	] ;


	rr:predicateObjectMap [
		rr:predicate fvc:height ;
		rr:objectMap [			
			rr:column "HEIGHT_CMS_KNOWN" ;
			rr:datatype xsd:double;
		] ;
	] ;

	rr:predicateObjectMap [
		rr:predicate fvc:weight ;
		rr:objectMap [			
			rr:column "WEIGHT_KG" ;
			rr:datatype xsd:double;
		] ;
	] ;

	rr:predicateObjectMap [
		rr:predicate fvc:BMI ;
		rr:objectMap [			
			rr:column "BMI" ;
			rr:datatype xsd:double;
		] ;
	] ;	

	rr:predicateObjectMap [
		rr:predicate fvc:hasDiagnosis;
		rr:objectMap [
		rr:parentTriplesMap <#diagnosis> ;
		rr:joinCondition [
			rr:child "RECORD_ID" ;
			rr:parent "RECORD_ID" ;
		] ;
		rr:joinCondition [
		    rr:child "DIAGNOSIS_DATE" ;
		    rr:parent "DIAGNOSIS_DATE" ;
		] ;
	] ;
	];

	rr:predicateObjectMap [
		rr:predicate fvc:hasANCA;
		rr:objectMap [
		rr:parentTriplesMap <#anca> ;
		rr:joinCondition [
			rr:child "RECORD_ID" ;
			rr:parent "RECORD_ID" ;
		] ;
		] ;
	];

	rr:predicateObjectMap [
		rr:predicate fvc:hasOrganPattern;
		rr:objectMap [
		rr:parentTriplesMap <#organ_pattern_generic> ;
		rr:joinCondition [
			rr:child "RECORD_ID" ;
			rr:parent "RECORD_ID" ;
		] ;
		] ;
	];

	rr:predicateObjectMap [
		rr:predicate fvc:hasOrganPattern;
		rr:objectMap [
		rr:parentTriplesMap <#organ_pattern_specific> ;
		rr:joinCondition [
			rr:child "RECORD_ID" ;
			rr:parent "RECORD_ID" ;
		] ;
		] ;
	];


	rr:predicateObjectMap [
		rr:predicate fvc:hasTreatment;
		rr:objectMap [
		rr:parentTriplesMap <#treatment> ;
		rr:joinCondition [
			rr:child "RECORD_ID" ;
			rr:parent "RECORD_ID" ;
		] ;
		] ;
	];
	
	
	rr:predicateObjectMap [
		rr:predicate fvc:hasTreatment;
		rr:objectMap [
		rr:parentTriplesMap <#treatment_induction> ;
		rr:joinCondition [
			rr:child "RECORD_ID" ;
			rr:parent "RECORD_ID" ;
		] ;
		] ;
	];

	rr:predicateObjectMap [
		rr:predicate fvc:hasTreatment;
		rr:objectMap [
		rr:parentTriplesMap <#treatment_maintenance> ;
		rr:joinCondition [
			rr:child "RECORD_ID" ;
			rr:parent "RECORD_ID" ;
		] ;
		] ;
	];
	
	rr:predicateObjectMap [
		rr:predicate fvc:hasComorbidities;
		rr:objectMap [
		rr:parentTriplesMap <#comorbidities> ;
		rr:joinCondition [
			rr:child "RECORD_ID" ;
			rr:parent "RECORD_ID" ;
		] ;
		] ;
	];

	rr:predicateObjectMap [
		rr:predicate fvc:hasConsent;
		rr:objectMap [
		rr:parentTriplesMap <#consent> ;
		rr:joinCondition [
			rr:child "RECORD_ID" ;
			rr:parent "RECORD_ID" ;
		] ;
		] ;
	];
	
.

<#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; ];
    ];	
	
.

<#consent>
	rr:logicalTable [ rr:sqlQuery """
	SELECT 			
		RECORD_ID,
		CASE 
			WHEN consent_obtained_for_regis___1 = 1 THEN 'Registry_Consent'	
		END AS CONSENT_ENCODING___1,	
		CASE 		
			WHEN consent_obtained_for_regis___2 = 1 THEN 'Biobanking_Consent'
		END AS CONSENT_ENCODING___2,
		CASE 
			WHEN consent_obtained_for_regis___3 = 1 THEN 'Future_Contact_Consent'
		END AS CONSENT_ENCODING___3,	
		CASE 		
			WHEN consent_obtained_for_regis___4 = 1 THEN 'All'
		END AS CONSENT_ENCODING___1, CONSENT_ENCODING___2, CONSENT_ENCODING___4,		
		CASE 		
			WHEN consent_obtained_for_regis___5 = 1 THEN 'No'
		END AS CONSENT_ENCODING___5,	
	FROM RKD
		""" ];
	
	rr:subjectMap [
		rr:template "http://data.fairvasc.ie/resource/rkd/overview/consent/{RECORD_ID}" ;
		rr:class fvc:Consent;
	] ;
	
 rr:predicateObjectMap [
		rr:predicate fvc:consentType;
		rr:objectMap [ rr:template "http://data.fairvasc.ie/resource/rkd/overview/consent/{CONSENT_ENCODING___1}";
			rr:datatype xsd:anyURI; ];
    ];
	
	rr:predicateObjectMap [
		rr:predicate fvc:consentType;
		rr:objectMap [ rr:template "http://data.fairvasc.ie/resource/rkd/overview/consent/CONSENT_ENCODING___2}";
			rr:datatype xsd:anyURI; ];
    ];	
	
    rr:predicateObjectMap [
		rr:predicate fvc:consentType;
		rr:objectMap [ rr:template "http://data.fairvasc.ie/resource/rkd/overview/consent/CONSENT_ENCODING___3}";
			rr:datatype xsd:anyURI; ];
    ];	

    rr:predicateObjectMap [
		rr:predicate fvc:hasConsentForDataUseInRegistry;
		rr:objectMap [ 
			rr:template "true";
			rr:datatype xsd:boolean; 
		];
    ];

    rr:predicateObjectMap [
		rr:predicate fvc:hasConsentForBiobanking;
		rr:objectMap [ 
			rr:template "true";
			rr:datatype xsd:boolean;  
		];
    ];	
	

    rr:predicateObjectMap [
		rr:predicate fvc:hasConsentForFutureContact;
		rr:objectMap [ 
			rr:template "true";
			rr:datatype xsd:boolean; 
		];
    ];	
	
	rr:predicateObjectMap [
		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;
		] ;
	] ;

.