mapping.ttl

@prefix d2rq: <http://www.wiwiss.fu-berlin.de/suhl/bizer/D2RQ/0.1#> .
@prefix rr: <http://www.w3.org/ns/r2rml#> .
@prefix rml: <http://semweb.mmlab.be/ns/rml#> .
@prefix ql: <http://semweb.mmlab.be/ns/ql#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix paladin: <http://research.tib.eu/paladin/vocab/> .

<#DB_source> a d2rq:Database;
  d2rq:jdbcDSN "SYNTH";
  d2rq:jdbcDriver "com.mysql.cj.jdbc.Driver";
  d2rq:username "";
  d2rq:password "".

<BCPatient_oral_drug>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, to_uri(od.drug) AS drug, to_uri(drug_type) AS drug_type FROM oral_drug od JOIN oral_drug_type odt USING (drug)";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/BC_HUPHM_{ehr}";
    rr:class paladin:BCPatient
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasOralDrug;
    rr:objectMap [
      rml:reference "drug";
      rr:termType rr:IRI;
    ];
  ] ;
  rr:predicateObjectMap [
    rr:predicate paladin:hasOralDrugType;
    rr:objectMap [
      rml:reference "drug_type";
      rr:termType rr:IRI;
    ];
  ] .

<BCPatient_family_history>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, cancer_cui, to_uri(description) AS description FROM family_history fh JOIN cui_description cd ON (fh.cancer_cui = cd.cui)";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/BC_HUPHM_{ehr}";
    rr:class paladin:BCPatient
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasFamilyCancerType;
    rr:objectMap [
      rr:parentTriplesMap <FamilyCancerType>
    ]
  ].

<FamilyCancerType>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, cancer_cui, to_uri(description) AS description FROM family_history fh JOIN cui_description cd ON (fh.cancer_cui = cd.cui)";
  ];
  rr:subjectMap [
    rml:reference "description";
    rr:termType rr:IRI;
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:constant <http://research.tib.eu/paladin/vocab/CancerType>;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasOriginalValue;
    rr:objectMap [
      rml:reference "cancer_cui";
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasCUIAnnotation;
    rr:objectMap [
      rr:template "http://research.tib.eu/paladin/entity/{cancer_cui}"
    ]
  ].

<BCPatient_radiotherapy_treatment_line>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT * FROM radiotherapy";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/BC_HUPHM_{ehr}";
    rr:class paladin:BCPatient
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasTreatmentEpisode;
    rr:objectMap [
      rr:parentTriplesMap <Treatment_Episode_Radiotherapy>
    ]
  ].

<Treatment_Episode_Radiotherapy>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT * FROM radiotherapy";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/{ehr}_Radiotherapy_{date_start}";
    rr:class paladin:TreatmentEpisode
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasTreatmentType;
    rr:objectMap [
      rr:parentTriplesMap <RadiotherapyTreatmentLine>
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:treatementLineStartDate;
    rr:objectMap [
      rml:reference "date_start";
      rr:datatype xsd:date
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:treatementLineEndingDate;
    rr:objectMap [
      rml:reference "date_end";
      rr:datatype xsd:date
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasEpisode;
    rr:objectMap [
      rr:parentTriplesMap <TreatmentLineNumber_Radiotherapy>
    ]
  ].

<RadiotherapyTreatmentLine>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT * FROM radiotherapy";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/BC_HUPHM_{ehr}_Radiotherapy_{n_radiotherapy}";
    rr:class paladin:Radiotherapy;
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasRadiotherapyRound;
    rr:objectMap [
      rr:parentTriplesMap <TreatmentLineNumber_Radiotherapy>
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:treatementLineStartDate;
    rr:objectMap [
      rml:reference "date_start";
      rr:datatype xsd:date
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:treatementLineEndingDate;
    rr:objectMap [
      rml:reference "date_end";
      rr:datatype xsd:date
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:treatmentLineDosage;
    rr:objectMap [
      rml:reference "dose_gy";
    ]
  ].

<TreatmentLineNumber_Radiotherapy>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT * FROM radiotherapy";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/TL_{n_radiotherapy}";
    rr:class paladin:RadiotherapyRound;
  ].

<BCPatient_surgery>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, surgery, to_uri(surgery) AS surgery_uri, n_surgery, date_year, date_month, date_day FROM surgery";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/BC_HUPHM_{ehr}";
    rr:class paladin:BCPatient
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasTreatmentEpisode;
    rr:objectMap [
      rr:parentTriplesMap <treatement_episode_surgery>
    ]
  ].

<treatement_episode_surgery>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, surgery, to_uri(surgery) AS surgery_uri, n_surgery, date_year, date_month, date_day FROM surgery";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/{ehr}_Surgery_{n_surgery}";
    rr:class paladin:TreatmentEpisode
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasTreatmentType;
    rr:objectMap [
      rr:parentTriplesMap <Treatment_Episode_surgery_surgery>
    ]
  ].

<Treatment_Episode_surgery_surgery>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, surgery, to_uri(surgery) AS surgery_uri, n_surgery, date_year, date_month, date_day FROM surgery";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/{ehr}_{surgery}_OncologicalSurgery_{n_surgery}";
    rr:class paladin:OncologicalSurgery
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:surgeryYear;
    rr:objectMap [
      rml:reference "date_year";
      rr:datatype xsd:int;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:surgeryMonth;
    rr:objectMap [
      rml:reference "date_month";
      rr:datatype xsd:int;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:surgeryDay;
    rr:objectMap [
      rml:reference "date_day";
      rr:datatype xsd:int;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasType;
    rr:objectMap [
      rr:parentTriplesMap <SurgeryType>
    ]
  ].

<SurgeryType>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, surgery, to_uri(surgery) AS surgery_uri, n_surgery, date_year, date_month, date_day FROM surgery";
  ];
  rr:subjectMap [
    rml:reference "surgery_uri";
    rr:termType rr:IRI;
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:template "http://research.tib.eu/paladin/vocab/SurgeryType";
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasOriginalValue;
    rr:objectMap [
      rml:reference "surgery";
    ]
  ].

<BCPatient_comorbidity>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, comorbidity AS comorbidity_orig, negated as negated_orig, to_uri(CASE WHEN comorbidity='smoker' THEN '' WHEN comorbidity='ex-smoker' THEN '' WHEN comorbidity='hta' THEN 'HTA' WHEN comorbidity='cardiac insufficiency' THEN 'Heart_failure' WHEN comorbidity='dislipemia' THEN 'Hypercholesterolemia' WHEN comorbidity='thyroid disease' THEN 'Thyroid_diseases' WHEN comorbidity='musculoskeletal disease' THEN 'Musculoskeletal_diseases' WHEN comorbidity='renal disease' THEN 'renal_disease_uncharacterized' WHEN comorbidity='gastrointestinal disease' THEN 'Gastrointestinal' WHEN comorbidity='psychiatric disorder' THEN 'Mental_disorder' WHEN comorbidity='insomnia' THEN 'Sleeplessness' WHEN comorbidity='liver disease' THEN 'Liver_diseases' WHEN comorbidity='autoimmune disease' THEN 'Autoimmune_diseases' WHEN comorbidity='lung disease' THEN 'Lung_diseases' WHEN comorbidity='transplant' THEN 'Transplantation' ELSE comorbidity END) AS comorbidity, to_uri(CASE WHEN comorbidity='smoker' THEN 'CurrentSmoker' WHEN comorbidity='ex-smoker' THEN 'PreviousSmoker' ELSE '' END) AS smokingHabit, to_uri(CASE WHEN negated=0 THEN 'NoComorbidity' ELSE 'WithComorbidity' END) AS negated FROM comorbidity";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/BC_HUPHM_{ehr}";
    rr:class paladin:BCPatient
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasComorbidityStatus;
    rr:objectMap [
      rr:parentTriplesMap <positive_negative_comorbidity>
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasComorbidity;
    rr:objectMap [
      rr:parentTriplesMap <disorder_comorbidity>
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasSmokingHabit;
    rr:objectMap [
      rr:parentTriplesMap <smoking_habit_comorbidity>
    ]
  ].

<positive_negative_comorbidity>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, comorbidity AS comorbidity_orig, negated as negated_orig, to_uri(CASE WHEN comorbidity='smoker' THEN '' WHEN comorbidity='ex-smoker' THEN '' WHEN comorbidity='hta' THEN 'HTA' WHEN comorbidity='cardiac insufficiency' THEN 'Heart_failure' WHEN comorbidity='dislipemia' THEN 'Hypercholesterolemia' WHEN comorbidity='thyroid disease' THEN 'Thyroid_diseases' WHEN comorbidity='musculoskeletal disease' THEN 'Musculoskeletal_diseases' WHEN comorbidity='renal disease' THEN 'renal_disease_uncharacterized' WHEN comorbidity='gastrointestinal disease' THEN 'Gastrointestinal' WHEN comorbidity='psychiatric disorder' THEN 'Mental_disorder' WHEN comorbidity='insomnia' THEN 'Sleeplessness' WHEN comorbidity='liver disease' THEN 'Liver_diseases' WHEN comorbidity='autoimmune disease' THEN 'Autoimmune_diseases' WHEN comorbidity='lung disease' THEN 'Lung_diseases' WHEN comorbidity='transplant' THEN 'Transplantation' ELSE comorbidity END) AS comorbidity, to_uri(CASE WHEN comorbidity='smoker' THEN 'CurrentSmoker' WHEN comorbidity='ex-smoker' THEN 'PreviousSmoker' ELSE '' END) AS smokingHabit, to_uri(CASE WHEN negated=0 THEN 'NoComorbidity' ELSE 'WithComorbidity' END) AS negated FROM comorbidity";
  ];
  rr:subjectMap [
    rml:reference "negated";
    rr:termType rr:IRI;
  ];
  rr:termType rr:IRI;
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:constant <http://research.tib.eu/paladin/vocab/ComorbidityStatus>;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasOriginalValue;
    rr:objectMap [
      rml:reference "negated_orig";
    ]
  ].

<disorder_comorbidity>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, comorbidity AS comorbidity_orig, negated as negated_orig, to_uri(CASE WHEN comorbidity='smoker' THEN '' WHEN comorbidity='ex-smoker' THEN '' WHEN comorbidity='hta' THEN 'HTA' WHEN comorbidity='cardiac insufficiency' THEN 'Heart_failure' WHEN comorbidity='dislipemia' THEN 'Hypercholesterolemia' WHEN comorbidity='thyroid disease' THEN 'Thyroid_diseases' WHEN comorbidity='musculoskeletal disease' THEN 'Musculoskeletal_diseases' WHEN comorbidity='renal disease' THEN 'renal_disease_uncharacterized' WHEN comorbidity='gastrointestinal disease' THEN 'Gastrointestinal' WHEN comorbidity='psychiatric disorder' THEN 'Mental_disorder' WHEN comorbidity='insomnia' THEN 'Sleeplessness' WHEN comorbidity='liver disease' THEN 'Liver_diseases' WHEN comorbidity='autoimmune disease' THEN 'Autoimmune_diseases' WHEN comorbidity='lung disease' THEN 'Lung_diseases' WHEN comorbidity='transplant' THEN 'Transplantation' ELSE comorbidity END) AS comorbidity, to_uri(CASE WHEN comorbidity='smoker' THEN 'CurrentSmoker' WHEN comorbidity='ex-smoker' THEN 'PreviousSmoker' ELSE '' END) AS smokingHabit, to_uri(CASE WHEN negated=0 THEN 'NoComorbidity' ELSE 'WithComorbidity' END) AS negated FROM comorbidity";
  ];
  rr:subjectMap [
    rml:reference "comorbidity";
    rr:termType rr:IRI;
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:constant <http://research.tib.eu/paladin/vocab/Disorder>;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasOriginalValue;
    rr:objectMap [
      rml:reference "comorbidity_orig";
    ]
  ].

<smoking_habit_comorbidity>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, comorbidity AS comorbidity_orig, negated as negated_orig, to_uri(CASE WHEN comorbidity='smoker' THEN '' WHEN comorbidity='ex-smoker' THEN '' WHEN comorbidity='hta' THEN 'HTA' WHEN comorbidity='cardiac insufficiency' THEN 'Heart_failure' WHEN comorbidity='dislipemia' THEN 'Hypercholesterolemia' WHEN comorbidity='thyroid disease' THEN 'Thyroid_diseases' WHEN comorbidity='musculoskeletal disease' THEN 'Musculoskeletal_diseases' WHEN comorbidity='renal disease' THEN 'renal_disease_uncharacterized' WHEN comorbidity='gastrointestinal disease' THEN 'Gastrointestinal' WHEN comorbidity='psychiatric disorder' THEN 'Mental_disorder' WHEN comorbidity='insomnia' THEN 'Sleeplessness' WHEN comorbidity='liver disease' THEN 'Liver_diseases' WHEN comorbidity='autoimmune disease' THEN 'Autoimmune_diseases' WHEN comorbidity='lung disease' THEN 'Lung_diseases' WHEN comorbidity='transplant' THEN 'Transplantation' ELSE comorbidity END) AS comorbidity, to_uri(CASE WHEN comorbidity='smoker' THEN 'CurrentSmoker' WHEN comorbidity='ex-smoker' THEN 'PreviousSmoker' ELSE '' END) AS smokingHabit, to_uri(CASE WHEN negated=0 THEN 'NoComorbidity' ELSE 'WithComorbidity' END) AS negated FROM comorbidity";
  ];
  rr:subjectMap [
    rml:reference "smokingHabit";
    rr:termType rr:IRI;
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:constant <http://research.tib.eu/paladin/vocab/SmokingHabit>;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasOriginalValue;
    rr:objectMap [
      rml:reference "comorbidity_orig";
    ]
  ].

<BCPatient_tumor_grade>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, grade FROM tumor_grade";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/BC_HUPHM_{ehr}";
    rr:class paladin:BCPatient
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:tumorGrade;
    rr:objectMap [
      rml:reference "grade";
    ]
  ].

<BCPatient_tnm_stadification>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT tnm.*, p.diagnosis_date, (CASE WHEN p.neoadjuvant LIKE '%no%' THEN NULL ELSE p.first_treatment_date END) AS neoadjuvant_derived_date, p.neoadjuvant, to_uri(CASE WHEN t_category = 'IS' THEN 'In_Situ' ELSE CONCAT('t', t_category) END) AS url_diag_tumor_size, to_uri(CONCAT('n', n_category)) AS url_diag_lymph_nodes, to_uri(CONCAT('m', m_category)) AS url_diag_metastatis, to_uri(CASE WHEN t_category_after_neoadj = 'IS' THEN 'In_Situ' WHEN t_category_after_neoadj IS NULL THEN '' ELSE CONCAT('t', t_category_after_neoadj) END) AS url_neoadj_tumor_size, to_uri(CASE WHEN n_category_after_neoadj IS NULL THEN '' ELSE CONCAT('n', n_category_after_neoadj) END) AS url_neoadj_lymph_nodes, to_uri(CASE WHEN m_category_after_neoadj IS NULL THEN '' ELSE CONCAT('m', m_category_after_neoadj) END) AS url_neoadj_metastatis FROM tumor_tnm tnm JOIN patient p USING (ehr)";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/BC_HUPHM_{ehr}";
    rr:class paladin:BCPatient
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasTNMstageAssessment;
    rr:objectMap [
      rr:parentTriplesMap <TNM_assessment_diagnosis>
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasTNMstageAssessment;
    rr:objectMap [
      rr:parentTriplesMap <TNM_assessment_NeoadjuvantTherapy>
    ]
  ].

<TNM_assessment_diagnosis>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT tnm.*, p.diagnosis_date, (CASE WHEN p.neoadjuvant LIKE '%no%' THEN NULL ELSE p.first_treatment_date END) AS neoadjuvant_derived_date, p.neoadjuvant, to_uri(CASE WHEN t_category = 'IS' THEN 'In_Situ' ELSE CONCAT('t', t_category) END) AS url_diag_tumor_size, to_uri(CONCAT('n', n_category)) AS url_diag_lymph_nodes, to_uri(CONCAT('m', m_category)) AS url_diag_metastatis, to_uri(CASE WHEN t_category_after_neoadj = 'IS' THEN 'In_Situ' WHEN t_category_after_neoadj IS NULL THEN '' ELSE CONCAT('t', t_category_after_neoadj) END) AS url_neoadj_tumor_size, to_uri(CASE WHEN n_category_after_neoadj IS NULL THEN '' ELSE CONCAT('n', n_category_after_neoadj) END) AS url_neoadj_lymph_nodes, to_uri(CASE WHEN m_category_after_neoadj IS NULL THEN '' ELSE CONCAT('m', m_category_after_neoadj) END) AS url_neoadj_metastatis FROM tumor_tnm tnm JOIN patient p USING (ehr)";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/{ehr}_Diagnosis_StageAssessment";
    rr:class paladin:TNMstageAssessment
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:isAssessedDuring;
    rr:objectMap [
      rr:constant "Diagnosis";
      rr:termType rr:Literal;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:isAssessedOn;
    rr:objectMap [
      rml:reference "diagnosis_date";
      rr:datatype xsd:date ;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasStage;
    rr:objectMap [
      rml:reference "stage_diagnosis";
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasTNMstage;
    rr:objectMap [
      rr:parentTriplesMap <TNM_Stage_diagnosis_tnm_stadification>
    ]
  ].

<TNM_Stage_diagnosis_tnm_stadification>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT tnm.*, p.diagnosis_date, (CASE WHEN p.neoadjuvant LIKE '%no%' THEN NULL ELSE p.first_treatment_date END) AS neoadjuvant_derived_date, p.neoadjuvant, to_uri(CASE WHEN t_category = 'IS' THEN 'In_Situ' ELSE CONCAT('t', t_category) END) AS url_diag_tumor_size, to_uri(CONCAT('n', n_category)) AS url_diag_lymph_nodes, to_uri(CONCAT('m', m_category)) AS url_diag_metastatis, to_uri(CASE WHEN t_category_after_neoadj = 'IS' THEN 'In_Situ' WHEN t_category_after_neoadj IS NULL THEN '' ELSE CONCAT('t', t_category_after_neoadj) END) AS url_neoadj_tumor_size, to_uri(CASE WHEN n_category_after_neoadj IS NULL THEN '' ELSE CONCAT('n', n_category_after_neoadj) END) AS url_neoadj_lymph_nodes, to_uri(CASE WHEN m_category_after_neoadj IS NULL THEN '' ELSE CONCAT('m', m_category_after_neoadj) END) AS url_neoadj_metastatis FROM tumor_tnm tnm JOIN patient p USING (ehr)";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/{stage_diagnosis}";
    rr:class paladin:TNMstage
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:cancerStageTNM_TumorSize;
    rr:objectMap [
      rr:parentTriplesMap <Diagnosis_TNM_TumorSize>
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:cancerStageTNM_LymphNodesInvolvement;
    rr:objectMap [
      rr:parentTriplesMap <Diagnosis_TNM_LymphNodesInvolvement>
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:cancerStageTNM_MetastatisStage;
    rr:objectMap [
      rr:parentTriplesMap <Diagnosis_TNM_MetastatisStage>
    ]
  ].

<Diagnosis_TNM_TumorSize>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT tnm.*, p.diagnosis_date, (CASE WHEN p.neoadjuvant LIKE '%no%' THEN NULL ELSE p.first_treatment_date END) AS neoadjuvant_derived_date, p.neoadjuvant, to_uri(CASE WHEN t_category = 'IS' THEN 'In_Situ' ELSE CONCAT('t', t_category) END) AS url_diag_tumor_size, to_uri(CONCAT('n', n_category)) AS url_diag_lymph_nodes, to_uri(CONCAT('m', m_category)) AS url_diag_metastatis, to_uri(CASE WHEN t_category_after_neoadj = 'IS' THEN 'In_Situ' WHEN t_category_after_neoadj IS NULL THEN '' ELSE CONCAT('t', t_category_after_neoadj) END) AS url_neoadj_tumor_size, to_uri(CASE WHEN n_category_after_neoadj IS NULL THEN '' ELSE CONCAT('n', n_category_after_neoadj) END) AS url_neoadj_lymph_nodes, to_uri(CASE WHEN m_category_after_neoadj IS NULL THEN '' ELSE CONCAT('m', m_category_after_neoadj) END) AS url_neoadj_metastatis FROM tumor_tnm tnm JOIN patient p USING (ehr)";
  ];
  rr:subjectMap [
    rml:reference "url_diag_tumor_size";
    rr:termType rr:IRI;
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:constant <http://research.tib.eu/paladin/vocab/TumorSize>;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:tumorSize_staging_method;
    rr:objectMap <Diagnosis_tnm_t_staging_method_Function_bc_clinical_notes_HUPHM_tnm_stadification> ;
    rr:termType rr:Literal ;
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:tumorSize_staging_category;
    rr:objectMap [
      rml:reference "t_category";
    ]
  ].

<Diagnosis_TNM_LymphNodesInvolvement>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT tnm.*, p.diagnosis_date, (CASE WHEN p.neoadjuvant LIKE '%no%' THEN NULL ELSE p.first_treatment_date END) AS neoadjuvant_derived_date, p.neoadjuvant, to_uri(CASE WHEN t_category = 'IS' THEN 'In_Situ' ELSE CONCAT('t', t_category) END) AS url_diag_tumor_size, to_uri(CONCAT('n', n_category)) AS url_diag_lymph_nodes, to_uri(CONCAT('m', m_category)) AS url_diag_metastatis, to_uri(CASE WHEN t_category_after_neoadj = 'IS' THEN 'In_Situ' WHEN t_category_after_neoadj IS NULL THEN '' ELSE CONCAT('t', t_category_after_neoadj) END) AS url_neoadj_tumor_size, to_uri(CASE WHEN n_category_after_neoadj IS NULL THEN '' ELSE CONCAT('n', n_category_after_neoadj) END) AS url_neoadj_lymph_nodes, to_uri(CASE WHEN m_category_after_neoadj IS NULL THEN '' ELSE CONCAT('m', m_category_after_neoadj) END) AS url_neoadj_metastatis FROM tumor_tnm tnm JOIN patient p USING (ehr)";
  ];
  rr:subjectMap [
    rml:reference "url_diag_lymph_nodes";
    rr:termType rr:IRI;
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:constant <http://research.tib.eu/paladin/vocab/LymphNodesInvolvement>;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:lymphNodesInvolvement_staging_method;
    rr:objectMap <Diagnosis_tnm_n_staging_method_Function_bc_clinical_notes_HUPHM_tnm_stadification> ;
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:lymphNodesInvolvement_staging_category;
    rr:objectMap [
      rml:reference "n_category";
    ]
  ].

<Diagnosis_TNM_MetastatisStage>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT tnm.*, p.diagnosis_date, (CASE WHEN p.neoadjuvant LIKE '%no%' THEN NULL ELSE p.first_treatment_date END) AS neoadjuvant_derived_date, p.neoadjuvant, to_uri(CASE WHEN t_category = 'IS' THEN 'In_Situ' ELSE CONCAT('t', t_category) END) AS url_diag_tumor_size, to_uri(CONCAT('n', n_category)) AS url_diag_lymph_nodes, to_uri(CONCAT('m', m_category)) AS url_diag_metastatis, to_uri(CASE WHEN t_category_after_neoadj = 'IS' THEN 'In_Situ' WHEN t_category_after_neoadj IS NULL THEN '' ELSE CONCAT('t', t_category_after_neoadj) END) AS url_neoadj_tumor_size, to_uri(CASE WHEN n_category_after_neoadj IS NULL THEN '' ELSE CONCAT('n', n_category_after_neoadj) END) AS url_neoadj_lymph_nodes, to_uri(CASE WHEN m_category_after_neoadj IS NULL THEN '' ELSE CONCAT('m', m_category_after_neoadj) END) AS url_neoadj_metastatis FROM tumor_tnm tnm JOIN patient p USING (ehr)";
  ];
  rr:subjectMap [
    rml:reference "url_diag_metastatis";
    rr:termType rr:IRI;
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:constant <http://research.tib.eu/paladin/vocab/MetastatisStage>;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:metastatisStage_staging_category;
    rr:objectMap [
      rml:reference "m_category";
    ]
  ].

<TNM_assessment_NeoadjuvantTherapy>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT tnm.*, p.diagnosis_date, (CASE WHEN p.neoadjuvant LIKE '%no%' THEN NULL ELSE p.first_treatment_date END) AS neoadjuvant_derived_date, p.neoadjuvant, to_uri(CASE WHEN t_category = 'IS' THEN 'In_Situ' ELSE CONCAT('t', t_category) END) AS url_diag_tumor_size, to_uri(CONCAT('n', n_category)) AS url_diag_lymph_nodes, to_uri(CONCAT('m', m_category)) AS url_diag_metastatis, to_uri(CASE WHEN t_category_after_neoadj = 'IS' THEN 'In_Situ' WHEN t_category_after_neoadj IS NULL THEN '' ELSE CONCAT('t', t_category_after_neoadj) END) AS url_neoadj_tumor_size, to_uri(CASE WHEN n_category_after_neoadj IS NULL THEN '' ELSE CONCAT('n', n_category_after_neoadj) END) AS url_neoadj_lymph_nodes, to_uri(CASE WHEN m_category_after_neoadj IS NULL THEN '' ELSE CONCAT('m', m_category_after_neoadj) END) AS url_neoadj_metastatis FROM tumor_tnm tnm JOIN patient p USING (ehr)";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/{ehr}_AfterNeoadjuvantTherapy_StageAssessment";
    rr:class paladin:TNMstageAssessment
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:isAssessedDuring;
    rr:objectMap [
      rr:constant "AfterNeoadjuvantTherapy";
      rr:termType rr:Literal;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:isAssessedOn;
    rr:objectMap [
      rml:reference "neoadjuvant_derived_date";
      rr:datatype xsd:date ;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasStage;
    rr:objectMap [
      rml:reference "stage_after_neo";
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasTNMstage;
    rr:objectMap [
      rr:parentTriplesMap <TNM_Stage_NeoadjuvantTherapy>
    ]
  ].

<TNM_Stage_NeoadjuvantTherapy>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT tnm.*, p.diagnosis_date, (CASE WHEN p.neoadjuvant LIKE '%no%' THEN NULL ELSE p.first_treatment_date END) AS neoadjuvant_derived_date, p.neoadjuvant, to_uri(CASE WHEN t_category = 'IS' THEN 'In_Situ' ELSE CONCAT('t', t_category) END) AS url_diag_tumor_size, to_uri(CONCAT('n', n_category)) AS url_diag_lymph_nodes, to_uri(CONCAT('m', m_category)) AS url_diag_metastatis, to_uri(CASE WHEN t_category_after_neoadj = 'IS' THEN 'In_Situ' WHEN t_category_after_neoadj IS NULL THEN '' ELSE CONCAT('t', t_category_after_neoadj) END) AS url_neoadj_tumor_size, to_uri(CASE WHEN n_category_after_neoadj IS NULL THEN '' ELSE CONCAT('n', n_category_after_neoadj) END) AS url_neoadj_lymph_nodes, to_uri(CASE WHEN m_category_after_neoadj IS NULL THEN '' ELSE CONCAT('m', m_category_after_neoadj) END) AS url_neoadj_metastatis FROM tumor_tnm tnm JOIN patient p USING (ehr)";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/{stage_after_neo}";
    rr:class paladin:TNMstage
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:cancerStageTNM_TumorSize;
    rr:objectMap [
       rr:parentTriplesMap <NeoadjuvantTherapy_TNM_TumorSize>
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:cancerStageTNM_LymphNodesInvolvement;
    rr:objectMap [
      rr:parentTriplesMap <NeoadjuvantTherapy_TNM_LymphNodesInvolvement>
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:cancerStageTNM_MetastatisStage;
    rr:objectMap [
      rr:parentTriplesMap <NeoadjuvantTherapy_TNM_MetastatisStage>
    ]
  ].

<NeoadjuvantTherapy_TNM_TumorSize>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT tnm.*, p.diagnosis_date, (CASE WHEN p.neoadjuvant LIKE '%no%' THEN NULL ELSE p.first_treatment_date END) AS neoadjuvant_derived_date, p.neoadjuvant, to_uri(CASE WHEN t_category = 'IS' THEN 'In_Situ' ELSE CONCAT('t', t_category) END) AS url_diag_tumor_size, to_uri(CONCAT('n', n_category)) AS url_diag_lymph_nodes, to_uri(CONCAT('m', m_category)) AS url_diag_metastatis, to_uri(CASE WHEN t_category_after_neoadj = 'IS' THEN 'In_Situ' WHEN t_category_after_neoadj IS NULL THEN '' ELSE CONCAT('t', t_category_after_neoadj) END) AS url_neoadj_tumor_size, to_uri(CASE WHEN n_category_after_neoadj IS NULL THEN '' ELSE CONCAT('n', n_category_after_neoadj) END) AS url_neoadj_lymph_nodes, to_uri(CASE WHEN m_category_after_neoadj IS NULL THEN '' ELSE CONCAT('m', m_category_after_neoadj) END) AS url_neoadj_metastatis FROM tumor_tnm tnm JOIN patient p USING (ehr)";
  ];
  rr:subjectMap [
    rml:reference "url_neoadj_tumor_size";
    rr:termType rr:IRI;
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:constant <http://research.tib.eu/paladin/vocab/TumorSize>;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:tumorSize_staging_method;
    rr:objectMap <NeoadjuvantTherapy_tnm_t_staging_method_Function_bc_clinical_notes_HUPHM_tnm_stadification> ;
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:tumorSize_staging_category;
    rr:objectMap [
      rml:reference "t_category_after_neoadj";
    ]
  ].

<NeoadjuvantTherapy_TNM_LymphNodesInvolvement>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT tnm.*, p.diagnosis_date, (CASE WHEN p.neoadjuvant LIKE '%no%' THEN NULL ELSE p.first_treatment_date END) AS neoadjuvant_derived_date, p.neoadjuvant, to_uri(CASE WHEN t_category = 'IS' THEN 'In_Situ' ELSE CONCAT('t', t_category) END) AS url_diag_tumor_size, to_uri(CONCAT('n', n_category)) AS url_diag_lymph_nodes, to_uri(CONCAT('m', m_category)) AS url_diag_metastatis, to_uri(CASE WHEN t_category_after_neoadj = 'IS' THEN 'In_Situ' WHEN t_category_after_neoadj IS NULL THEN '' ELSE CONCAT('t', t_category_after_neoadj) END) AS url_neoadj_tumor_size, to_uri(CASE WHEN n_category_after_neoadj IS NULL THEN '' ELSE CONCAT('n', n_category_after_neoadj) END) AS url_neoadj_lymph_nodes, to_uri(CASE WHEN m_category_after_neoadj IS NULL THEN '' ELSE CONCAT('m', m_category_after_neoadj) END) AS url_neoadj_metastatis FROM tumor_tnm tnm JOIN patient p USING (ehr)";
  ];
  rr:subjectMap [
    rml:reference "url_neoadj_lymph_nodes";
    rr:termType rr:IRI;
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:constant <http://research.tib.eu/paladin/vocab/LymphNodesInvolvement>;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:lymphNodesInvolvement_staging_method;
    rr:objectMap <NeoadjuvantTherapy_tnm_n_staging_method_Function_bc_clinical_notes_HUPHM_tnm_stadification> ;
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:lymphNodesInvolvement_staging_category;
    rr:objectMap [
      rml:reference "n_category_after_neoadj";
    ]
  ].

<NeoadjuvantTherapy_TNM_MetastatisStage>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT tnm.*, p.diagnosis_date, (CASE WHEN p.neoadjuvant LIKE '%no%' THEN NULL ELSE p.first_treatment_date END) AS neoadjuvant_derived_date, p.neoadjuvant, to_uri(CASE WHEN t_category = 'IS' THEN 'In_Situ' ELSE CONCAT('t', t_category) END) AS url_diag_tumor_size, to_uri(CONCAT('n', n_category)) AS url_diag_lymph_nodes, to_uri(CONCAT('m', m_category)) AS url_diag_metastatis, to_uri(CASE WHEN t_category_after_neoadj = 'IS' THEN 'In_Situ' WHEN t_category_after_neoadj IS NULL THEN '' ELSE CONCAT('t', t_category_after_neoadj) END) AS url_neoadj_tumor_size, to_uri(CASE WHEN n_category_after_neoadj IS NULL THEN '' ELSE CONCAT('n', n_category_after_neoadj) END) AS url_neoadj_lymph_nodes, to_uri(CASE WHEN m_category_after_neoadj IS NULL THEN '' ELSE CONCAT('m', m_category_after_neoadj) END) AS url_neoadj_metastatis FROM tumor_tnm tnm JOIN patient p USING (ehr)";
  ];
  rr:subjectMap [
    rml:reference "url_neoadj_metastatis";
    rr:termType rr:IRI;
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:constant <http://research.tib.eu/paladin/vocab/MetastatisStage>;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:metastatisStage_staging_category;
    rr:objectMap [
      rml:reference "m_category_after_neoadj";
    ]
  ].

<BCPatient>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT *, to_uri(neoadjuvant) AS neoadjuvant_uri, to_bool_uri(er_positive) AS er_positive_uri, to_bool_uri(pr_positive) AS pr_positive_uri, to_bool_uri(her2_overall_positive) AS her2_overall_positive_uri FROM patient";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/BC_HUPHM_{ehr}";
    rr:class paladin:BCPatient
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:id_ehr;
    rr:objectMap [
      rml:reference "ehr"
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:birthDate;
    rr:objectMap [
      rml:reference "birth_date";
      rr:datatype xsd:date;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:diagnosisDate;
    rr:objectMap [
      rml:reference "diagnosis_date";
      rr:datatype xsd:date;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:age;
    rr:objectMap [
      rml:reference "age_at_diagnosis";
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasOncologicalTreatmentLine;
    rr:objectMap [
      rr:parentTriplesMap <OncologicalTreatmentLine_bc_clinical_notes_patient>
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:firstSurgeryDate;
    rr:objectMap [
      rml:reference "surgery_date";
      rr:datatype xsd:date;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:deathDate;
    rr:objectMap [
      rml:reference "death_date";
      rr:datatype xsd:date;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:deathAge;
    rr:objectMap [
      rml:reference "age_at_death";
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:relapseYear;
    rr:objectMap [
      rml:reference "recurrence_year";
      rr:datatype xsd:gYear;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasNeoadjuvantTherapy;
    rr:objectMap [
      rr:parentTriplesMap <NeoadjuvantTherapy_bc_clinical_notes_patient>
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:estrogenPositive;
    rr:objectMap [
      rr:parentTriplesMap <estrogen_positive_bc_clinical_notes_patient>
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:progesteronePositive;
    rr:objectMap [
      rr:parentTriplesMap <progesterone_positive_bc_clinical_notes_patient>
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:her2Positive;
    rr:objectMap [
      rr:parentTriplesMap <her2_positive_bc_clinical_notes_patient>
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:ki67;
    rr:objectMap [
      rml:reference "ki67_percent_max_simp";
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasMenarcheAge;
    rr:objectMap [
      rml:reference "menarche_age";
      rr:datatype xsd:int;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasMenopauseAge;
    rr:objectMap [
      rml:reference "menopause_age";
      rr:datatype xsd:int;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasEarlyMenopause;
    rr:objectMap [
      rml:reference "menopause_pre";
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:gravidity;
    rr:objectMap [
      rml:reference "pregnancy"
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:abortion;
    rr:objectMap [
      rml:reference "abort"
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:parity;
    rr:objectMap [
      rml:reference "birth"
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:cSection;
    rr:objectMap [
      rml:reference "caesarean"
    ]
  ].

<OncologicalTreatmentLine_bc_clinical_notes_patient>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT *, to_uri(neoadjuvant) AS neoadjuvant_uri, to_bool_uri(er_positive) AS er_positive_uri, to_bool_uri(pr_positive) AS pr_positive_uri, to_bool_uri(her2_overall_positive) AS her2_overall_positive_uri FROM patient";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/BC_HUPHM_{ehr}_OncologicalTL_1";
    rr:class paladin:OncologicalTreatmentLine
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:treatementLineStartDate;
    rr:objectMap [
      rml:reference "first_treatment_date";
      rr:datatype xsd:date
    ]
  ].

<NeoadjuvantTherapy_bc_clinical_notes_patient>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT *, to_uri(neoadjuvant) AS neoadjuvant_uri, to_bool_uri(er_positive) AS er_positive_uri, to_bool_uri(pr_positive) AS pr_positive_uri, to_bool_uri(her2_overall_positive) AS her2_overall_positive_uri FROM patient";
  ];
  rr:subjectMap [
    rml:reference "neoadjuvant_uri";
    rr:termType rr:IRI;
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:constant <http://research.tib.eu/paladin/vocab/NeoadjuvantTherapy>;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasOriginalValue;
    rr:objectMap [
      rml:reference "neoadjuvant";
    ]
  ].

<estrogen_positive_bc_clinical_notes_patient>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT *, to_uri(neoadjuvant) AS neoadjuvant_uri, to_bool_uri(er_positive) AS er_positive_uri, to_bool_uri(pr_positive) AS pr_positive_uri, to_bool_uri(her2_overall_positive) AS her2_overall_positive_uri FROM patient";
  ];
  rr:subjectMap [
    rml:reference "er_positive_uri";
    rr:termType rr:IRI;
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:constant <http://research.tib.eu/paladin/vocab/EstrogenPositive>;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasOriginalValue;
    rr:objectMap [
      rml:reference "er_positive";
    ]
  ].

<progesterone_positive_bc_clinical_notes_patient>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT *, to_uri(neoadjuvant) AS neoadjuvant_uri, to_bool_uri(er_positive) AS er_positive_uri, to_bool_uri(pr_positive) AS pr_positive_uri, to_bool_uri(her2_overall_positive) AS her2_overall_positive_uri FROM patient";
  ];
  rr:subjectMap [
    rml:reference "pr_positive_uri";
    rr:termType rr:IRI;
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:constant <http://research.tib.eu/paladin/vocab/ProgesteronePositive>;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasOriginalValue;
    rr:objectMap [
      rml:reference "pr_positive";
    ]
  ].

<her2_positive_bc_clinical_notes_patient>
  a rr:TriplesMap;
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT *, to_uri(neoadjuvant) AS neoadjuvant_uri, to_bool_uri(er_positive) AS er_positive_uri, to_bool_uri(pr_positive) AS pr_positive_uri, to_bool_uri(her2_overall_positive) AS her2_overall_positive_uri FROM patient";
  ];
  rr:subjectMap [
    rml:reference "her2_overall_positive_uri";
    rr:termType rr:IRI;
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:constant <http://research.tib.eu/paladin/vocab/HER2Positive>;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasOriginalValue;
    rr:objectMap [
      rml:reference "her2_overall_positive";
    ]
  ].

<BCPatient_chemotherapy_treatment_episode>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, date, cycle_number, cs.id_schema, SPLIT_STR(name, ' + ', 1) AS drug1, SPLIT_STR(name, ' + ', 2) AS drug2, SPLIT_STR(name, ' + ', 3) AS drug3, SPLIT_STR(name, ' + ', 4) AS drug4, to_uri(REPLACE(CAP_FIRST(name), ' + ', '_')) AS uri_schema FROM chemoterapy_cycle cc JOIN chemoterapy_schema cs USING(id_schema)";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/BC_HUPHM_{ehr}";
    rr:class paladin:BCPatient
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasTreatmentEpisode;
    rr:objectMap [
      rr:parentTriplesMap <Treatment_Episode_Chemotherap>
    ]
  ].

<Treatment_Episode_Chemotherapy>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, date, cycle_number, cs.id_schema, SPLIT_STR(name, ' + ', 1) AS drug1, SPLIT_STR(name, ' + ', 2) AS drug2, SPLIT_STR(name, ' + ', 3) AS drug3, SPLIT_STR(name, ' + ', 4) AS drug4, to_uri(REPLACE(CAP_FIRST(name), ' + ', '_')) AS uri_schema FROM chemoterapy_cycle cc JOIN chemoterapy_schema cs USING(id_schema)";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/{ehr}_Chemotherapy_{date}";
    rr:class paladin:TreatmentEpisode
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasTreatmentType;
    rr:objectMap [
      rr:parentTriplesMap <Treatment_Type_Chemotherapy>
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:treatementLineDate;
    rr:objectMap [
      rml:reference "date";
      rr:datatype xsd:date
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasEpisode;
    rr:objectMap [
      rr:parentTriplesMap <TreatmentLineCycle_chemotherapy_drugs>
    ]
  ].

<Treatment_Type_Chemotherapy>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, date, cycle_number, cs.id_schema, SPLIT_STR(name, ' + ', 1) AS drug1, SPLIT_STR(name, ' + ', 2) AS drug2, SPLIT_STR(name, ' + ', 3) AS drug3, SPLIT_STR(name, ' + ', 4) AS drug4, to_uri(REPLACE(CAP_FIRST(name), ' + ', '_')) AS uri_schema FROM chemoterapy_cycle cc JOIN chemoterapy_schema cs USING(id_schema)";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/{ehr}_Chemotherapy_{cycle_number}_{id_schema}";
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
       rr:constant <http://research.tib.eu/paladin/vocab/Chemotherapy>;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasTreatmentLineCycle;
    rr:objectMap [
      rr:parentTriplesMap <TreatmentLineCycle_chemotherapy_drugs>
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasDrugSchema;
    rr:objectMap [
      rr:parentTriplesMap <chemotherapy_drug_schema>
    ]
  ].

<chemotherapy_drug_schema>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, date, cycle_number, cs.id_schema, SPLIT_STR(name, ' + ', 1) AS drug1, SPLIT_STR(name, ' + ', 2) AS drug2, SPLIT_STR(name, ' + ', 3) AS drug3, SPLIT_STR(name, ' + ', 4) AS drug4, to_uri(REPLACE(CAP_FIRST(name), ' + ', '_')) AS uri_schema FROM chemoterapy_cycle cc JOIN chemoterapy_schema cs USING(id_schema)";
  ];
  rr:subjectMap [
    rml:reference "uri_schema";
    rr:termType rr:IRI;
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:constant <http://research.tib.eu/paladin/vocab/BreastCancerDrugSchema>;
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasDrug1;
    rr:objectMap [
      rr:parentTriplesMap <Treatment_Episode_Chemotherapy_schema_drug_1>
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasDrug2;
    rr:objectMap [
      rr:parentTriplesMap <Treatment_Episode_Chemotherapy_schema_drug_2>
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasDrug3;
    rr:objectMap [
      rr:parentTriplesMap <Treatment_Episode_Chemotherapy_schema_drug_3>
    ]
  ];
  rr:predicateObjectMap [
    rr:predicate paladin:hasDrug4;
    rr:objectMap [
      rr:parentTriplesMap <Treatment_Episode_Chemotherapy_schema_drug_4>
    ]
  ].

<Treatment_Episode_Chemotherapy_schema_drug_1>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, date, cycle_number, cs.id_schema, SPLIT_STR(name, ' + ', 1) AS drug1, SPLIT_STR(name, ' + ', 2) AS drug2, SPLIT_STR(name, ' + ', 3) AS drug3, SPLIT_STR(name, ' + ', 4) AS drug4, to_uri(REPLACE(CAP_FIRST(name), ' + ', '_')) AS uri_schema FROM chemoterapy_cycle cc JOIN chemoterapy_schema cs USING(id_schema)";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/{drug1}";
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:constant <http://research.tib.eu/paladin/vocab/BreastCancerOncologicalDrug>;
    ]
  ].

<Treatment_Episode_Chemotherapy_schema_drug_2>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, date, cycle_number, cs.id_schema, SPLIT_STR(name, ' + ', 1) AS drug1, SPLIT_STR(name, ' + ', 2) AS drug2, SPLIT_STR(name, ' + ', 3) AS drug3, SPLIT_STR(name, ' + ', 4) AS drug4, to_uri(REPLACE(CAP_FIRST(name), ' + ', '_')) AS uri_schema FROM chemoterapy_cycle cc JOIN chemoterapy_schema cs USING(id_schema)";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/{drug2}";
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:constant <http://research.tib.eu/paladin/vocab/BreastCancerOncologicalDrug>;
    ]
  ].

<Treatment_Episode_Chemotherapy_schema_drug_3>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, date, cycle_number, cs.id_schema, SPLIT_STR(name, ' + ', 1) AS drug1, SPLIT_STR(name, ' + ', 2) AS drug2, SPLIT_STR(name, ' + ', 3) AS drug3, SPLIT_STR(name, ' + ', 4) AS drug4, to_uri(REPLACE(CAP_FIRST(name), ' + ', '_')) AS uri_schema FROM chemoterapy_cycle cc JOIN chemoterapy_schema cs USING(id_schema)";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/{drug3}";
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:constant <http://research.tib.eu/paladin/vocab/BreastCancerOncologicalDrug>;
    ]
  ].

<Treatment_Episode_Chemotherapy_schema_drug_4>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, date, cycle_number, cs.id_schema, SPLIT_STR(name, ' + ', 1) AS drug1, SPLIT_STR(name, ' + ', 2) AS drug2, SPLIT_STR(name, ' + ', 3) AS drug3, SPLIT_STR(name, ' + ', 4) AS drug4, to_uri(REPLACE(CAP_FIRST(name), ' + ', '_')) AS uri_schema FROM chemoterapy_cycle cc JOIN chemoterapy_schema cs USING(id_schema)";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/{drug4}";
  ];
  rr:predicateObjectMap [
    rr:predicate rdf:type;
    rr:objectMap [
      rr:constant <http://research.tib.eu/paladin/vocab/BreastCancerOncologicalDrug>;
    ]
  ].

<TreatmentLineCycle_chemotherapy_drugs>
  rml:logicalSource [
    rml:source <#DB_source>;
    rml:query "SELECT ehr, date, cycle_number, cs.id_schema, SPLIT_STR(name, ' + ', 1) AS drug1, SPLIT_STR(name, ' + ', 2) AS drug2, SPLIT_STR(name, ' + ', 3) AS drug3, SPLIT_STR(name, ' + ', 4) AS drug4, to_uri(REPLACE(CAP_FIRST(name), ' + ', '_')) AS uri_schema FROM chemoterapy_cycle cc JOIN chemoterapy_schema cs USING(id_schema)";
  ];
  rr:subjectMap [
    rr:template "http://research.tib.eu/paladin/entity/{cycle_number}";
    rr:class paladin:TreatmentLineCycle
  ].