Condition-Mapping.md

+# Condition Mapping
+
+:information_source: All ICD Code will also be mapped to a Snomed Code. The mapping information is available in OMOP in the `public.MATERIALIZED VIEW.icd_snomed_domain_lookup`, which is generated from ICD10GM Vocabulary (CONCEPT) and CONCEPT_RELATIONSHIP tables. 
+
+## Condition to CONDITION_OCCURRENCE
+| Source | Target | Comments |
+| :---------------- | :---------------------- | :------------------------------------------------- |
+|                   | condition_occurrence_id |this id is automatic generated in database          |
+| subject.reference | person_id               | the `person_id` from PERSON                        |
+| code.coding.code | condition_concept_id <br> condition_source_value <br> condition_source_concept_id | both primary and secondary ICD codes are written here |
+| recordedDate <br> onsetPeriod.start <br> onsetDateTimeType | condition_start_date <br> condition_start_datetime | one of the resources is used |
+|  | condition_type_concept_id| the data _`rank`_ from `Encounter` is used here <br> 1-> HD (44786627) <br> 2-> ND (44786629) |
+| Encounter.reference | visit_occurrence_id | the `visit_occurrence_id` from VISIT_OCCURRENCE |
+| |visit_detail_id| the `visit_detail_id` from VISIT_DETAIL|
+|code.coding.extension|condition_status_concept_id <br> condition_status_resource_value|__A__(ausgeschlossene Diagnose) -> __37116688__ <br> __G__(gesicherte Diagnose) -> __4230359__ <br> __V__(Verdachtsdiagnose)-> __4033240__ <br> __Z__(symptomloser Zustand nach der betreffende Diagnose)-> __4284245__|
+
+## Condition to MEASUREMENT
+| Source | Target | Comments |
+| :--------------- | :-------------------- | :---------------------------------------- |
+|                  | measurement_id        |this id is automatic generated in database |
+|subject.reference |  person_id            | the `person_id` from PERSON               |
+| code.coding.code |measurement_concept_id <br> measurement_source_value <br> measurement_source_concept_id| _Analogous to CONDITION_OCCURRENCE_           |
+|recordedDate <br> onsetPeriod.start <br> onsetDateTimeType |measurement_date <br> measurement_datetime|_Analogous to CONDITION_OCCURRENCE_|
+| |measurement_type_concept_id|_Analogous to CONDITION_OCCURRENCE_|
+|Encounter.reference |visit_occurrence_id|the `visit_occurrence_id` from VISIT_OCCURRENCE|
+| |visit_detail_id|the `visit_detail_id` from VISIT_DETAIL|
+
+## Condition to OBSERVATION
+| Source | Target | Comments |
+| :--------------- | :-------------------- | :---------------------------------------- |
+|                  | observation_id        |this id is automatic generated in database |
+|subject.reference |  person_id            | the `person_id` from PERSON               |
+| code.coding.code |observation_concept_id <br> observation_source_value <br> observation_source_concept_id| _Analogous to CONDITION_OCCURRENCE_           |
+|recordedDate <br> onsetPeriod.start <br> onsetDateTimeType |observation_date <br> observation_datetime|_Analogous to CONDITION_OCCURRENCE_|
+| |observation_type_concept_id|_Analogous to CONDITION_OCCURRENCE_|
+|Encounter.reference |visit_occurrence_id|the `visit_occurrence_id` from VISIT_OCCURRENCE|
+| |visit_detail_id|the `visit_detail_id` from VISIT_DETAIL|
+
+## Condition to PROCEDURE_OCCURRENCE
+| Source | Target | Comments |
+| :--------------- | :-------------------- | :---------------------------------------- |
+|                  | procedure_occurrence_id|this id is automatic generated in database |
+|subject.reference |  person_id            | the `person_id` from PERSON               |
+| code.coding.code |procedure_concept_id <br> procedure_source_value <br> procedure_source_concept_id| _Analogous to CONDITION_OCCURRENCE_           |
+|recordedDate <br> onsetPeriod.start <br> onsetDateTimeType |procedure_date <br> procedure_datetime|_Analogous to CONDITION_OCCURRENCE_|
+| |procedure_type_concept_id|_Analogous to CONDITION_OCCURRENCE_|
+|Encounter.reference |visit_occurrence_id|the `visit_occurrence_id` from VISIT_OCCURRENCE|
+| |visit_detail_id|the `visit_detail_id` from VISIT_DETAIL|
+
+
+## Example
+
+### Input Condition Resource
+
+```json
+{
+    "id": "id-1",
+    "code": {
+        "coding": [{
+                "code": "Z71 Z50.1",
+                "system": "http://fhir.de/CodeSystem/dimdi/icd-10-gm",
+                "version": "2018",
+                "extension": [{
+                        "url": "http://fhir.de/StructureDefinition/icd-10-gm-haupt-kreuz",
+                        "valueCoding": {
+                            "code": "Z71",
+                            "system": "http://fhir.de/CodeSystem/dimdi/icd-10-gm",
+                            "version": "2018"
+                        }
+                    }
+                ]
+            }
+        ]
+    },
+    "meta": {
+        "source": "#p21"
+    },
+    "subject": {
+        "reference": "Patient/pid.001"
+    },
+    "encounter": {
+        "reference": "Encounter/cid.001"
+    },
+    "identifier": [{
+            "value": "id-1",
+            "system": "https://miracum.org/fhir/NamingSystem/identifier/P21SurrogateConditionId"
+        }
+    ],
+    "recordedDate": "2018-02-15T17:25:00+00:00",
+    "resourceType": "Condition"
+}
+```
+
+### Output OMOP tables
++ CONDITION_OCCURRENCE
+
+|condition_occurrence_id|person_id|condition_concept_id|condition_start_date|condition_start_datetime|condition_type_concept_id|visit_occurrence_id|condition_source_value|condition_source_concept_id|
+|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|
+|1|1|2000001173|2018-02-15|2018-02-15 17:25:00|44786627|1|Z71|4254477|
+|2|1|2000001425|2018-02-15|2018-02-15 17:25:00|44786627|1|Z50.1|4238738|
+
++ FACT_RELATIONSHIP
+
+|domain_concept_id_1|fact_id_1|domain_concept_id_2|fact_id_2|relationship_concept_id|
+|:----:|:----:|:----:|:----:|:----:|
+|10|1|27|2|44818770|
+|27|2|10|1|44818868|
\ No newline at end of file