Condition-Mapping.md

@@ -6,26 +6,26 @@
 ## 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 | 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_end_date <br> condition_end_datetime | |
-|  | condition_type_concept_id| the data _`rank`_ from `Encounter` is used here <br> 1-> HD (44786627) <br> 2-> ND (44786629) |
-|code.coding.extension|condition_status_concept_id |__A__(ausgeschlossene Diagnose) -> __37116688__ <br> __G__(gesicherte Diagnose) -> __4230359__ <br> __V__(Verdachtsdiagnose)-> __4033240__ <br> __Z__(symptomloser Zustand nach der betreffende Diagnose)-> __4284245__|
+| | condition_occurrence_id |This id is generated for each condition resource automatically. |
+| subject.reference or <br> subject.identifier.value | person_id | The patient reference is used to search for the person_id in FHIR_ID_TO_OMOP_ID_MAP. |
+|  | condition_concept_id | SNOMED concept associated with the ICD code from condition_source_value without special characters |
+| recordedDate <br> onsetPeriod.start <br> onsetDateTime.value | condition_start_date <br> condition_start_datetime | |
+| onsetPeriod.end | condition_end_date <br> condition_end_datetime | |
+|  | condition_type_concept_id| the data _`rank`_ from `Encounter` is used here <br> value: 1 -> concept_id: 44786627 (HD) <br> value: 2 -> concept_id: 44786629 (ND) |
+|code.coding.extension|condition_status_concept_id | See mapping table in [DiagnoseSicherheitLookup.java](https://gitlab.miracum.org/miracum/etl/fhir-to-omop/-/blob/master/src/main/java/org/miracum/etl/fhirtoomop/lookups/DiagnoseSicherheitLookup.java) |
 | | :x: stop_reason | |
 | | :x: provider_id | |
-| Encounter.reference | visit_occurrence_id | the `visit_occurrence_id` from VISIT_OCCURRENCE |
-| |visit_detail_id| the `visit_detail_id` from VISIT_DETAIL|
-| code.coding.code | condition_source_value <br> condition_source_concept_id |
-| | condition_source_concept_id | |
-|code.coding.extension|condition_status_source_value|__A__(ausgeschlossene Diagnose) -> __37116688__ <br> __G__(gesicherte Diagnose) -> __4230359__ <br> __V__(Verdachtsdiagnose)-> __4033240__ <br> __Z__(symptomloser Zustand nach der betreffende Diagnose)-> __4284245__|
+| encounter.reference or <br> encounter.identifier.value | visit_occurrence_id | The encounter reference is used to search for the visit_occurrence_id in FHIR_ID_TO_OMOP_ID_MAP. |
+| |visit_detail_id| See post processing for visit_detail_id |
+| code.coding.code | condition_source_value | ICD-code WHERE system = "http://fhir.de/CodeSystem/dimdi/icd-10-gm" | 
+| | condition_source_concept_id | ICD-code from condition_source_value <br> CONCEPT.concept_id WHERE CONCEPT.concept_code = condition_source_value |
+|code.coding.extension|condition_status_source_value| |
 
 ## Condition to MEASUREMENT
 | Source | Target | Comments |
 | :--------------- | :-------------------- | :---------------------------------------- |
-|                  | measurement_id        |this id is automatic generated in database |
-|subject.reference |  person_id            | the `person_id` from PERSON               |
+| | measurement_id |This id is generated for each condition resource automatically. |
+| subject.reference or <br> subject.identifier.value | person_id | The patient reference is used to search for the person_id in FHIR_ID_TO_OMOP_ID_MAP. |
 | code.coding.code |measurement_concept_id| _Analogous to CONDITION_OCCURRENCE_           |
 |recordedDate <br> onsetPeriod.start <br> onsetDateTimeType |measurement_date <br> measurement_datetime|_Analogous to CONDITION_OCCURRENCE_|
 | | :x: measurement_time | |
@@ -36,8 +36,8 @@
 | | :x: unit_concept_id | |
 | | :x: range_low | |
 | | :x: range_high | |
-|Encounter.reference |visit_occurrence_id|the `visit_occurrence_id` from VISIT_OCCURRENCE|
-| |visit_detail_id|the `visit_detail_id` from VISIT_DETAIL|
+| encounter.reference or <br> encounter.identifier.value | visit_occurrence_id | The encounter reference is used to search for the visit_occurrence_id in FHIR_ID_TO_OMOP_ID_MAP. |
+| |visit_detail_id| See post processing for visit_detail_id |
 | code.coding.code |measurement_source_value| _Analogous to CONDITION_OCCURRENCE_           |
 | code.coding.code |measurement_source_concept_id| _Analogous to CONDITION_OCCURRENCE_           |
 | | :x: unit_source_value | |
@@ -46,16 +46,16 @@
 ## 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               |
+| | procedure_occurrence_id|This id is generated for each condition resource automatically. |
+| subject.reference or <br> subject.identifier.value | person_id | The patient reference is used to search for the person_id in FHIR_ID_TO_OMOP_ID_MAP. |
 | code.coding.code |procedure_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_|
 | | :x: modifier_concept_id | |
 | | :x: quantity | |
 | | :x: provider_id | |
-|Encounter.reference |visit_occurrence_id|the `visit_occurrence_id` from VISIT_OCCURRENCE|
-| |visit_detail_id|the `visit_detail_id` from VISIT_DETAIL|
+| encounter.reference or <br> encounter.identifier.value | visit_occurrence_id | The encounter reference is used to search for the visit_occurrence_id in FHIR_ID_TO_OMOP_ID_MAP. |
+| |visit_detail_id| See post processing for visit_detail_id |
 | code.coding.code |procedure_source_value| _Analogous to CONDITION_OCCURRENCE_           |
 | code.coding.code |procedure_source_concept_id| _Analogous to CONDITION_OCCURRENCE_           |
 | | :x: modifier_source_value | |
@@ -63,8 +63,8 @@
 ## Condition to OBSERVATION
 | Source | Target | Comments |
 | :--------------- | :-------------------- | :---------------------------------------- |
-|                  | observation_id        |this id is automatic generated in database |
-|subject.reference |  person_id            | the `person_id` from PERSON               |
+| | observation_id |This id is generated for each condition resource automatically. |
+| subject.reference or <br> subject.identifier.value | person_id | The patient reference is used to search for the person_id in FHIR_ID_TO_OMOP_ID_MAP. |
 | code.coding.code |observation_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_|
@@ -73,8 +73,8 @@
 | | :x: qualifier_concept_id | |
 | | :x: unit_concept_id | |
 | | :x: provider_id | |
-|Encounter.reference |visit_occurrence_id|the `visit_occurrence_id` from VISIT_OCCURRENCE|
-| |visit_detail_id|the `visit_detail_id` from VISIT_DETAIL|
+| encounter.reference or <br> encounter.identifier.value | visit_occurrence_id | The encounter reference is used to search for the visit_occurrence_id in FHIR_ID_TO_OMOP_ID_MAP. |
+| |visit_detail_id| See post processing for visit_detail_id |
 | code.coding.code |observation_source_value| _Analogous to CONDITION_OCCURRENCE_           |
 | code.coding.code |observation_source_concept_id| _Analogous to CONDITION_OCCURRENCE_           |
 | | :x: unit_source_value | |
@@ -83,7 +83,7 @@
 ## Condition to DATA_PERSISTANT_MAP
 | Source| Target | Comments |
 | ------ | ------ | ------ |
-|  | data_id | This id is generated for each encounter resource automatically. |
+|  | data_id | This id is generated for each condition resource automatically. |
 |  | type | default value: "ENCOUNTER" |
 |  | data_one | It represents the visit_start_date of the visit_occurrence. |
 |  | data_two | It represents the visit_end_date of the visit_occurrence. |