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Update Condition Mapping authored by Henke, Elisa's avatar Henke, Elisa
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Condition-Mapping.md
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## 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 | |
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| | :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 | |
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## 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 | |
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## 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_|
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| | :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 | |
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## 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. |
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