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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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:information_source: This mapper will check the right domain for the SNOMED code and then mapps it to the right table in OMOP CDM. :information_source: This mapper will check the right domain for the SNOMED code and then mapps it to the right table in OMOP CDM.
## Condition to CONDITION_OCCURRENCE ## Condition to CONDITION_OCCURRENCE
| Source | Target | Comments | | FHIR | FHIR - required | OMOP | OMOP - required | Comments |
| :---------------- | :---------------------- | :------------------------------------------------- | | :------: | :------: | :------: |:------: |:------: |
| | condition_occurrence_id |This id is generated for each condition resource automatically. | | | | condition_occurrence_id | :heavy_check_mark:| 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. | | subject.reference or <br> subject.identifier.value | | person_id | :heavy_check_mark: | 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 | | | | condition_concept_id | :heavy_check_mark: | SNOMED concept associated with the ICD code from condition_source_value without special characters |
| recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | condition_start_date <br> condition_start_datetime | | | recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | | condition_start_date | :heavy_check_mark: | |
| onsetPeriod.end | condition_end_date <br> condition_end_datetime | | | recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | | condition_start_datetime | | |
| | condition_type_concept_id| See post processing for diagnosis rank. | | onsetPeriod.end | | condition_end_date | | |
|code.coding.extension|condition_status_concept_id | See mapping in source_to_concept_map. | | onsetPeriod.end | | condition_end_datetime | | |
| | :x: stop_reason | | | | | condition_type_concept_id| :heavy_check_mark: | See post processing for diagnosis rank. |
| | :x: provider_id | | |code.coding.extension| | condition_status_concept_id | | See mapping in source_to_concept_map. |
| 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. | | | | :x: stop_reason | | |
| |visit_detail_id| See post processing for visit_detail_id | | | | :x: provider_id | | |
| code.coding.code | condition_source_value | ICD-code WHERE system = "http://fhir.de/CodeSystem/dimdi/icd-10-gm" | | 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. |
| | condition_source_concept_id | ICD-code from condition_source_value <br> CONCEPT.concept_id WHERE CONCEPT.concept_code = condition_source_value | | | |visit_detail_id| | See post processing for visit_detail_id |
|code.coding.extension|condition_status_source_value| | | 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 ## Condition to MEASUREMENT
| Source | Target | Comments | | FHIR | FHIR - required | OMOP | OMOP - required | Comments |
| :--------------- | :-------------------- | :---------------------------------------- | | :------: | :------: |:------: |:------: |:------: |
| | measurement_id |This id is generated for each condition resource automatically. | | | | measurement_id | :heavy_check_mark: | 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. | | subject.reference or <br> subject.identifier.value | | person_id | :heavy_check_mark: | The patient reference is used to search for the person_id in FHIR_ID_TO_OMOP_ID_MAP. |
| |measurement_concept_id| SNOMED concept associated with the ICD code from measurement_source_value without special characters | | | |measurement_concept_id| :heavy_check_mark: | SNOMED concept associated with the ICD code from measurement_source_value without special characters |
|recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value |measurement_date <br> measurement_datetime|| |recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | |measurement_date |:heavy_check_mark:| |
| | :x: measurement_time | | |recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | |measurement_datetime|| |
| |measurement_type_concept_id| See post processing for diagnosis rank. | | | | :x: measurement_time | | |
| | :x: operator_concept_id | | | | |measurement_type_concept_id| :heavy_check_mark: | See post processing for diagnosis rank. |
| | :x: value_as_number | | | | | :x: operator_concept_id | | |
| | :x: value_as_concept_id | | | | | :x: value_as_number | | |
| | :x: unit_concept_id | | | | | :x: value_as_concept_id | | |
| | :x: range_low | | | | | :x: unit_concept_id | | |
| | :x: range_high | | | | | :x: range_low | | |
| 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. | | | | :x: range_high | | |
| |visit_detail_id| See post processing for visit_detail_id | | 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. |
| code.coding.code |measurement_source_value| ICD-code WHERE system = "http://fhir.de/CodeSystem/dimdi/icd-10-gm" | | | |visit_detail_id| | See post processing for visit_detail_id |
| |measurement_source_concept_id| ICD-code from measurement_source_value <br> CONCEPT.concept_id WHERE CONCEPT.concept_code = measurement_source_value | | code.coding.code | |measurement_source_value || ICD-code WHERE system = "http://fhir.de/CodeSystem/dimdi/icd-10-gm" |
| | :x: unit_source_value | | | | |measurement_source_concept_id| | ICD-code from measurement_source_value <br> CONCEPT.concept_id WHERE CONCEPT.concept_code = measurement_source_value |
| | :x: value_source_value | | | | | :x: unit_source_value | | |
| | | :x: value_source_value | | |
## Condition to PROCEDURE_OCCURRENCE ## Condition to PROCEDURE_OCCURRENCE
| Source | Target | Comments | | FHIR |FHIR - required | OMOP | OMOP - required | Comments |
| :--------------- | :-------------------- | :---------------------------------------- | |:------: |:------: |:------: |:------: |:------: |
| | procedure_occurrence_id|This id is generated for each condition resource automatically. | | | | procedure_occurrence_id| :heavy_check_mark: |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. | | subject.reference or <br> subject.identifier.value | | person_id | :heavy_check_mark: | The patient reference is used to search for the person_id in FHIR_ID_TO_OMOP_ID_MAP. |
| |procedure_concept_id| SNOMED concept associated with the ICD code from procedure_source_value without special characters | | | |procedure_concept_id| :heavy_check_mark: | SNOMED concept associated with the ICD code from procedure_source_value without special characters |
|recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value |procedure_date <br> procedure_datetime| | |recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | |procedure_date| :heavy_check_mark: | |
| |procedure_type_concept_id| See post processing for diagnosis rank. | |recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | |procedure_datetime| | |
| | :x: modifier_concept_id | | | | |procedure_type_concept_id| :heavy_check_mark: |See post processing for diagnosis rank. |
| | :x: quantity | | | | | :x: modifier_concept_id | | |
| | :x: provider_id | | | | | :x: quantity | | |
| 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. | | | | :x: provider_id | | |
| |visit_detail_id| See post processing for visit_detail_id | | 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. |
| code.coding.code |procedure_source_value| ICD-code WHERE system = "http://fhir.de/CodeSystem/dimdi/icd-10-gm" | | | |visit_detail_id| |See post processing for visit_detail_id |
| |procedure_source_concept_id| ICD-code from procedure_source_value <br> CONCEPT.concept_id WHERE CONCEPT.concept_code = procedure_source_value | | code.coding.code | |procedure_source_value| | ICD-code WHERE system = "http://fhir.de/CodeSystem/dimdi/icd-10-gm" |
| | :x: modifier_source_value | | | | |procedure_source_concept_id| | ICD-code from procedure_source_value <br> CONCEPT.concept_id WHERE CONCEPT.concept_code = procedure_source_value |
| | | :x: modifier_source_value | | |
## Condition to OBSERVATION ## Condition to OBSERVATION
| Source | Target | Comments | | FHIR | FHIR - required | OMOP | OMOP - required | Comments |
| :--------------- | :-------------------- | :---------------------------------------- | |:------: |:------: |:------: |:------: |:------: |
| | observation_id |This id is generated for each condition resource automatically. | | | | observation_id | :heavy_check_mark: |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. | | subject.reference or <br> subject.identifier.value | | person_id | :heavy_check_mark: | The patient reference is used to search for the person_id in FHIR_ID_TO_OMOP_ID_MAP. |
| |observation_concept_id| SNOMED concept associated with the ICD code from observation_source_value without special characters | | | |observation_concept_id| :heavy_check_mark: | SNOMED concept associated with the ICD code from observation_source_value without special characters |
|recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value |observation_date <br> observation_datetime| | |recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | |observation_date|:heavy_check_mark: | |
| |observation_type_concept_id| See post processing for diagnosis rank. | |recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | |observation_datetime| | |
| | :x: value_as_number | | | | |observation_type_concept_id| :heavy_check_mark: |See post processing for diagnosis rank. |
| | :x: value_as_string | | | | | :x: value_as_number | | |
| | :x: value_as_concept_id | | | | | :x: value_as_string | | |
| | :x: qualifier_concept_id | | | | | :x: value_as_concept_id | | |
| | :x: unit_concept_id | | | | | :x: qualifier_concept_id | | |
| | :x: provider_id | | | | | :x: unit_concept_id | | |
| 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. | | | | :x: provider_id | | |
| |visit_detail_id| See post processing for visit_detail_id | | 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. |
| code.coding.code |observation_source_value| ICD-code WHERE system = "http://fhir.de/CodeSystem/dimdi/icd-10-gm" | | | |visit_detail_id| | See post processing for visit_detail_id |
| |observation_source_concept_id| ICD-code from observation_source_value <br> CONCEPT.concept_id WHERE CONCEPT.concept_code = observation_source_value | | code.coding.code | |observation_source_value| | ICD-code WHERE system = "http://fhir.de/CodeSystem/dimdi/icd-10-gm" |
| | :x: unit_source_value | | | | |observation_source_concept_id| | ICD-code from observation_source_value <br> CONCEPT.concept_id WHERE CONCEPT.concept_code = observation_source_value |
| | :x: qualifier_source_value | | | | | :x: unit_source_value | | |
| | | :x: qualifier_source_value | | |
## Condition to POST_PROCESS_MAP ## Condition to POST_PROCESS_MAP
| Source| Target | Comments | | FHIR | OMOP | Comments |
| ------ | ------ | ------ | | ------ | ------ | ------ |
| | data_id | This id is generated for each condition resource automatically. | | | data_id | This id is generated for each condition resource automatically. |
| | type | default value: "CONDITION" | | | type | default value: "CONDITION" |
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