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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_occurrence_id | :heavy_check_mark:| 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 | :heavy_check_mark: | 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 | :heavy_check_mark: | 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 | :heavy_check_mark: | | | recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | :heavy_check_mark: <br> <br> | condition_start_date | :heavy_check_mark: | |
| recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | | condition_start_datetime | | | | recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | :heavy_check_mark: <br> <br> | condition_start_datetime | | |
| onsetPeriod.end | | condition_end_date | | | | onsetPeriod.end | | condition_end_date | | |
| onsetPeriod.end | | condition_end_datetime | | | | onsetPeriod.end | | condition_end_datetime | | |
| | | condition_type_concept_id| :heavy_check_mark: | See post processing for diagnosis rank. | | | | condition_type_concept_id| :heavy_check_mark: | See post processing for diagnosis rank. |
...@@ -21,7 +21,7 @@ ...@@ -21,7 +21,7 @@
| | | :x: provider_id | | | | | | :x: provider_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. | | 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 | | | |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" | | code.coding.code | :heavy_check_mark: | 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 | | | | 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| | | |code.coding.extension| |condition_status_source_value| | |
...@@ -31,8 +31,8 @@ ...@@ -31,8 +31,8 @@
| | | measurement_id | :heavy_check_mark: | 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 | :heavy_check_mark: | 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| :heavy_check_mark: | 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 |:heavy_check_mark:| | |recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | :heavy_check_mark: <br> <br> |measurement_date |:heavy_check_mark:| |
|recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | |measurement_datetime|| | |recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | :heavy_check_mark: <br> <br> |measurement_datetime|| |
| | | :x: measurement_time | | | | | | :x: measurement_time | | |
| | |measurement_type_concept_id| :heavy_check_mark: | See post processing for diagnosis rank. | | | |measurement_type_concept_id| :heavy_check_mark: | See post processing for diagnosis rank. |
| | | :x: operator_concept_id | | | | | | :x: operator_concept_id | | |
...@@ -43,7 +43,7 @@ ...@@ -43,7 +43,7 @@
| | | :x: range_high | | | | | | :x: range_high | | |
| 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. | | 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 | | | |visit_detail_id| | See post processing for visit_detail_id |
| code.coding.code | |measurement_source_value || ICD-code WHERE system = "http://fhir.de/CodeSystem/dimdi/icd-10-gm" | | code.coding.code | :heavy_check_mark: |measurement_source_value || ICD-code WHERE system = "http://fhir.de/CodeSystem/dimdi/icd-10-gm" |
| | |measurement_source_concept_id| | ICD-code from measurement_source_value <br> CONCEPT.concept_id WHERE CONCEPT.concept_code = measurement_source_value | | | |measurement_source_concept_id| | ICD-code from measurement_source_value <br> CONCEPT.concept_id WHERE CONCEPT.concept_code = measurement_source_value |
| | | :x: unit_source_value | | | | | | :x: unit_source_value | | |
| | | :x: value_source_value | | | | | | :x: value_source_value | | |
...@@ -54,15 +54,15 @@ ...@@ -54,15 +54,15 @@
| | | procedure_occurrence_id| :heavy_check_mark: |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 | :heavy_check_mark: | 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| :heavy_check_mark: | 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| :heavy_check_mark: | | |recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | :heavy_check_mark: <br> <br> |procedure_date| :heavy_check_mark: | |
|recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | |procedure_datetime| | | |recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | :heavy_check_mark: <br> <br> |procedure_datetime| | |
| | |procedure_type_concept_id| :heavy_check_mark: |See post processing for diagnosis rank. | | | |procedure_type_concept_id| :heavy_check_mark: |See post processing for diagnosis rank. |
| | | :x: modifier_concept_id | | | | | | :x: modifier_concept_id | | |
| | | :x: quantity | | | | | | :x: quantity | | |
| | | :x: provider_id | | | | | | :x: provider_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. | | 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 | | | |visit_detail_id| |See post processing for visit_detail_id |
| code.coding.code | |procedure_source_value| | ICD-code WHERE system = "http://fhir.de/CodeSystem/dimdi/icd-10-gm" | | code.coding.code | :heavy_check_mark: |procedure_source_value| | ICD-code WHERE system = "http://fhir.de/CodeSystem/dimdi/icd-10-gm" |
| | |procedure_source_concept_id| | ICD-code from procedure_source_value <br> CONCEPT.concept_id WHERE CONCEPT.concept_code = procedure_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 | | | | | | :x: modifier_source_value | | |
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| | | observation_id | :heavy_check_mark: |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 | :heavy_check_mark: | 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| :heavy_check_mark: | 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|:heavy_check_mark: | | |recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | :heavy_check_mark: <br> <br> |observation_date|:heavy_check_mark: | |
|recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | |observation_datetime| | | |recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | :heavy_check_mark: <br> <br> |observation_datetime| | |
| | |observation_type_concept_id| :heavy_check_mark: |See post processing for diagnosis rank. | | | |observation_type_concept_id| :heavy_check_mark: |See post processing for diagnosis rank. |
| | | :x: value_as_number | | | | | | :x: value_as_number | | |
| | | :x: value_as_string | | | | | | :x: value_as_string | | |
...@@ -83,20 +83,20 @@ ...@@ -83,20 +83,20 @@
| | | :x: provider_id | | | | | | :x: provider_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. | | 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 | | | |visit_detail_id| | See post processing for visit_detail_id |
| code.coding.code | |observation_source_value| | ICD-code WHERE system = "http://fhir.de/CodeSystem/dimdi/icd-10-gm" | | code.coding.code | :heavy_check_mark: |observation_source_value| | ICD-code WHERE system = "http://fhir.de/CodeSystem/dimdi/icd-10-gm" |
| | |observation_source_concept_id| | ICD-code from observation_source_value <br> CONCEPT.concept_id WHERE CONCEPT.concept_code = observation_source_value | | | |observation_source_concept_id| | ICD-code from observation_source_value <br> CONCEPT.concept_id WHERE CONCEPT.concept_code = observation_source_value |
| | | :x: unit_source_value | | | | | | :x: unit_source_value | | |
| | | :x: qualifier_source_value | | | | | | :x: qualifier_source_value | | |
## Condition to POST_PROCESS_MAP ## Condition to POST_PROCESS_MAP
| FHIR | OMOP | Comments | | FHIR | FHIR - required | OMOP | OMOP - required | 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" |
| id | data_one | | | id | | data_one | | |
| recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | data_two | "v" + the linkage between visit_occurrence_id and the *_start_datetime | | recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | :heavy_check_mark: <br> <br> | data_two | | "v" + the linkage between visit_occurrence_id and the *_start_datetime |
| | omop_id | This id represents the person_id of the person table. | | | | omop_id | | This id represents the person_id of the person table. |
| code.coding.code | omop_table | It represents the linkage between the primary and the secondary ICD code including indication of the respective domain. | | code.coding.code | :heavy_check_mark: | omop_table | | It represents the linkage between the primary and the secondary ICD code including indication of the respective domain. |
## Example ## Example
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