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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 |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 | |
| recordedDate or <br> onsetPeriod.start or <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) |
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| | 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_|
|recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value |measurement_date <br> measurement_datetime|_Analogous to CONDITION_OCCURRENCE_|
| | :x: measurement_time | |
| |measurement_type_concept_id|_Analogous to CONDITION_OCCURRENCE_|
| | :x: operator_concept_id | |
......@@ -49,7 +49,7 @@
| | 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_|
|recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value |procedure_date <br> procedure_datetime|_Analogous to CONDITION_OCCURRENCE_|
| |procedure_type_concept_id|_Analogous to CONDITION_OCCURRENCE_|
| | :x: modifier_concept_id | |
| | :x: quantity | |
......@@ -66,7 +66,7 @@
| | 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_|
|recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value |observation_date <br> observation_datetime|_Analogous to CONDITION_OCCURRENCE_|
| |observation_type_concept_id|_Analogous to CONDITION_OCCURRENCE_|
| | :x: value_as_number | |
| | :x: value_as_string | |
......@@ -84,11 +84,11 @@
| Source| Target | Comments |
| ------ | ------ | ------ |
| | 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. |
| | type | default value: "CONDITION" |
| 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 |
| | omop_id | This id represents the person_id of the person table. |
| | omop_table | default value: "observation_period" |
| code.coding.code | omop_table | It represents the linkage between the primary and the secondary ICD code including indication of the respective domain. |
## Example
......@@ -145,4 +145,4 @@
|data_id|type|data_one|data_two|omop_id|omop_table|
|:----:|:----:|:----:|:----:|:----:|:----:|
| 1 | ENCOUNTER | 2018-02-13 | 2018-02-23 | 1 | observation_period |
\ No newline at end of file
| 1 | CONDITION | id-1 | v:1:2018-02-15 17:25:00 | 1 | Z71:Condition:Z50.1:Condition |
\ No newline at end of file