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Condition-Mapping.md
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# Condition Mapping # Condition Mapping
![fhir-to-omop-Condition.drawio](uploads/833c8e6c2f269d2d959dacb375ca353b/fhir-to-omop-Condition.drawio.png) ![fhir-to-omop-Condition.drawio](uploads/7113207ade657ef5482d6f837764de5c/fhir-to-omop-Condition.drawio.png)
:information_source: All ICD codes will also be mapped to a SNOMED Code. The mapping information is available in OMOP in the `cds_etl_helper.MATERIALIZED VIEW.icd_snomed_domain_lookup`, which is generated from ICD10GM vocabulary (CONCEPT) and CONCEPT_RELATIONSHIP tables. :information_source: All ICD codes will also be mapped to a SNOMED Code. The mapping information is available in OMOP in the `cds_etl_helper.MATERIALIZED VIEW.icd_snomed_domain_lookup`, which is generated from ICD10GM vocabulary (CONCEPT) and CONCEPT_RELATIONSHIP tables.
...@@ -16,7 +16,7 @@ ...@@ -16,7 +16,7 @@
| 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: | default value: 44803913 (Diagnosis) or <br> See post processing for diagnosis rank. | | | | condition_type_concept_id| :heavy_check_mark: | default value: 44803913 (Diagnosis) or <br> See post processing for diagnosis rank. |
|code.coding.code.extension.valueCoding.code | | condition_status_concept_id | | Extension WHERE system = "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_DIAGNOSESICHERHEIT" <br> See mapping in source_to_concept_map for Diagnostic Conf.| |code.coding.code.extension.valueCoding.code | | condition_status_concept_id | | Extension WHERE system = "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_DIAGNOSESICHERHEIT" <br> Detailed mapping is in SOURCE_TO_CONCEPT_MAP, where source_vocabulary_id is __Diagnostic Conf.__ |
| | | :x: stop_reason | | | | | | :x: stop_reason | | |
| | | :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 VISIT_OCCURRENCE. | | encounter.reference or <br> encounter.identifier.value | | visit_occurrence_id | | The encounter reference is used to search for the visit_occurrence_id in VISIT_OCCURRENCE. |
...@@ -24,8 +24,8 @@ ...@@ -24,8 +24,8 @@
| code.coding.code | :heavy_check_mark: | 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.code.extension.valueCoding.code | | condition_status_source_value| | Extension WHERE system = "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_DIAGNOSESICHERHEIT"| |code.coding.code.extension.valueCoding.code | | condition_status_source_value| | Extension WHERE system = "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_DIAGNOSESICHERHEIT"|
| id | | fhir_logical_id | | | | id | | fhir_logical_id | | prefix "con-"|
| identifier.value| | fhir_identifier | | | | identifier.value| | fhir_identifier | | prefix "con-"|
## Condition to MEASUREMENT ## Condition to MEASUREMENT
| FHIR | FHIR - required | OMOP | OMOP - required | Comments | | FHIR | FHIR - required | OMOP | OMOP - required | Comments |
...@@ -39,7 +39,7 @@ ...@@ -39,7 +39,7 @@
| | |measurement_type_concept_id| :heavy_check_mark: | default value: 44803913 (Diagnosis) or <br> See post processing for diagnosis rank. | | | |measurement_type_concept_id| :heavy_check_mark: | default value: 44803913 (Diagnosis) or <br> See post processing for diagnosis rank. |
| | | :x: operator_concept_id | | | | | | :x: operator_concept_id | | |
| | | :x: value_as_number | | | | | | :x: value_as_number | | |
| code.coding.code.extension.valueCoding.code | | value_as_concept_id | | Extension WHERE system = "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_DIAGNOSESICHERHEIT" <br> See mapping in source_to_concept_map for Diagnostic Conf. | | code.coding.code.extension.valueCoding.code | | value_as_concept_id | | Extension WHERE system = "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_DIAGNOSESICHERHEIT" <br> Detailed mapping is in SOURCE_TO_CONCEPT_MAP, where source_vocabulary_id is __Diagnostic Conf.__ |
| | | :x: unit_concept_id | | | | | | :x: unit_concept_id | | |
| | | :x: range_low | | | | | | :x: range_low | | |
| | | :x: range_high | | | | | | :x: range_high | | |
...@@ -49,8 +49,8 @@ ...@@ -49,8 +49,8 @@
| | |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 | | |
| code.coding.code.extension.valueCoding.code | | value_source_value | | Extension WHERE system = "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_DIAGNOSESICHERHEIT" | | code.coding.code.extension.valueCoding.code | | value_source_value | | Extension WHERE system = "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_DIAGNOSESICHERHEIT" |
| id | | fhir_logical_id | | | | id | | fhir_logical_id | |prefix "con-"|
| identifier.value| | fhir_identifier | | | | identifier.value| | fhir_identifier | |prefix "con-" |
## Condition to PROCEDURE_OCCURRENCE ## Condition to PROCEDURE_OCCURRENCE
| FHIR |FHIR - required | OMOP | OMOP - required | Comments | | FHIR |FHIR - required | OMOP | OMOP - required | Comments |
...@@ -61,7 +61,7 @@ ...@@ -61,7 +61,7 @@
|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 | :heavy_check_mark: <br> <br> |procedure_date| :heavy_check_mark: | |
|recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | :heavy_check_mark: <br> <br> |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: |default value: 44803913 (Diagnosis) or <br> See post processing for diagnosis rank. | | | |procedure_type_concept_id| :heavy_check_mark: |default value: 44803913 (Diagnosis) or <br> See post processing for diagnosis rank. |
| code.coding.code.extension.valueCoding.code | | modifier_concept_id | | Extension WHERE system = "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_DIAGNOSESICHERHEIT" <br> See mapping in source_to_concept_map for Diagnostic Conf. | | code.coding.code.extension.valueCoding.code | | modifier_concept_id | | Extension WHERE system = "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_DIAGNOSESICHERHEIT" <br> Detailed mapping is in SOURCE_TO_CONCEPT_MAP, where source_vocabulary_id is __Diagnostic Conf.__ |
| | | :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 VISIT_OCCURRENCE. | | encounter.reference or <br> encounter.identifier.value | | visit_occurrence_id | | The encounter reference is used to search for the visit_occurrence_id in VISIT_OCCURRENCE. |
...@@ -69,8 +69,8 @@ ...@@ -69,8 +69,8 @@
| code.coding.code | :heavy_check_mark: |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 |
| code.coding.code.extension.valueCoding.code | | modifier_source_value | | Extension WHERE system = "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_DIAGNOSESICHERHEIT" | | code.coding.code.extension.valueCoding.code | | modifier_source_value | | Extension WHERE system = "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_DIAGNOSESICHERHEIT" |
| id | | fhir_logical_id | | | | id | | fhir_logical_id | | prefix "con-"|
| identifier.value| | fhir_identifier | | | | identifier.value| | fhir_identifier | | prefix "con-"|
## Condition to OBSERVATION ## Condition to OBSERVATION
...@@ -86,7 +86,7 @@ ...@@ -86,7 +86,7 @@
| | | :x: value_as_number | | | | | | :x: value_as_number | | |
| | | :x: value_as_string | | | | | | :x: value_as_string | | |
| | | :x: value_as_concept_id | | | | | | :x: value_as_concept_id | | |
| code.coding.code.extension.valueCoding.code | | qualifier_concept_id | | Extension WHERE system = "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_DIAGNOSESICHERHEIT" <br> See mapping in source_to_concept_map for Diagnostic Conf. | | code.coding.code.extension.valueCoding.code | | qualifier_concept_id | | Extension WHERE system = "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_DIAGNOSESICHERHEIT" <br> Detailed mapping is in SOURCE_TO_CONCEPT_MAP, where source_vocabulary_id is __Diagnostic Conf.__ |
| | | :x: unit_concept_id | | | | | | :x: unit_concept_id | | |
| | | :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 VISIT_OCCURRENCE. | | encounter.reference or <br> encounter.identifier.value | | visit_occurrence_id | | The encounter reference is used to search for the visit_occurrence_id in VISIT_OCCURRENCE. |
...@@ -95,8 +95,8 @@ ...@@ -95,8 +95,8 @@
| | |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 | | |
| code.coding.code.extension.valueCoding.code | | qualifier_source_value | | Extension WHERE system = "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_DIAGNOSESICHERHEIT" | | code.coding.code.extension.valueCoding.code | | qualifier_source_value | | Extension WHERE system = "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_DIAGNOSESICHERHEIT" |
| id | | fhir_logical_id | | | | id | | fhir_logical_id | |prefix "con-" |
| identifier.value| | fhir_identifier | | | | identifier.value| | fhir_identifier | | prefix "con-"|
### Information for ICD site localization ### Information for ICD site localization
| FHIR | FHIR - required | OMOP | OMOP - required | Comments | | FHIR | FHIR - required | OMOP | OMOP - required | Comments |
...@@ -106,7 +106,7 @@ ...@@ -106,7 +106,7 @@
| | |observation_concept_id| :heavy_check_mark: | SNOMED concept associated with the value from observation_source_value <br> See mapping in source_to_concept_map. | | | |observation_concept_id| :heavy_check_mark: | SNOMED concept associated with the value from observation_source_value <br> See mapping in source_to_concept_map. |
|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 | :heavy_check_mark: <br> <br> |observation_date|:heavy_check_mark: | |
|recordedDate or <br> onsetPeriod.start or <br> onsetDateTime.value | :heavy_check_mark: <br> <br> |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: |default value: 38000280 (Observation recorded from EHR) | | | |observation_type_concept_id| :heavy_check_mark: |default value: 32817 (EHR) |
| | | :x: value_as_number | | | | | | :x: value_as_number | | |
| code.coding.code.extension.valueCoding.code | | value_as_string | | Extension WHERE system = "http://fhir.de/CodeSystem/kbv/s-icd-seitenlokalisation" | | code.coding.code.extension.valueCoding.code | | value_as_string | | Extension WHERE system = "http://fhir.de/CodeSystem/kbv/s-icd-seitenlokalisation" |
| | | :x: value_as_concept_id | | | | | | :x: value_as_concept_id | | |
...@@ -115,12 +115,12 @@ ...@@ -115,12 +115,12 @@
| | | :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 VISIT_OCCURRENCE. | | encounter.reference or <br> encounter.identifier.value | | visit_occurrence_id | | The encounter reference is used to search for the visit_occurrence_id in VISIT_OCCURRENCE. |
| | | :x: visit_detail_id| | | | | | :x: visit_detail_id| | |
| code.coding.code.extension.valueCoding.code | |observation_source_value| | Extension WHERE system = "http://fhir.de/CodeSystem/kbv/s-icd-seitenlokalisation" | | code.coding.code.extension.valueCoding.code | |observation_source_value| | Extension WHERE url = "http://fhir.de/StructureDefinition/seitenlokalisation" |
| | | :x: observation_source_concept_id| | | | | | :x: observation_source_concept_id| | |
| | | :x: unit_source_value | | | | | | :x: unit_source_value | | |
| | | :x: qualifier_source_value | | | | | | :x: qualifier_source_value | | |
| id | | fhir_logical_id | | | | id | | fhir_logical_id | | prefix "con-"|
| identifier.value| | fhir_identifier | | | | identifier.value| | fhir_identifier | | prefix "con-"|
## Condition to POST_PROCESS_MAP ## Condition to POST_PROCESS_MAP
...@@ -133,8 +133,8 @@ ...@@ -133,8 +133,8 @@
| code.coding.code | :heavy_check_mark: | data_two | | It represents the linkage between the secondary ICD code and its respective domain. | | code.coding.code | :heavy_check_mark: | data_two | | It represents the linkage between the secondary ICD code and its respective domain. |
| | | omop_id | | This id represents the person_id of the PERSON table. | | | | omop_id | | This id represents the person_id of the PERSON table. |
| | | omop_table | | default value: "primary_secondary_icd" | | | | omop_table | | default value: "primary_secondary_icd" |
| id | | fhir_logical_id | | | | id | | fhir_logical_id | | prefix "con-"|
| identifier.value| | fhir_identifier | | | | identifier.value| | fhir_identifier | |prefix "con-" |
### Information for ICD site localization ### Information for ICD site localization
| FHIR | FHIR - required | OMOP | OMOP - required | Comments | | FHIR | FHIR - required | OMOP | OMOP - required | Comments |
...@@ -145,8 +145,8 @@ ...@@ -145,8 +145,8 @@
| code.coding.code | :heavy_check_mark: | data_two | | It represents the linkage between the ICD code its respective domain. | | code.coding.code | :heavy_check_mark: | data_two | | It represents the linkage between the ICD code its respective domain. |
| | | omop_id | | This id represents the person_id of the PERSON table. | | | | omop_id | | This id represents the person_id of the PERSON table. |
| | | omop_table | | default value: "site_localization" | | | | omop_table | | default value: "site_localization" |
| id | | fhir_logical_id | | | | id | | fhir_logical_id | | prefix "con-"|
| identifier.value| | fhir_identifier | | | | identifier.value| | fhir_identifier | | prefix "con-"|
## Example ## Example
...@@ -215,25 +215,25 @@ ...@@ -215,25 +215,25 @@
|condition_occurrence_id|person_id|condition_concept_id|condition_start_date|condition_start_datetime|condition_type_concept_id|visit_occurrence_id|condition_source_value|condition_source_concept_id|condition_status_source_value|condition_status_concept_id|fhir_logical_id|fhir_identifier| |condition_occurrence_id|person_id|condition_concept_id|condition_start_date|condition_start_datetime|condition_type_concept_id|visit_occurrence_id|condition_source_value|condition_source_concept_id|condition_status_source_value|condition_status_concept_id|fhir_logical_id|fhir_identifier|
|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:| |:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|
|1|1|4295950|2018-02-15|2018-02-15 17:25:00|44786627|1|Z71|37097751|G|4230359|id-1|id-1| |1|1|4295950|2018-02-15|2018-02-15 17:25:00|44786627|1|Z71|37097751|G|4230359|con-id-1|con-id-1|
|2|1|4238738|2018-02-15|2018-02-15 17:25:00|44786627|1|Z50.1|37097284|G|4230359|id-1|id-1| |2|1|4238738|2018-02-15|2018-02-15 17:25:00|44786627|1|Z50.1|37097284|G|4230359|con-id-1|con-id-1|
+ OBSERVATION + OBSERVATION
Information for ICD site localization Information for ICD site localization
|observation_id|person_id|observation_concept_id|observation_date|observation_datetime|observation_type_concept_id|value_as_string|visit_occurrence_id|observation_source_value|fhir_logical_id|fhir_identifier| |observation_id|person_id|observation_concept_id|observation_date|observation_datetime|observation_type_concept_id|value_as_string|visit_occurrence_id|observation_source_value|fhir_logical_id|fhir_identifier|
|----|----|----|----|----|----|----|----|----|----|----| |----|----|----|----|----|----|----|----|----|----|----|
|1|1|4197258|2018-02-15|2018-02-15 17:25:00|38000280|B|1|B|id-1|id-1| |1|1|4197258|2018-02-15|2018-02-15 17:25:00|32817|B|1|B|con-id-1|con-id-1|
+ POST_PROCESS_MAP + POST_PROCESS_MAP
Information for primary and secondary ICD Information for primary and secondary ICD
|data_id|type|data_one|data_two|omop_id|omop_table|fhir_logical_id|fhir_identifier| |data_id|type|data_one|data_two|omop_id|omop_table|fhir_logical_id|fhir_identifier|
|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:| |:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|
| 1 | CONDITION | Z71:Condition | Z50.1:Condition | 1 | primary_secondary_icd |id-1|id-1| | 1 | CONDITION | Z71:Condition | Z50.1:Condition | 1 | primary_secondary_icd |con-id-1|con-id-1|
Information for ICD site localization Information for ICD site localization
|data_id|type|data_one|data_two|omop_id|omop_table|fhir_logical_id|fhir_identifier| |data_id|type|data_one|data_two|omop_id|omop_table|fhir_logical_id|fhir_identifier|
|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:| |:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|
| 2 | CONDITION | B:Observation | Z71:Condition | 1 | site_localization |id-1|id-1| | 2 | CONDITION | B:Observation | Z71:Condition | 1 | site_localization |con-id-1|con-id-1|
| 3 | CONDITION | B:Observation | Z50.1:Condition | 1 | site_localization |id-1|id-1| | 3 | CONDITION | B:Observation | Z50.1:Condition | 1 | site_localization |con-id-1|con-id-1|