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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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...@@ -16,14 +16,14 @@ ...@@ -16,14 +16,14 @@
| 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. |
| | | :x: condition_status_concept_id | | | |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.|
| | | :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. |
| | | :x: visit_detail_id| | | | | | :x: visit_detail_id| | |
| 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 |
| | | :x: condition_status_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"|
| id | | fhir_logical_id | | | | id | | fhir_logical_id | | |
| identifier.value| | fhir_identifier | | | | identifier.value| | fhir_identifier | | |
...@@ -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 | | |
| | | :x: value_as_concept_id | | | | 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. |
| | | :x: unit_concept_id | | | | | | :x: unit_concept_id | | |
| | | :x: range_low | | | | | | :x: range_low | | |
| | | :x: range_high | | | | | | :x: range_high | | |
...@@ -48,7 +48,7 @@ ...@@ -48,7 +48,7 @@
| code.coding.code | :heavy_check_mark: |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 | | | | 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 | | |
| identifier.value| | fhir_identifier | | | | identifier.value| | fhir_identifier | | |
...@@ -61,14 +61,14 @@ ...@@ -61,14 +61,14 @@
|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. |
| | | :x: modifier_concept_id | | | | 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. |
| | | :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. |
| | | :x: visit_detail_id| | | | | | :x: visit_detail_id| | |
| 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 |
| | | :x: modifier_source_value | | | | 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 | | |
| identifier.value| | fhir_identifier | | | | identifier.value| | fhir_identifier | | |
...@@ -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 | | |
| | | :x: qualifier_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. |
| | | :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. |
...@@ -94,7 +94,7 @@ ...@@ -94,7 +94,7 @@
| code.coding.code | :heavy_check_mark: |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 | | | | 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 | | |
| identifier.value| | fhir_identifier | | | | identifier.value| | fhir_identifier | | |
...@@ -122,30 +122,6 @@ ...@@ -122,30 +122,6 @@
| id | | fhir_logical_id | | | | id | | fhir_logical_id | | |
| identifier.value| | fhir_identifier | | | | identifier.value| | fhir_identifier | | |
### Information for diagnostic confidence
| FHIR | FHIR - required | OMOP | OMOP - required | Comments |
|:------: |:------: |:------: |:------: |:------: |
| | | 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 PERSON. |
| | |observation_concept_id| :heavy_check_mark: | See mapping in source_to_concept_map for Diagnostic Conf. |
|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| | |
| | |observation_type_concept_id| :heavy_check_mark: |default value: 38000280 (Observation recorded from EHR) |
| | | :x: value_as_number | | |
| code.coding.code.extension.valueCoding.code | | value_as_string | | Extension WHERE system = "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_DIAGNOSESICHERHEIT" |
| | | value_as_concept_id | | See mapping in source_to_concept_map for Diagnostic Conf. |
| | | :x: qualifier_concept_id | | |
| | | :x: unit_concept_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. |
| | | :x: visit_detail_id| | |
| code.coding.code.extension.valueCoding.code | |observation_source_value| | Extension WHERE system = "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_DIAGNOSESICHERHEIT" |
| | | observation_source_concept_id| | See mapping in source_to_concept_map for Diagnostic Conf. |
| | | :x: unit_source_value | | |
| | | :x: qualifier_source_value | | |
| id | | fhir_logical_id | | |
| identifier.value| | fhir_identifier | | |
## Condition to POST_PROCESS_MAP ## Condition to POST_PROCESS_MAP
### Information for primary and secondary ICD ### Information for primary and secondary ICD
...@@ -172,18 +148,6 @@ ...@@ -172,18 +148,6 @@
| id | | fhir_logical_id | | | | id | | fhir_logical_id | | |
| identifier.value| | fhir_identifier | | | | identifier.value| | fhir_identifier | | |
### Information for diagnostic confidence
| FHIR | FHIR - required | OMOP | OMOP - required | Comments |
| ------ | ------ | ------ | ------ | ------ |
| | | data_id | | This id is generated for each condition resource automatically. |
| | | type | | default value: "CONDITION" |
| code.coding.code.extension.valueCoding.code | | data_one | | diagnosticConfidence + ":Observation" |
| 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_table | | default value: "diagnostic_confidence" |
| id | | fhir_logical_id | | |
| identifier.value| | fhir_identifier | | |
## Example ## Example
### Input Condition Resource ### Input Condition Resource
...@@ -249,10 +213,10 @@ ...@@ -249,10 +213,10 @@
### Output OMOP tables ### Output OMOP tables
+ CONDITION_OCCURRENCE + CONDITION_OCCURRENCE
|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|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|id-1|id-1| |1|1|4295950|2018-02-15|2018-02-15 17:25:00|44786627|1|Z71|37097751|G|4230359|id-1|id-1|
|2|1|4238738|2018-02-15|2018-02-15 17:25:00|44786627|1|Z50.1|37097284|id-1|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|
+ OBSERVATION + OBSERVATION
...@@ -261,11 +225,6 @@ Information for ICD site localization ...@@ -261,11 +225,6 @@ Information for ICD site localization
|----|----|----|----|----|----|----|----|----|----|----| |----|----|----|----|----|----|----|----|----|----|----|
|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|38000280|B|1|B|id-1|id-1|
Information for diagnostic confidence
|observation_id|person_id|observation_concept_id|observation_date|observation_datetime|observation_type_concept_id|value_as_string|value_as_concept_id|visit_occurrence_id|observation_source_value|observation_source_concept_id|fhir_logical_id|fhir_identifier|
|----|----|----|----|----|----|----|----|----|----|----|----|----|
|1|1|4230359|2018-02-15|2018-02-15 17:25:00|38000280|G|4230359|1|G|4230359|id-1|id-1|
+ POST_PROCESS_MAP + POST_PROCESS_MAP
Information for primary and secondary ICD Information for primary and secondary ICD
...@@ -278,9 +237,3 @@ Information for ICD site localization ...@@ -278,9 +237,3 @@ Information for ICD site localization
|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:| |:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|
| 2 | CONDITION | B:Observation | Z71:Condition | 1 | site_localization |id-1|id-1| | 2 | CONDITION | B:Observation | Z71:Condition | 1 | site_localization |id-1|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 |id-1|id-1|
Information for diagnostic confidence
|data_id|type|data_one|data_two|omop_id|omop_table|fhir_logical_id|fhir_identifier|
|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|
| 4 | CONDITION | G:Observation | Z71:Condition | 1 | diagnostic_confidence |id-1|id-1|
| 5 | CONDITION | G:Observation | Z50.1:Condition | 1 | diagnostic_confidence |id-1|id-1|
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