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feat: added mapping of severity authored by Henke, Elisa's avatar Henke, Elisa
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Condition-Mapping.md
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...@@ -116,7 +116,31 @@ ...@@ -116,7 +116,31 @@
| 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 url = "http://fhir.de/StructureDefinition/seitenlokalisation" | | code.coding.code.extension.valueCoding.code | |observation_source_value| | Extension WHERE url = "http://fhir.de/StructureDefinition/seitenlokalisation" |
| | | :x: observation_source_concept_id| | | | | | observation_source_concept_id| | SNOMED concept associated with the value from observation_source_value <br> See mapping in source_to_concept_map. |
| | | :x: unit_source_value | | |
| | | :x: qualifier_source_value | | |
| id | | fhir_logical_id | | prefix "con-"|
| identifier.value| | fhir_identifier | | prefix "con-"|
### Information for severity
| 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: | SNOMED-code from observation_source_value <br> CONCEPT.concept_id WHERE CONCEPT.concept_code = observation_source_value AND CONCEPT.vocabulary_id = 'SNOMED' |
|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: 32817 (EHR) |
| | | :x: value_as_number | | |
| severity.coding.code | | value_as_string | | |
| | | :x: value_as_concept_id | | |
| | | :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| | |
| severity.coding.code | |observation_source_value| | |
| | | observation_source_concept_id| | SNOMED-code from observation_source_value <br> CONCEPT.concept_id WHERE CONCEPT.concept_code = observation_source_value AND CONCEPT.vocabulary_id = 'SNOMED'|
| | | :x: unit_source_value | | | | | | :x: unit_source_value | | |
| | | :x: qualifier_source_value | | | | | | :x: qualifier_source_value | | |
| id | | fhir_logical_id | | prefix "con-"| | id | | fhir_logical_id | | prefix "con-"|
...@@ -142,12 +166,24 @@ ...@@ -142,12 +166,24 @@
| | | 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" |
| code.coding.code.extension.valueCoding.code | | data_one | | siteLocalization + ":Observation" | | code.coding.code.extension.valueCoding.code | | data_one | | siteLocalization + ":Observation" |
| 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 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: "site_localization" | | | | omop_table | | default value: "site_localization" |
| id | | fhir_logical_id | | prefix "con-"| | id | | fhir_logical_id | | prefix "con-"|
| identifier.value| | fhir_identifier | | prefix "con-"| | identifier.value| | fhir_identifier | | prefix "con-"|
### Information for severity
| FHIR | FHIR - required | OMOP | OMOP - required | Comments |
| ------ | ------ | ------ | ------ | ------ |
| | | data_id | | This id is generated for each condition resource automatically. |
| | | type | | default value: "CONDITION" |
| severity.coding.code | | data_one | | severity + ":Observation" |
| code.coding.code | :heavy_check_mark: | data_two | | It represents the linkage between the diagnosis code and its respective domain. |
| | | omop_id | | This id represents the person_id of the PERSON table. |
| | | omop_table | | default value: "severity" |
| id | | fhir_logical_id | | prefix "con-"|
| identifier.value| | fhir_identifier | | prefix "con-"|
## Example ## Example
### Input Condition Resource ### Input Condition Resource
...@@ -190,6 +226,17 @@ ...@@ -190,6 +226,17 @@
} }
] ]
}, },
"severity":[
{
"coding":[
{
"code":"24484000",
"system":"http://snomed.info/sct",
"display":"Severe"
}
]
}
],
"meta":{ "meta":{
"source":"#p21" "source":"#p21"
}, },
...@@ -221,9 +268,14 @@ ...@@ -221,9 +268,14 @@
+ 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|observation_source_concept_id|fhir_logical_id|fhir_identifier|
|----|----|----|----|----|----|----|----|----|----|----| |----|----|----|----|----|----|----|----|----|----|----|
|1|1|4197258|2018-02-15|2018-02-15 17:25:00|32817|B|1|B|con-id-1|con-id-1| |1|1|4197258|2018-02-15|2018-02-15 17:25:00|32817|B|1|B|4197258|con-id-1|con-id-1|
Information for severity
|observation_id|person_id|observation_concept_id|observation_date|observation_datetime|observation_type_concept_id|value_as_string|visit_occurrence_id|observation_source_value|observation_source_concept_id|fhir_logical_id|fhir_identifier|
|----|----|----|----|----|----|----|----|----|----|----|
|2|1|4087703|2018-02-15|2018-02-15 17:25:00|32817|24484000|1|24484000|4197258|con-id-1|con-id-1|
+ POST_PROCESS_MAP + POST_PROCESS_MAP
...@@ -237,3 +289,9 @@ Information for ICD site localization ...@@ -237,3 +289,9 @@ Information for ICD site localization
|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:| |:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|
| 2 | CONDITION | B:Observation | Z71:Condition | 1 | site_localization |con-id-1|con-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 |con-id-1|con-id-1| | 3 | CONDITION | B:Observation | Z50.1:Condition | 1 | site_localization |con-id-1|con-id-1|
Information for severity
|data_id|type|data_one|data_two|omop_id|omop_table|fhir_logical_id|fhir_identifier|
|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|
| 4 | CONDITION | 24484000:Observation | Z71:Condition | 1 | severity |con-id-1|con-id-1|
| 5 | CONDITION | 24484000:Observation | Z50.1:Condition | 1 | severity |con-id-1|con-id-1|