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Updated Condition Mapping authored by Henke, Elisa's avatar Henke, Elisa
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Condition-Mapping.md
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:information_source: All Orpha codes will be mapped to a SNOMED Code. The mapping information is available in OMOP in the `cds_etl_helper.TABLE.orpha_snomed_mapping`.
:information_source: All ICD10GM codes will 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 ICD10GM codes will be mapped to a Standard Concept. The mapping information is available in OMOP in the `cds_etl_helper.MATERIALIZED VIEW.icd10gm_standard_lookup`, which is generated from ICD10GM vocabulary (CONCEPT) and CONCEPT_RELATIONSHIP tables.
:information_source: This mapper will check the right domain for the SNOMED code and then maps it to the right table in OMOP CDM.
:information_source: This mapper will check the right domain for the Standard Concept and then maps it to the right table in OMOP CDM.
## Condition to CONDITION_OCCURRENCE
| FHIR | FHIR - required | OMOP | OMOP - required | Comments |
| :------: | :------: | :------: |:------: |:------: |
| | | 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 PERSON. |
| | | condition_concept_id | :heavy_check_mark: | standard concept (SNOMED) associated with the source code from condition_source_value |
| | | condition_concept_id | :heavy_check_mark: | standard concept associated with the source code from condition_source_value |
| 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 | :heavy_check_mark: <br> <br> | condition_start_datetime | | |
| onsetPeriod.end | | condition_end_date | | |
......@@ -38,7 +38,7 @@
| :------: | :------: |:------: |:------: |:------: |
| | | 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 PERSON. |
| | |measurement_concept_id| :heavy_check_mark: | standard concept (SNOMED) associated with the source code from condition_source_value |
| | |measurement_concept_id| :heavy_check_mark: | standard concept associated with the source code from condition_source_value |
|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 | :heavy_check_mark: <br> <br> |measurement_datetime|| |
| | | :x: measurement_time | | |
......@@ -63,7 +63,7 @@
|:------: |:------: |:------: |:------: |:------: |
| | | 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 PERSON. |
| | |procedure_concept_id| :heavy_check_mark: | standard concept (SNOMED) associated with the source code from condition_source_value |
| | |procedure_concept_id| :heavy_check_mark: | standard concept associated with the source code from condition_source_value |
|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| | |
| | |procedure_type_concept_id| :heavy_check_mark: |default value: 32817 (EHR) |
......@@ -85,7 +85,7 @@
|:------: |:------: |:------: |:------: |:------: |
| | | 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: | standard concept (SNOMED) associated with the source code from condition_source_value |
| | |observation_concept_id| :heavy_check_mark: | standard concept associated with the source code from condition_source_value |
|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) |
......@@ -109,20 +109,20 @@
|:------: |:------: |:------: |:------: |:------: |
| | | 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 concept associated with the value from observation_source_value <br> See mapping in source_to_concept_map. |
| code.coding.code.extension.valueCoding.code | |observation_concept_id| :heavy_check_mark: | Extension WHERE system = "http://fhir.de/CodeSystem/kbv/s-icd-seitenlokalisation" <br> Detailed mapping is in SOURCE_TO_CONCEPT_MAP, where source_vocabulary_id is __Localization__ |
|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 | | |
| 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 | | |
| | | qualifier_concept_id | | default value: 4181514 (Finding site) |
| | | :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 url = "http://fhir.de/StructureDefinition/seitenlokalisation" |
| | | observation_source_concept_id| | SNOMED concept associated with the value from observation_source_value <br> See mapping in source_to_concept_map. |
| | | :x: observation_source_concept_id| | |
| | | :x: unit_source_value | | |
| | | :x: qualifier_source_value | | |
| id | | fhir_logical_id | | prefix "con-"|
......@@ -323,19 +323,23 @@
```
### Output OMOP tables
+ CONDITION_OCCURRENCE
+ PROCEDURE_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|condition_status_source_value|condition_status_concept_id|fhir_logical_id|fhir_identifier|
|procedure_occurrence_id|person_id|procedure_concept_id|procedure_date|procedure_datetime|procedure_type_concept_id|visit_occurrence_id|procedure_source_value|procedure_source_concept_id|modifier_source_value|modifier_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|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|con-id-1|con-id-1|
|1|1|4295950|2018-02-15|2018-02-15 17:25:00|32817|1|Z71|37097751|G|32893|con-id-1|con-id-1|
+ OBSERVATION
Information for ICD
|observation_id|person_id|observation_concept_id|observation_date|observation_datetime|observation_type_concept_id|visit_occurrence_id|observation_source_value|observation_source_concept_id|qualifier_source_value|qualifier_concept_id|fhir_logical_id|fhir_identifier|
|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|
|4|1|4238738|2018-02-15|2018-02-15 17:25:00|32817|1|Z50.1|37097284|G|32893|con-id-1|con-id-1|
Information for site localization
|observation_id|person_id|observation_concept_id|observation_date|observation_datetime|observation_type_concept_id|value_as_string|qualifier_concept_id|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|4181514|1|B|4197258|con-id-1|con-id-1|
|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|32817|B|1|B|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|qualifier_concept_id|visit_occurrence_id|observation_source_value|observation_source_concept_id|fhir_logical_id|fhir_identifier|
......