Condition-Mapping.md

 # Condition Mapping
 ![fhir-to-omop-Condition](uploads/3bc2c0d4b1d61d3533873daea4330c74/fhir-to-omop-Condition.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: Condition ressources can contain multiple codes from different terminologies such as Orpha, ICD10GM or SNOMED. If multiple mappings occurr in one Condition ressource, only one terminology is mapped to OMOP CDM. The mapping order is as follows: Orpha -> ICD10GM -> SNOMED.
+
+: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: This mapper will check the right domain for the SNOMED code and then maps it to the right table in OMOP CDM.
 
@@ -10,19 +14,19 @@
 | :------: | :------: | :------: |:------: |:------: |
 | | | 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: | SNOMED concept associated with the ICD code from condition_source_value without special characters |
+| | | condition_concept_id | :heavy_check_mark: | standard concept (SNOMED) 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 | | |
 | 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: 32817 (EHR) |
 |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: 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 | :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 |
+| code.coding.code | :heavy_check_mark: | condition_source_value | | Orpha/ICD10GM/SNOMED source code | 
+| | | condition_source_concept_id | | concept id of the source code from 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"|
 | id | | fhir_logical_id | | prefix "con-"|
 | identifier.value| | fhir_identifier | | prefix "con-"|
@@ -32,11 +36,11 @@
 | :------: | :------: |:------: |:------: |:------: |
 | | | 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: | SNOMED concept associated with the ICD code from measurement_source_value without special characters |
+| | |measurement_concept_id| :heavy_check_mark: | standard concept (SNOMED) 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 | | |
-| | |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: 32817 (EHR) |
 | | | :x: operator_concept_id | | |
 | | | :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> Detailed mapping is in SOURCE_TO_CONCEPT_MAP, where source_vocabulary_id is __Diagnostic Conf.__ |
@@ -45,8 +49,8 @@
 | | | :x: range_high | | |
 | 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 | :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 |
+| code.coding.code | :heavy_check_mark: |measurement_source_value || Orpha/ICD10GM/SNOMED source code |
+| | |measurement_source_concept_id| | concept id of the source code from condition_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" |
 | id | | fhir_logical_id | |prefix "con-"|
@@ -57,32 +61,32 @@
 |:------: |:------: |:------: |:------: |:------: |
 | | | 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: | SNOMED concept associated with the ICD code from procedure_source_value without special characters |
+| | |procedure_concept_id| :heavy_check_mark: | standard concept (SNOMED) 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: 44803913 (Diagnosis) or <br> See post processing for diagnosis rank. |
+| | |procedure_type_concept_id| :heavy_check_mark: |default value: 32817 (EHR) |
 | 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: 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 | :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 |
+| code.coding.code | :heavy_check_mark: |procedure_source_value| | Orpha/ICD10GM/SNOMED source code |
+| | |procedure_source_concept_id| | concept id of the source code from condition_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 | | prefix "con-"|
 | identifier.value| | fhir_identifier | | prefix "con-"|
 
 ## Condition to OBSERVATION
 
-### Information for ICD diagnosis
+### Information for diagnosis
 | 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 concept associated with the ICD code from observation_source_value without special characters |
+| | |observation_concept_id| :heavy_check_mark: | standard concept (SNOMED) 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: 44803913 (Diagnosis) or <br> See post processing for diagnosis rank. |
+| | |observation_type_concept_id| :heavy_check_mark: |default value: 32817 (EHR) |
 | | | :x: value_as_number | | |
 | | | :x: value_as_string | | |
 | | | :x: value_as_concept_id | | |
@@ -91,14 +95,14 @@
 | | | :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 | :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 |
+| code.coding.code | :heavy_check_mark: |observation_source_value| | Orpha/ICD10GM/SNOMED source code |
+| | |observation_source_concept_id| | concept id of the source code from condition_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" |
 | id | | fhir_logical_id | |prefix "con-" |
 | identifier.value| | fhir_identifier | | prefix "con-"|
 
-### Information for ICD site localization
+### Information for site localization
 | FHIR | FHIR - required | OMOP | OMOP - required | Comments |
 |:------: |:------: |:------: |:------: |:------: |
 | | | observation_id | :heavy_check_mark: |This id is generated for each condition resource automatically. |
@@ -184,7 +188,7 @@
 | id | | fhir_logical_id | | prefix "con-"|
 | identifier.value| | fhir_identifier | |prefix "con-" |
 
-### Information for ICD site localization
+### Information for site localization
 | FHIR | FHIR - required | OMOP | OMOP - required | Comments |
 | ------ | ------ | ------ | ------ | ------ |
 | | | data_id | | This id is generated for each condition resource automatically. |
@@ -326,7 +330,7 @@
 
 + OBSERVATION
 
-Information for ICD site localization
+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|
@@ -348,7 +352,7 @@ Information for primary and secondary ICD
 |:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|
 | 1 | CONDITION | Z71:Condition | Z50.1:Condition | 1 | primary_secondary_icd |con-id-1|con-id-1|
 
-Information for ICD site localization
+Information for site localization
 |data_id|type|data_one|data_two|omop_id|omop_table|fhir_logical_id|fhir_identifier|
 |:----:|:----:|:----:|:----:|:----:|:----:|:----:|:----:|
 | 2 | CONDITION | B:27 | 4197258 | 1 | site_localization |con-id-1|con-id-1|