Condition-Mapping.md

@@ -7,16 +7,16 @@
 
 :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|