Merge branch 'OHDSI:master' into master

docs/CPRD/CPRD_Additional_STEM.md

@@ -36,7 +36,7 @@ These concatenated source values will then be mapped to standard concepts using
 | concept_id |  | Map the source value (add_int.enttype + '-' + add_int.category + '-' + add_int.description + '-' + add_int.data) to a concept using the [SOURCE_TO_STANDARD_QUERY](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_STANDARD.sql) with the filters: <br><br>   WHERE source_vocabulary_id = 'JNJ_CPRD_ADD_ENTTYPE'  AND standard_concept = 'S'  AND target_invalid_reason is NULL  | |
 | source_value |  | Concatenate add_int.enttype + '-' + add_int.category + '-' + add_int.description + '-' + add_int.data. |  This will retain the information from the entity table about the record and the specific data field being mapped. Please refer to [appendix 2](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/CPRD/Appendix_2_Additional_Table_Descriptions.xlsx) which is a table showing the enttypes and data_field descriptions from the additional table and counts of each. |
 | source_concept_id |  | 0 | |
-| type_concept_id |  | Use **32851** - Health professional filled survey |  
+| type_concept_id |  | Use **32817** - EHR |  
 | unit_concept_id |  | Look up add_int.unit_source_value in the CONCEPT table where vocabulary_id = 'UCUM' and standard_concept = 'S' and invalid_reason is NULL. |  |
 | unit_source_value | add_int.unit_source_value |  | |
 | start_date | add_int.eventdate |  | For the additional table, the adid is used to link back to the clinical table to get the eventdate. |

docs/CPRD/CPRD_Clinical_STEM.md

@@ -38,4 +38,4 @@ Any record with one of the SARS-COV-2 read codes listed below should be mapped t
 | concept_id | medcode | Use the medcode to link to the medical table to find the read code. Use the [SOURCE_TO_STANDARD](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_STANDARD.sql) query to map the read code to standard concept(s) with the following filters: <br> <br>  Where source_vocabulary_id = 'Read'  and Target_standard_concept = 'S'  and target_invalid_reason is NULL<br><br>*BE CAREFUL - READ CODES ARE CASE SENSITIVE*. If there is no mapping available, set concept_id to zero. | See the query [CPRD_Clinical_Medcodes.sql](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/CPRD/Queries/CPRD_Clinical_Medcodes.sql) as a high-level look at the domains covered by this table and how the link to the medical table should be made. |
 | source_value | medical.read_code | Use the medcode to link to the medical table to find the read code. Store read code as source_value. | |
 | source_concept_id | medcode | Use the medcode to link to the medical table to find the read code.     Use the [SOURCE_TO_SOURCE](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_SOURCE.sql) query to map the read code to a source concept id with the following filters:<br><br> Where source_vocabulary_id = 'Read' <br><br>*BE CAREFUL - READ CODES ARE CASE SENSITIVE*. If there is no mapping available set source_concept_id to zero. | |
-| type_concept_id |  | Use **32827** - EHR encounter record |  |
+| type_concept_id |  | Use **32817** - EHR |  |

docs/CPRD/CPRD_Death.md

@@ -34,7 +34,7 @@ Per CPRD cause-specific mortality is not reliably recorded in the General Practi
 PERSON_ID|Patient.Patid||
 DEATH_DATE|Patient.Deathdate|
 DEATH_DATETIME|Set time to 00:00:00 UTC Tz||
-DEATH_TYPE_CONCEPT_ID|32815 (Death Certificate)
+DEATH_TYPE_CONCEPT_ID|32817 (EHR)
 CAUSE_OF_DEATH_CONCEPT_ID|0||
 CAUSE_OF_DEATH_SOURCE_VALUE|0||
-CAUSE_SOURCE_CONCEPT_ID|0||
+CAUSE_SOURCE_CONCEPT_ID|0||

docs/CPRD/CPRD_Immunisation_STEM.md

@@ -29,4 +29,4 @@ In the below table, only the relevant STEM fields are shown. Any fields that do
 | concept_id | medcode | Use the medcode to link to the medical table to find the read code. Use the [SOURCE_TO_STANDARD](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_STANDARD.sql) query to map the read code to standard concept(s) with the following filters: <br> <br>  Where source_vocabulary_id = 'Read'  and Target_standard_concept = 'S'  and target_invalid_reason is NULL<br><br>*BE CAREFUL - READ CODES ARE CASE SENSITIVE*. If there is no mapping available, set concept_id to zero.  | See the query [CPRD_Immunisation_Medcodes.sql](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/CPRD/Queries/CPRD_Immunisation_Medcodes.sql) as a high-level look at the domains covered by this table and how the link to the medical table should be made. |
 | source_value | medical.read_code | Use the medcode to link to the medical table to find the read code. Store read code as source_value. |  |
 | source_concept_id | medcode | Use the medcode to link to the medical table to find the read code.     Use the [SOURCE_TO_SOURCE](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_SOURCE.sql) query to map the read code to a source concept id with the following filters:<br><br> Where source_vocabulary_id = 'Read' <br><br>*BE CAREFUL - READ CODES ARE CASE SENSITIVE*. If there is no mapping available set source_concept_id to zero. | |
-| type_concept_id |  | Use **32827** - EHR encounter record |  |
+| type_concept_id |  | Use **32818** - EHR administration |  |

docs/CPRD/CPRD_Person.md

@@ -26,15 +26,19 @@ The patients in the CDM are restricted to the subset of all CPRD patients deemed
 | month_of_birth | mob |  | Mob is only populated for children, if 0 set as NULL |
 | day_of_birth |  |  |  |
 | birth_datetime |  |  |  |
-| race_concept_id |  | 0 |  |
-| ethnicity_concept_id |  | 0 |  It could be possible to write an algorithm in the future using the Read codes that are available for a patient. |
+| race_concept_id |  | STEM.concept_id | populate if STEM.concept_id has domain 'Race'  |
+| ethnicity_concept_id |  | 0 |   |
 | location_id |  |  |  |
 | provider_id |  |  |  |
 | care_site_id | patid | Last 3 digits of patient.patid is the practice identifier and can be used in the CARE_SITE table to lookup the care_site_id. |  |
 | person_source_value | patid |  |  |
 | gender_source_value | gender |  | 'M' if gender = 1, 'F' if gender = 2 |
 | gender_source_concept_id |  | 0 |  |
-| race_source_value |  |  |  |
-| race_source_concept_id |  | 0 |  |
-| ethnicity_source_value |  |  |  |
-| ethnicity_source_concept_id |  | 0 |  |
+| race_source_value |  | STEM.source_value | populate if STEM.concept_id has domain 'Race'  |
+| race_source_concept_id |  | STEM.source_concept_id | populate if STEM.concept_id has domain 'Race' |
+| ethnicity_source_value |  |  |  | 
+
+## Change log
+
+### 08-Aug-2023
+- added rule: populate Race from the STEM table

docs/CPRD/CPRD_Referral_STEM.md

@@ -38,5 +38,5 @@ Any record with one of the SARS-COV-2 read codes listed below should be mapped t
 | concept_id | medcode | Use the medcode to link to the medical table to find the read code. Use the [SOURCE_TO_STANDARD](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_STANDARD.sql) query to map the read code to standard concept(s) with the following filters: <br> <br>  Where source_vocabulary_id = 'Read'  and Target_standard_concept = 'S'  and target_invalid_reason is NULL<br><br>*BE CAREFUL - READ CODES ARE CASE SENSITIVE*. If there is no mapping available, set concept_id to zero. | See [CPRD_Referral_Medcodes.sql](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/CPRD/Queries/CPRD_Referral_Medcodes.sql) for an idea of how the codes in the referral table map to the vocabulary and how the link between the referral table and medical table should be made.  |
 | source_value | medical.read_code | Use the medcode to link to the medical table to find the read code. Store read code as source_value. |  |  |
 | source_concept_id | medcode | Use the medcode to link to the medical table to find the read code.     Use the [SOURCE_TO_SOURCE](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_SOURCE.sql) query to map the read code to a source concept id with the following filters:<br><br> Where source_vocabulary_id = 'Read' <br><br>*BE CAREFUL - READ CODES ARE CASE SENSITIVE*. If there is no mapping available set source_concept_id to zero. | |
-| type_concept_id |  | Use **32842** - EHR referral record |  |
+| type_concept_id |  | Use **32817** - EHR |  |
 

docs/CPRD/CPRD_Visit_Detail.md

@@ -29,7 +29,7 @@ For datetime fields, set time to midnight 00:00:00.
 | visit_detail_start_datetime | eventdate | Use the same logic used to set visit_detail_start_date. Set time to 00:00:00 |  |
 | visit_detail_end_date |  | Set as visit_detail_start_date  | |
 | visit_detail_end_datetime |  | Set as visit_detail_start_datetime |  |
-| visit_detail_type_concept_id |  | Use **32827** - EHR encounter record |  |
+| visit_detail_type_concept_id |  | Use **32817** - EHR |  |
 | provider_id | staffid |  |  |
 | care_site_id | patid | Use the last three digits of the patid (removing leading zeros) to look up the care_site_id in the care_site table. |  |
 | visit_detail_source_value | constype | Use the consid to link back to the consultation table. Use the constype from the consultation table as the visit_detail_source_value. If there are two based on how the visit detail was defined, choose one. |  |

docs/CPRD/CPRD_Visit_Occurrence.md

@@ -25,7 +25,7 @@ For datetime fields, set time to midnight 00:00:00.
 | visit_start_datetime | visit_detail_start_datetime | |  |
 | visit_end_date | visit_detail_end_date | | |
 | visit_end_datetime | visit_detail_end_datetime ||  |
-| visit_type_concept_id |  | Use **32827** - EHR encounter record |  |
+| visit_type_concept_id |  | Use **32817** - EHR |  |
 | provider_id | visit_detail.provider_id | Choose one provider_id if a patient saw more than one provider on the same day. |  |
 | care_site_id | visit_detail.care_site_id| |  |
 | visit_source_value | visit_detail_source_value | Choose one visit_detail_source_value for this field if a patient had more than one visit_detail_source_value on the same day. |  |

docs/CPRD_Aurum/CPRD_Aurum_Observation_STEM.md

@@ -33,7 +33,7 @@ In the below table, only the relevant STEM fields are shown.
 | type_concept_id |  | Set all from observation as **32840** - observation recorded from EHR |  |
 | range_high | numrangehigh | |
 | range_low | numrangelow | |
-| unit_concept_id | numunitid | Lookup up the unitid in the lookup tables and use the [SOURCE_TO_STANDARD](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_STANDARD.sql) query to map either the numunitid to standard concept(s) with the following filters: <br> <br>  Where source_vocabulary_id in ('UCUM', 'CPRD_Units')  and target_standard_concept = 'S'  and target_invalid_reason is NULL |
+| unit_concept_id | numunitid | Lookup up the unitid in the lookup tables and use the [SOURCE_TO_STANDARD](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_STANDARD.sql) query to map either the numunitid to standard concept(s) with the following filters: <br> <br>  Where source_vocabulary_id in ('UCUM', 'CPRD_Units')  and target_standard_concept = 'S'  and target_invalid_reason is NULL<br>When numinitid is NULL, set unit_concept_id = NULL |
 | unit_source_value | numunitid | Lookup the unitid in the lookup tables and put the english version of the unit here |
 | value_as_number | value | |
 | value_source_value | value | |

docs/IBM_CCAE_MDCR/CCAE_MDCR_stem_inpatient_admissions.md

@@ -58,7 +58,7 @@ For every record in STEM there should be 1 row record in VISIT_DETAIL (n:1 join)
 | UNIQUE_DEVICE_ID | - | NULL | - |
 | UNIT_CONCEPT_ID | - | 0 | - |
 | UNIT_SOURCE_VALUE | - | NULL | - |
-| VALUE_AS_CONCEPT_ID | - | 0 | - |
+| VALUE_AS_CONCEPT_ID | PDX<br>DX1-15<br>PPROC<br>PROC1-15 | TARGET_VALUE_AS_CONCEPT_ID from the Source_to_Standard Query (resulting from  **'Maps to value'** relationsip);<br> See SOURCE_CONCEPT_ID field logic of how to define SOURCE_CONCEPT_ID being mapped| - |
 | VALUE_AS_NUMBER | - | NULL | - |
 | VALUE_AS_STRING | - | NULL | - |
 | VALUE_SOURCE_VALUE | - | NULL | - |
@@ -91,4 +91,7 @@ For every record in STEM there should be 1 row record in VISIT_DETAIL (n:1 join)
     * Remove any duplicate records 
     * Set VISIT_PROVID and VISIT_PROVSTD as PPROV and PROVCAT
   * As data is being assigned a CONCEPT_ID check the domain, this tells you what domain table the data should land.<br><br>If the CONCEPT = 0 the PDX, DX1-15 rows should land in **CONDITION_OCCURRENCE** and the PPROC, PROC1-15 should land in the **PROCEDURE_OCCURRENCE** table. 
-    * Instead any code without a mapping is assigned a CONCEPT_ID of zero and a DOMAIN_ID of OBSERVATION.
+    * Instead any code without a mapping is assigned a CONCEPT_ID of zero and a DOMAIN_ID of OBSERVATION.
+
+### Aug-01-2023
+ - Added 'Maps to value' logic

docs/IBM_CCAE_MDCR/CCAE_MDCR_stem_inpatient_services.md

@@ -63,7 +63,7 @@ Records will be written from the INPATIENT_SERVICES table mapping the field REVC
 | UNIQUE_DEVICE_ID | - | NULL | - |
 | UNIT_CONCEPT_ID | - | 0 | - |
 | UNIT_SOURCE_VALUE | - | NULL | - |
-| VALUE_AS_CONCEPT_ID | - | 0 | - |
+| VALUE_AS_CONCEPT_ID | PDX<br>DX1-5<br>PPROC<br>PROC1 | TARGET_VALUE_AS_CONCEPT_ID from the Source_to_Standard Query (resulting from  **'Maps to value'** relationsip);<br> See SOURCE_CONCEPT_ID field logic of how to define SOURCE_CONCEPT_ID being mapped| - |
 | VALUE_AS_NUMBER | - | NULL | - |
 | VALUE_AS_STRING | - | NULL | - |
 | VALUE_SOURCE_VALUE | - | NULL | - |
@@ -97,3 +97,6 @@ Records will be written from the INPATIENT_SERVICES table mapping the field REVC
 * Added CONDITION_STATUS_CONCEPT_ID information
 
 * Added information on how to map revenue codes
+
+ ### Aug-01-2023
+ - Added 'Maps to value' logic

docs/IBM_CCAE_MDCR/CCAE_MDCR_stem_lab.md

@@ -75,7 +75,7 @@ IF RESULT > -999999.99999 THEN DO;
 | LOT_NUMBER | - | NULL | - |
 | MODIFIER_CONCEPT_ID | - | NULL | - |
 | MODIFIER_SOURCE_VALUE | - | NULL | - |
-| OPERATOR_CONCEPT_ID | - | 0 | - |
+| OPERATOR_CONCEPT_ID | - | NULL | - |
 | QUANTITY | - | NULL | - |
 | RANGE_HIGH | REFHIGH | - | - |
 | RANGE_LOW | REFLOW | - | - |