Merge pull request #22 from OHDSI/null-vs-0-for-value_as_concept_id,-…

…operator_concept_id value_as_concept_id and operator_concept_id can be NULL
OHDSI · Sep 13, 2023 · 4123ce0 · 4123ce0
2 parents a740da0 + 97ab817
commit 4123ce0
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Showing 7 changed files with 9 additions and 9 deletions.
diff --git a/docs/CPRD_Aurum/CPRD_Aurum_Observation_STEM.md b/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 | |
diff --git a/docs/IBM_CCAE_MDCR/CCAE_MDCR_stem_lab.md b/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 | - | - |

diff --git a/docs/JMDC/JMDC_Measurement.md b/docs/JMDC/JMDC_Measurement.md
@@ -27,7 +27,7 @@ When an ICD10 code in the **diagnosis** table maps to a concept in the Measureme
 |     measurement_source_concept_id    |     standard_disease_code    |          |     Lookup icd10_level4_code in diagnosis_master table, and   use vocab to map to source concept.    |
 |     provider_id    |     medical_facility_id    |     Use dummy provider corresponding to the institute    |     Use dummy provider corresponding to the institute    |
 |     measurement_datetime    |          |          |          |
-|     operator_concept_id    |          |          |          |
+|     operator_concept_id    |          |    NULL      |          |
 |     value_as_number    |          |          |          |
 |     value_as_concept_id    |          |          |     Lookup icd10_level4_code in diagnosis_master table, and use 'Maps to value' vocabulary relationship to map to standard concept. If such relationship is absent set to NULL  |
 |     unit_concept_id    |          |         |        |

diff --git a/docs/JMDC/JMDC_Observation.md b/docs/JMDC/JMDC_Observation.md
@@ -57,7 +57,7 @@ The **annual_health_checkup** table is a wide table with one row per date and ma
 |     observation_datetime    |          |          |          |
 |     value_as_number    |   Put the numeric value of the column here.        |          |          |
 |     value_as_string    |          |          |          |
-|     value_as_concept_id    |        |    | See the mapping file [here](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/JMDC/Vocab%20Updates/Annual_Health_Checkup_Mapping.xlsx) for how to map the categorical values to concept ids.        |
+|     value_as_concept_id    |        | If the source categorical value is null, set  value_as_concept_id  to NULL  | See the mapping file [here](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/JMDC/Vocab%20Updates/Annual_Health_Checkup_Mapping.xlsx) for how to map the categorical values to concept ids.        |
 |     qualifier_concept_id    |          |          |          |
 |     unit_concept_id    |          |   See the mapping file [here](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/JMDC/Vocab%20Updates/Annual_Health_Checkup_Mapping.xlsx) for what the correct unit_concept_id should be.   |          |
 |     visit_detail_id    |          |          |          |

diff --git a/docs/OPTUM_PANTHER/Optum_Panther_Labs_STEM.md b/docs/OPTUM_PANTHER/Optum_Panther_Labs_STEM.md
@@ -34,7 +34,7 @@ description: "OPTUM EHR Labs table to STEM"
 | range_low | normal_range |Parse upper bound (split on hyphen), second piece | |
 | value_as_number | test_result | If value of test_result is numeric put in value_as_number| |
 | value_as_string | test_result | If value of test_result is NOT numeric put in value_as_string | |
-| value_as_concept_id | test_result |If value of test_result is NOT numeric use the [SOURCE_TO_STANDARD](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_STANDARD.sql) query to map the code to standard concept(s) with the following filters: <br> <br>  Where source_vocabulary_id = 'JNJ_OPTUM_EHR_LABRES'  and Target_standard_concept = 'S'  and target_invalid_reason is NULL<br><br>If there is no mapping available, set concept_id to zero. | |
+| value_as_concept_id | test_result |If value of test_result is NOT numeric use the [SOURCE_TO_STANDARD](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_STANDARD.sql) query to map the code to standard concept(s) with the following filters: <br> <br>  Where source_vocabulary_id = 'JNJ_OPTUM_EHR_LABRES'  and Target_standard_concept = 'S'  and target_invalid_reason is NULL<br><br>If there is no mapping available, set value_as_concept_id to zero. If test_result is NULL or numeric, set value_as_concept_id to NULL | |
 | value_source_value | test_result | | |
 | verbatim_end_date |   | | |
 | days_supply |  | | |

diff --git a/docs/OPTUM_PANTHER/Optum_Panther_NLP_Measurement_STEM.md b/docs/OPTUM_PANTHER/Optum_Panther_NLP_Measurement_STEM.md
@@ -36,7 +36,7 @@ description: "OPTUM EHR NLP_Measurement table to STEM"
 | range_low |  | | |
 | value_as_number | measurement_value | If value of measurement_value is numeric put in value_as_number| |
 | value_as_string | measurement_value | If value of measurement_value is NOT numeric put in value_as_string | |
-| value_as_concept_id | measurement_value |If value of obs_result is NOT numeric use the [SOURCE_TO_STANDARD](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_STANDARD.sql) query to map the code to standard concept(s) with the following filters: <br> <br>  Where source_vocabulary_id = 'JNJ_OPTUM_EHR_LABRES'  and Target_standard_concept = 'S'  and target_invalid_reason is NULL<br><br>If there is no mapping available, set concept_id to zero. | |
+| value_as_concept_id | measurement_value |If value of obs_result is NOT numeric use the [SOURCE_TO_STANDARD](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_STANDARD.sql) query to map the code to standard concept(s) with the following filters: <br> <br>  Where source_vocabulary_id = 'JNJ_OPTUM_EHR_LABRES'  and Target_standard_concept = 'S'  and target_invalid_reason is NULL<br><br>If there is no mapping available, set value_as_concept_id to zero.<br>If  value of obs_result is numeric OR null, set value_as_concept_id to null  | |
 | value_source_value | measurement_value | | |
 | verbatim_end_date |   | | |
 | days_supply |  | | |

diff --git a/docs/OPTUM_PANTHER/Optum_Panther_Observations_STEM.md b/docs/OPTUM_PANTHER/Optum_Panther_Observations_STEM.md
@@ -27,14 +27,14 @@ description: "OPTUM EHR Observations table to STEM"
 |source_value|obs_type|||
 | source_concept_id |0 || |
 | type_concept_id | 32831  | EHR Note| | 
-| operator_concept_id |0 | | |
-| unit_concept_id | obs_unit  | Map to UCUM vocabulary using a CASE-SENSITIVE matching; if no match if found, match to the JNJ_UNITS STCM. If no match is found in either vocabulary, set this field to 0.| |
+| operator_concept_id |NULL | | |
+| unit_concept_id | obs_unit  | Map to UCUM vocabulary using a CASE-SENSITIVE matching; if no match if found, match to the JNJ_UNITS STCM. If no match is found in either vocabulary, set this field to 0. If there'so source unit, set unit_concept_id to NULL| |
 | unit_source_value | obs_unit | | |
 | range_high | |  | | 
 | range_low |  | | |
 | value_as_number | obs_result | If value of obs_result is numeric put in value_as_number| |
 | value_as_string | obs_result | If value of obs_result is NOT numeric put in value_as_string | |
-| value_as_concept_id | obs_result |If value of obs_result is NOT numeric use the [SOURCE_TO_STANDARD](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_STANDARD.sql) query to map the code to standard concept(s) with the following filters: <br> <br>  Where source_vocabulary_id = 'JNJ_OPTUM_EHR_LABRES'  and Target_standard_concept = 'S'  and target_invalid_reason is NULL<br><br>If there is no mapping available, set concept_id to zero. | |
+| value_as_concept_id | obs_result |If value of obs_result is NOT numeric use the [SOURCE_TO_STANDARD](https://github.com/OHDSI/ETL-LambdaBuilder/blob/master/docs/Standard%20Queries/SOURCE_TO_STANDARD.sql) query to map the code to standard concept(s) with the following filters: <br> <br>  Where source_vocabulary_id = 'JNJ_OPTUM_EHR_LABRES'  and Target_standard_concept = 'S'  and target_invalid_reason is NULL<br><br>If there is no mapping available, set value_as_concept_id to zero. If value of obs_result is numeric OR NULL, set value_as_concept_id to NULL  | |
 | value_source_value | obs_type | | |
 | verbatim_end_date |   | | |
 | days_supply |  | | |