How to remap source concepts and standard concepts when going from an old CDM to a new CDM with updated vocab:
Step 1: Start with original source_concept_id as it is given in the original CDM. Using the source-to-source query, identify the source_code and source_vocabulary_id.
Step 2: Use the source_code and source_vocabulary_id you found in step 1 and find the correct source_concept_id through the source-to-source query where the date of the event falls between the valid_start_date and valid_end_date of the concept.
Note most of the source concepts will likely stay the same but there are some drug codes that are reused and therefore will change source concepts.
Step 3: Map the new source_concept_id to a standard concept_id using the Source-to-Standard Query.
Reading from OBSERVATION
| Destination Field | Source field | Logic | Comment field |
|---|---|---|---|
| DOMAIN_ID | - | - | This should be the domain_id of the standard concept in the CONCEPT_ID field. If a code is mapped to CONCEPT_ID 0, put the domain_id as Observation |
| PERSON_ID | PERSON_ID | - | - |
| VISIT_OCCURRENCE_ID | VISIT_OCCURRENCE_ID | - | - |
| VISIT_DETAIL_ID | VISIT_DETAIL_ID | - | - |
| PROVIDER_ID | PROVIDER_ID | - | - |
| ID | OBSERVATION_ID | - | |
| CONCEPT_ID | OBSERVATION_SOURCE_CONCEPT_ID | Use the Source-to-Standard Query. Lookup the target concept that the source concept maps to. If there are multiple target concepts, create multiple records. | |
| SOURCE_VALUE | OBSERVATION_SOURCE_VALUE | - | - |
| SOURCE_CONCEPT_ID | OBSERVATION_SOURCE_CONCEPT_ID OBSERVATION_SOURCE_VALUE | Please see the logic above for assigning the proper source and standard concepts. | - |
| TYPE_CONCEPT_ID | OBSERVATION_TYPE_CONCEPT_ID | - | - |
| START_DATE | OBSERVATION_DATE | - | - |
| START_DATETIME | OBSERVATION_DATETIME | - | - |
| END_DATE | - | - | - |
| END_DATETIME | - | - | - |
| VERBATIM_END_DATE | - | - | - |
| DAYS_SUPPLY | - | - | - |
| DOSE_UNIT_SOURCE_VALUE | - | - | - |
| LOT_NUMBER | - | - | - |
| MODIFIER_CONCEPT_ID | - | - | - |
| MODIFIER_SOURCE_VALUE | - | - | - |
| OPERATOR_CONCEPT_ID | - | - | - |
| QUANTITY | - | - | - |
| RANGE_HIGH | - | - | - |
| RANGE_LOW | - | - | - |
| REFILLS | - | - | - |
| ROUTE_CONCEPT_ID | - | - | - |
| ROUTE_SOURCE_VALUE | - | - | - |
| SIG | - | - | - |
| STOP_REASON | - | - | - |
| UNIQUE_DEVICE_ID | - | - | - |
| UNIT_CONCEPT_ID | UNIT_CONCEPT_ID | - | - |
| UNIT_SOURCE_VALUE | UNIT_SOURCE_VALUE | - | - |
| VALUE_AS_CONCEPT_ID | VALUE_AS_CONCEPT_ID | - | - |
| VALUE_AS_NUMBER | VALUE_AS_NUMBER | - | - |
| VALUE_AS_STRING | VALUE_AS_STRING | - | - |
| VALUE_SOURCE_VALUE | - | - | - |
| ANATOMIC_SITE_CONCEPT_ID | - | - | - |
| DISEASE_STATUS_CONCEPT_ID | - | - | - |
| SPECIMEN_SOURCE_ID | - | - | - |
| ANATOMIC_SITE_SOURCE_VALUE | - | - | - |
| DISEASE STATUS_SOURCE_VALUE | - | - | - |
| CONDITION_STATUS_CONCEPT_ID | - | - | - |
| CONDITION_STATUS_SOURCE_VALUE | - | - | - |
| EVENT_ID | - | - | - |
| EVENT_FIELD_CONCEPT_ID | - | - | - |
| VALUE_AS_DATETIME | - | - | - |
| QUALIFIER_CONCEPT_ID | QUALIFIER_CONCEPT_ID | - | - |
| QUALIFIER_SOURCE_VALUE | QUALIFIER_SOURCE_VALUE | - | - |