CDM Table: STEM

The STEM table is a staging area where source codes like ICD9 codes will first be mapped to concept_ids. The STEM table itself is an amalgamation of the OMOP event tables to facilitate record movement. This means that all fields present across the OMOP event tables are present in the STEM table. After a record is mapped and staged, the domain of the concept_id dictates which OMOP table (CONDITION_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, MEASUREMENT, OBSERVATION, DEVICE_EXPOSURE) the record will move to. Please see the STEM → CDM mapping files for a description of which STEM fields move to which STEM tables.

Key Conventions

  • IBM removes decimal points from ICD diagnosis. When mapping to the OMOP Vocabulary the decimal points need to also be removed from the Vocabulary concept code in order to map between the source and the vocabulary.

  • Only keep records with valid ICD9CM or ICD10CM diagnoses, the DXVER variable in all tables indicates the ICD version to map to. If DXVER=9 then use ICD9CM; if DXVER=0 then use ICD10CM otherwise if DXVER is null then use a date filter:
    • If before October 1, 2015 use ICD9CM
    • If after October 1, 2015 use ICD10CM (OUTPATIENT_SERVICES use SVCDATE, INPATIENT_SERVICES use ADMDATE, FACILITY_HEADER use SVCDATE, and INPATIENT_ADMISSIONS use ADMDATE).
  • Valid Codes 1) ICD9CM must start with 0-9, V or E, and non-numeric character is not allowed in other positions. 2) If ICD9CM starts with 0-9 or V, length should be between 3 and 5; if starts with E, length should be between 4 and 5. 3) ICD10CM must be between 3 and 7 digits

Fields in the STEM table

Field
ID
DOMAIN_ID
PERSON_ID
VISIT_OCCURRENCE_ID
PROVIDER_ID
START_DATETIME
CONCEPT_ID
SOURCE_CONCEPT_ID
TYPE_CONCEPT_ID
OPERATOR_CONCEPT_ID
UNIT_CONCEPT_ID
UNIT_SOURCE_VALUE
START_DATE
END_DATE
RANGE_HIGH
RANGE_LOW
VALUE_AS_NUMBER
VALUE_AS_STRING
VALUE_AS_CONCEPT_ID
VALUE_SOURCE_VALUE
END_DATETIME
VERBATIM_END_DATE
DAYS_SUPPLY
DOSE_UNIT_SOURCE_VALUE
LOT_NUMBER
MODIFIER_CONCEPT_ID
MODIFIER_SOURCE_VALUE
QUANTITY
REFILLS
ROUTE_CONCEPT_ID
ROUTE_SOURCE_VALUE
SIG
STOP_REASON
UNIQUE_DEVICE_ID
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_FIELD_CONCEPT_ID 
 EVENT_ID 
 QUALIFIER_CONCEPT_ID 
 QUALIFIER_SOURCE_VALUE 
 SIG 
 SOURCE_VALUE 
 VALUE_AS_DATETIME 
 VISIT_DETAIL_ID 

Table of contents


Please contact Clair Blacketer (https://github.com/clairblacketer) if you have any questions