Value Set mapping table and Terminology Code Mapping Table Structure - National-Clinical-Cohort-Collaborative/Data-Ingestion-and-Harmonization GitHub Wiki

Value Set mapping table and Terminology Code Mapping Table Structure Explained.

The static iteration of the value set mapping table is established once for each Common Data Model (CDM) model. Conversely, the dynamically generated rendition of the terminology based mapping table is freshly generated within every pipeline ingestion process, specifically tailored to accommodate terminology-based codes found in the each data partner's source data. This approach guarantees the adaptability of the mapping table to the unique needs of each data source transformation, offering flexibility and precision in concept translation throughout the conversion of source data to the OMOP CDM.


columns description
DATA_SOURCE It name of the data source refers to the source data Common Data Model abbreviated name, i.e. OMOP, ACT, TriNetX, or PCORnet.
TBL_NAME CDM table name where specifid value is found in the data source
TABLE_COLUMN_NAME column name within the table list in the CDM_TBL_NAME column where the data values is found.
SRC_CD permissible data values, it is often an enumerated list of permissble values found in the source data.
SRC_CD_DESCRIPTION Description of the value listed in the SRC_CD column.
TARGET_CONCEPT_ID This is the standardized concept identifier that represents a clinical event, measurement, observation, drug or procedure in OMOP CDM. The target_concept_id is a field used to represent the concept that is the focus or target of a particular record in the source database.
TARGET_CONCEPT_NAME The text description associated with the target_concept_id
TARGET_DOMAIN_ID The domain id represents the various tables in the OMOP CDM. It is used to categorize and classify data into different domains based on the type of healthcare information it represents. In essence, this field referes to the table where the target concept should be inserted into. It serves as a way to codify and standardize the clinical content of the data in a consistent manner.
TARGET_VOCABULARY_ID The vocabulary id represents the standardized vocabulary or the terminology from which the concept code is derived. The source of the concept code in the source data in the SRC_CD column is often terminology based coded value. Some commonly used vocabularies in the source data include: SNOMED, RxNorm, LOINC, ICD10CM, ICD0PCS, CPT4, HCPCS and NDC. The vocabulary_id and the concept_code field uniquely identifies a concept within a specific vocabulary.
TARGET_CONCEPT_CLASS_ID This field is used to categorize concepts based on their class or category. It helps to organize concepts into groups that share similar characteristics or properties.
TARGET_STANDARD_CONCEPT The target_standard_concept column is used to identify the standard representation of a concept within a vocabulary. This column helps to distinguish between standard and non-standard. The possible values in this column can be S(standard), C(classification), D(Deprecated), or null.
TARGET_CONCEPT_CODE This column represents the codified data element or the equivalent code found in the source data that is associated with the concept within a specific vocabulary. For example, SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Rapid immunoassay laboratory test is equivalent to LOINC(Logical Observation Identifiers Names and Codes) 97097-0. The corresponding codified value of the concept in source_cd column LOINC code 97097-0 is represented in this field.
TARGET_TBL_COLUMN_NAME used as a reference to specify the location of data element in the source data.
PREDICATE_ID It defaults to omoprel:maps_to. Currently, not generated. However, it is used to describe the mapping relationship between the source data and the OMOP target concept. The OMOP relationship of "Maps to" is used, which can be either skos:exactMatch or skos:broadMatch. The common mapping predicates are explained here.
PREDICATE_label It defaults to "Maps to".
CONFIDENCE mapping confidence