1.3 Mapping vocabularies from source to target
The data vocabularies employed were the Systematic Nomenclature of
Medicine Clinical Terms (SNOMED CT) for diagnosis codes, RxNorm
Extension for drugs, and Logical Observation Identifiers Names and Codes
(LOINC) for laboratory tests and vitals measurements9-11. In general, ETL was performed if the concept was
available in the respective vocabularies and could be mapped via
database joins with the OMOP concept table based on “Concept Name”. In
the upper branch of Figure 2, under the “Conditions” subgroup in the
data source, the concept of “J18.9 (Pneumonia, unspecified)” in the
International Classification of Diseases, 10threvision (ICD-10) could be mapped to “233604007 (Pneumonia)” in SNOMED
CT, which was mapped to the OMOP standard concept identifier “255848”.
If the concept did not exist in the OMOP vocabulary, it was mapped
through a manual conversion process to an OMOP concept identifier. An
example of this process is shown in the lower branch of Figure 2 and
explained under ‘1.4 Drug Exposures’.