Vocab.OMOP_Extension - OHDSI/Vocabulary-v5.0 GitHub Wiki

Scope of the vocabulary

OMOP Extension is an in-house multi-domain terminology system, created and maintained by the OHDSI community. The concepts that could not be found among existing standardised vocabularies can be added to the OMOP Extension vocabulary if they possess interest within the community.

Some use cases are out of scope for OMOP Extension and require their terminologies:

Drug Domain that goes to the RxNorm Extension vocabulary
Genomic data (OMOP Genomic vocabulary)
Cancer data (Cancer modifier vocabulary)
Units (UCUM vocabulary)

OMOP Extension appeared in OMOP during the COVID-19 Study-a-thon as the urgent response to the needs for observational research on COVID-19, and the first concepts were devoted to COVID-19 diagnosis, lab tests, and epidemiological features.

Currently, it has become a large collection of scales (psychiatric, quality of life, ophthalmic, etc.), concepts to represent a history of events, measurements (cardiac, parasites detection, lung function assessment, etc.), procedures, substances, and continues to expand and improve.

The content is authored by the OHDSI vocabulary team or may be suggested through the community contribution.

Concept names

Concept names are built according to the principle of naming in SNOMED. Concept name provides each code with a structured fully specified name that unambiguously describes its meaning. The concept name is defined in a reference language (the language of first use). Less common names and translations to other languages find their place in the CONCEPT_SYNONYM table as synonyms.

Concept codes

Concept codes have an “OMOP” prefix in the beginning to provide code uniqueness. E. g. “OMOP4873907” for Respiratory infection caused by COVID-19.

Domains

Classic domains are used in the OMOP Extension vocabulary: Condition, Measurement, Observation, Procedure. They are assigned according to CDM specification.

Concept_classes

Concept classes are assigned according to the logic of SNOMED. So the same concept classes are used in the OMOP Extension. E. g. “Event”, “Qualifier Value”, “Substance”, “Staging / Scales” etc.

One concept class outside of SNOMED logic is the Precoordinated pair. This class is used for precoordinated Question/answer and Variable/Value pairs.

Standard concepts

All concepts are Standard, excluding concepts that have lost relevance and become non-standard.

Internal and external relationships

Internal relationships include hierarchical “Is a/Subsumes” relationships and “Maps to” for non-standard concepts.