Appendix B — OMOP Domains

The OMOP CDM v5.4 organizes clinical data into domains, each stored in one or more tables. Understanding domains is essential for building correct cohort criteria, analyses, and for mapping extended data types (genomics, imaging) into the standardized model.

Domain Reference

Domain	Primary Table	Standard Vocabulary	Description
Condition	condition_occurrence	SNOMED CT	Diagnoses, problems, clinical findings
Drug	drug_exposure	RxNorm	Drug prescriptions, dispensings, administrations
Measurement	measurement	LOINC	Lab tests, vital signs, clinical assessments with numeric or categorical values
Procedure	procedure_occurrence	SNOMED CT, CPT4, HCPCS	Medical procedures performed on patients
Observation	observation	SNOMED CT, LOINC	Clinical facts, survey responses, social determinants of health
Visit	visit_occurrence	OMOP Visit	Healthcare encounters (inpatient, outpatient, ED, telehealth)
Visit Detail	visit_detail	OMOP Visit	Sub-encounters within a visit (e.g. individual department stays)
Device	device_exposure	SNOMED CT	Medical devices used (implants, prosthetics, monitors)
Death	death	SNOMED CT, ICD10CM	Cause of death and mortality status
Specimen	specimen	SNOMED CT	Biological specimens collected
Note	note	---	Unstructured clinical notes (text)
Note NLP	note_nlp	---	NLP-extracted entities from clinical notes

Genomics and the Measurement Domain

Parthenon's Genomics module maps genomic variant data into the OMOP CDM using the Measurement domain. This follows the OHDSI Genomic CDM Working Group conventions:

Genomic Data Element	OMOP Mapping	Details
Genetic variant (SNV, indel)	measurement row	measurement_concept_id maps to a genomic measurement concept; value_as_concept_id encodes the variant allele
Gene name	measurement.measurement_source_value	HUGO gene symbol (e.g., BRCA1, TP53) stored as source value
Variant classification	measurement.value_as_concept_id	Pathogenic, Likely Pathogenic, VUS, Benign, etc. mapped to OMOP concepts
Zygosity	measurement.qualifier_concept_id	Heterozygous, Homozygous, Hemizygous
Allele frequency	measurement.value_as_number	Variant allele frequency (0.0 -- 1.0)

VCF to OMOP Pipeline

When you upload a VCF file in the Genomics module, Parthenon parses variants and creates corresponding measurement rows linked to the patient via person_id. ClinVar annotations are stored as additional measurement attributes. This allows genomic variants to participate in standard OMOP cohort definitions and analyses alongside clinical data.

Imaging and the Procedure Domain

DICOM imaging studies are mapped into the OMOP CDM using the Procedure domain, following radiology procedure coding conventions:

Imaging Data Element	OMOP Mapping	Details
Imaging study (e.g., CT Chest)	procedure_occurrence row	procedure_concept_id maps to the CPT4/SNOMED procedure concept for the imaging modality
Study date	procedure_date	Date the imaging study was performed
Modality (CT, MR, US, XR)	procedure_source_value	DICOM modality code stored as source value
Imaging report findings	note row	Radiology report text linked to the procedure via visit_occurrence_id
NLP-extracted findings	note_nlp + condition_occurrence	Structured findings extracted from radiology reports may also create condition rows

DICOM Metadata

Parthenon stores the full DICOM metadata (study UID, series UID, SOP instance UID, pixel data references) in its own imaging tables (imaging_studies, imaging_series, imaging_instances). The procedure_occurrence row links the OMOP clinical record to the imaging metadata via procedure_occurrence_id, enabling cohort definitions that combine imaging criteria with standard clinical criteria.

Standard Vocabularies by Domain

Condition Domain

• Standard: SNOMED CT (OMOP concept class: Clinical Finding, Disorder)
• Source: ICD-10-CM, ICD-10, ICD-9-CM, MedDRA, Read codes

Drug Domain

• Standard: RxNorm (Ingredient, Clinical Drug, Clinical Drug Form)
• Source: NDC, NDF-RT, GPI, AMIS, Multilex

Measurement Domain

• Standard: LOINC
• Source: LOINC (local labs may use LOINC directly), custom lab codes
• Genomic extension: Genomic variant measurements use LOINC panel codes (e.g., LOINC 81247-9 for master HL7 genetic variant reporting)

Procedure Domain

• Standard: SNOMED CT, CPT4, HCPCS
• Source: ICD-10-PCS, ICD-9-CM procedures, local procedure codes
• Imaging extension: CPT4 radiology codes (70000--79999 range) map imaging studies to procedures

CDM v5.4 Key Tables

Person Table

Column	Type	Description
person_id	BIGINT	Unique person identifier
gender_concept_id	INT	OMOP gender concept (8507=Male, 8532=Female)
year_of_birth	INT	Birth year
race_concept_id	INT	OMOP race concept
ethnicity_concept_id	INT	OMOP ethnicity concept

Condition Occurrence Table

Column	Type	Description
condition_occurrence_id	BIGINT	Row identifier
person_id	BIGINT	Foreign key to person
condition_concept_id	INT	Standard SNOMED concept
condition_start_date	DATE	Onset date
condition_end_date	DATE	Resolution date (optional)
condition_type_concept_id	INT	Source of record (EHR, claims, etc.)
condition_source_value	VARCHAR	Original ICD code
condition_source_concept_id	INT	Concept mapped from source code

Measurement Table (Including Genomic Variants)

Column	Type	Description
measurement_id	BIGINT	Row identifier
person_id	BIGINT	Foreign key to person
measurement_concept_id	INT	Standard LOINC concept
measurement_date	DATE	Date of measurement
value_as_number	NUMERIC	Numeric result (lab value, allele frequency)
value_as_concept_id	INT	Categorical result concept (variant classification)
unit_concept_id	INT	Unit of measure concept
measurement_source_value	VARCHAR	Original code or gene symbol

Procedure Occurrence Table (Including Imaging)

Column	Type	Description
procedure_occurrence_id	BIGINT	Row identifier
person_id	BIGINT	Foreign key to person
procedure_concept_id	INT	Standard CPT4/SNOMED concept
procedure_date	DATE	Date procedure was performed
procedure_type_concept_id	INT	Source of record
procedure_source_value	VARCHAR	Original code or DICOM modality

Observation Period

The observation_period table defines the windows during which a person's data is expected to be complete. OMOP-based analyses restrict to events within observation periods to avoid bias from incomplete records.

Column	Description
observation_period_start_date	Start of continuous observation
observation_period_end_date	End of continuous observation
period_type_concept_id	How the period was defined (insurance enrollment, EHR registration, etc.)

Genomic and Imaging Data Outside Observation Periods

Genomic test results and imaging studies must fall within a patient's observation period to be included in cohort definitions and analyses. If your genomic or imaging data has dates outside the observation period, those records will be excluded from OMOP-standard analyses. Ensure observation periods are updated when integrating new data sources.