How the Observational Medical Outcomes Partnership (OMOP) vocabulary are structured

All participant data are transformed into Observational Medical Outcomes Partnership (OMOP) standard vocabulary where possible. For example, the condition type II diabetes may be recorded as ICD9 code 250.00 in one electronic health record (EHR) or ICD10 code E11 in another. This data are transformed such that all the codes (called source codes) are re-assigned a standard vocabulary code (e.g., SNOMED 44054006). In addition, all survey data are assigned a Participant Provided Information (PPI) vocabulary code and mapped to a corresponding standard vocabulary when possible.

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Below is a list of the EHR domains or program data and their most commonly used respective source and standard vocabularies. The OMOP community maintains a searchable database of all standardized vocabularies it supports called ATHENA. You can search, browse, and/or download vocabularies and standard codes associated with your All of Us data interests there.

Domain Source Vocabulary Standard Vocabulary
Conditions ICD9, ICD10 SNOMED
Measurements LOINC or institutional specific codes LOINC
Drugs NDC RxNORM
Procedures ICD9, ICD10, CPT SNOMED
Program Physical Measurements PPI SNOMED, LOINC, PPI
Survey Questions & Answers PPI SNOMED, LOINC, PPI

ICD = International Classification of Diseases
SNOMED = Systematized Nomenclature of Medicine
LOINC = Logical Observation Identifiers Names and Codes
NDC = National Drug Code
CPT = Current Procedural Terminology
PPI = Participant Provided Information

 

As mentioned above, the OMOP common data model (CDM) is a relational database made up of different tables that relate to each other by foreign keys (XXXX_ID values; e.g., PERSON_ID or PROVIDER_ID). The OMOP tables referenced by the Researcher Workbench tools are as follows: 

Table Standard Vocabulary
Person Contains basic demographic information describing a participant, including biological sex, birth date, race, and ethnicity.
Visit_occurence Captures encounters with healthcare providers or similar events. Contains the type of visit a person has (outpatient care, inpatient care, or long-term care), as well as the date and duration information. Rows in other tables can reference this table, for example, condition_occurrences related to a specific visit.
Condition_occurence Indicates the presence of a disease or medical condition stated as a diagnosis, a sign, or symptom, which is either observed by a provider or reported by the patient.
Drug_exposure Captures records about the utilization of a medication. Drug exposures include prescription and over-the-counter medicines, vaccines, and large-molecule biologic therapies. Radiological devices ingested or applied locally do not count as drugs. Drug exposure is inferred from clinical events associated with orders, prescriptions written, pharmacy dispensing, procedural administrations, and other patient-reported information.
Measurement Contains both orders and results of a systematic and standardized examination or testing of a participant or participant's sample, including laboratory tests, vital signs, quantitative findings from pathology reports, etc.
Procedure_occurrence Contains records of activities or processes ordered by or carried out by a healthcare provider on the patient to have a diagnostic or therapeutic purpose.
Observation Captures clinical facts about a person obtained in the context of an examination, questioning, or a procedure. Any data that cannot be represented by another domain, such as social and lifestyle facts, medical history, and family history, are recorded here.
Device_exposure Captures information about a person's exposure to a foreign physical object or instrument which is used for diagnostic or therapeutic purposes. Devices include implantable objects, blood transfusions, medical equipment and supplies, other instruments used in medical procedures, and material used in clinical care. 
Death Contains the clinical events surrounding how and when a participant dies.

 

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