OMOP CDM Database
After OMOP ETL and mapping process, we will save the mapped records into databases. Either SQL Server, PostgreSQL will be good choises for data storage.
Database Architecture
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CDM
Table Name
Description
Action
PERSON
This table serves as the central identity management for all Persons in the database. It contains records that uniquely ...
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OBSERVATION_PERIOD
This table contains records which define spans of time during which two conditions are expected to hold: (i) Clinical Ev...
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VISIT_OCCURRENCE
This table contains Events where Persons engage with the healthcare system for a duration of time. They are often also c...
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VISIT_DETAIL
The VISIT_DETAIL table is an optional table used to represents details of each record in the parent VISIT_OCCURRENCE tab...
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CONDITION_OCCURRENCE
This table contains records of Events of a Person suggesting the presence of a disease or medical condition stated as a ...
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DRUG_EXPOSURE
This table captures records about the exposure to a Drug ingested or otherwise introduced into the body. A Drug is a bio...
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PROCEDURE_OCCURRENCE
This table contains records of activities or processes ordered by, or carried out by, a healthcare provider on the patie...
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DEVICE_EXPOSURE
The Device domain captures information about a person's exposure to a foreign physical object or instrument which is use...
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MEASUREMENT
The MEASUREMENT table contains records of Measurements, i.e. structured values (numerical or categorical) obtained throu...
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OBSERVATION
The OBSERVATION table captures clinical facts about a Person obtained in the context of examination, questioning or a pr...
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DEATH
The death domain contains the clinical event for how and when a Person dies. A person can have up to one record if the s...
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NOTE
The NOTE table captures unstructured information that was recorded by a provider about a patient in free text (in ASCII,...
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NOTE_NLP
The NOTE_NLP table encodes all output of NLP on clinical notes. Each row represents a single extracted term from a note....
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SPECIMEN
The specimen domain contains the records identifying biological samples from a person.
FACT_RELATIONSHIP
The FACT_RELATIONSHIP table contains records about the relationships between facts stored as records in any table of the...
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LOCATION
The LOCATION table represents a generic way to capture physical location or address information of Persons and Care Site...
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CARE_SITE
The CARE_SITE table contains a list of uniquely identified institutional (physical or organizational) units where health...
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PROVIDER
The PROVIDER table contains a list of uniquely identified healthcare providers. These are individuals providing hands-on...
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PAYER_PLAN_PERIOD
The PAYER_PLAN_PERIOD table captures details of the period of time that a Person is continuously enrolled under a specif...
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COST
The COST table captures records containing the cost of any medical event recorded in one of the OMOP clinical event tabl...
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DRUG_ERA
A Drug Era is defined as a span of time when the Person is assumed to be exposed to a particular active ingredient. A Dr...
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DOSE_ERA
A Dose Era is defined as a span of time when the Person is assumed to be exposed to a constant dose of a specific active...
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CONDITION_ERA
A Condition Era is defined as a span of time when the Person is assumed to have a given condition. Similar to Drug Eras,...
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EPISODE
The EPISODE table aggregates lower-level clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_...
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EPISODE_EVENT
The EPISODE_EVENT table connects qualifying clinical events (such as CONDITION_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCU...
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METADATA
The METADATA table contains metadata information about a dataset that has been transformed to the OMOP Common Data Model...
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CDM_SOURCE
The CDM_SOURCE table contains detail about the source database and the process used to transform the data into the OMOP ...
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LOCATION_HISTORY
This table contains location history for all entities, Person, CARESITE, ETC
DEVICE_EXPOSURE_ERA
Table contains device exposure eras allowing for up to a 1 calendar day overlap
ICU_ERA
Table contains device exposure eras allowing for up to a 1 calendar day overlap
FINAL_AKI
Custom AKI status derived table.
OUTCOMES
Custom Outcome table derived from other tables.
IC3_CUSTOMIZED
Table Name
Description
Action
FILE_PROCCESSING_TABLE
This table contains field level mappings for the OMOP upload/conversion ETL
CARE_SITE_MAPPING
This table contains alias mappings between care sites to reconcile different names for the same site
OMOP_MAPPING
This table is a wide mapping table between source values and OMOP concepts
DATABASE_UPDATES
This table contains information pertaining to database updates (e.g. CRUD operations)
COHORT_DEF
COHORT Definition for prismap_studies
RESULTS
Table Name
Description
Action
COHORT
The COHORT table contains records of subjects that satisfy a given set of criteria for a duration of time. The definitio...
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COHORT_DEFINITION
The COHORT_DEFINITION table contains records defining a Cohort derived from the data through the associated description ...
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VOCAB
Table Name
Description
Action
CONCEPT
The Standardized Vocabularies contains records, or Concepts, that uniquely identify each fundamental unit of meaning use...
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VOCABULARY
The VOCABULARY table includes a list of the Vocabularies collected from various sources or created de novo by the OMOP c...
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DOMAIN
The DOMAIN table includes a list of OMOP-defined Domains the Concepts of the Standardized Vocabularies can belong to. A ...
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CONCEPT_CLASS
The CONCEPT_CLASS table is a reference table, which includes a list of the classifications used to differentiate Concept...
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CONCEPT_RELATIONSHIP
The CONCEPT_RELATIONSHIP table contains records that define direct relationships between any two Concepts and the nature...
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RELATIONSHIP
The RELATIONSHIP table provides a reference list of all types of relationships that can be used to associate any two con...
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CONCEPT_SYNONYM
The CONCEPT_SYNONYM table is used to store alternate names and descriptions for Concepts.
CONCEPT_ANCESTOR
The CONCEPT_ANCESTOR table is designed to simplify observational analysis by providing the complete hierarchical relatio...
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SOURCE_TO_CONCEPT_MAP
The source to concept map table is a legacy data structure within the OMOP Common Data Model, recommended for use in ETL...
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DRUG_STRENGTH
The DRUG_STRENGTH table contains structured content about the amount or concentration and associated units of a specific...
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