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Emory Conventions

Emory-specific additions to the OMOP CDM. Standard OHDSI conventions are not modified — only additions are made to support Emory's research community (e.g., data provenance, PII for re-identification across sources). OHDSI tools ignore additional columns and tables, so these additions do not interfere with standard tooling.

Quick reference — what's on this page

Tables — Emory-added mapping and PII tables:

Fields — Emory-added columns across CDM tables:

OMOP-CDM v5.4 Data Model Conventions

Origin: OHDSI

OHDSI's General, Vocabulary, and Mapping conventions are all observed by Emory, as of site access date, April 23, 2025. The following listed conventions are specific to Emory's implementation of the CDM and are not part of the standard OMOP CDM conventions.

Tables

Several tables have been added to the CDM to support the needs of Emory's research community. These tables are not part of the standard OMOP CDM but have been created to enhance data management and analysis capabilities.

ID stability

IDs in these mapping tables (except person_id in OMOP_PII.PATIENT) are not stable between loads. Do not use them as durable identifiers across data refreshes.

CARE_SITE_MAPPING — CDW and Epic

Care site ID generation and source tracking. IDs are assigned first from CDW care sites, then by appending incremental IDs for Epic care sites.

CDM Field Description ETL Convention Type PK FK
care_site_id Unique identifier for the care site Generated in this table for the final care_site OMOP table. Not stable between loads. Integer Yes —
care_site_source_value Source value for the care site Source value differs between CDW and Epic with regard to FK values varchar — CDW: lkp_location.location_key; Epic: clarity_pos.pos_id
care_site_source Database source Hardcoded for either Epic or CDW sources varchar — —
LOCATION_MAPPING — CDW and Epic

Location ID generation and source tracking. IDs are assigned first from CDW, then by appending incremental IDs for Epic.

CDM Field Description ETL Convention Type PK FK
location_id Unique identifier for the location Generated in this table for the final location OMOP table. Not stable between loads. Integer Yes —
location_source_value Source value for the location Source value differs between CDW and Epic. Epic's source values are concatenated when present (or '' if null): 1) PATIENT.ADD_LINE_1, 2) PATIENT.ADD_LINE_2, 3) PATIENT.CITY, 4) ZC_STATE.ABBR, 5) PATIENT.ZIP, 6) ZC_COUNTY.COUNTY_C varchar — CDW: lkp_facility.facility_key; Epic: see concatenation
location_source Database source Hardcoded for either Epic or CDW sources varchar — —
PROVIDER_MAPPING — CDW and Epic

Provider deduplication across CDW and Epic. Deduplication is based on NPI only, given sparse details elsewhere for trusted matching. This limitation is noted in Known Issues.

CDM Field Description ETL Convention Type PK FK
provider_id Unique identifier for the provider Generated in this table for the final provider OMOP table. Not stable between loads. Integer Yes —
provider_source_value Source value for the provider Source value differs between CDW and Epic. NPI-based deduplication across sources where possible varchar — CDW: lkp_personnel.personnel_id; Epic: clarity_ser.prov_id
provider_source Database source Hardcoded for either Epic or CDW sources varchar — —
VISIT_OCCURRENCE_MAPPING — CDW and Epic

Visit occurrence linking across sources. Deduplication is NPI-based where possible; limitations are noted in Known Issues.

CDM Field Description ETL Convention Type PK FK
visit_occurrence_id Unique identifier for the visit occurrence Generated in this table for the final visit_occurrence OMOP table. Not stable between loads. Integer Yes —
visit_occurrence_source_value Source value for the encounter Source value differs between CDW and Epic varchar — CDW: fact_encounter.encounter_key; Epic: PAT_ENC_HSP.PAT_ENC_CSN_ID or PAT_ENC.PAT_ENC_CSN_ID
visit_occurrence_source Database source Hardcoded for either Epic or CDW sources varchar — —

Hidden Tables

The following tables are viewable by only certain members of a research team, given the sensitive nature of the data. They are protected from view so cannot be found in the OMOP schema. The schema.table convention is therefore used to identify the table in our production database.

OMOP_PII.PATIENT — CDW and Epic (restricted access)

Restricted

This table contains protected health information (PHI) and is only accessible to authorized team members.

The person_id in this table is stable over time and across loads, unlike the mapping table IDs above.

Identity fields

CDM Field Description Type FK
person_id Unique identifier for the person in the CDM integer CDW: lkp_master_patient.person_id; Epic: deident_driver.person_id
epic_pat_id Unique identifier in Epic varchar Epic: patient.epic_pat_id
pat_mrn_id Emory MRN from Epic. Often matches empi_nbr but not always due to CDW data collisions varchar Epic: patient.pat_mrn_id
empi_nbr CDW EMPI from Cerner varchar CDW: lkp_patient.empi_nbr

Name fields

CDM Field Description Type FK
epic_pat_last_nm Last name (Epic) varchar Epic: patient.pat_last_name
cdw_pat_last_nm Last name (CDW) varchar CDW: lkp_patient.patient_last_nm
epic_pat_first_nm First name (Epic) varchar Epic: patient.pat_first_name
cdw_pat_first_nm First name (CDW) varchar CDW: lkp_patient.patient_first_nm
epic_middle_name Middle name (Epic) varchar Epic: patient.pat_middle_name
cdw_middle_name Middle name (CDW) varchar CDW: lkp_patient.patient_middle_nm
epic_maiden_name Maiden name (Epic) varchar Epic: patient_2.maiden_name
cdw_maiden_name Maiden name (CDW) varchar CDW: lkp_patient.patient_maiden_nm

Demographics and contact fields

CDM Field Description Type FK
epic_birth_date Date of birth (Epic) date Epic: patient.birth_date
cdw_birth_date Date of birth (CDW) date CDW: lkp_patient.birth_day_key
epic_sex Sex/gender (Epic) varchar Epic: zc_sex.name
cdw_sex Sex/gender (CDW) varchar CDW: lkp_patient.gender_desc
epic_ssn SSN (Epic) varchar Epic: patient.ssn
cdw_ssn SSN (CDW) varchar CDW: lkp_patient.patient_ssn_nbr
epic_zip Zip code (Epic) varchar Epic: patient.zip_code
cdw_zip Zip code (CDW) varchar CDW: lkp_patient.patient_address_zip_desc
epic_email_address Email (Epic) varchar Epic: patient.email_address
cdw_email_address Email (CDW) varchar CDW: lkp_patient.patient_email_address_nm
epic_phone_cell Cell phone (Epic) — currently hardcoded to null varchar —
cdw_phone_cell Cell phone (CDW) varchar CDW: lkp_patient.patient_phone_cell_nbr

Fields

General

These columns are added to standard OMOP CDM tables across the database to provide granular data provenance.

_source_primary_key

The primary key used to obtain the most granular data available to achieve distinct rows in the final OMOP table housing this column (e.g., drug_exposure._source_primary_key; measurement._source_primary_key).

Aggregation across the primary key in a particular table may sometimes be required, as there are many changes to data in an EHR system that are not relevant to how data is represented in the OMOP CDM. For example, a patient's drug order may have been ordered by one clinician, modified by the pharmacist, cancelled by staff by mistake, and then re-added by the pharmacist. For research purposes, we are only interested in the final state of the drug order.

_source_primary_key_source

The exact location where the _source_primary_key was obtained. This should be nearly machine-readable, with the caveat being aggregations. For aggregations (such as taking a minimum table primary key where all other values are distinct for the row), the function used is appended to the database.table.column name following a caret ^.

For example, a drug administration from Epic data might be: clarity_onprem_omop.order_med.order_med_id^MIN().