Introduction

This tables below contain an overview of which standard OHDSI tools make use of which OMOP CDM fields. The goal is to inform ETL developers, tooling developers and CDM extensions.

  • For ETL developers it helps to have guidance on which fields to prioritise in the mapping. Most value will be gained from populating fields support across the OHDSI tooling.
  • For OHDSI tooling developers, this page provides insight in the gaps of support and can drive future development efforts.
  • For CDM extensions, it helps to known what it means for an OMOP CDM table/field to be part of the standard. In other words: what OHDSI tooling do we at least expect to support the new extensions?

Currently four OHDSI tools have been evaluated: DataQualityDashboard, Achilles, Atlas (Data Sources and Cohort creation) and Feature Extraction.

Criteria

Tool Supports CDM Field if Link to resource used
DataQualityDashboard Part of Field Level checks https://github.com/OHDSI/DataQualityDashboard/blob/main/inst/csv/OMOP_CDMv5.4_Field_Level.csv
Achilles Covered by at least one Achilles analysis https://github.com/OHDSI/Achilles/blob/main/inst/csv/achilles/achilles_analysis_details.csv
Atlas Data Sources A statistic based on the field is shown in a ‘Data Sources’ visualisation https://atlas-demo.ohdsi.org/
Atlas Cohort Used in te Atlas User Interface for cohort definition criteria (directly, or via ‘Add attribute’) https://atlas-demo.ohdsi.org/
Feature Extraction Used in one of the Feature Extraction analyses https://github.com/OHDSI/FeatureExtraction/blob/main/inst/csv/

General criteria: - ✔️ if the field essential for OMOP CDM definition (Primary Key, Foreign Key) e.g. person_id not explicitly used, but essential. (if the PK is marked as False, it typically means the whole table is not used in the tool e.g. _source_value fields that are used for traceability in ETL) - ❗ if field is used by the tool, but not in a meaningful way. e.g. provider_id in Achilles only checked for a valid foreign key to the provider table.

Tooling Support for OMOP fields

Abbreviations  
PK Primary Key
SV Source Value (for data quality / etl validation)
BC Backwards Compatibility, to support CDM <v5.4
FC Forwards Compatibility, to easy support for CDM v6 in the future.

Person

cdmTableName cdmFieldName Special Fields DQD (v1.0) Achilles (v1.7) Atlas Cohort (v2.10) Atlas Cohort (v2.12) Atlas Data Sources (v2.12) Feature Extraction (v3.2) Comment
PERSON person_id PK ✔️ ✔️ ✔️ ✔️ ✔️ ✔️
PERSON gender_concept_id ✔️ ✔️ ✔️ ✔️ ✔️ ✔️
PERSON year_of_birth ✔️ ✔️ ✔️ ✔️ ✔️ ✔️
PERSON month_of_birth ✔️ ✔️ ❗ ❗ ❗ ❗
PERSON day_of_birth ✔️ ❗ ❗ ❗ ❗ ❗
PERSON birth_datetime FC ✔️ ❗ ❗ ❗ ❗ ❗
PERSON race_concept_id ✔️ ✔️ ✔️ ✔️ ✔️ ✔️
PERSON ethnicity_concept_id ✔️ ✔️ ✔️ ✔️ ✔️ ✔️
PERSON location_id ✔️ ❗ ❗ ❗ ❗ ❗ Achilles only does FK check
PERSON provider_id ✔️ ❗ ❗ ❗ ❗ ❗ Achilles only does FK check
PERSON care_site_id ✔️ ❗ ❗ ❗ ❗ ❗ Achilles only does FK check
PERSON person_source_value SV ✔️ ❗ ❗ ❗ ❗ ❗
PERSON gender_source_value SV ✔️ ❗ ❗ ❗ ❗ ❗
PERSON gender_source_concept_id ✔️ ❗ ❗ ❗ ❗ ❗
PERSON race_source_value SV ✔️ ❗ ❗ ❗ ❗ ❗
PERSON race_source_concept_id ✔️ ❗ ❗ ❗ ❗ ❗
PERSON ethnicity_source_value SV ✔️ ❗ ❗ ❗ ❗ ❗
PERSON ethnicity_source_concept_id ✔️ ❗ ❗ ❗ ❗ ❗

Observation Period

cdmTableName cdmFieldName Special Fields DQD (v1.0) Achilles (v1.7) Atlas Cohort (v2.10) Atlas Cohort (v2.12) Atlas Data Sources (v2.12) Feature Extraction (v3.2) Comment
OBSERVATION_PERIOD observation_period_id PK ✔️ ✔️ ✔️ ✔️ ✔️ ✔️
OBSERVATION_PERIOD person_id Pid ✔️ ✔️ ✔️ ✔️ ✔️ ✔️
OBSERVATION_PERIOD observation_period_start_date ✔️ ✔️ ✔️ ✔️ ✔️ ✔️
OBSERVATION_PERIOD observation_period_end_date ✔️ ✔️ ✔️ ✔️ ✔️ ✔️
OBSERVATION_PERIOD period_type_concept_id ✔️ ✔️ ✔️ ✔️ ❗ ❗

Visit Occurrence

cdmTableName cdmFieldName Special Fields DQD (v1.0) Achilles (v1.7) Atlas Cohort (v2.10) Atlas Cohort (v2.12) Atlas Data Sources (v2.12) Feature Extraction (v3.2) Comment
VISIT_OCCURRENCE visit_occurrence_id PK ✔️ ✔️ ✔️ ✔️ ✔️ ✔️
VISIT_OCCURRENCE person_id Pid ✔️ ✔️ ✔️ ✔️ ✔️ ✔️
VISIT_OCCURRENCE visit_concept_id ✔️ ✔️ ✔️ ✔️ ✔️ ✔️
VISIT_OCCURRENCE visit_source_concept_id ✔️ ✔️ ✔️ ✔️ ❗ ❗
VISIT_OCCURRENCE visit_source_value SV ✔️ ❗ ❗ ❗ ❗ ❗
VISIT_OCCURRENCE visit_start_date ✔️ ✔️ ✔️ ✔️ ✔️ ✔️ Achilles check 1900
VISIT_OCCURRENCE visit_start_datetime FC ✔️ ❗ ❗ ❗ ❗ ❗
VISIT_OCCURRENCE visit_end_date ✔️ ✔️ ✔️ ✔️ ❗ ✔️
VISIT_OCCURRENCE visit_end_datetime FC ✔️ ❗ ❗ ❗ ❗ ❗
VISIT_OCCURRENCE visit_type_concept_id ✔️ ✔️ ✔️ ✔️ ❗ ❗
VISIT_OCCURRENCE provider_id ✔️ ❗ ✔️ ✔️ ❗ ❗ Atlas uses provider.specialty_concept_id
VISIT_OCCURRENCE care_site_id ✔️ ❗ ✔️ ✔️ ❗ ❗ Achilles only does FK check, Atlas uses care_site.place_of_service_concept_id
VISIT_OCCURRENCE admitted_from_concept_id ✔️ ❗ ❗ ❗ ❗ ❗
VISIT_OCCURRENCE admitted_from_source_value SV ✔️ ❗ ❗ ❗ ❗ ❗ Achilles check 1900
VISIT_OCCURRENCE discharged_to_concept_id ✔️ ❗ ❗ ❗ ❗ ❗
VISIT_OCCURRENCE discharged_to_source_value SV ✔️ ❗ ❗ ❗ ❗ ❗ Achilles check 1900
VISIT_OCCURRENCE preceding_visit_occurrence_id ✔️ ❗ ❗ ❗ ❗ ❗

Episode

cdmTableName cdmFieldName Special Fields DQD (v1.0) Achilles (v1.7) Atlas Cohort (v2.10) Atlas Cohort (v2.12) Atlas Data Sources (v2.12) Feature Extraction (v3.2) Comment
EPISODE episode_id PK ✔️ ❗ ❗ ❗ ❗ ❗
EPISODE person_id Pid ✔️ ❗ ❗ ❗ ❗ ❗
EPISODE episode_concept_id ✔️ ❗ ❗ ❗ ❗ ❗
EPISODE episode_start_date ✔️ ❗ ❗ ❗ ❗ ❗
EPISODE episode_start_datetime FC ✔️ ❗ ❗ ❗ ❗ ❗
EPISODE episode_end_date ✔️ ❗ ❗ ❗ ❗ ❗
EPISODE episode_end_datetime FC ✔️ ❗ ❗ ❗ ❗ ❗
EPISODE episode_parent_id ✔️ ❗ ❗ ❗ ❗ ❗
EPISODE episode_number ✔️ ❗ ❗ ❗ ❗ ❗
EPISODE episode_object_concept_id ✔️ ❗ ❗ ❗ ❗ ❗
EPISODE episode_type_concept_id ✔️ ❗ ❗ ❗ ❗ ❗
EPISODE episode_source_value SV ✔️ ❗ ❗ ❗ ❗ ❗
EPISODE episode_source_concept_id ✔️ ❗ ❗ ❗ ❗ ❗

This was an effort by the CDM Working Group in 2022. *Credits: Clair Blacketer, Maxim Moinat, Nitin Park