Abstract

This is a synthetic patient dataset in the OMOP Common Data Model v5.2, originally released by the CMS and accessed via BigQuery. The dataset includes 24 tables and records for 2 million synthetic patients from 2008 to 2010.

Methodology

This dataset takes on the format of the Observational Medical Outcomes Partnership Common Data Model (OMOP CDM). As shown in the diagram below, the purpose of the Common Data Model is to convert various distinctly-formatted datasets into a well-known, universal format with a set of standardized vocabularies. See the diagram below from the Observational Health Data Sciences and Informatics (OHDSI) webpage.

https://redivis.com/fileUploads/d1a95a4e-074a-44d1-92e5-9adfd2f4068a%3E" alt="Why-CDM.png">

Such universal data models ultimately enable researchers to streamline the analysis of observational medical data. For more information regarding the OMOP CDM, refer to the OHSDI OMOP site.

Usage

%3Cli%3EFor documentation regarding the source data format from the Center for Medicare and Medicaid Services (CMS), refer to the %3Ca href="https://www.cms.gov/Research-Statistics-Data-and-Systems/Downloadable-Public-Use-Files/SynPUFs/DE_Syn_PUF"%3ECMS Synthetic Public Use File%3C/a%3E.%3C/li%3E

%3Cli%3EFor information regarding the conversion of the CMS data file to the OMOP CDM v5.2, refer to %3Ca href="https://github.com/OHDSI/ETL-CMS"%3Ethis OHDSI GitHub page%3C/a%3E. %3C/li%3E

%3Cli%3EFor information regarding each of the 24 tables in this dataset, including more detailed variable metadata, see %3Ca href="https://github.com/OHDSI/CommonDataModel/wiki"%3Ethe OHDSI CDM GitHub Wiki page%3C/a%3E. All variable labels and descriptions as well as table descriptions come from this Wiki page. Note that this GitHub page includes information primarily regarding the 6.0 version of the CDM and that this dataset works with the 5.2 version. %3C/li%3E

The Synthetic Patient Data in OMOP Dataset is a synthetic database released by the Centers for Medicare and Medicaid Services (CMS) Medicare Claims Synthetic Public Use Files (SynPUF). It is synthetic data containing 2008-2010 Medicare insurance claims for development and demonstration purposes. It has been converted to the Observational Medical Outcomes Partnership (OMOP) common data model from its original form, CSV, by the open source community as released on GitHub Please refer to the CMS Linkable 2008–2010 Medicare Data Entrepreneurs’ Synthetic Public Use File (DE-SynPUF) User Manual for details regarding how DE-SynPUF was created." This public dataset is hosted in Google BigQuery and is included in BigQuery's 1TB/mo of free tier processing. This means that each user receives 1TB of free BigQuery processing every month, which can be used to run queries on this public dataset. Watch this short video to learn how to get started quickly using BigQuery to access public datasets. What is BigQuery .

Abstract

MarketScan databases in the OMOP data model (https://www.ohdsi.org/data-standardization/the-common-data-model/)

The Synthea generated data is provided here as a 1,000 person (1k), 100,000 person (100k), and 2,800,000 persom (2.8m) data sets in the OMOP Common Data Model format. SyntheaTM is a synthetic patient generator that models the medical history of synthetic patients. Our mission is to output high-quality synthetic, realistic but not real, patient data and associated health records covering every aspect of healthcare. The resulting data is free from cost, privacy, and security restrictions. It can be used without restriction for a variety of secondary uses in academia, research, industry, and government (although a citation would be appreciated). You can read our first academic paper here: https://doi.org/10.1093/jamia/ocx079

BackgroundThe use of routinely collected health data for secondary research purposes is increasingly recognised as a methodology that advances medical research, improves patient outcomes, and guides policy. This secondary data, as found in electronic medical records (EMRs), can be optimised through conversion into a uniform data structure to enable analysis alongside other comparable health metric datasets. This can be achieved with the Observational Medical Outcomes Partnership Common Data Model (OMOP-CDM), which employs a standardised vocabulary to facilitate systematic analysis across various observational databases. The concept behind the OMOP-CDM is the conversion of data into a common format through the harmonisation of terminologies, vocabularies, and coding schemes within a unique repository. The OMOP model enhances research capacity through the development of shared analytic and prediction techniques; pharmacovigilance for the active surveillance of drug safety; and ‘validation’ analyses across multiple institutions across Australia, the United States, Europe, and the Asia Pacific. In this research, we aim to investigate the use of the open-source OMOP-CDM in the PATRON primary care data repository.MethodsWe used standard structured query language (SQL) to construct, extract, transform, and load scripts to convert the data to the OMOP-CDM. The process of mapping distinct free-text terms extracted from various EMRs presented a substantial challenge, as many terms could not be automatically matched to standard vocabularies through direct text comparison. This resulted in a number of terms that required manual assignment. To address this issue, we implemented a strategy where our clinical mappers were instructed to focus only on terms that appeared with sufficient frequency. We established a specific threshold value for each domain, ensuring that more than 95% of all records were linked to an approved vocabulary like SNOMED once appropriate mapping was completed. To assess the data quality of the resultant OMOP dataset we utilised the OHDSI Data Quality Dashboard (DQD) to evaluate the plausibility, conformity, and comprehensiveness of the data in the PATRON repository according to the Kahn framework.ResultsAcross three primary care EMR systems we converted data on 2.03 million active patients to version 5.4 of the OMOP common data model. The DQD assessment involved a total of 3,570 individual evaluations. Each evaluation compared the outcome against a predefined threshold. A ’FAIL’ occurred when the percentage of non-compliant rows exceeded the specified threshold value. In this assessment of the primary care OMOP database described here, we achieved an overall pass rate of 97%.ConclusionThe OMOP CDM’s widespread international use, support, and training provides a well-established pathway for data standardisation in collaborative research. Its compatibility allows the sharing of analysis packages across local and international research groups, which facilitates rapid and reproducible data comparisons. A suite of open-source tools, including the OHDSI Data Quality Dashboard (Version 1.4.1), supports the model. Its simplicity and standards-based approach facilitates adoption and integration into existing data processes.

The CPRD Primary Care and Linked Data OMOP CDM database contains longitudinal routinely-collected health records (EHR data) from UK primary care practices, and hospital episode data provided by NHS England. The data has been transformed into a common format (data model) using an open community data standard and structure from the OHDSI standardised vocabularies. The approach allows organisation, standardisation and common representation of medical terms and variables that have been obtained from various clinical data sources. Access to anonymised data from CPRD is subject to a full licence agreement containing detailed terms and conditions of use. Anonymised patient datasets can be extracted for researchers against specific study specifications, following protocol approval.

The OMOP Common Data Model allows for the systematic analysis of disparate observational databases. The concept behind this approach is to transform data contained within those databases into a common format (data model) as well as a common representation (terminologies, vocabularies, coding schemes), and then perform systematic analyses using a library of standard analytic routines that have been written based on the common format.

The DOMAIN table includes a list of OMOP-defined Domains the Concepts of the Standardized Vocabularies can belong to. A Domain defines the set of allowable Concepts for the standardized fields in the CDM tables.

The Person Domain contains records that uniquely identify each patient in the source data who is time at-risk to have clinical observations recorded within the source systems.

This dataset is an extract from the Bradford Royal Infirmary EPR system. This contains current and some historical data, and is based on extracting the relevant tables from EPR, mapping to the OMOP schema and outputting in omop cdm 5.3 format.

BackgroundThe use of routinely collected health data for secondary research purposes is increasingly recognised as a methodology that advances medical research, improves patient outcomes, and guides policy. This secondary data, as found in electronic medical records (EMRs), can be optimised through conversion into a uniform data structure to enable analysis alongside other comparable health metric datasets. This can be achieved with the Observational Medical Outcomes Partnership Common Data Model (OMOP-CDM), which employs a standardised vocabulary to facilitate systematic analysis across various observational databases. The concept behind the OMOP-CDM is the conversion of data into a common format through the harmonisation of terminologies, vocabularies, and coding schemes within a unique repository. The OMOP model enhances research capacity through the development of shared analytic and prediction techniques; pharmacovigilance for the active surveillance of drug safety; and ‘validation’ analyses across multiple institutions across Australia, the United States, Europe, and the Asia Pacific. In this research, we aim to investigate the use of the open-source OMOP-CDM in the PATRON primary care data repository.MethodsWe used standard structured query language (SQL) to construct, extract, transform, and load scripts to convert the data to the OMOP-CDM. The process of mapping distinct free-text terms extracted from various EMRs presented a substantial challenge, as many terms could not be automatically matched to standard vocabularies through direct text comparison. This resulted in a number of terms that required manual assignment. To address this issue, we implemented a strategy where our clinical mappers were instructed to focus only on terms that appeared with sufficient frequency. We established a specific threshold value for each domain, ensuring that more than 95% of all records were linked to an approved vocabulary like SNOMED once appropriate mapping was completed. To assess the data quality of the resultant OMOP dataset we utilised the OHDSI Data Quality Dashboard (DQD) to evaluate the plausibility, conformity, and comprehensiveness of the data in the PATRON repository according to the Kahn framework.ResultsAcross three primary care EMR systems we converted data on 2.03 million active patients to version 5.4 of the OMOP common data model. The DQD assessment involved a total of 3,570 individual evaluations. Each evaluation compared the outcome against a predefined threshold. A ’FAIL’ occurred when the percentage of non-compliant rows exceeded the specified threshold value. In this assessment of the primary care OMOP database described here, we achieved an overall pass rate of 97%.ConclusionThe OMOP CDM’s widespread international use, support, and training provides a well-established pathway for data standardisation in collaborative research. Its compatibility allows the sharing of analysis packages across local and international research groups, which facilitates rapid and reproducible data comparisons. A suite of open-source tools, including the OHDSI Data Quality Dashboard (Version 1.4.1), supports the model. Its simplicity and standards-based approach facilitates adoption and integration into existing data processes.

The COST table captures records containing the cost of any medical event recorded in one of the OMOP clinical event tables such as DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, VISIT_OCCURRENCE, VISIT_DETAIL, DEVICE_OCCURRENCE, OBSERVATION or MEASUREMENT.

BackgroundThe use of routinely collected health data for secondary research purposes is increasingly recognised as a methodology that advances medical research, improves patient outcomes, and guides policy. This secondary data, as found in electronic medical records (EMRs), can be optimised through conversion into a uniform data structure to enable analysis alongside other comparable health metric datasets. This can be achieved with the Observational Medical Outcomes Partnership Common Data Model (OMOP-CDM), which employs a standardised vocabulary to facilitate systematic analysis across various observational databases. The concept behind the OMOP-CDM is the conversion of data into a common format through the harmonisation of terminologies, vocabularies, and coding schemes within a unique repository. The OMOP model enhances research capacity through the development of shared analytic and prediction techniques; pharmacovigilance for the active surveillance of drug safety; and ‘validation’ analyses across multiple institutions across Australia, the United States, Europe, and the Asia Pacific. In this research, we aim to investigate the use of the open-source OMOP-CDM in the PATRON primary care data repository.MethodsWe used standard structured query language (SQL) to construct, extract, transform, and load scripts to convert the data to the OMOP-CDM. The process of mapping distinct free-text terms extracted from various EMRs presented a substantial challenge, as many terms could not be automatically matched to standard vocabularies through direct text comparison. This resulted in a number of terms that required manual assignment. To address this issue, we implemented a strategy where our clinical mappers were instructed to focus only on terms that appeared with sufficient frequency. We established a specific threshold value for each domain, ensuring that more than 95% of all records were linked to an approved vocabulary like SNOMED once appropriate mapping was completed. To assess the data quality of the resultant OMOP dataset we utilised the OHDSI Data Quality Dashboard (DQD) to evaluate the plausibility, conformity, and comprehensiveness of the data in the PATRON repository according to the Kahn framework.ResultsAcross three primary care EMR systems we converted data on 2.03 million active patients to version 5.4 of the OMOP common data model. The DQD assessment involved a total of 3,570 individual evaluations. Each evaluation compared the outcome against a predefined threshold. A ’FAIL’ occurred when the percentage of non-compliant rows exceeded the specified threshold value. In this assessment of the primary care OMOP database described here, we achieved an overall pass rate of 97%.ConclusionThe OMOP CDM’s widespread international use, support, and training provides a well-established pathway for data standardisation in collaborative research. Its compatibility allows the sharing of analysis packages across local and international research groups, which facilitates rapid and reproducible data comparisons. A suite of open-source tools, including the OHDSI Data Quality Dashboard (Version 1.4.1), supports the model. Its simplicity and standards-based approach facilitates adoption and integration into existing data processes.

BackgroundThe use of routinely collected health data for secondary research purposes is increasingly recognised as a methodology that advances medical research, improves patient outcomes, and guides policy. This secondary data, as found in electronic medical records (EMRs), can be optimised through conversion into a uniform data structure to enable analysis alongside other comparable health metric datasets. This can be achieved with the Observational Medical Outcomes Partnership Common Data Model (OMOP-CDM), which employs a standardised vocabulary to facilitate systematic analysis across various observational databases. The concept behind the OMOP-CDM is the conversion of data into a common format through the harmonisation of terminologies, vocabularies, and coding schemes within a unique repository. The OMOP model enhances research capacity through the development of shared analytic and prediction techniques; pharmacovigilance for the active surveillance of drug safety; and ‘validation’ analyses across multiple institutions across Australia, the United States, Europe, and the Asia Pacific. In this research, we aim to investigate the use of the open-source OMOP-CDM in the PATRON primary care data repository.MethodsWe used standard structured query language (SQL) to construct, extract, transform, and load scripts to convert the data to the OMOP-CDM. The process of mapping distinct free-text terms extracted from various EMRs presented a substantial challenge, as many terms could not be automatically matched to standard vocabularies through direct text comparison. This resulted in a number of terms that required manual assignment. To address this issue, we implemented a strategy where our clinical mappers were instructed to focus only on terms that appeared with sufficient frequency. We established a specific threshold value for each domain, ensuring that more than 95% of all records were linked to an approved vocabulary like SNOMED once appropriate mapping was completed. To assess the data quality of the resultant OMOP dataset we utilised the OHDSI Data Quality Dashboard (DQD) to evaluate the plausibility, conformity, and comprehensiveness of the data in the PATRON repository according to the Kahn framework.ResultsAcross three primary care EMR systems we converted data on 2.03 million active patients to version 5.4 of the OMOP common data model. The DQD assessment involved a total of 3,570 individual evaluations. Each evaluation compared the outcome against a predefined threshold. A ’FAIL’ occurred when the percentage of non-compliant rows exceeded the specified threshold value. In this assessment of the primary care OMOP database described here, we achieved an overall pass rate of 97%.ConclusionThe OMOP CDM’s widespread international use, support, and training provides a well-established pathway for data standardisation in collaborative research. Its compatibility allows the sharing of analysis packages across local and international research groups, which facilitates rapid and reproducible data comparisons. A suite of open-source tools, including the OHDSI Data Quality Dashboard (Version 1.4.1), supports the model. Its simplicity and standards-based approach facilitates adoption and integration into existing data processes.

The RELATIONSHIP table provides a reference list of all types of relationships that can be used to associate any two concepts in the CONCEPT_RELATIONSHP table.

The PAYER_PLAN_PERIOD table captures details of the period of time that a Person is continuously enrolled under a specific health Plan benefit structure from a given Payer.

The CONCEPT_RELATIONSHIP table contains records that define direct relationships between any two Concepts and the nature or type of the relationship.

The 'Drug' domain captures records about the utilization of a Drug when ingested or otherwise introduced into the body.

The PROVIDER table contains a list of uniquely identified healthcare providers. These are individuals providing hands-on healthcare to patients, such as physicians, nurses, midwives, physical therapists etc.

DECOVID, a multi-centre research consortium, was founded in March 2020 by two United Kingdom (UK) National Health Service (NHS) Foundation Trusts (comprising three acute care hospitals) and three research institutes/universities: University Hospitals Birmingham (UHB), University College London Hospitals (UCLH), University of Birmingham, University College London and The Alan Turing Institute. The original aim of DECOVID was to share harmonised electronic health record (EHR) data from UCLH and UHB to enable researchers affiliated with the DECOVID consortium to answer clinical questions to support the COVID-19 response.   ​​   ​​The DECOVID database has now been placed within the infrastructure of PIONEER, a Health Data Research (HDR) UK funded data hub that contains data from acute care providers, to make the DECOVID database accessible to external researchers not affiliated with the DECOVID consortium.  

This highly granular dataset contains 256,804 spells and 165,414 hospitalised patients. The data includes demographics, serial physiological measurements, laboratory test results, medications, procedures, drugs, mortality and readmission.

Geography: UHB is one of the largest NHS Trusts in England, providing direct acute services & specialist care across four hospital sites, with 2.2 million patient episodes per year, 2750 beds & > 120 ITU bed capacity. UCLH provides first-class acute and specialist services in six hospitals in central London, seeing more than 1 million outpatient and 100,000 admissions per year. Both UHB and UCLH have fully electronic health records. Data has been harmonised using the OMOP data model. Data set availability: Data access is available via the PIONEER Hub for projects which will benefit the public or patients. This can be by developing a new understanding of disease, by providing insights into how to improve care, or by developing new models, tools, treatments, or care processes. Data access can be provided to NHS, academic, commercial, policy and third sector organisations. Applications from SMEs are welcome. There is a single data access process, with public oversight provided by our public review committee, the Data Trust Committee. Contact pioneer@uhb.nhs.uk or visit www.pioneerdatahub.co.uk for more details.

Available supplementary data: Matched controls; ambulance and community data. Unstructured data (images). We can provide the dataset in other common data models and can build synthetic data to meet bespoke requirements.

Available supplementary support: Analytics, model build, validation & refinement; A.I. support. Data partner support for ETL (extract, transform & load) processes. Bespoke and “off the shelf” Trusted Research Environment (TRE) build and run. Consultancy with clinical, patient & end-user and purchaser access/ support. Support for regulatory requirements. Cohort discovery. Data-driven trials and “fast screen” services to assess population size.