OMOP Tool Evaluation
- Daniel Popham
Owned by Daniel Popham
Detailed Information
| Name | Description | URL | Will be used for project | Notes | Evaluation Date | Tool Availability Date |
|---|---|---|---|---|---|---|
| CDM R package | https://ohdsi.github.io/Hades/rSetup.html | Yes, required for other tools | Needed for most tools to run. | 11/3/2023 | 11/6/2023 | |
| Data Quality Dashboard | Runs a set of > 3500 data quality checks against an OMOP CDM instance and is required to be run on all databases prior to participating in an OHDSI network research study. | https://github.com/OHDSI/DataQualityDashboard | Yes | Highly suggested to use for initial project data mapping. Setup Instructions: https://raw.githubusercontent.com/OHDSI/DataQualityDashboard/main/inst/doc/DataQualityDashboard.pdf | 11/3/2023 | Local Usage via R - 12/29/2023 Web Server Usage - WIP |
| Achilles | Performs a set of broad database characterizations against an OMOP CDM instance. | https://github.com/OHDSI/Achilles https://www.ohdsi.org/web/wiki/doku.php?id=documentation:software:achilles | Yes | Needed for ARES and ATLAS to run. | 11/3/2023 | 12/29/2023 |
| ARES | Display the results from both the ACHILLES and DataQualityDashboard packages to support data quality and characterization research. | Yes | Suggested by Jared Houghtaling of Tufts Medicine. | 11/3/2023 | 8/14/2024 | |
| ATLAS | Useful for defining cohorts, creating data characterizations, and producing models that can be trained in R. | No | Suggested by Jared Houghtaling of Tufts Medicine, however cannot find installation link yet. Reassessed on 2/15/24 during OMOP office hours. Cohort creation will be useful for unit testing and possibly identifying patients for future projects. | 2/15/2024 | ||
| Rabbit-In-A-Hat/WhiteRabbit | An application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit. | https://github.com/OHDSI/WhiteRabbit | No | Suggested by Jared Houghtaling of Tufts Medicine. Used for generating simple synthetic data based on real data input. Might not be needed for this initial project. | 11/3/2023 | |
| Feature Extraction | It is designed to generate features (covariates) for a cohort generated using the OMOP CDM. | No | As of Nov 2023, this tool does not appear to be needed for the current requirements. | 11/3/2023 | ||
| Cohort Diagnostics | Used to critically evaluate cohort phenotypes. | No | As of Nov 2023, this tool does not appear to be needed for the current requirements. | 11/3/2023 |
References
- Installing R - R is needed to support several of the OMOP tools
- OMOP Version Support - Official wiki page showing latest OMOP version and tools that support the latest version