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OHDSI Gold Standard Phenotype Library Working Group

This update provides an overview of the progress made in the implementation of the OHDSI Gold Standard Phenotype Library. It includes information on the design, evaluation, and architecture of the library, as well as the development of a preliminary example viewer app. The update also discusses the need for restructuring data in JSON format, decoupling data in the viewer app, and the plans for testing, feedback, and deployment of the library.

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OHDSI Gold Standard Phenotype Library Working Group

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  1. OHDSI Gold Standard Phenotype Library Working Group Library Architecture and Implementation: Progress Update and Next Steps Aaron Potvien March 26, 2019

  2. Gold Standard Phenotype Library Phenotypes Design Evaluation Rule-Based(Heuristic) Computable(Probabilistic) Chart Review(Annotations) Automated(Algorithmic) Library Architecture and Implementation

  3. Gold Standard Phenotype Library Preliminary Work and Brainstorming Example Viewer App Developed Library Architecture Formulation Example Viewer App Deployed Demonstrate External File Reading Flagship Use Case Program for Simplified Inputs Test and Feedback (Alpha/Beta) Transition Data to Final Location Onward!

  4. Gold Standard Phenotype Library Preliminary Work and Brainstorming Example Viewer App Developed Library Architecture Formulation Example Viewer App Deployed Demonstrate External File Reading Flagship Use Case Program for Simplified Inputs Test and Feedback (Alpha/Beta) Transition Data to Final Location Onward!

  5. Preliminary Work Phenotypes • Development of Use Cases • 2019 Kick-off: GSPL Group Formation with biweekly meetings • Brainstorming, presentations, and discussion • Breakdown of Design/Evaluation portions and assignment of task leads Design Evaluation Rule-Based(Heuristic) Computable(Probabilistic) Chart Review(Annotations) Automated(Algorithmic) Library Architecture and Implementation

  6. Library Architecture Formulation End User Authors Librarians Validators

  7. Example Viewer Application Developed

  8. Example Viewer Application Deployed To Access: data.ohdsi.org

  9. Demonstrate External File Reading 1) Need to restructure data in JSON format 2) Need to decouple the data in the viewer app from the app itself OHDSI/ShinyDeploy OHDSI/PhenotypeLibrary Hosts the app Hosts the data Get JSON

  10. Flagship Use Case • Going forward with the first “real” phenotype… • What will this group’s flagship example definition be? • Any volunteers to put forward one definition for this use? • Any volunteers to validate this definition, once it’s available?

  11. Program for Simplified Inputs • JSON data might look something like this: • Any ideas for a form-like structure that can automatically check data validity and JSONify it? • What should submission to the library look like?

  12. Testing and Feedback (Alpha/Beta) • Once we’ve established our Flagship Example, we should repeat the process for a few other hand-curated examples. • Ideally, we would have multiple participants to get a variety of experiences with the library. • This gives us a chance to work out any kinks before we deploy it to the larger community. • Think “Alpha” or “Beta” testing.

  13. After that… • Deployment • Assignment of roles (e.g. who will be the librarians) • Dissemination at the OHDSI Symposium, Forums, etc. • (And plenty of other details to be accounted for along the way!)

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