EHR-Based Phenotyping Tools

Created by the Collaboratory Phenotypes, Data Standards, and Data Quality Core

Tools for ResearchOn this page, you will find a series of recommendations for collecting and querying data from electronic health records for patient characteristics and clinical features. These phenotype definition recommendations are intended to support the conduct of pragmatic clinical trials, as well as encourage standardized reporting of baseline characteristics of research populations in interventional and observational studies. Also included are resources for identifying additional phenotype definitions through literature search or other groups engaged in electronic phenotyping. Background information on the identification, evaluation, and implementation of phenotype definitions is available in the Living Textbook chapter.

The information presented is continually evaluated and updated as new use cases, phenotype definitions, and phenotype validation results become known. All recommended phenotype definitions are also available directly from the NIH Collaboratory Knowledge Repository.

Please note: all documents listed below open as Adobe PDFs. If you do not have software that can open a PDF, click here to download a free version of Adobe Acrobat Reader.

Recommended Phenotype Definitions

Common Conditions

Resources for Additional Phenotype Definitions

This work was supported by a cooperative agreement (U54 AT007748) from the NIH Common Fund for the NIH Health Care Systems Research Collaboratory. Recommendations are produced by members of the NIH Collaboratory Phenotypes, Data Standards, and Data Quality Core. The material has not been fully vetted or endorsed by the NIH, the Collaboratory Steering Committee, or all Collaboratory members.

Originally published on June 27, 2014.
Last updated November 11, 2015.

  • We encourage comment, including updated information on formal validation or institutional experience with any of the referenced phenotype definitions, or suggestions, corrections, or clarifications regarding our supporting information or interpretation.
  • Questions or comments can be submitted via email. Please add “Living Textbook” to the Subject line of the email.