The PhenX Toolkit

Abstract

The PhenX (consensus measures for Phenotypes and eXposures) Toolkit (https://www.phenxtoolkit.org) is a freely available, web-based catalog of measurement protocols recommended for use in research with human participants. Use of PhenX protocols promotes collaborative study design and facilitates data sharing and cross-study analysis. PhenX protocols are recommended by domain experts using a consensus process that includes community input. The Toolkit is an established resource that includes protocols across 30 research domains (e.g., Demographics, Cardiovascular, Diabetes) and six focused collections (e.g., Substance Use, Use Disorders, and Recovery, Mental Health Research) that add depth in key research areas. The Toolkit provides detailed protocols and bioinformatics tools to incorporate PhenX protocols during study design. The PhenX Toolkit has over 6,000 registered users and has been recommended in over 700 NIH Notices of Funding Opportunities (NOFOs).
The Substance Use and Recovery Working Group (WG), co-chaired by Dr. Anne Buu (UTHealth Houston) and Dr. John Kelly (Harvard Medical School), recommended 30 new protocols and added a new specialty collection for Substance Use Recovery, released in 2025. The WG addressed the topic areas of medical cannabis use, polysubstance use, and substance use recovery. They also identified updates to language and imagery that reflect modern concepts in PhenX protocols across multiple domains and collections.
The Cardiovascular – Expansion WG, led by Dr. Matthew Allison (UCSD) and Dr. Mark Weiner (Regeneron), will identify new protocols to add to the existing Cardiovascular Domain. The WG is considering the following topic areas: cardiovascular diseases, pulmonary diseases, and blood disorders. We will present the WG’s preliminary list of recommended cardiovascular protocols.
PhenX protocols are associated with various data standards to promote interoperability and data reuse. They are represented by Logical Observation Identifiers Names and Codes (LOINC) codes, which are commonly used in clinical settings to increase compatibility with electronic health records. PhenX protocols are also being implemented as HL7® FHIR® Questionnaire Resources annotated with metadata and associated biomedical standards to enhance their integration into clinical and computational workflows.