PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability

May 12, 2016
Free for AMIA members and students of Academic Forum member institutions; Others: $50
Jacqueline Kirby, MS; Joshua Denny, MD, MS, FACMI

PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability

Author Jacqueline Kirby will discuss this month's JAMIA Journal Club selection:

Kirby JC, Speltz P, Rasmussen LV, et al. PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability. J Am Med Inform Assoc. 2016 Mar 28. pii: ocv202. doi: 10.1093/jamia/ocv202. [Epub ahead of print]


Jacqueline Kirby, MS, Project Manager: Before coming to Vanderbilt, Jacqueline Kirby had project management and data analysis experience in a number of areas within the health care industry. She manages diverse projects related to development and implementation of informatics infrastructure supporting the use of clinical data. Locally, she manages the Vanderbilt research data warehouses; as part of larger consortia, she has been the project manager for the Mid-South Clinical Data Research Network with PCORI, eMERGE, and the Clinical Decision Support Consortium. As project manager of the eMERGE Network, she has managed the development of the collaborative space for phenotype algorithm development, PheKB. Additionally, she has managed projects to create the eMERGE Network’s Record Counter; Clinical Decision Support Knowledge Base (CDS-KB); and Sequence, Phenotype, and Pharmacogenomics Integration Exchange (SPHINX). SPHINX is a web-based tool for exploring data for hypothesis generation, especially around drug response implications of genetic variation. In addition, Jacqueline Kirby is involved with other data collection efforts.  

Joshua C. Denny, MD, MS, FACMI, has primary research interests in the development of tools to identify phenotypic traits from electronic health records (EHR) to allow for clinical and genomic analyses of EMR-linked genetic data, and implementation of personalized medicine into clinical care. He is the primary developer of the phenome-wide association study (PheWAS) method which will be used in this project and he has had substantial experience in the design, development, and implementation of EHR data mining algorithms, and was the primary author of several natural language processing systems to support phenotype extraction algorithms for genomic research projects. To date, Dr. Denny has led >40 genome-wide and candidate gene association studies using EHR data linked to genetic data and performed PheWAS using data from seven different sites. He serves as the principal investigator for the Synthetic Derivative, the de-identified version of the electronic medical record at Vanderbilt, and is co-chair of the eMERGE phenotype and pharmacogenomics workgroups. Dr. Denny has training in biomedical informatics, computer science, epidemiology, and biostatistics.


  • 40-minute discussion between the authors and the JAMIA Student Editorial Board moderators including salient features of the published study and its potential impact on practice.
  • 20-minute discussion of questions submitted by listeners via the webinar tools.


  • Follow @AMIAinformatics and #JAMIAJC for Journal Club information.
  • Participants also receive short feedback surveys to evaluate the JAMIA JC webinar.


JAMIA Journal Club managers are JAMIA Student Editorial Board members:

Mary Regina Boland, MA, Department of Biomedical Informatics, Columbia University

Matthew K. Breitenstein, PhD, Department of Health Sciences Research, Mayo Clinic


The PubMed citation for the paper under discussion is:

Kirby JC, Speltz P, Rasmussen LV, et al. PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability. J Am Med Inform Assoc. 2016 Mar 28. pii: ocv202. doi: 10.1093/jamia/ocv202. [Epub ahead of print]

The abstract is available here.

Fee Statement

Students who are not AMIA members, but whose academic institutions are members of the Academic Forum, are eligible for a complimentary JAMIA Journal Club registration. Please contact Susanne Arnold at for the discount code. In the email, please include: full name, Academic Department, and the primary Academic Forum representative of that Academic Department. Note that AMIA Student memberships are $45, which allow access to JAMIA, all JAMIA Journal Clubs, and other webinars of interest to the biomedical informatics community. 

Statement of Purpose

Healthcare generated data have become an important source for clinical and genomic research. Often investigators create and iteratively refine phenotype algorithms to achieve high positive predictive values (PPVs) or sensitivity, thereby identifying true cases and controls. These algorithms achieve greatest utility when validated and shared by multiple healthcare systems.
Institutions that engage in clinical and genomic research will want to assess the value of Phenotype KnowledgeBase (PheKB,, an online environment to support reuse as well as their own building, sharing, and validating electronic phenotype algorithms. 

Target Audience

The target audience for this activity is professionals and students interested in biomedical and health informatics.

Learning Objective

After this live activity, the participant should be better able to:

  • Assess the value of PheKB for one’s institution or network for the use, production, refining, or validation of phenotype algorithms derived from aggregated health care data 


Jacqueline Kirby, MS
Senior IT Project Manager
Vanderbilt University Medical Center
Nashville, TN

Joshua C. Denny, MD, MS, FACMI
Assistant Professor
Departments of Biomedical Informatics and Medicine
Vanderbilt University School of Medicine
Nashville, TN

Accreditation Statement

The American Medical Informatics Association is accredited by the Accreditation Council for Continuing Medical Education to provide continuing medical education for physicians.

Credit Designation Statement

The American Medical Informatics Association designates this live activity for a maximum of 1 AMA PRA Category 1 Credit(s). Physicians should claim only the credit commensurate with the extent of their participation in the activity. 

Criteria for Successful Completion

Completion of this live activity is demonstrated by:

  • Viewing the live webinar
  • Optional submission of questions via webinar feature; option to follow @AMIAinformatics and tweet via #JAMIAJC
  • Completion of the evaluation survey at and 
  • Verification of attendance through the participant's electronic report through the individual login at 

The physician participant will be able to generate a CME certificate through the AMIA automated system. 
For a certificate of completion, contact

Commercial Support

No commercial support was received for this activity.

Disclosure Policy

As a provider accredited by the ACCME, AMIA requires that everyone who is in a position to control the content of an educational activity disclose all relevant financial relationships with any commercial interest for 12 months prior to the educational activity.

The ACCME considers relationships of the person involved in the CME activity to include financial relationships of a spouse or partner.

Faculty and planners who refuse to disclose relevant financial relationships will be disqualified from participating in the CME activity. For an individual with no relevant financial relationship(s), the participants must be informed that no conflicts of interest or financial relationship(s) exist.

AMIA uses a number of methods to resolve potential conflicts of interest, including: limiting content of the presentation to that which has been reviewed by one or more peer reviewers; ensuring that all scientific research referred to conforms to generally accepted standards of experimental design, data collection, and analysis; undertaking review of the educational activity by a content reviewer to evaluate for potential bias, balance in presentation, evidence-based content or other indicators of integrity, and absence of bias; monitoring the educational activity to evaluate for commercial bias in the presentation; and/or reviewing participant feedback to evaluate for commercial bias in the activity.

Disclosures for this Activity

These faculty, planners, and staff who are in a position to control the content of this activity disclose that they and their life partners have no relevant financial relationships with commercial interests: 

Faculty: Jacqueline Kirby, Josh Denny
JAMIA Journal Club planners: Mary Regina Boland, Matthew Breitenstein
AMIA staff: Susanne Arnold, Pesha Rubinstein

JAMIA Journal Club planner Michael Chiang discloses the following:

  • Received Grant/Research support from the National Institutes of Health
  • Is an unpaid member of the Scientific Advisory Board of Clarity Medical Systems

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  • Click “Apply for Credits" link for meeting or event you attended.
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Contact Info

For questions about content or CE, email