2019 May JAMIA Journal Club Webinar

May 9, 2019
Free for AMIA members; $50 for non-members.
Chunhua Weng, PhD

Criteria2Query: a natural language interface to clinical databases for cohort definition

Co-author Chunhua Weng will discuss this month's JAMIA Journal Club selection:

Yuan C, Ryan PB, Ta C, et al. Criteria2Query: a natural language interface to clinical databases for cohort definition. J Am Med Inform Assoc. 2019 Apr 1;26(4):294-305. doi: 10.1093/jamia/ocy178. [Article]


Chunhua Weng, PhD
Associate Professor of Biomedical Informatics
Department of Biomedical Informatics
Columbia University
New York, NY

Dr. Chunhua Weng is a tenured Associate Professor of Biomedical Informatics at Columbia University and an elected fellow of the American College of Medical Informatics (ACMI). She has also been co-leading the Biomedical Informatics Resource for the Columbia CTSA (The Irving Institute for Clinical and Translational Science) since 2011. Dr. Weng holds a Ph.D. in Biomedical and Health Informatics from University of Washington at Seattle. As an active researcher in the field of Clinical Research Informatics since 2000, Dr. Weng has published extensively on text knowledge engineering for optimizing clinical research eligibility criteria, electronic screening methods for clinical trial recruitment, EHR data quality assessment and data analytics, and EHR phenotyping. 


  • 35-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.
  • 25-minute discussion of questions submitted by listeners via the webinar tools and moderated by JAMIA Student Editorial Board members


JAMIA Journal Club managers and monthly moderators are JAMIA Student Editorial Board members:

Kelson Zawack, PhD, Postdoctoral Fellow, Biostatistics Department, Yale University, New Haven, CT 

Tiffany J. Callahan, MPH, PhD Candidate, Computational Bioscience Program at the University of Colorado Denver Anschutz Medical Campus, Aurora, CO


Alejandro Schuler, PhD, Data Scientist at Kaiser Permanente Division of Research, Oakland, CA 


The PubMed citation for the paper under discussion is:

Yuan C, Ryan PB, Ta C, et al. Criteria2Query: a natural language interface to clinical databases for cohort definition. J Am Med Inform Assoc. 2019 Apr 1;26(4):294-305. doi: 10.1093/jamia/ocy178. [Article]

Student Access

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 susanne@amia.org 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 $50, which allow access to JAMIA, all JAMIA Journal Clubs, and other webinars of interest to the biomedical informatics community. 

Statement of Purpose

In the medical domain, there are few studies on natural language interfaces to patient-level databases. Before Criteria2Query, no system existed to support natural language querying of complex cohort eligibility criteria. Criteria2Query makes three important contributions by:
(1) Implementing a systematic information extraction pipeline to parse free-text clinical research eligibility criteria into a structured and computable representation;
(2) Improving the interoperability between eligibility criteria and clinical databases by representing eligibility criteria using the OMOP CDM; and
(3) Enabling the autonomy of clinicians and researchers during cohort definition using a novel natural language interface.

Target Audience

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

Learning Objectives

The general learning objective for all of the JAMIA Journal Club webinars is that participants will

  • Use a critical appraisal process to assess article validity and to gauge article findings' relevance to practice

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

  • Develop a natural language interface to standards-based clinical databases
  • Practice the use of open-science principles to enable portable biomedical computing 

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
  • Viewing CME information at registration
  • Optional submission of questions via webinar feature
  • Completion of the evaluation survey available after the webinar
  • Physicians only: request CME credit and receive certificate

For a certificate of completion, contact Pesha@amia.org.

Note that the archived webinar does not offer continuing education credit. 

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: 

JAMIA Journal Club Faculty: Chunhua Weng
JAMIA Journal Club planners: Michael Chiang, Kelson Zawack, Tiffany J. Callahan, Alejandro Schuler
AMIA staff: Susanne Arnold, Pesha Rubinstein

Contact Info

For questions about content or CE, email Pesha@amia.org. For questions about webinar access, email Susanne@amia.org.