2020 July JAMIA Journal Club Webinar

July 9, 2020
Free for AMIA members and non-members; no fee.
David Oniani; Feichen Shen, PhD

Constructing Co-occurrence Network Embeddings to Assist Association Extraction for COVID-19 and Other Coronavirus Infectious Diseases

A JAMIA Journal Club webinar – part of AMIA’s COVID-19 Resource Center

Co-authors David Oniani and Feichen Shen, PhD discuss this month's JAMIA Journal Club selection:

Oniani D, Jiang G, Liu H, Shen F. Constructing Co-occurrence Network Embeddings to Assist Association Extraction for COVID-19 and Other Coronavirus Infectious Diseases [published online ahead of print, 2020 May 27]. J Am Med Inform Assoc. 2020;ocaa117. [Article]


David Oniani
Mayo Clinic
Kern Center for the Science of Health Care Delivery
Rochester, MN

David Oniani is an undergraduate student double majoring in computer science and mathematics. He is currently a research and development intern in the Kern Center for the Science of Health Care Delivery at Mayo Clinic. His interests include artificial intelligence, information and knowledge management, and emerging technologies.

Feichen Shen, PhD
Assistant Professor of Biomedical Informatics
Division of Digital Health Sciences
Mayo Clinic
Rochester MN

Dr. Feichen Shen is an Assistant Professor of Biomedical Informatics and an Associate Consultant in the Division of Digital Health Sciences at Mayo Clinic. His primary research focus is to improve health care delivery and facilitate translational studies by developing machine/deep learning methodologies and applications. Specifically, Dr. Shen is interested in AI-driven rare disease differential diagnosis and precision medicine informatics.


  • 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:


Maryam Zolnoori, PhD, Postdoctoral Research Fellow, Department of Digital Health Sciences and Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN


Travis Goodwin, PhD, graduated from the University of Texas at Dallas with a PhD in Computer Science. He is currently a postdoctoral research fellow at the U.S. National Library of Medicine of the National Institutes of Health. 



Statement of Purpose

Featuring a large number of scientific articles related to COVID-19, CORD-19 is a valuable resource that facilitates the research study of COVID-19 and related coronaviruses. CORD-19-on-FHIR is a Linked Data version of CORD-19. It is represented in the RDF format and provides an easy way to extract co-occurred associations (e.g., of chemicals, mutations, etc).

In this study, we applied an existing network embeddings model (node2vec) over a co-occurrence network derived from CORD-19-on-FHIR, in order to facilitate association detection and knowledge discovery for COVID-19 and related coronavirus infectious diseases.

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:

  • Identify and discuss the general process of constructing a co-occurrence network (in this case, using CORD-19-on-FHIR)
  • Apply node2vec to generate co-occurrence network embeddings
  • Demonstrate results with a web-based user-friendly tool

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.

The live webinar only offers CME credit. The recording on our website will be openly available for learners, but will not offer CME credit.

Commercial Support

No commercial support was received for this 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 presenters: David Oniani and Feichen Shen
JAMIA Journal Club planners: Michael Chiang, Travis Goodwin, Maryam Zolnoori
AMIA staff: Susanne Arnold, Pesha Rubinstein

Contact Info

For questions about webinar access, email Susanne@amia.org.

Instructions for Claiming CME Credit

Use the link in the chat area to claim credit; in a few days you will receive an email with your CME certificate.
If you require a certificate of participation, contact Pesha@amia.org