NLP Workshop

Use of Natural Language Processing to Extract Information from Clinical Text

June 15, 2017
8:30 am to 5:00 pm (Registration starts at 7:45 am)

Great Room (Building 31, Room 1503A)
FDA White Oak Campus
10903 New Hampshire Ave
Silver Spring, MD 20993



The objective of this workshop is to identify current and emerging natural language processing (NLP) efforts being applied to unstructured text such as clinical notes or narratives in electronic health records (EHRs). The workshop will provide insights into utility and challenges in designing and implementing NLP systems to capture relevant or missing information from clinical notes or text for monitoring postmarketing safety surveillance and informing the design and execution of clinical trials for medical products, which include drugs, biologics, and devices. The workshop will include panel discussion sessions to provide stakeholders with a forum to discuss natural language processing with experts in the field.

The workshop will focus on whether NLP can be applied to unstructured text in clinical notes to:

  • Identify indication or reason for medical product use, adverse outcomes or events associated with use of these products, and confounders or personal behaviors that may modify risks associated with use of these products
  • Support protocol design, feasibility, recruitment efforts and execution of clinical trials


Please click here to view more information about this workshop on the FDA's website.



This workshop is open to the public.  The intended audience includes researchers, industry, public health agencies, the clinical community, and other stakeholders using or interested in using NLP, either by itself or as part of a system, to harness relevant information from unstructured text in clinical notes or narratives in EHRs.

There is no cost to attend, but pre-registration is required. Attendees may attend in person or remotely via webinar (link will be sent to registrants). Attendees arriving in person should allocate sufficient time to clear the security screening process.


Non-FDA attendees and FDA contractors/ORISE fellows: Click here to register.
FDA employees: Click here to register.


Workshop Agenda

The agenda is shown below. A PDF version will be available for download soon.

Time Topic Speaker

7:45 am





8:30 am


Rita Ouellet-Hellstrom, PhD, MPH

8:35 am


Opening Remarks - FDA’s interest in NLP for pharmacoepidemiology and other uses


Robert Ball, MD, MPH

9:00 am


A brief review of recent literature on clinical NLP


Russ Altman, MD, PhD
Stanford University



Moderator: Russ Altman, MD, PhD (Stanford University)

9:30 am


NLP extraction of disease activity measures


Brian Sauer, PhD, MS
University of Utah

10:00 am


Novel NLP for longitudinal analysis of patient records identifying medication treatment patterns, side effects, and adherence


Murthy Devarakonda, PhD
IBM Research

10:30 am



10:45 am


Mining the EHR to understand disease, drugs, and adverse events

Nigam Shah, MBBS, PhD
Stanford University

11:15 am


Panel Discussion - Addressing the strengths and limitations of NLP solutions

Panelists: Robert Ball, MD, MPH (FDA/CDER), Isaac Chang, PhD (FDA/CDRH), Murthy Devarakonda, PhD (IBM Research), Rita Ouellet-Hellstrom, PhD, MPH (FDA/CDER), Brian Sauer, PhD, MS (University of Utah), Nigam Shah, MBBS, PhD (Stanford University), Mark Walderhaug, PhD (FDA/CBER)



Russ Altman, MD, PhD (Stanford University)

12:30 pm


Lunch (on your own)




Moderator: Mark Walderhaug, PhD (FDA/CBER)

1:30 pm


Adapting clinical NLP methods for multi-site medical products research

David Carrell, PhD
Kaiser Permanente Washington Health Research Institute

2:00 pm


Leveraging NLP and diverse data sources to mine drug repositioning, adverse drug events, and patient-reported medication outcome information

Hongfang Liu, PhD
Mayo Clinic

2:30 pm


Flexible NLP for varied applications and data sources, including cohort selection and adverse event coding/validation

David Milward, PhD

3:00 pm


Lessons learned from NLP implementations at FDA

Mitra Rocca, PhD

3:45 pm


Panel Discussion - Can NLP alone or as part of a system address FDA's and the healthcare community’s needs?

Panelists: David Carrell, PhD (Kaiser Permanente Washington Health Research Institute), Isaac Chang, PhD (FDA/CDRH), Hongfang Liu, PhD (Mayo Clinic), David Milward, PhD (Linguamatics), Rita Ouellet-Hellstrom, PhD, MPH (FDA/CDER), Mitra Rocca, PhD (FDA/CDER)



Mark Walderhaug, PhD (FDA/CBER)


4:45 pm


Closing Remarks


Dragutin Petkovic, PhD
San Francisco State University


Lodging and Transportation

Details on lodging and transportation options can be found on FDA's webpage.


Please contact Lawrence Lin at with any questions.