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OHDSI Natural Language Processing Working Group
Objective
The primary goal of the NLP working group is to promote the use of textual information from Electronic Health Records (EHRs) for observational studies under the OHDSI umbrella. To facilitate this objective, the group will develop methods and software that can be implemented to utilize clinical text for studies by the OHDSI community.
Project Lead
Project Coordinator
OHDSI NLP WG Monthly Meeting
When: Second Wednesday of every month at 1 PM - 2 PM CT
Where: Click here to join the meeting
Monthly Meeting: Upcoming - December 14, 2022
Agenda
- Invited talk: Dr. Yanjun Gao, University of Wisconsin
Title: Hierarchical Annotation for Building a Suite of Clinical Natural Language Processing Tasks Abstract: Applying methods in natural language processing on electronic health records (EHR) data has attracted rising interests. Existing corpus and annotation focus on modeling textual features and relation prediction. However, there are a paucity of annotated corpus built to model clinical diagnostic thinking, a processing involving text understanding, domain knowledge abstraction and reasoning. In this talk, I will introduce a hierarchical annotation schema with three tasks to address clinical text understanding, clinical reasoning and summarization. We create an annotated corpus based on a large collection of publicly available daily progress notes, a type of EHR that is time-sensitive, problem-oriented, and well-documented by the format of Subjective, Objective, Assessment and Plan (SOAP). I will present the experiment results of applying state-of-the-art language models to this new suite. I will also talk about how this new suite of tasks could perform the paradigm shift of clinical NLP from information extraction and outcome prediction to diagnostic reasoning, and ultimately to effective clinical decision support systems for physicians at the bedside care.
Presenter:
Dr. Yanjun Gao is a postdoc research associate in the Critical Care Medicine (ICU) Data Science Lab in the Division of Allergy, Pulmonary and Critical Care Medicine within the Department of Medicine. She serves on the organizing committee of 2022 National NLP Clinical Challenges (N2C2), and Graph-based Natural Language Processing Workshop (TextGraphs). She has publications across major NLP and AI conferences including ACL, COLING, CoNLL, and reviews for several NLP and clinical informatics conferences and journals. Her current focus is developing NLP models for diagnostic reasoning using clinical text and medical knowledge.
Ongoing Projects
- Clinical Abbreviations
- Post-acute sequelae of SARS-CoV-2 infection (PASC) study
- Extraction, Transformation, and Load Process (ETL)
- Note type normalization
- Open source Python NLP package
Past Projects
- Note_NLP table
- COVID-19 testing normalization (TestNorm)
- Note type
- NLP tools: NLP Wrappers; THEIA; Ananke
Participants
A noncomprehensive list of participants: Click here
Upcoming Meeting Dates (2022)
- December 14
Repository
- NLP Tools in OHDSI GitHub https://github.com/OHDSI/NLPTools
- OHDSIananke https://github.com/thepanacealab/OHDSIananke
Past WG meetings (Agenda/Minutes/Recordings)
2022
2021
2019
2018
2017
2016
2015
Microsoft Teams meeting
