Applications of Natural Language Processing in Clinical Research and Practice

AbstractRapid growth in adoption of electronic health records (EHRs) has led to an unprecedented expansion in the availability of large longitudinal datasets. Large initiatives such as the Electronic Medical Records and Genomics (eMERGE) Network, the Patient-Centered Outcomes Research Network (PCORNet), and the Observational Health Data Science and Informatics (OHDSI) consortium, have been established and have reported successful applications of secondary use of EHRs in clinical research and practice. In these applications, natural language processing (NLP) technologies have played a crucial role as much of detailed patient information in EHRs is embedded in narrative clinical documents. Meanwhile, a number of clinical NLP systems, such as MedLEE, MetaMap/MetaMap Lite, cTAKES, and MedTagger have been developed and utilized to extract useful information from diverse types of clinical text, such as clinical notes, radiology reports, and pathology reports. Success stories in applying these tools have been reported widely. Despite the demonstrated success of NLP in the clinical domain, methodologies and tools developed for the clinical NLP are still underknown and underutilized by students and experts in the general NLP domain, mainly due to the limited exposure to EHR data. Through this tutorial, we would like to introduce NLP methodologies and tools developed in the clinical domain, and showcase the real-world NLP applications in clinical research and practice at Mayo Clinic (the No. 1 national hospital ranked by the U.S. News & World Report) and the University of Minnesota (the No. 41 best global universities ranked by the U.S. News & World Report). We will review NLP techniques in solving clinical problems and facilitating clinical research, the state-of-the art clinical NLP tools, and share collaboration experience with clinicians, as well as publicly available EHR data and medical resources, and finally conclude the tutorial with vast opportunities and challenges