Natural Language Processing (NLP)

Mortality is an indicator of the severity of the impact of an event on the population. In France mortality surveillance is part of the syndromic surveillance system SurSaUD and is carried out by Santé publique France, the French public health agency. The set-up of an Electronic Death Registration System (EDRS) in 2007 enabled to receive in real-time medical causes of death in free-text format. This data source was considered as reactive and valuable to implement a reactive mortality surveillance system using medical causes of death (1). The reactive mortality surveillance system is based on the monitoring of Mortality Syndromic Groups (MSGs). An MSG is defined as a cluster of medical causes of death (pathologies, syndromes, symptoms) that meet the objectives of early detection and impact assessment of events (2). Since causes of death are entered in free-text format, their automatic classifications into MSGs require the use of natural language processing methods. We observe a constant increase in the use of these methods to classify medical information and for health surveillance over the last two decades (3).

Objective: This study aims to implement and evaluate two automatic classification methods of free-text medical causes of death into Mortality Syndromic Groups (MSGs) in order to be used for reactive mortality surveillance.

Opioid overdoses have emerged within the last five to ten years to be a major public health concern. The high potential for fatal events, disease transmission, and addiction all contribute to negative outcomes. However, what is currently known about opioid use and overdose is generally gathered from emergency room data, public surveys, and mortality data. In addition, opioid overdoses are a non-reportable condition. As a result, state/national standardized procedures for surveillance or reporting have not been developed, and local government monitoring is frequently not specific enough to capture and track all opioid overdoses. Lastly, traditional means of data collection for conditions such as heart disease through hospital networks or insurance companies are not necessarily applicable to opioid overdoses, due to the often short disease course of addiction and lack of consistent health care visits. Overdose patients are also reluctant to follow-up or provide contact information due to law enforcement or personal reasons. Furthermore, collected data related to overdoses several months or years after the fact are useless in terms of short-term outreach. Therefore, given the potentially brief timeline of addiction or use to negative outcome, the current project set to create a near real-time surveillance and treatment/outreach system for opioid overdoses using an already existing EMS data collection framework.

Objective: To develop and implement a classifcation algorithm to identify likely acute opioid overdoses from text fields in emergency medical services (EMS) records.

Emergency department (ED) syndromic surveillance relies on a chief complaint, which is often a free-text field, and may contain misspelled words, syntactic errors, and healthcare-specific and/or facility-specific abbreviations. Cleaning of the chief complaint field may improve syndrome capture sensitivity and reduce misclassification of syndromes. We are building a spell-checker, customized with language found in ED corpora, as our first step in cleaning our chief complaint field. This exercise would elucidate the value of pre-processing text and would lend itself to future work using natural language processing (NLP) techniques, such as topic modeling. Such a tool could be extensible to other datasets that contain free-text fields, including electronic reportable disease lab and case reporting.

Objective: To share progress on a custom spell-checker for emergency department chief complaint free-text data and demonstrate a spell-checker validation Shiny application.

Despite considerable effort since the turn of the century to develop Natural Language Processing (NLP) methods and tools for detecting negated terms in chief complaints, few standardised methods have emerged. Those methods that have emerged (e.g. the NegEx algorithm) are confined to local implementations with customised solutions. Important reasons for this lack of progress include (a) limited shareable datasets for developing and testing methods (b) jurisdictional data silos, and (c) the gap between resource-constrained public health practitioners and technical solution developers, typically university researchers and industry developers. To address these three problems ISDS, funded by a grant from the Defense Threat Reduction Agency, organized a consultancy meeting at the University of Utah designed to bring together (a) representatives from public health departments, (b) university researchers focused on the development of computational methods for public health surveillance, (c) members of public health oriented non-governmental organisations, and (d) industry representatives, with the goal of developing a roadmap for the development of validated, standardised and portable resources (methods and data sets) for negation detection in clinical text used for public health surveillance.

Objective: This abstract describes an ISDS initiative to bring together public health practitioners and analytics solution developers from both academia and industry to define a roadmap for the development of algorithms, tools, and datasets to improve the capabilities of current text processing algorithms to identify negated terms (i.e. negation detection).

PyConTextKit is a web-based platform that extracts entities from clinical text and provides relevant metadata - for example, whether the entity is negated or hypothetical - using simple lexical clues occurring in the window of text surrounding the entity. The system provides a flexible framework for clinical text mining, which in turn expedites the development of new resources and simplifies the resulting analysis process. PyConTextKit is an extension of an existing Python implementation of the ConText algorithm, which has been used successfully to identify patients with an acute pulmonary embolism and to identify patients with findings consistent with seven syndromes. Public health practitioners are beginning to have access to clinical symptoms, findings, and diagnoses from the EMR. Making use of this data is difficult, because much of it is in the form of free text. Natural language processing techniques can be leveraged to make sense of this text, but such techniques often require technical expertise. PyConTextKit provides a web-based interface that makes it easier for the user to perform concept identification for surveillance. We describe the development of a web based application - PyConTextKit - to support text mining of clinical reports for public health surveillance.

Objective

We describe the development of a web based application - PyConTextKit - to support text mining of clinical reports for public health surveillance.