Extending an Uncertainty Taxonomy for Suspected Pneumonia Case Review

Natural language processing algorithms that accurately screen clinical documents for suspected pneumonia must extract and reason about whether these mentions provide evidence that supports, refutes, or represents uncertainty. Our efforts extend existing algorithms [1] and taxonomies [2] that can be leveraged by NLP tools for more accurate handling of uncertainty for suspected pneumonia case review.


September 11, 2017

Classifying Supporting, Refuting, or Uncertain Evidence for Pneumonia Case Review

Characterizing mentions found in clinical texts that support, refute, or represent uncertainty for suspected pneumonia is one area where automated Natural Language Processing (NLP) screening algorithms could be improved. Mentions of uncertainty and negation commonly occur in clinical texts, and opportunities exist to extend existing algorithms [1] and taxonomies [2].

October 10, 2017

#wheezing: A Content Analysis of Asthma-Related Tweets

Recently, a growing number of studies have made use of Twitter to track the spread of infectious disease. These investigations show that there are reliable spikes in traffic related to keywords associated with the spread of infectious diseases like Influenza [1], as well as other Syndromes [2]. However, little research has been done using Social Media to monitor chronic conditions like Asthma, which do not spread from sufferer to sufferer.

January 19, 2018

An ISDS-Based Initiative for Conventions for Biosurveillance Data Analysis Methods

Twelve years into the 21st century, after publication of hundreds of articles and establishment of numerous biosurveillance systems worldwide, there is no agreement among the disease surveillance community on most effective technical methods for public health data monitoring. Potential utility of such methods includes timely anomaly detection, threat corroboration and characterization, follow-up analysis such as case linkage and contact tracing, and alternative uses such as providing supplementary information to clinicians and policy makers.

January 24, 2018

A web-based platform to support text mining of clinical reports for public health surveillance

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.

May 02, 2019

Evaluating Syndrome Definitions in the Extended Syndromic Surveillance Ontology

The Extended Syndromic Surveillance Ontology (ESSO) is an open source terminological ontology designed to facilitate the text mining of clinical reports in English [1,2]. At the core of ESSO are 279 clinical concepts (for example, fever, confusion, headache, hallucination, fatigue) grouped into eight syndrome categories (rash, hemorrhagic, botulism, neurological, constitutional, influenza-like-illness, respiratory, and gastrointestinal). In addition to syndrome groupings, each concept is linked to synonyms, variant spellings and UMLS Concept Unique Identifiers.

May 02, 2019

Using cKASS to facilitate knowledge authoring and sharing for syndromic surveillance

Mining text for real-time syndromic surveillance usually requires a comprehensive knowledge base (KB) which contains detailed information about concepts relevant to the domain, such as disease names, symptoms, drugs, and radiology findings. Two such resources are the Biocaster Ontology [1] and the Extended Syndromic Surveillance Ontology (ESSO) [2]. However, both these resources are difficult to manipulate, customize, reuse and extend without knowledge of ontology development environments (like Protege) and Semantic Web standards (like RDF and OWL).

May 02, 2019

Unstructured Free-text Data and Meaningful Use

In 2010, as rules for the Centers for Medicaid and Medicare Electronic Heatlh Record (EHR) Incentive Programs (Meaningful Use)(1), were finalized, ISDS became aware of a trend towards new EHR systems capturing or sending emergency department (ED) chief complaint (CC) data as structured variables without including the free-text. This perceived shift in technology was occurring in the absence of consensus-based technical requirements for syndromic surveillance and survey data on the value of free-text CC to public health practice.

May 02, 2019

Developing an application ontology for mining clinical reports: the extended syndromic surveillance ontology

Ontologies representing knowledge from the public health and surveillance domains currently exist. However, they focus on infectious diseases (infectious disease ontology), reportable diseases (PHSkbFretired) and internet surveillance from news text (BioCaster ontology), or are commercial products (OntoReason public health ontology). From the perspective of biosurveillance text mining, these ontologies do not adequately represent the kind of knowledge found in clinical reports.

June 14, 2019

Challenges in adapting an natural language processing system for real-time surveillance

We are developing a Bayesian surveillance system for realtime surveillance and characterization of outbreaks that incorporates a variety of data elements, including free-text clinical reports. An existing natural language processing (NLP) system called Topaz is being used to extract clinical data from the reports. Moving the NLP system from a research project to a real-time service has presented many challenges.



Adapt an existing NLP system to be a useful component in a system performing real-time surveillance.

June 18, 2019


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