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The study sought to describe the literature describing clinical reasoning ontology (CRO)-based clinical decision support systems (CDSSs) and identify and classify the medical knowledge and reasoning concepts and their properties within these ontologies to guide future research.

Academic medical centers and health systems are increasingly challenged with supporting appropriate secondary use of clinical data. Enterprise data warehouses have emerged as central resources for these data, but often require an informatician to extract meaningful information, limiting direct access by end users. To overcome this challenge, we have developed Leaf, a lightweight self-service web application for querying clinical data from heterogeneous data models and sources.

Pharmacogenomics (PGx) clinical decision support integrated into the electronic health record (EHR) has the potential to provide relevant knowledge to clinicians to enable individualized care. However, past experience implementing PGx clinical decision support into multiple EHR platforms has identified important clinical, procedural, and technical challenges. Commercial EHRs have been widely criticized for the lack of readiness to implement precision medicine. Herein, we share our experiences and lessons learned implementing new [...]

We implement 2 different multitask learning (MTL) techniques, hard parameter sharing and cross-stitch, to train a word-level convolutional neural network (CNN) specifically designed for automatic extraction of cancer data from unstructured text in pathology reports. We show the importance of learning related information extraction (IE) tasks leveraging shared representations across the tasks to achieve state-of-the-art performance in classification accuracy and computational efficiency.

This study focuses on the task of automatically assigning standardized (topical) subject headings to free-text sentences in clinical nursing notes. The underlying motivation is to support nurses when they document patient care by developing a computer system that can assist in incorporating suitable subject headings that reflect the documented topics. Central in this study is performance evaluation of several text classification methods to assess the feasibility of developing such a [...]

Our objectives were to identify educational interventions designed to equip medical students or residents with knowledge or skills related to various uses of electronic health records (EHRs), summarize and synthesize the results of formal evaluations of these initiatives, and compare the aims of these initiatives with the prescribed EHR-specific competencies for undergraduate and postgraduate medical education.

Accurate and complete information about medications and related information is crucial for effective clinical decision support and precise health care. Recognition and reduction of adverse drug events is also central to effective patient care. The goal of this research is the development of a natural language processing (NLP) system to automatically extract medication and adverse drug event information from electronic health records. This effort was part of the 2018 n2c2 [...]

Phenotyping patients using electronic health record (EHR) data conventionally requires labeled cases and controls. Assigning labels requires manual medical chart review and therefore is labor intensive. For some phenotypes, identifying gold-standard controls is prohibitive. We developed an accurate EHR phenotyping approach that does not require labeled controls.

We aimed to impute uncoded self-harm in administrative claims data of individuals with major mental illness (MMI), characterize self-harm incidence, and identify factors associated with coding bias.