Termviewer – A Web Application for Streamlined Human Phenotype Ontology (HPO) Tagging and Document Annotation

Abstract

Clinical notes from electronic health records (EHRs) contain a large amount of clinical phenotype data on patients that can provide insights into the phenotypic presentation of various diseases. A number of Natural Language Processing (NLP) algorithms have been utilized in the past few years to annotate medical concepts, such as Human Phenotype Ontology (HPO) terms, from clinical notes. However, efficient use of NLP algorithms requires the use of high‐quality clinical notes with phenotype descriptions, and erroneous annotations often exist in results from these NLP algorithms. Manual review by human experts is often needed to compile the correct phenotype information on individual patients. Here we develop TermViewer, a web application that allows multi‐party collaborative annotation and quality assessment of clinical notes that have already been processed and tagged by NLP algorithms. TermViewer allows users to view clinical notes with HPO terms highlighted, and to easily classify high‐quality notes and revise incorrect tagging of HPO terms. Currently, TermViewer combines MetaMap and cTAKES, two of the most widely used NLP tools for tagging medical terms, and identifies where these two tools agree and disagree, allowing users to perform collaborative manual reviews of computationally generated HPO annotations. TermViewer can be a stand‐alone tool for analyzing notes or become part of a machine‐learning pipeline where tagged HPO terms can be used as additional input data. TermViewer is available at https://github.com/WGLab/TermViewer.