Christopher G. Chute

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Measures of semantic similarity between concepts are widely used in Natural Language Processing. In this article, we show how six existing domain-independent measures can be adapted to the biomedical domain. These measures were originally based on WordNet, an English lexical database of concepts and relations. In this research, we adapt these measures to(More)
We aim to build and evaluate an open-source natural language processing system for information extraction from electronic medical record clinical free-text. We describe and evaluate our system, the clinical Text Analysis and Knowledge Extraction System (cTAKES), released open-source at http://www.ohnlp.org. The cTAKES builds on existing open-source(More)
Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing and decision support. BioPortal (http://bioportal.bioontology.org) is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF,(More)
A unified model for text categorization and text retrieval is introduced. We use a training set of manually categorized documents to learn word-category associations, and use these associations to predict the categories of arbitrary documents. Similarly, we use a training set of queries and their related documents to obtain empirical associations between(More)
INTRODUCTION The eMERGE (electronic MEdical Records and GEnomics) Network is an NHGRI-supported consortium of five institutions to explore the utility of DNA repositories coupled to Electronic Medical Record (EMR) systems for advancing discovery in genome science. eMERGE also includes a special emphasis on the ethical, legal and social issues related to(More)
The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees(More)
OBJECTIVE To identify patients with heart failure (HF) by using language contained in the electronic medical record (EMR). METHODS We validated 2 methods of identifying HF through the EMR, which offers transcription of clinical notes within 24 hours or less of the encounter. The first method was natural language processing (NLP) of the EMR text. The(More)
As the size and complexity of medical terminologies increase, terminology modelers are increasingly hampered by lack of tools and methods to manage the development process. This paper presents our use and ongoing evaluation of a description-logic classifier to support cognitive scalability of the underlying terminology and our enhancements to that(More)