James J. Cimino

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OBJECTIVE Development of a general natural-language processor that identifies clinical information in narrative reports and maps that information into a structured representation containing clinical terms. DESIGN The natural-language processor provides three phases of processing, all of which are driven by different knowledge sources. The first phase(More)
OBJECTIVE Develop a knowledge-based representation for a controlled terminology of clinical information to facilitate creation, maintenance, and use of the terminology. DESIGN The Medical Entities Dictionary (MED) is a semantic network, based on the Unified Medical Language System (UMLS), with a directed acyclic graph to represent multiple hierarchies.(More)
Builders of medical informatics applications need controlled medical vocabularies to support their applications and it is to their advantage to use available standards. In order to do so, however, these standards need to address the requirements of their intended users. Over the past decade, medical informatics researchers have begun to articulate some of(More)
The objective of this work is to investigate the feasibility of conceptual similarity metrics in the framework of the Unified Medical Language System (UMLS). We have investigated an approach based on the minimum number of parent links between concepts, and evaluated its performance relative to human expert estimates on three sets of concepts for three(More)
OBJECTIVE Clinical questions are often long and complex and take many forms. We have built a clinical question answering system named AskHERMES to perform robust semantic analysis on complex clinical questions and output question-focused extractive summaries as answers. DESIGN This paper describes the system architecture and a preliminary evaluation of(More)
This paper describes a large case study that explores the applicability of ontology reasoning to problems in the medical domain. We investigate whether it is possible to use such reasoning to automate common clinical tasks that are currently labor intensive and error prone, and focus our case study on improving cohort selection for clinical trials. An(More)
We have developed several prototype applications which integrate clinical systems with on-line information resources by using patient data to drive queries in response to user information needs. We refer to these collectively as infobuttons because they are evoked with a minimum of keyboard entry. We make use of knowledge in our terminology, the Medical(More)
OBJECTIVE To develop and test a method for automatically detecting inconsistencies between the parent-child is-a relationships in the Metathesaurus and the ancestor-descendant relationships in the Semantic Network of the Unified Medical Language System (UMLS). METHODS We exploited the fact that each Metathesaurus concept is assigned one or more semantic(More)
WebCIS is a Web-based clinical information system. It sits atop the existing Columbia University clinical information system architecture, which includes a clinical repository, the Medical Entities Dictionary, an HL7 interface engine, and an Arden Syntax based clinical event monitor. WebCIS security features include authentication with secure tokens,(More)
The published medical literature and online medical resources are important sources to help physicians make patient treatment decisions. Traditional sources used for information retrieval (e.g., PubMed) often return a list of documents in response to a user's query. Frequently the number of returned documents from large knowledge repositories is large and(More)