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Research Paper: A General Natural-language Text Processor for Clinical Radiology
- C. Friedman, P. Alderson, J. Austin, J. Cimino, Stephen B. Johnson
- Computer ScienceJ. Am. Medical Informatics Assoc.
- 1 March 1994
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, using radiology as the test domain.
GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles
- C. Friedman, Pauline Kra, Hong Yu, M. Krauthammer, A. Rzhetsky
- Biology, Computer ScienceISMB
- 1 June 2001
A system is presented that extracts and structures information about cellular pathways from the biological literature in accordance with a knowledge model that was developed earlier and implemented by modifying an existing medical natural language processing system.
Novel Data‐Mining Methodologies for Adverse Drug Event Discovery and Analysis
- R. Harpaz, W. DuMouchel, N. Shah, D. Madigan, P. Ryan, C. Friedman
- Computer Science, MedicineClinical pharmacology and therapeutics
- 1 June 2012
An overview of recent methodological innovations and data sources used to support ADE discovery and analysis is provided.
Mining multi-item drug adverse effect associations in spontaneous reporting systems
It is demonstrated that multi-item ADEs are present and can be extracted from the FDA’s adverse effect reporting system using the method proposed, suggesting that the method is a valid approach for the initial identification of multi- item ADEs.
Exploiting Semantic Relations for Literature-Based Discovery
We propose using semantic predications to enhance literature-based discovery (LBD) systems, which currently depend exclusively on co-occurrence of words or concepts in target documents. In this…
Two biomedical sublanguages: a description based on the theories of Zellig Harris
A Study of Abbreviations in Clinical Notes
A study of a two-step model for building a clinical abbreviation database: first, abbreviations in a text corpus were detected and then a sense inventory was built for those that were found, and a sense inventories from two different knowledge sources were used.
Information theory applied to the sparse gene ontology annotation network to predict novel gene function
A novel approach, information theory-based semantic similarity (ITSS), to automatically predict molecular functions of genes based on existing GO annotations is proposed, able to generate highly accurate predictions in sparsely annotated portions of GO, where previous algorithms have failed.
Disambiguating Ambiguous Biomedical Terms in Biomedical Narrative Text: An Unsupervised Method
This paper presents a two-phase unsupervised method to build a WSD classifier for an ambiguous biomedical term W, which demonstrated that classifiers trained on the derived sense-tagged corpora achieved an overall accuracy of about 97%, with greater than 90% accuracy for each individual ambiguous term.
Research Paper: Active Computerized Pharmacovigilance Using Natural Language Processing, Statistics, and Electronic Health Records: A Feasibility Study
- Xiaoyan Wang, G. Hripcsak, M. Markatou, C. Friedman
- MedicineJ. Am. Medical Informatics Assoc.
- 1 May 2009
This study provides a framework for the development of active, high-throughput and prospective systems which could potentially unveil drug safety profiles throughout their entire market life, and is the first study using comprehensive unstructured data from the EHR for pharmacovigilance.