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First published February 28, 2007 as JAMIA PrePrint; doi:10.1197/jamia.M2321
Journal of the American Medical Informatics Association 2007;14(3):355-360
© 2007 American Medical Informatics Association

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Submitted on November 17, 2006
Accepted on February 8, 2007

NeuroExtract: Facilitating Neuroscience-Oriented Retrieval from Broadly-Focused Bioscience Databases using Text-based Query Mediation

Chiquito J. Crasto PhD1*, Peter Masiar MS2, Gordon M. Shepherd PhD, MPhil3, and Perry L. Miller MD, PhD4

Affiliation of the authors: 1 Department of Neurobiology, Yale University, New Haven, CT; Center for Medical Informatics, Yale University, New Haven, CT ; 2 Center for Medical Informatics, Yale University, New Haven, CT; 3 Department of Neurobiology, Yale University, New Haven, CT ; 4 Center for Medical Informatics, Yale University, New Haven, CT; Department of Anesthesiology, Yale University, New Haven, CT; Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT

* To whom correspondence should be addressed.

This paper describes NeuroExtract, a pilot system which facilitates the integrated retrieval of Internet-based information relevant to the neurosciences. The approach involved extracting descriptive metadata from the sources using domain-specific queries; retrieving, processing and organizing the data into structured text files; searching the data files using text-based queries; and, providing the results in a web page along with descriptions to entries and URL links to the original sources. NeuroExtract has been implemented for three bioscience resources, SWISSPROT, GEO and PDB, which provide neuroscience-related information as sub-topics. We discuss several issues that arose in the course of NeuroExtract's implementation. This project is a first step in exploring how this general approach might be used, in conjunction with other query mediation approaches, to facilitate the integration of many Internet-accessible resources relevant to the neurosciences.




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[Abstract] [Full Text] [PDF]


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