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NeuroExtract: Facilitating Neuroscience-oriented Retrieval from Broadly-focused Bioscience Databases Using Text-based Query Mediation

^a Department of Neurobiology, Yale University, New Haven, CT
^b Center for Medical Informatics, Yale University, New Haven, CT
^c Department of Anesthesiology, Yale University, New Haven, CT
^d Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT

^_* Correspondence and reprints: Chiquito Crasto, PhD, Center for Medical Informatics, 300 George Street, Suite 501, New Haven, CT 06511 (Email: chiquito.crasto{at}yale.edu).

Received for publication: 11/17/06; accepted for publication: 02/08/07.

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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