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Bioinformatics Advance Access originally published online on December 17, 2004
Bioinformatics 2005 21(4):430-438; doi:10.1093/bioinformatics/bti187
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Bioinformatics vol. 21 issue 4 © Oxford University Press 2005; all rights reserved.

An architecture for biological information extraction and representation

Aditya Vailaya *, Peter Bluvas , Robert Kincaid , Allan Kuchinsky , Michael Creech and Annette Adler

Agilent Laboratories 3500 Deer Creek Road, MS 26U-16, Palo Alto, CA 94304, USA

*To whom correspondence should be addressed.

Motivations: Technological advances in biomedical research are generating a plethora of heterogeneous data at a high rate. There is a critical need for extraction, integration and management tools for information discovery and synthesis from these heterogeneous data.

Results: In this paper, we present a general architecture, called ALFA, for information extraction and representation from diverse biological data. The ALFA architecture consists of: (i) a networked, hierarchical, hyper-graph object model for representing information from heterogeneous data sources in a standardized, structured format; and (ii) a suite of integrated, interactive software tools for information extraction and representation from diverse biological data sources. As part of our research efforts to explore this space, we have currently prototyped the ALFA object model and a set of interactive software tools for searching, filtering, and extracting information from scientific text. In particular, we describe BioFerret, a meta-search tool for searching and filtering relevant information from the web, and ALFA Text Viewer, an interactive tool for user-guided extraction, disambiguation, and representation of information from scientific text. We further demonstrate the potential of our tools in integrating the extracted information with experimental data and diagrammatic biological models via the common underlying ALFA representation.

Contact: aditya_vailaya{at}agilent.com


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