Text Mining for Metabolic Pathways, Signaling Cascades, and Protein Networks

doi:10.1126/stke.2832005pe21

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Sci. STKE, 10 May 2005
Vol. 2005, Issue 283, p. pe21
[DOI: 10.1126/stke.2832005pe21]

PERSPECTIVES

Text Mining for Metabolic Pathways, Signaling Cascades, and Protein Networks

Robert Hoffmann¹, Martin Krallinger¹, Eduardo Andres¹, Javier Tamames², Christian Blaschke², and Alfonso Valencia¹^*

¹Protein Design Group, National Center for Biotechnology, CNB-CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
²BioAlmai, Tres Cantos, Madrid, Spain.

Summary: The complexity of the information stored in databases and publications on metabolic and signaling pathways, the high throughput of experimental data, and the growing number of publications make it imperative to provide systems to help the researcher navigate through these interrelated information resources. Text-mining methods have started to play a key role in the creation and maintenance of links between the information stored in biological databases and its original sources in the literature. These links will be extremely useful for database updating and curation, especially if a number of technical problems can be solved satisfactorily, including the identification of protein and gene names (entities in general) and the characterization of their types of interactions. The first generation of openly accessible text-mining systems, such as iHOP (Information Hyperlinked over Proteins), provides additional functions to facilitate the reconstruction of protein interaction networks, combine database and text information, and support the scientist in the formulation of novel hypotheses. The next challenge is the generation of comprehensive information regarding the general function of signaling pathways and protein interaction networks.

*Corresponding author. E-mail: valencia{at}cnb.uam.es

Citation: R. Hoffmann, M. Krallinger, E. Andres, J. Tamames, C. Blaschke, A. Valencia, Text Mining for Metabolic Pathways, Signaling Cascades, and Protein Networks. Sci. STKE 2005, pe21 (2005).

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