Abstract
A large amount of biological knowledge today is only available from full-text research papers. Since neither manual database curators nor users can keep up with the rapidly expanding volume of scientific literature, natural language processing approaches are becoming increasingly important for bioinformatic projects.
In this paper, we go beyond simply extracting information from full-text articles by describing an architecture that supports targeted access to information from biological databases using the results derived from text mining of research papers, thereby integrating information from both sources within a biological application.
The described architecture is currently being used to extract information about protein mutations from full-text research papers. Text mining results drive the retrieval of sequence information from protein databases and the employment of algorithmic sequence analysis tools, which facilitate further data access from protein structure databases. Complex mapping of NLP derived text annotations to protein structures allows the rendering, with 3D structure visualization, of information not available in databases of mutation annotations.
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References
Altschul, S.F., Gish, W., Miller, W., Meyers, E.W., Lipman, D.J.: Basic Local Alignment Search Tool. Journal of Molecular Biology 215(3), 403–410 (1990)
Baker, C.J.O., Witte, R.: Enriching Protein Structure Visualizations with Mutation Annotations Obtained by Text Mining Protein Engineering Literature. In: The 3rd Canadian Working Conference on Computational Biology (CCCB 2004), Markham, Ontario, October 4 (2004) Co-located with IBM CASCON
Corney, D.P.A., Buxton, B.F., Langdon, W.B., Jones, D.T.: BioRAT: extracting biological information from full-length papers. Bioinformatics (November 22, 2004)
Couto, F.M., Silva, M.J., Coutinho, P.: ProFAL: PROtein Functional Annotation through Literature. In: JISBD, pp. 747–756 (2003)
Cunningham, H., Maynard, D., Bontcheva, K., Tablan, V.: GATE: A framework and graphical development environment for robust NLP tools and applications. In: Proceedings of the 40th Anniversary Meeting of the ACL (2002)
Gabdoulline, R.R., Hoffmann, R., Leitnern, F., Wade, R.C.: ProSAT: functional annotation of protein 3D structures. Bioinformatics 19(13), 1723–1725 (2003)
Kawabata, T., Ota, M., Nishikawa, K.: The protein mutant database. Nucleaic Acid Research 27(1) (1999)
Marchler-Bauer, A., Panchenko, A.R., Shoemaker, B.A., Thiessen, P.A., Geer, L.Y., Bryant, S.H.: CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Research 30(1), 281–283 (2002)
Müller, H.-M., Kenny, E.E., Sternberg, P.W.: Textpresso: An Ontology-Based Information Retrieval and Extraction System for Biological Literature. PLoS Biology 2(11), 1984–1998 (2004), www.plosbiology.org
Pearson, W.R., Lipman, D.J.: Improved tools for biological sequence comparison. Proc. of the National Academy of Sciences of the USA 85(8) (1988)
Schomburg, I., Chang, A., Ebeling, C., Gremse, M., Heldt, C., Huhn, G., Schomburg, D.: BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Research, 32 (2004)
Thompson, J.D., Higgins, D.G., Gibson, T.J.: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research 22(22), 4673–4680 (1994)
Witte, R.: An Integration Architecture for User-Centric Document Creation, Retrieval, and Analysis. In: Proceedings of the VLDB Workshop on Information Integration on the Web (IIWeb), Toronto, Canada, August 30, pp. 141–144 (2004)
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Witte, R., Baker, C.J.O. (2005). Combining Biological Databases and Text Mining to Support New Bioinformatics Applications. In: Montoyo, A., Muńoz, R., Métais, E. (eds) Natural Language Processing and Information Systems. NLDB 2005. Lecture Notes in Computer Science, vol 3513. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11428817_28
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DOI: https://doi.org/10.1007/11428817_28
Publisher Name: Springer, Berlin, Heidelberg
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