Abstract
BLID (Bio-Logical Intelligent Database) is a bioinformatic system designed to help biologists extract new knowledge from raw genome data by providing high-level facilities for both data browsing and analysis. We describe BLID’s novel data browsing system which is based on the idea of Logical Information Systems. This enables combined querying and navigation of data in BLID (extracted from public bioinformatic repositories). The browsing language is a logic especially designed for bioinformatics. It currently includes sequence motifs, taxonomies, and macromolecule structures, and it is designed to be easily extensible, as it is composed of reusable components. Navigation is tightly combined with this logic, and assists users in browsing a genome through a form of human-computer dialog.
This project is funded by the BBSRC grant 21BEP17028.
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References
Brachman, R.J.: On the epistemological status of semantic nets. In: Findler, N.V. (ed.) Associative Networks: Representation of Knowledge and Use of Knowledge by Examples, Academic Press, New York (1979)
Cornell, M., et al.: GIMS – a data warehouse for storage and analysis of genome sequence and functional data. In: IEEE Int. Symp. on Bioinformatics and Bioengineering, pp. 15–22. IEEE Press, Los Alamitos (2001)
de Raedt, L.: A perspective on inductive databases. SIGKDD Explorations 4(2), 69–77 (2002)
Ferré, S., Ridoux, O.: A framework for developing embeddable customized logics. In: Pettorossi, A. (ed.) LOPSTR 2001. LNCS, vol. 2372, pp. 191–215. Springer, Heidelberg (2002)
Ferré, S., Ridoux, O.: The use of associative concepts in the incremental building of a logical context. In: Angelova, G., Priss, U., Corbett, D. (eds.) ICCS 2002. LNCS (LNAI), vol. 2393, pp. 299–313. Springer, Heidelberg (2002)
Ferré, S., Ridoux, O.: An introduction to logical information systems. Information Processing & Management (2003) (to appear)
Ganter, B., Kuznetsov, S.: Formalizing hypotheses with concepts. In: Mineau, G., Ganter, B. (eds.) ICCS 2000. LNCS, vol. 1867, pp. 342–356. Springer, Heidelberg (2000)
Godin, R., Missaoui, R., April, A.: Experimental comparison of navigation in a Galois lattice with conventional information retrieval methods. International Journal of Man-Machine Studies 38(5), 747–767 (1993)
Goffeau, A., et al.: The Yeast genome directory. Nature 387, 1–105 (1997)
King, R.D., Karwath, A., Clare, A., Dehaspe, L.: Genome scale prediction of protein functional class from sequence using data mining. In: Ramakrishnan, R., et al. (eds.) ACM SIGKDD Int. Conf. Knowledge Discovery and Data Mining, pp. 384–389. ACM, New York (2000)
Muggleton, S., De Raedt, L.: Inductive logic programming: Theory and methods. Journal of Logic Programming 19(20), 629–679 (1994)
Ouali, M., King, R.D.: Cascaded multiple classifiers for secondary structure prediction. Prot. Sci. 9, 1162–1176 (2000)
Wille, R.: Restructuring lattice theory: an approach based on hierarchies of concepts. In: Ordered Sets, pp. 445–470. Reidel, Dordrechtz (1982)
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Ferré, S., King, R.D. (2004). BLID: An Application of Logical Information Systems to Bioinformatics. In: Eklund, P. (eds) Concept Lattices. ICFCA 2004. Lecture Notes in Computer Science(), vol 2961. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24651-0_5
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DOI: https://doi.org/10.1007/978-3-540-24651-0_5
Publisher Name: Springer, Berlin, Heidelberg
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