Abstract
Difficulties in integrating information resources (IRs) in molecular biology are due to a complex hierarchical and/or network organization of data, to their heterogeneity, complex interrelations, insufficient formalization, and to incompleteness. To overcome these difficulties, a digital library called GeneExpress has been under development in the Institute of Cytology and Genetics of the Siberian Division of Russian Academy of Sciences. This system, which belongs to a new class of information systems, integrates a great number of data-bases and hundreds of computer programs designed for processing information on the structure and functions of DNA, RNA, and proteins. The foundation of our approach is provided by hypertext integration, integration on the basis of a unified object-oriented environment by mapping the data into a canonical model with the use of specially designed mediators, and semantic data integration. A prototype of an implementation of this approach used in the current version of GeneExpress is described.
Similar content being viewed by others
Explore related subjects
Discover the latest articles, news and stories from top researchers in related subjects.References
Catalog of Databases in Molecular Biology, http://www.infobiogen.fr/services/dbcat/.
Catalog of Programs for Analyzing Data in Molecular Biology, http://www.ebi.ac.uk/biocat/.
Kolchanov, N.A., Ponomarenko, M.P., Kel, A.E., Kondrakhin, Yu.V., Frolov, A.S., Kolpakov, F.A., Kel, O.V., Ananko, E.A., Ignatieva, E.V., Podkolodnaya, O.A., Stepanenko, I.L., Merkulova, T.I., Babenko, V.N., Vorobiev, D.G., Lavryushev, S.V., Ponomarenko, Yu.V., Kochetov, A.V., Kolesov, G.B., Podkolodny, N.L., Milanesi, L., Wingender, E., Heinemeyer, T., and Solovyev, V.V., GeneExpress: A Computer System for Description, Analysis, and Recognition of Regulatory Sequences of the Eukaryotic Genome,ISBM, 1998, pp. 95–104.
Digital Library GeneExpress, http://wwwmgs.bionet.nsc.ru/mgs/systems/geneexpress/.
Kolchanov, N.A., Ponomarenko, M.P., Frolov, A.S., Ananko, E.A., Kolpakov, F.A., Ignatieva, E.V., Podkolodnaya, O.A., Goryachkovskaya, T.N., Stepanenko, I.L., Merkulova, T.I., Babenko, V.V., Ponomarenko, Yu.V., Kochetov, A.V., Podkolodny, N.L., Vorobiev, D.V., Lavryushev, S.V., Grigorovich, D.A., Kondrakhin, Yu.V., Milanesi, L., Wingender, E., Solovyev, V.V., and Overton, G.C., Integrated Databases and Computer Systems for Studying Eukaryotic Gene Expression,Bioinformatics, 1999, vol. 15, no. 7, pp. 669–686.
Ratner, V.A., Biology-Modular Principle of the Organization of Evolution in Molecular Genetics Control Systems,Genetika, 1992, vol. 28, no. 3, pp. 5–25.
Ratner, V.A.,Molekulyarno geneticheskie sistemy upravleniya (Molecular Genetics Control Systems), Novosibirsk: Nauka, 1975.
Knowledge Discovery through Data Mining: What is Knowledge Discovery? Tandem Computers, 1996.
Kalinichenko, L.A.,Metody i sredstva integratsii neodnorodnykh baz dannykh (Methods and Means for Integration of Heterogeneous Databases), Moscow, Nauka, 1983.
Kalinichenko, L.A., Integration of Heterogeneous Semistructured Data Models in the Canonical One,Trudy loi Vserossiiskoi nauchnoi konferentsii Elektronnye biblioteki: perspectivnye metody i tekhnologii (Proc. First All-Russian Conf. Digital Libraries: Advanced Methods and Technologies), St. Petersburg, 1999, pp. 3–15.
Etzold, T. and Argos P., SRS—an Indexing and Retrieval Tool for Flat File Data Libraries.Comput. Appl. Biosci, 1993, vol. 9, pp. 49–57.
UML Specification,OMG Documents ad/97-08-02-ad/97-08-09.
Kolpakov, F.A., Ananko, E.A., Kolesov, G.B., and Kolchanov, N.A., GeneNet: A Gene Network Database and Its Automated Visualization,Bioinformatics, 1998, vol. 14, pp. 529–537.
Kolpakov, F.A. and Ananko, E.A., Interactive Data Input into the GeneNet Database,Bioinformatics, 1999, vol. 15, pp. 713–714.
Kolpakov, F.A. and Babenko, V.N., Computer System MGL—a Tool for Retrieving, Graphical Representation, and Analysis of Regulatory Genome Sequences,Mol. Biol., 1997, vol. 31, no. 4, pp. 647–655.
Grant Linking Biological Databases Using CORBA, http://corba.ebi.ac.uk/CORBA_grant/.
Common Object Request Broker Architecture. Version 2.3, Object Management Group,OMG Documents formal/99-07-01-formal/99-07-28.
Kalinichenko, L.A. and Kogalovsky, M.R., OMG Standards: Interface Definition Language in the CORBA Architecture,SUBD, 1996, no. 2.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Kolpakov, F.A., Podkolodnyi, N.L., Lavryushev, S.V. et al. Methods for integration of heterogeneous information resources in molecular biology in the digital library GeneExpress. Program Comput Soft 26, 170–176 (2000). https://doi.org/10.1007/BF02759316
Issue Date:
DOI: https://doi.org/10.1007/BF02759316