Skip to main content
SpringerLink
Log in

Methods for integration of heterogeneous information resources in molecular biology in the digital library GeneExpress

  • Published:
Programming and Computer Software Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Catalog of Databases in Molecular Biology, http://www.infobiogen.fr/services/dbcat/.

  2. Catalog of Programs for Analyzing Data in Molecular Biology, http://www.ebi.ac.uk/biocat/.

  3. 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.

  4. Digital Library GeneExpress, http://wwwmgs.bionet.nsc.ru/mgs/systems/geneexpress/.

  5. 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.

    Article  Google Scholar 

  6. 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.

    Google Scholar 

  7. Ratner, V.A.,Molekulyarno geneticheskie sistemy upravleniya (Molecular Genetics Control Systems), Novosibirsk: Nauka, 1975.

    Google Scholar 

  8. Knowledge Discovery through Data Mining: What is Knowledge Discovery? Tandem Computers, 1996.

  9. Kalinichenko, L.A.,Metody i sredstva integratsii neodnorodnykh baz dannykh (Methods and Means for Integration of Heterogeneous Databases), Moscow, Nauka, 1983.

    Google Scholar 

  10. 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.

  11. 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.

    Google Scholar 

  12. UML Specification,OMG Documents ad/97-08-02-ad/97-08-09.

  13. 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.

    Article  Google Scholar 

  14. Kolpakov, F.A. and Ananko, E.A., Interactive Data Input into the GeneNet Database,Bioinformatics, 1999, vol. 15, pp. 713–714.

    Article  Google Scholar 

  15. 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.

    Google Scholar 

  16. Grant Linking Biological Databases Using CORBA, http://corba.ebi.ac.uk/CORBA_grant/.

  17. Common Object Request Broker Architecture. Version 2.3, Object Management Group,OMG Documents formal/99-07-01-formal/99-07-28.

  18. Kalinichenko, L.A. and Kogalovsky, M.R., OMG Standards: Interface Definition Language in the CORBA Architecture,SUBD, 1996, no. 2.

Download references

Author information

Authors and Affiliations

  1. Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, pr. Akademika Lavrent'eva 10, 630090, Novosibirsk, Russia

    F. A. Kolpakov, N. L. Podkolodnyi, S. V. Lavryushev, D. A. Grigorovich, M. P. Ponomarenko & N. A. Kolchanov

Authors
  1. F. A. Kolpakov
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. N. L. Podkolodnyi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. S. V. Lavryushev
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. D. A. Grigorovich
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. M. P. Ponomarenko
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. N. A. Kolchanov
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints 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

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF02759316

Keywords

Search

Navigation