Advertisement

Semantic Visualization of Biochemical Databases

  • Esteban Zimányi
  • Sabri Skhiri dit Gabouje
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3226)

Abstract

Extracting and visualizing information from biochemical databases is one of the most important challenges in biochemical research. The huge quantity and high complexity of the data available force the biologist to use sophisticated tools for extracting and interpreting accurately the information extracted from the database. These tools must define a graphical semantics associated to the data semantics in accordance with biologist usages. The aim of these tools is to display complex biochemical networks in a readable and understandable way. In this paper we define the notion of customizable representation model, which allows the biologist to change the graphical semantics associated to the data semantics. The approach is also generic since our graphical semantics is common to several kinds of biochemical networks. We also defined adaptive graph layout algorithms taking into account the particular semantics of biochemical networks. We show how we implemented these notions in the BioMaze project.

Keywords

Representation Model Interaction Graph Data Semantic Biochemical Network Graphical Element 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Wheeler, D.L.: GenBank. Nucleic Acids Research 31(1), 23–27 (2003)CrossRefGoogle Scholar
  2. 2.
    Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.-C., Estreicher, A., Gasteiger, E., Martin, L.J., Michoud, K., O’Donovan, C., Phan, I., Pilbout, S., Schneider, M.: The Swiss-Prot protein sequence database and its supplement TrEMBL. Nucleic Acids Research 31, 365–370 (2003)CrossRefGoogle Scholar
  3. 3.
    Cook, D.L., Farley, J.F., Tapscott, S.J.: A basis for visual language for describing, archiving and analyzing functional models of complex biochemical systems. Genome Biology 2(4), research0012 (2001)Google Scholar
  4. 4.
    Deville, Y., Gilbert, D., van Helden, J., Wodak, S.: An overview of data models for the analysis of biochemical pathways. Briefings in Bioinformatics 4(3), 246–259 (2003)CrossRefGoogle Scholar
  5. 5.
    Englebert, V., Hainaut, J.-L.: DB-Main: A next generation meta-case. Information Systems 24(2), 99–112 (1999)CrossRefGoogle Scholar
  6. 6.
    Kanehisa, M., Goto, S., Kawashima, S., Nakaya, A.: The Kegg database at GenomeNet. Nucleic acid research 4(3), 246–259 (2003)Google Scholar
  7. 7.
    Karp, P., Paley, S., Romero, P.: The pathway tools software.Bioinformatics vol.18(Suppl. 1), S225-S232 (2002)Google Scholar
  8. 8.
    Kohn, K.W.: Molecular interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems. Molecular Biology of the Cell 10, 2703–2734 (1999)Google Scholar
  9. 9.
    Lemer, C., Antezana, E., Couche, F., Fays, F., Santolaria, X., Janky, R., Deville, Y., Richelle, J., Wodak, S.J.: The aMAZE LightBench: a web interface to a relational database of cellular processes. Nucleic Acids Research 32 ,D443–D444Google Scholar
  10. 10.
    Maimon, R., Browning, S.: Diagrammatic Notation and Computational Structure of Gene Network. In: Proc. of the 2nd Int. Conf. on Systems Biology (2001)Google Scholar
  11. 11.
    Parent, C., Spaccapietra, S., Zimányi, E.: Murmur: Database management of multiple representation. In: Proc. of the AAAI-2000 Workshop on Spatial and Temporal Granularity, pp. 83-86 (2000)Google Scholar
  12. 12.
    Shavor, S., D’Anjou, J., Fairbrother, S., Kehn, D., Kellerman, J., McCarthy, P.: The Java Developer’s Guide to Eclipse. Addison-Wesley, Reading (2003)Google Scholar
  13. 13.
    van Helden, J., Naim, A., Mancuso, R., Eldridge, M., Wernish, L., Glibert, D., Wodak, S.: Representing and analysing molecular and cellular function in computer. Biol. Chem. 381(9–10), 921–935 (2000)CrossRefGoogle Scholar
  14. 14.
    van Helden, J., Naim, A., Lemer, C., Mancuso, R., Eldridge, M., Wodak, S.: From molecular activities and processes to biological function. Briefings in Bioinformatics 2(1), 81–93 (2001)CrossRefGoogle Scholar
  15. 15.
    Van Roy, P., Brand, P., Duchier, D., Haridi, S., Henz, M., Schulte, C.: Logic programming in the context of multiparadigm programming: The Oz experience. Theory and Practice of Logic Programming 3(6), 717–763 (2003)zbMATHCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Esteban Zimányi
    • 1
  • Sabri Skhiri dit Gabouje
    • 1
  1. 1.Department of Informatics & Networks, Faculty of EngineeringUniversité Libre de BruxellesBrusselsBelgium

Personalised recommendations