Abstract
We examined the process of virtualization to deal with data intensive problems. Since data integration is a first-order priority in systems biology, we started developing a new method to manipulate data models through ordinary metadata transactions, i.e. by preserving the original data format stored in resources. After discussing why metamodels are made for, and the interplay of modeling languages in metamodel design, we presented a systemic metamodel-driven strategy to integrate semantically heterogeneous data.
Keywords
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.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Spring, M.B., Jennings, M.C.: Virtual reality and abstract data: virtualizing information. Virtual Reality World 1(1), c-m (1993)
Moore, R.W.: Integrating Data and Information Management. In: International Supercomputer Conference, Heidelberg (D), June 22-25 (2004)
Auffray, C., Imbeau, S., Roux-Rouquié, M., Hood, L.: C. R. Biologies. From functional genomics to systems biology 326, 879–892 (2003)
Franza, B.R.: From play to laws: Language in Biology. Sci. STKE, pe9 (2004)
Sauro, H., Hucka, M., Finney, A., Wellock, C., Bolouri, H., Doyle, J., Kitano, H.: Omics: A journal of integrative biology 7, 355–372 (2003)
Garvey, T.D., Lincoln, P., Pedersen, C.J., Martin, D., Johnson, M.: Omics: A journal of integrative biology 7, 411–420 (2003)
http://www.cellml.org/public/specification/20021106/index.html
Cook, D.L., Farley, J.F., Tapscott, S.J.: A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems. Genome Biology 2(4) (2001) research0012.1-0012.10
Kohn, K.W.: Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Mol. Biol. Cell 10(8), 2703–2734 (1999)
Pirson, I., Fortemaison, N., jacobs, C., Dremier, S., Dumont, J., Maenhaut, C.: The visual display of regulatory information and networks. Trends Cell Biol. 10(10), 404–408 (2000)
Maimon, R., Browning, S.: Diagramatic Notation and Computational Structure of Gene Networks. In: The Second International Conference on Systems Biology, Pasadena (2001)
Kitano, H.: A Graphical Notation for Biological Networks. BIOSILICO 1, 169–176 (2003)
Schulze-Kremer, S.: Ontologies for Molecular Biology. In: Proc. of 3rd Pacific Symposium on Biocomputing, PSB 1998, pp. 693–704 (1998)
Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel- Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium, Nat. Genet. 25, 25–29 (2000)
Rzhetsky, A., Koike, T., Kalachikov, S., Gomez, S., Krauthammer, M., Kaplan, S., Kra, P., Russo, J., Friedman, C.: A knowledge model for analysis and simulation of regulatory networks. Bioinformatics 16(12), 1120–1128 (2000)
Paton, R.C.: Diagrammatic Representations for Modelling Biological Knowledge. BioSystems 66, 43–53 (2002)
Roux-Rouquié, M., Le Moigne., J.L.: The systemic paradigm and its relevance for modeling biological functions. C. R. Biologies, Special Issue: Model driven Acquisition 325, 419–430 (2002)
Soto., M.: Semantic approach of virtual worlds interoperability. In: Capps, M. (ed.) Proceedings of IEEE WET-ICE 1997, Cambridge, MA. IEEE Press, Los Alamitos (1997)
Regev, A., Shapiro, E.: Cells as computation. Nature 419(6905), 343 (2002)
Roux-Rouquié, M., Renner, J., Sautejeau, G., Rosenthal-Sabroux, C.: Modeling Systems and Processes in Molecular Biology with active objects. In: Objects in bio- and chem-informatics (OiBCI 2002), OMG conference, Washington, USA (2002)
Roux-Rouquié, M., Caritey, N., Gaubert, L., Rosenthal-Sabroux, C.: Using the Unified Modeling Language (UML) to guide systemic description of biological processes and systems Biosystems (2004) (in press)
Kam, N., Irun, R., Cohen, H.D.: The Immune System as a Reactive System: Modeling T Cell Activation With Statecharts. In: IEEE 2001 Symposia on Human Centric Computing Languages and Environments (HCC 2001), Stresa, Italy, September 05-07 (2001)
Spellman, M.P., Troup, C., Sarkans, U., Chevitz, S., Berhnart, D., Sherlock, G., Ball, C., Lepage, M., Swiatek, M., Marks, W.:, Goncalves, J., Markel, S., Iordan, D., Shojatalab, M., Pizarro, A., White, J., Hubley, R., Deutsch, E., Senger, M., Aronow, B., Robinson, A., Bassett, D., Stoeckert Jr., C., Brazma, A.: Genome Biology 3(9) (2002), research0046.1 0046.9
Bader, G.D., Hogue, C.W.V.: BIND-a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bioinformatics 16, 465–477 (2000)
Karp, P.D., Riley, M., Paley, S.M., Pellegrini-Toole, A., Krummenacker, M.: Eco- Cyc: Encyclopedia of E. Coli Genes and Metabolism. Nucleic Acid Res. 27, 55–58 (1999)
Hodges, P.E., McKee, A.H.Z., David, B.P., Payne, W.E., Garrels, J.I.: The Yeast Proteome Database (YPD): a Model for the Organization and Presentation of Genome-Wide Funtional Dat. Nucleic Acid Res. 27, 69–73 (1999)
Kaneshisa, M.: A Database for Post-Genome Analysis. Trends genet. 13, 375–376 (1997)
Korenblat, K., Priami, C.: Extraction of Pi-calculus specifications from a UML sequence and state diagrams. DEGAS IST-2001-32072, technical report, #DIT-03-07 (2003)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Roux-Rouquié, M., Soto, M. (2005). Virtualization in Systems Biology: Metamodels and Modeling Languages for Semantic Data Integration. In: Priami, C. (eds) Transactions on Computational Systems Biology I. Lecture Notes in Computer Science(), vol 3380. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-32126-2_3
Download citation
DOI: https://doi.org/10.1007/978-3-540-32126-2_3
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-25422-5
Online ISBN: 978-3-540-32126-2
eBook Packages: Computer ScienceComputer Science (R0)