Abstract
A multimodal network (MMN) is a novel graph-theoretic formalism designed to capture the structure of biological networks and to represent relationships derived from multiple biological databases. MMNs generalize the standard notions of graphs and hypergraphs, which are the bases of current diagrammatic representations of biological phenomena and incorporate the concept of mode. Each vertex of an MMN is a biological entity, a biot, while each modal hyperedge is a typed relationship, where the type is given by the mode of the hyperedge. The current paper defines MMNs and concentrates on the structural aspects of MMNs. A companion paper develops MMNs as a representation of the semantics of biological networks and discusses applications of the MMNs in managing complex biological data. The MMN model has been implemented in a database system containing multiple kinds of biological networks.
- I. Pirson, N. Fortemaison, C. Jacobs, S. Dremier, J.E. Dumont, and C. Maenhaut, "The Visual Display of Regulatory Information and Networks," Trends in Cell Biology, vol. 10, pp. 404-408, 2000.Google ScholarCross Ref
- K. Fukuda and T. Takagi, "Knowledge Representation of Signal Transduction Pathways," Bioinformatics, vol. 17, no. 9, pp. 829-837, 2001.Google ScholarCross Ref
- S. Xanthoudakis and D.W. Nicholson, "Heat-Shock Proteins as Death Determinants," Nature Cell Biology, vol. 2, pp. E163-E165, 2000.Google ScholarCross Ref
- P. Holme, M. Huss, and H. Jeong, "Subnetwork Hierarchies of Biochemical Pathways," Bioinformatics, vol. 19, no. 4, pp. 532-538, 2003.Google ScholarCross Ref
- S. Schuster, T. Pfeiffer, F. Moldenhauer, I. Koch, and T. Dandekar, "Exploring the Pathway Structure of Metabolism: Decomposition into Subnetworks and Application to Mycoplasma pneumoniae," Bioinformatics, vol. 18, no. 2, pp. 351-361, 2002.Google ScholarCross Ref
- H. Ma and A.-P. Zeng, "Reconstruction of Metabolic Networks from Genome Data and Analysis of Their Global Structure for Various Organisms," Bioinformatics, vol. 19, no. 2, pp. 270-277, 2003.Google ScholarCross Ref
- C.V. Forst, C. Flamm, I.L. Hofacker, and P.F. Stadler, "Algebraic Comparison of Metabolic Networks, Phylogenetic Inference, and Metabolic Innovation," BMC Bioinformatics, vol. 7, no. 67, Feb. 2006.Google Scholar
- L.S. Heath, "Networks in Bioinformatics," Proc. Int'l Symp. Parallel Architectures, Algorithms, and Networks (I-SPAN '02), pp. 141-150, 2002. Google ScholarDigital Library
- A.A. Sioson and L.S. Heath, "Some Fundamental Operations on Multimodal Networks in Biology," Philippine Computing J., vol. 1, no. 2, pp. 13-22, Dec. 2006.Google Scholar
- L.S. Heath and A.A. Sioson, "Semantics of Multimodal Network Models," IEEE/ACM Trans. Computational Biology and Bioinformatics , vol. 6, no. 2, pp. 271-280, Apr.-June 2009. Google ScholarDigital Library
- A.A. Sioson, "Multimodal Networks in Biology," Virginia Polytechnic Inst. and State Univ., Nov. 2005.Google Scholar
- M. Stonebraker and G. Kemnitz, "The POSTGRES Next-Generation Database Management System," Comm. ACM, vol. 34, pp. 78- 92, 1991. Google ScholarDigital Library
- M. Benjamins, C.D.R. Lindveld, and R. van Nes, "Multimodal Travel Choice Modeling Using a Supernetwork Approach," Proc. 81st Transportation Research Board Ann. Meeting, 2002.Google Scholar
- K. Uchida, A. Sumalee, D. Watling, and R. Connors, "Study on Optimal Frequency Design Problem for Multimodal Network Using Probit-Based User Equilibrium Assignment," Transportation Research Board, no. 1923, pp. 236-245, 2005.Google ScholarCross Ref
- H. Abrach, S. Bhatti, J. Carlson, H. Dai, J. Rose, A. Sheth, B. Shuckler, J. Deng, and R. Han, "Mantis: System Support for Multimodal Networks of In-Situ Sensors," Proc. Second ACM Int'l Workshop Wireless Sensor Networks and Applications (WSNA), 2003. Google ScholarDigital Library
- C. Berge, Hypergraphs. North-Holland, 1989.Google Scholar
- G. Gallo, G. Longo, S. Pallottino, and S. Nguyen, "Directed Hypergraphs and Applications," Discrete Applied Math., vol. 42, pp. 177-201, 1993. Google ScholarDigital Library
- M.K. Campbell and S.O. Farrell, Biochemistry, fourth ed. Thomson Brooks/Cole, 2005.Google Scholar
- W.H. Elliott and D.C. Elliott, Biochemistry and Molecular Biology. Oxford Univ. Press, 1997.Google Scholar
- D.B. West, Introduction to Graph Theory, second ed. Prentice Hall, 2001.Google Scholar
- B.C. Pierce, Basic Category Theory for Computer Scientists (Foundations of Computing). MIT Press, 1991. Google ScholarDigital Library
- Kyoto Encyclopedia of Genes and Genomes (KEGG) Website, http://www.kegg.org/, 2008.Google Scholar
- J.-M. Bruey, C. Ducasse, P. Bonniaud, L. Ravagnan, S.A. Susin, C. Diaz-Latoud, S. Gurbuxani, A.-P. Arrigo, G. Kroemer, E. Solary, and C. Garrido, "HSP27 Negatively Regulates Cell Death by Interacting with Cytochrome c," Nature Cell Biology, vol. 2, pp. 645-652, 2000.Google ScholarCross Ref
- A. Saleh, S.M. Srinivasula, L. Balkir, and P.D. Robbins, "Negative Regulation of the APAF-1 Apoptosome by HSP70," Nature Cell Biology, vol. 2, pp. 476-483, 2000.Google ScholarCross Ref
- H.M. Beere, B.B. Wolf, K. Cain, D.D. Mosser, A. Mahboubi, T. Kuwana, P. Tailor, R.I. Morimoto, and G.M. Cohen, "Heat-Shock Protein 70 Inhibits Apoptosis by Preventing Recruitment of Procaspase-9 to the APAF-1 Apoptosome," Nature Cell Biology, vol. 2, pp. 469-475, 2000.Google ScholarCross Ref
- M. Kanehisa, S. Goto, S. Kawashima, and A. Nakaya, "The KEGG Databases at GenomeNet," Nucleic Acids Research, vol. 30, no. 1, pp. 42-46, 2002.Google ScholarCross Ref
- M. Kanehisa, S. Goto, S. Kawashima, Y. Okuno, and M. Hattori, "The KEGG Resources for Deciphering the Genome," Nucleic Acids Research, vol. 32, pp. D277-D280, 2004.Google ScholarCross Ref
- R.G. Alscher, B.I. Chevone, L.S. Heath, and N. Ramakrishnan, "Expresso--A Problem Solving Environment for Bioinformatics: Finding Answers with Microarray Technology," Proc. High Performance Computing Symp., Advanced Simulation Technologies Conf. (HPC '01), pp. 64-69, 2001.Google Scholar
- A.A. Sioson, J.I. Watkinson, C. Vasquez-Robinet, M. Ellis, M. Shukla, D. Kumar, N. Ramakrishnan, L.S. Heath, R. Grene, B.I. Chevone, K. Kadafar, and L.T. Watson, "Expresso and Chips: Creating a Next Generation Microarray Experiment Management System," Proc. Int'l Parallel and Distributed Processing Symp. Next Generation Software Systems Workshop (IPDPS '03), p. 209b, Apr. 2003. Google ScholarDigital Library
Index Terms
- Multimodal Networks: Structure and Operations
Recommendations
Semantics of Multimodal Network Models
A multimodal network (MMN) is a novel graph-theoretic formalism designed to capture the structure of biological networks and to represent relationships derived from multiple biological databases. MMNs generalize the standard notions of graphs and ...
Hamilton-chain saturated hypergraphs
We say that a hypergraph H is hamiltonian path (cycle) saturated if H does not contain an open (closed) hamiltonian chain but by adding any new edge we create an open (closed) hamiltonian chain in H. In this paper we ask about the smallest size of an r-...
Line Graphs of Helly Hypergraphs
A natural generalization of the notion of domino introduced and investigated in [T. Kloks, D. Kratsch, and H. Müller, Dominoes, Lecture Notes in Comput. Sci. 903, Springer-Verlag, Berlin, 1995, pp. 106--120] is considered. A graph is called an r-mino if ...
Comments