Entity grammar systems: A grammatical tool for studying the hierarchal structures of biological systems
- Yun Wang
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The hierarchal structures of biological systems are the typical complex hierarchal dynamical structures in the physical world, the effective investigations on which could not be performed with the existing formal grammar systems. To meet the needs of the investigation on these kinds of systems, especially the emerging field of system biology, a grammatical tool was proposed in the present article. Because the grammatical toolmainly deals with the systems composed of structured entities, they are called entity grammar systems (EGSs). The structure of entities in EGSs have the general form of the objects in the physical world, which means EGSs could be used as a tool to study the complex system composed of many objects with different structures, just like the biological systems. The article contains the formal definition of EGSs and the hierarchy of EGSs, which is congruent with the Chomsky hierarchy. The relationship between EGSs and array grammar systems, graph grammar systems, tree grammar systems, multi-set grammar systems are discussed to show the generative power of EGSs. At the end of the present article, the steps to define new grammar systems with the form of EGS are provided and the possible applicable fields of EGSs are discussed.
- Abe, N. and H. Mamitsuka (1997). Predicting protein secondary structure using stochastic tree grammars. Mach. Learn. 29, 275–301. CrossRef
- Adleman, L. (1994). Molecular computation of solutions to combinatorial problems. Science 266, 1021–1024.
- Berry, G. and G. Boudol (1996). The chemical abstract machine. Theor. Comput. Sci. 96, 217–248. CrossRef
- Book, R. and F. Otto (1993). String Rewriting Systems, Berlin, Heidelberg: Springer.
- Brendel, V. and H. G. Busse (1984). Genome structure described by formal languages. Nucleic Acids Res. 12, 2561–2568.
- Brown, R. and A. Heyworth (1999). Using rewriting systems to compute Kan extensions and induced actions of categories. Department of Mathematics, University of Bangor, UK.
- Csuhaj-Varju, E., J. Dassow, J. Kelemen and G. H. Paun (1994). Grammar Systems: A Grammatical Approach to Distribution and Cooperation, London: Gordon and Breach Science Publishers.
- Dershowiz, N. and I. P. Jouannaud (1990). Rewrite systems, in Handbook of Theoretical Computer Science, Vol. B: Formal Models and Semantics, J. van Leuwen (Ed.), Amsterdam: Elsevier, pp. 243–320.
- Fernau, H., R. Freund and M. Holzer (1999). Regulated array grammars of finite index. Part I: theoretical investigations, in Grammatical Models of Multi-agent Systems (1999), G. H. Paun and A. Salomaa (Eds), Amsterdam, Netherlands: Gordon and Breach Science Publishers.
- Head, T. (1987). Formal language theory and DNA: an analysis of generative capacity of recombinant behaviors. Bull. Math. Biol. 49, 737–759. CrossRef
- Head, T. (1992). Splicing schemes and DNA, in Lindermayer Systems: Impact on Theoretical Computer Science, Computer Graphics and Developmental Biology, G. Rozenberg and A. Salomaa (Eds), Berlin, Heidelberg: Springer, pp. 371–383.
- Head, T., G. H. Paun and D. Pixton (1997). Language theory and molecular genetics, in Handbook of Language Theory, vol. 2, chapter 7, G. Rozenberg and A. Salomaa (Eds), Berlin, Heidelberg: Springer.
- Kari, L. (1996). DNA computers: tomorrow’s reality. Bulletin of EATCS 59, 256–266.
- Kudlek, M., C. Martinvide and G. H. Paun (2000). Toward FMT (Formal Macroset Theory), in Pre-proceedings of the Workshop on Multiset Processing (Curtea de Arges, August 21–25, 2000), pp. 149–158.
- Lindenmayer, A. (1968). Mathematical models for cellular interaction in development, I and II. J. Theor. Biol. 18, 280–315. CrossRef
- Paun, G. H. (Ed.), (1995). Artificial Life; Grammatical Models, Bucharest: Black Sea University Press.
- Przytycka, T., R. Srinivasan and G. D. Rose (2002). Recursive domains in proteins. Protein Sci. 11, 409–417. CrossRef
- Rozenberg, G. and E. Welzl (1986). Boundary NLC graph grammars—basic definitions, normal forms, and complexity. Information and Control 69, 136–167. CrossRef
- Salomaa, A. (1973). Formal Language, Reading, MA: Academic Press.
- Schultz, J., F. Milpetz, P. Bork and C. P. Ponting (1998). SMART, a simple modular architecture research tool: identification of signalling domains. Proc. Natl Acad. Sci. USA 95, 5857–5864. CrossRef
- Searls, D. B. (1988). Proc. 7th Natl Conf. Artif. Intell., Menlo Park, CA: AAAI Press, pp. 386–391.
- Searls, D. B. (2002). The language of gene. Nature 420, 211–217. CrossRef
- Simeoni, M. and M. Staniszkis (1999). Cooperating graph grammar systems, in Grammatical Models of Multi-agent Systems, G. H. Paun and A. Salomaa (Eds), Amsterdam, Netherlands: Gordon and Breach Science Publishers.
- Syropoulos, A. (2000). Mathematics of multisets, in Pre-proceedings of the Workshop on Multiset Processing (Curtea de Arges, August 21–25, 2000), pp. 286–295.
- Westhead, D. R., T. W. Slidel, T. P. Flores and J. M. Thornton (1999). Protein structural topology: automated analysis and diagrammatic representation. Protein Sci. 8, 897–904.
- Entity grammar systems: A grammatical tool for studying the hierarchal structures of biological systems
Bulletin of Mathematical Biology
Volume 66, Issue 3 , pp 447-471
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- Yun Wang (1)
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- 1. National Laboratory of Protein Engineering, Peking University, Beijing, 100871, China