Bibliography of Journal: Proc Int Conf Intell Syst Mol Biol

  1. Baker, P.G., Brass, A., Bechhofer, S., Goble, C.A., Paton, N.W., and Stevens, R.. "TAMBIS--Transparent Access to Multiple Bioinformatics Information Sources." Proc Int Conf Intell Syst Mol Biol. vol. 6. 1998. pp. 25-34.
    [ .pdf ] [ .ps ] [ PubMed ] [ WebSite ]

    The TAMBIS project aims to provide transparent access to disparate biological databases and analysis tools, enabling users to utilize a wide range of resources with the minimum of effort. A prototype system has been developed that includes a knowledge base of biological terminology (the biological Concept Model), a model of the underlying data sources (the Source Model) and a 'knowledge-driven' user interface. Biological concepts are captured in the knowledge base using a description logic called GRAIL. The Concept Model provides the user with the concepts necessary to construct a wide range of multiple-source queries, and the user interface provides a flexible means of constructing and manipulating those queries. The Source Model provides a description of the underlying sources and mappings between terms used in the sources and terms in the biological Concept Model. The Concept Model and Source Model provide a level of indirection that shields the user from source details, providing a high level of source transparency. Source independent, declarative queries formed from terms in the Concept Model are transformed into a set of source dependent, executable procedures. Query formulation, translation and execution is demonstrated using a working example.

    Keywords: Artificial Intelligence ; *Computational Biology ; Databases Factual ; User-Computer Interface


  2. Hofestadt, R.. "Grammatical formalization of metabolic processes." Proc Int Conf Intell Syst Mol Biol. vol. 1. 1993. pp. 181-9.
    [ PubMed ]

    In the field of biotechnology and medicine it is of interest to model and simulate metabolic processes. The usual methods to model metabolic pathways are chemical descriptions and differential equations. Moreover, the graph theoretical aspect is discussed and the development of expert systems is in process. In this paper we present the formalization of metabolic processes. Our formalization is based on the theory of formal languages. This formalization is called genetic grammar and represents an expansion of the Semi-Thue-System.

    Keywords: *Computer Simulation ; *Expert Systems ; Gene Expression ; *Metabolism ; *Models Biological ; Programming Languages


  3. Mavrovouniotis, M.L.. "Identification of localized and distributed bottlenecks in metabolic pathways." Proc Int Conf Intell Syst Mol Biol. vol. 1. 1993. pp. 275-83.
    [ PubMed ]

    The usual thermodynamic evaluation, based solely on the Standard Gibbs Energy of reaction, does not take into account the permissible ranges of concentrations of metabolites, and it faces further difficulties when, instead of isolated reactions, we are examining whole pathways. For pathways, we seek not only to decide whether they are feasible but also to pinpoint the pathway segment that causes any thermodynamic difficulties. We define a set of scaled quantities which reformulate the thermodynamic-feasibility problem for the whole pathway. We present an algorithm which analyzes individual reactions and selective construction of larger subpathways and uncovers localized and distributed thermodynamic bottlenecks of the biotransformation. This type of thermodynamic treatment contributes to the effort to include more physical, chemical, and biological factors in the computer-aided analysis of metabolic pathways.

    Keywords: *Algorithms ; *Computer Simulation ; Glycolysis ; *Metabolism ; *Models Biological ; *Thermodynamics


  4. Mavrovouniotis, M.L.. "Describing multiple levels of abstraction in the metabolism." Proc Int Conf Intell Syst Mol Biol. vol. 2. 1994. pp. 294-302.
    [ PubMed ]

    We discuss some central issues that arise in the computer representation of the metabolism and its subsystems. We provide a framework for the representation of metabolites and bioreactions at multiple levels of detail. The framework is based on defining an explicit linear mapping of metabolites and reactions from one level of detail to another. A simple reaction mechanism serves as an illustration and shows the emergence of the concept of a catalyst from metabolic abstraction levels.

    Keywords: Catalysis ; *Computer Simulation ; *Metabolism


  5. Reddy, V.N., Mavrovouniotis, M.L., and Liebman, M.N.. "Petri net representations in metabolic pathways." Proc Int Conf Intell Syst Mol Biol. vol. 1. 1993. pp. 328-36.
    [ PubMed ]

    The present methods for representing metabolic pathways are limited in their ability to handle complex systems, incorporate new information, and to provide for drawing qualitative conclusions from the structure of pathways. The theory of Petri nets is introduced as a tool for computer-implementable representation of pathways. Petri nets have the potential to overcome the present limitations, and through a multitude of properties, enable the preliminary qualitative analysis of pathways.

    Keywords: *Computer Simulation ; Fructose_metabolism ; Liver_metabolism ; *Metabolism ; *Models Biological