Box 5.2On Graphical Models

A large fraction of today's knowledge of biochemical or genetic regulatory networks is represented either as text or as cartoon-like diagrams. However, text has the disadvantage of being inherently ambiguous, and every reader must reinterpret the text of a journal article. Diagrams are usually informal, often confusing, and thus fail to present all of the information that is available to the presenter of the research. For example, the meanings of nodes and arcs within a diagram are inconsistent—one arrow may mean activation, but another arrow in the same diagram may mean transition of the state or translocation of materials.

To remedy this state of affairs, a system of graphical representation should be powerful enough to express sufficient information in a clearly visible and unambiguous way and should be supported by software tools. There are several criteria for a graphical notation system, including the following:

  1. Expressiveness. The notation system should be able to describe every possible relationship among the entities in a system—for example, those between genes and proteins in a biological model.
  2. Semantical unambiguity. Notation should be unambiguous. Different semantics should be assigned to different symbols that are clearly distinguishable.
  3. Visual unambiguity. Each symbol should be identified clearly and not be mistaken with other symbols. This feature should be maintained with low-resolution displays, using only black and white.
  4. Extension capability. The notation system should be flexible enough to add new symbols and relationships in a consistent manner. This may include the use of color coding to enhance expressiveness and readability, but information should not be lost even with black-and-white displays.
  5. Mathematical translation. The notation should be able to convert itself into mathematical formalisms, such as differential equations, so that it can be applied directly for numerical analysis.
  6. Software support. The notation should be supported by software for its drawing, viewing, editing, and translation into mathematical formalisms.

No current graphical notation system satisfies all of these criteria fully, although a number of systems satisfy some of them.1

SOURCE: Adapted by permission from H. Kitano, “A Graphical Notation for Biochemical Networks,” Biosilico 1(5):159-176. Copyright 2003 Elsevier.

1

See, for example, K.W. Kohn, “Molecular Interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems,” Molecular Biology of the Cell 10(8):2703-2734, 1999; K. Kohn, “Molecular Interaction Maps as Information Organizers and Simulation Guides,” Chaos 11(1):84-97, 2001.

From: 5, Computational Modeling and Simulation as Enablers for Biological Discovery

Cover of Catalyzing Inquiry at the Interface of Computing and Biology
Catalyzing Inquiry at the Interface of Computing and Biology.
National Research Council (US) Committee on Frontiers at the Interface of Computing and Biology; Wooley JC, Lin HS, editors.
Washington (DC): National Academies Press (US); 2005.
Copyright © 2005, National Academy of Sciences.

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