Extended Contact Maps

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Rule-based modeling provides a means to represent cell signaling systems in a way that captures site-specific details of molecular interactions. For rule-based models to be more widely understood and (re)used, conventions for model visualization and annotation are needed. We have developed the concepts of an extended contact map and a model guide for illustrating and annotating rule-based models. An extended contact map represents the scope of a model by providing an illustration of each molecule, molecular component, direct physical interaction, post-translational modification, and enzyme-substrate relationship considered in a model. A map can also illustrate allosteric effects, structural relationships among molecular components, and compartmental locations of molecules. A model guide associates elements of a contact map with annotation and elements of an underlying model, which may be fully or partially specified. A guide can also serve to document the biological knowledge upon which a model is based. An extended contact map and an associated guide can document knowledge of a cell signaling system in a form that is visual as well as executable. As a tool for model annotation, a map and guide can communicate the content of a model clearly and with precision, even for large models.

  • Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J, Hlavacek WS (2011) Mol. BioSyst. doi:10.1039/c1mb05077j

The paper with Appendices S1-S3 and supplemental figures is also available here.

Stencil package for OmniGraffle

  • Download the current version as a .tgz file here. The current version is 1.0. The following files are included in the package: templates.graffle, Contact Maps.gstencil and README.txt.

Example Map and Guide

The map below (you may need to log in to view the map) illustrates the model of Goldstein et al. (2002) and Faeder et al. (2003). A BNGL specification of this model is available here. A guide for this model is available here.

Example_Map.png

A version of this map in a style similar to Systems Biology Graphical Notation (SBGN) is here.

  • Goldstein B, Faeder JR, Hlavacek WS, Blinov ML, Redondo A, Wofsy C (2002) Mol. Immunol. 38, 1213-1219.
  • Faeder JR, Hlavacek WS, Reischl I, Blinov ML, Metzger H, Redondo A, Wofsy C, Goldstein B (2003) J. Immunol. 170, 3769-3781.
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