Abstract
Generation and usage of high-quality molecular signalling network maps can be augmented by standardizing notations, establishing curation workflows and application of computational biology methods to exploit the knowledge contained in the maps. In this manuscript, we summarize the major aims and challenges of assembling information in the form of comprehensive maps of molecular interactions. Mainly, we share our experience gained while creating the Atlas of Cancer Signalling Network. In the step-by-step procedure, we describe the map construction process and suggest solutions for map complexity management by introducing a hierarchical modular map structure. In addition, we describe the NaviCell platform, a computational technology using Google Maps API to explore comprehensive molecular maps similar to geographical maps and explain the advantages of semantic zooming principles for map navigation. We also provide the outline to prepare signalling network maps for navigation using the NaviCell platform. Finally, several examples of cancer high-throughput data analysis and visualization in the context of comprehensive signalling maps are presented.
Highlights
Similar to geographical maps, the representation of biological knowledge as a diagram facilitates the study of complex processes in the living cell, in a visual and insightful way.Goal of knowledge formalization The representation of biological processes as comprehensive signalling network maps has three major goals: (i) to generate a resource containing a formalized summary of biological findings from many research groups, (ii) to provide a platform for sharing information and discussing biological mechanisms and (iii) to create an analytical tool useful for high-throughput data integration and analysis.It can be helpful to systematically represent and formalize the molecular information distributed in thousands of scientific publications
Diagram of detailed molecular interactions with meaningful layout reflecting a certain biological process, which is graphically represented in CellDesigner tool and converted to NaviCell format for exploration and curation
Signalling processes of DNA repair are represented as biochemical reactions in CellDesigner diagram editor based on the standard Systems Biology Graphical Notation (SBGN) syntax [10], and the Systems Biology Markup Language (SBML), for further computational modelling of the map [14]
Summary
The representation of biological knowledge as a diagram facilitates the study of complex processes in the living cell, in a visual and insightful way.Goal of knowledge formalization The representation of biological processes as comprehensive signalling network maps has three major goals: (i) to generate a resource containing a formalized summary of biological findings from many research groups, (ii) to provide a platform for sharing information and discussing biological mechanisms and (iii) to create an analytical tool useful for high-throughput data integration and analysis.It can be helpful to systematically represent and formalize the molecular information distributed in thousands of scientific publications. Goal of knowledge formalization The representation of biological processes as comprehensive signalling network maps has three major goals: (i) to generate a resource containing a formalized summary of biological findings from many research groups, (ii) to provide a platform for sharing information and discussing biological mechanisms and (iii) to create an analytical tool useful for high-throughput data integration and analysis. We suggest the biological network map navigation facilitated by Google Maps technology and provide examples of data analysis and visualization in this context.
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