Abstract
BackgroundMolecular biology knowledge can be formalized and systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular interactions containing detailed and step-wise description of various cell mechanisms. It is difficult to explore these large maps, to organize discussion of their content and to maintain them. Several efforts were recently made to combine these capabilities together in one environment, and NaviCell is one of them.ResultsNaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. It is characterized by a combination of three essential features: (1) efficient map browsing based on Google Maps; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of interest in the context of signaling pathways and crosstalk between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell greatly facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive and user-friendly fashion due to an imbedded blogging system.ConclusionsNaviCell provides user-friendly exploration of large-scale maps of molecular interactions, thanks to Google Maps and WordPress interfaces, with which many users are already familiar. Semantic zooming which is used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization readable. In addition, NaviCell provides a framework for community-based curation of maps.
Highlights
Molecular biology knowledge can be formalized and systematically represented in a computerreadable form as a comprehensive map of molecular interactions
From our practical experience of map creation, maintenance and curation, we identified the lack of a tool that would offer simultaneously a) easy web-based navigation through the content of comprehensive maps of molecular interactions created according to the systems biology standards; b) visualization of the map at different scales in a readable form; c) possibility to collect the feedback of a user about the map’s content in an interactive manner
To fill this unoccupied but highlydemanded niche, we have developed NaviCell which uses Google Maps for navigation into the map, semantic zooming principles for exploring the map at various scales and the standard WordPress blogging system for collecting comments on the maps, providing a discussion forum for the community around the map’s content
Summary
Molecular biology knowledge can be formalized and systematically represented in a computerreadable form as a comprehensive map of molecular interactions. A parallel approach for formalizing the biological knowledge consists in creating graphical representations of the biochemical mechanisms in the form of maps of molecular interactions such as [13] and many others. The first large maps of metabolism, cell cycle, DNA repair have been created manually starting from the ‘60s and were not supported by any database structure [14,15] Such maps can be considered as a collection of biological diagrams, each depicting a particular cellular mechanism, assembled into a seamless whole, where the molecular players and their groups occupy particular “territories”. Molecules put close together on the map are assumed to have similar functional properties (though it is not always possible to achieve in practice) This geographical metaphor has certain advantages over the database representations for which no global visual image of pathways’ functional proximity and crosstalk exists
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