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. 2013 Oct 7;7:100.
doi: 10.1186/1752-0509-7-100.

NaviCell: A Web-Based Environment for Navigation, Curation and Maintenance of Large Molecular Interaction Maps

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Free PMC article

NaviCell: A Web-Based Environment for Navigation, Curation and Maintenance of Large Molecular Interaction Maps

Inna Kuperstein et al. BMC Syst Biol. .
Free PMC article

Abstract

Background: Molecular 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.

Results: NaviCell 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.

Conclusions: NaviCell 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.

Figures

Figure 1
Figure 1
General architecture of NaviCell environment.
Figure 2
Figure 2
NaviCell layout. (A) Map panel with top-level view of the modular RB-E2F map, (B) Fragment of the detailed view of the map with a callout and markers, (C) Selection panel with list of the map entities grouped per type.
Figure 3
Figure 3
NaviCell semantic zooming. The same area of the map is visualized at four different zoom levels; each image is twice smaller than in the preceding zoom level. (A) In the top-level view, boundaries of map modules are visualized, (B) In the pruned view, only the most important molecular cascades are visualized, (C) In the hidden details view, unreadable details (such as residue names) are hidden, (D) In the detailed view, entity names, modifications and reaction IDs are visible.
Figure 4
Figure 4
Module maps. (A) RB module on the Top-level view zoom, (B) RB module on the hidden-details view zoom, (C) RB module shown as a separate map.
Figure 5
Figure 5
Annotation post in the blog for the complex CDK2:cyclin A2*:p27Kip1*.

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