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Table 1 Comparison of NaviCell features with existing tools

From: NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

Feature Map browsers used in pathway databases Standalone tools
  KEGG Reactome Spike Wiki pathways BioCyc Panther NaviCell Cell publisher Pathways projector Cell designer Payao SBGN-ED GenMAPP PathVisio BioUML Cytoscape + plugins
Built-in SBGN support (not through external converters)   ×    × × × ×   × × ×    × ×
Map editing embedded in the tool (not through external editor)    × ×      × ×   × × × × ×
Possibility to change the layout    × ×       ×   × × × × ×
Adding user maps through web uploading     ×     ×    ×      
Analytical tools ×* ×*    ×* ×* under development   ×* ×* ×* ×* ×* ×* ×* ×*
Web interface × × × × × × × × ×   ×     × ×
Google Maps interface     ×    × × ×        
Semantic zooming   ×    ×   ×   ×        ×
Commenting map content by users     ×    × ×   × × ×    ×  
Browser Any type Any type Any type Any type Any type Any type Firefox Safari Chrome Firefox Safari Chrome IE Firefox Safari N/A N/A N/A N/A N/A Any type N/A
Reference 6 5 8 9 11 7   21 22 16 26 25 23 24 N/A 31,32
  1. * Analytical tools:
  2. Pathway projector- Data mapping, Path search, Sequence-based search (BLAST), Pathway prediction; KEGG- Data mapping, Pathways enrichment analysis; Reactome- Data mapping, Pathways enrichment analysis, Path search; CellDesigner- Simulation; Payao-analytical text-mining by PathText; SBGN-ED- Data mapping, Network analysis, Simulation; Panther- Data mapping; BioCyc-Pathway Tools Software; PathVisio- Data mapping, Pathways enrichment analysis; GenMAPP- Data mapping, Pathways enrichment analysis; BioUML- Simulation and analysis; Cytoscape-Various tools available through plugins.