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

BMC Systems Biology

Table 1 Comparison of NaviCell features with existing tools

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

^* Analytical tools:
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.

ISSN: 1752-0509