latest news

1.Feb.2012

Added circular bacterial genome map

21.Sep.2010

Added new pathway map "Biosynthesis of secondary metabolites"

11.Nov.2009

Pathway Projector paper published.

19.Sep.2009

Documentation is added.

19.Jul.2009

Reference map and webpage renewal

27.Nov.2008

Beta

example graphic

Introduction

The Pathway Projector was implemented according to the aforementioned requirements, including the availability of a large-scale comprehensive pathway map, pathways from a wide variety of organisms, and searching and mapping capabilities. Since it has been implemented as a web application, this software is cross-platform and requires no installation or maintenance. Moreover, use of the AJAX web development paradigm provides an intuitive user experience similar to that of desktop applications. The main pathway map of Pathway Projector was reconstructed from the popular KEGG Atlas layout by adding nodes for enzymes and genes. As an example, the map for E. coli K12 contains 1365 genes, 1813 enzymes, and 1572 metabolites. Circular and rectangular nodes represent metabolites and genes/enzymes, respectively, and the names of genes, enzymes, and metabolites are displayed within the map at high zoom levels by means of semantic zooming. Reaction edges are color coded according to the following pathway categories: aqua represents glycan biosynthesis and metabolism, blue represents carbohydrate metabolism, green represents lipid metabolism, red represents nucleotide metabolism, purple represents energy metabolism, yellow represents amino acid metabolism, pink represents metabolism of cofactors and vitamins, dark red represents biosynthesis of secondary metabolites, orange represents metabolism of other amino acids, and magenta represents biodegradation and metabolism of xenobiotics. Pathway Projector utilizes the Google Maps API for the implementation of zoomable user interface (ZUI) and enables smooth navigation through panning and zooming without page transitions using a mouse scroll wheel or double clicks. Every component in the pathway map shows more detailed information by clicking on the nodes, which opens up an information window containing annotations, such as chemical and structural formulas and links to external public databases. Users can therefore use Pathway Projector as a generic browser and as a gateway for various pathway-related resources.

Software

start Pathway Projector

Click here to start.

Documentations

Detailed documentation is available in here


Publication

Our manuscript describing this online resource is published by PLoS one journal with the title, "Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API". Click the above Publication to view the full-text of the manuscript.

Kono N, Arakawa K, Ogawa R, Kido N, Oshita K, Ikegami K, Tamaki S, Tomita M. (2009) Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API. PLoS One 2009 4(11):e7710

License

Important Notice: The software automatically utilizes KEGG data on the server side. Academic users may freely download the KEGG data as provided at the GenomeNet ftp site at ftp://ftp.genome.ad.jp/pub/kegg/, but non-academic users are requested to obtain a license agreement through the licensor, Pathway Solutions Inc., for installation of KEGG at their sites, for distribution or reselling of KEGG data, for software development and any other commercial activities that make use of KEGG, and also as end users of the third-party programs that access the KEGG ftp site.

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