The KEGG reference pathway maps and BRITE reference hierarchies are created in a general way to be applicable to all organisms; namely, in terms of the orthologs defined by K numbers. The organism-specific pathways and hierarchies can then be generated by converting K numbers to gene identifiers in a given organism. In the past year, the KEGG PATHWAY database has been completely renovated. All the pathway maps have been redrawn using a newly developed tool called KegSketch, which generates KGML+ (meaning KGML + SVG) files. Internally the database update procedure is now based on the text manipulation of these files rather than the color manipulation of image files. For outside services, the coloring procedure continues to be done on image files, but the image file format has been changed from GIF to PNG to accommodate more colors. As a result, there is now no distinction between the global map (6) and the regular pathway maps; they can be manipulated in the same way both in the new KEGG Atlas tool and the traditional image map viewer. Another new feature in
