A systematic comparison of the MetaCyc and KEGG pathway databases

BMC Bioinformatics

Table 1 Comparison of chemical compounds in MetaCyc and KEGG

Category	M(all)	M(base)	M(super)	K(all)	K(module)	K(map)	Common
All chemical compounds	11991			15161			5120 (0.23)
All reaction substrates	8891			6912			4232 (0.37)
Pathway reaction substrates	5523	5371	5523	4759	828	4759	2384 (0.30)

For each type of compound (row), we report the number of compounds in MetaCyc, the number of compounds in KEGG, and the number of compounds in common between MetaCyc and KEGG. “All chemical compounds” includes both compound classes and compound instances for MetaCyc; for KEGG it includes all compounds in the KEGG COMPOUND file. “All reaction substrates” is the union of all literal reaction substrates (reactants plus products) in the specified DB. M(all): all MetaCyc compounds; M(base): compounds in MetaCyc base pathways; M(super): compounds in MetaCyc super pathways; K(all): all KEGG compounds; K(module): compounds in KEGG module; K(map): compounds in KEGG map; Common: corresponding compounds by total number and by the Jaccard coefficient in parentheses.

ISSN: 1471-2105