A systematic comparison of the MetaCyc and KEGG pathway databases

BMC Bioinformatics

Table 9 A comparison of MetaCyc (M) and KEGG (K) pathway attributes, for those attributes where one hundred or more objects have a value for that attribute

Attributes are sorted based on frequency. KEGG pathway attribute data are pooled from all objects in the KEGG MODULE and MAP datasets (which include data from global pathways and pathway classes with no metabolic reaction data). Attribute Species specifies the organisms in which the pathway has been studied experimentally. Pathway-Links lists important substrates that connect to other metabolic pathways, whereas KEGG attribute Rel_Pathway links pathways to one another without specifying the compound in common. Taxonomic-Range describes the taxonomic groups in which the pathway is likely to be found; this information increases the accuracy of pathway prediction. Predecessors specifies for each reaction the reaction(s) that precede it in the pathway, and thus defines the connectivity structure of each pathway. KEGG encodes equivalent data in the “ECrel” relationship, obtained from the get_element_relations_by_pathway API function. Key-Reactions increases the accuracy of pathway prediction by specifying reactions whose presence is highly indicative of the pathway, and distinguish the pathway from other, similar pathways. Hypothetical-Reactions identifies pathway reactions that are speculative and have not been firmly established experimentally. The Disease attribute consists of links to the KEGG DISEASE dataset when disease-related genes encode enzymes for one or more reaction steps in the pathway.

ISSN: 1471-2105