Use IntPath to find the pathway interactions/edges

It is very common to find the papers explored the number of KEGG pathways present in reconstructed networks for real experimental data. The number of edges present in KEGG pathways are very useful as the real biological experimental data in this work, however this can be a very serious problem for the analysis. It has been well known by many excellent investigation, that effectiveness of pathway databases (especially like KEGG) is hindered by issues such as incompatible data formats, inconsistent molecular representations, inconsistent molecular relationship representations, inconsistent referrals to pathway names, and incomprehensive data from different databases[1]. Therefore the number of edges retrieved from KEGG pathways are very incomplete and limited, therefore may seriously limit the sufficient assessment of this comparative studies. 

There are effective and easy solutions for this problem, just use IntPath data and here the IntPath database[1] solves all those issues completely and accurately, the authors should try to build their work on comprehensive database like IntPath[1]. 

It take few seconds to retrieve the pathway edges from all the whole IntPath database, by using the “Online Toolkit”, choose the species “H. Sapiens” and the API “getIntPathGenePairs”, and in a second, one can get the most comprehensive and curated edges in IntPath database which contains 3 times more edges than KEGG. For more specific information of gene pairs(edges) of each specific pathways, the users can download the simple text format of the IntPath data in the download section. IntPath will be a more solid stepping stone for the comparative studies than KEGG. For retrieving the specific edges of each specific pathways, one can just use “getIntPathPathways” , the database will list all the pathway names, and then, the authors can choose the interested pathway names, and use the online toolkit “getPathwayInteraction” and input the pathway name below, then the comprehensive gene pairs(edges) will be displayed, the author can also retrieve the same information from the downloaded text format. 

Reference:

[1]Hufeng Zhou, Jingjing Jin, Haojun Zhang, Bo Yi, Michal Wozniak, and Limsoon Wong. "IntPath--an integrated pathway gene relationship database for model organisms and important pathogens." BMC systems biology 6, no. Suppl 2 (2012): S2.