Kegg: How Can I Get Data 'By Organism' As In: Get_Compounds_By_Organism...

Question

[Lo]

I would like to find out the most conventient way, to limit/filter results of a request 'by_compounds' or similar by an organism.

for instance get_pathways_by_compounds('C00024'); yields.

( Acetyl-CoA - pathways):


["path:ko00010", "path:ko00020", "path:ko00061", "path:ko00062", "path:ko00071", "path:ko00072", "path:ko00253", "path:ko00280", "path:ko00290", "path:ko00300", "path:ko00310", "path:ko00362", "path:ko00380", "path:ko00410", "path:ko00430", "path:ko00480", "path:ko00562", "path:ko00620", "path:ko00621", "path:ko00622", "path:ko00625", "path:ko00630", "path:ko00640", "path:ko00642", "path:ko00650", "path:ko00680", "path:ko00720", "path:ko00900", "path:ko01056", "path:ko01100", "path:ko01110", "path:ko01120", "path:ko04725", "path:ko04976", "path:map01060", "path:map01061", "path:map01062", "path:map01063", "path:map01064", "path:map01065", "path:map01066", "path:map01070"]

Kegg's description: link 'pathway_id' is a pathway identifier consisting of 'path' and a pathway number used in KEGG/PATHWAY. Pathway numbers prefixed by 'map' specify the reference pathway and pathways prefixed by the 'keggorg' specify pathways specific to the organism (e.g. 'path:map00020' means a reference pathway for the cytrate cycle and 'path:eco00020' means a same pathway of which E. coli genes are marked).

I would like to filter the results, or make a filtered request in the first place. For instance filtered by the organism E.coli.

Answer 1

[Sudeep]

Hi, since you are using kegg web api, it is very easy instead of get_pathways_by_compounds() method call list_pathways("eco") [eco -> three letter organism code for E. coli], you can find a tutorial here. KEGG uses a three letter organism code, you can find more examples of this three letter nomenclature in this file. Hope this helps

[Lo]

do you also know how to resolve the kegg ontologies? e.g. ko#num ?

Ideally i would like to get the pathway names instead of K-numbers when using ' get_pathways_by_compounds'. Or do you know of a sql database out there with all the Kegg orthologies?