Hi,

I don't know your informatic skills, but you could start by taking a look at the rather new KEGG rest API. If your organism is already inside the KEGG database retrieving all its pathways is relatively easy. Assume your organism is Homo sapiens (Kegg code "hsa"), you just need to open your browser and go to this page (notice the URL). This example gives you all the pathways AND the human genes associated to them.

To get info about a gene (for instance hsa:10) just go to this page (again, notice how the URL is built).

To get info about a pathway (for instance hsa:10) just go to this page.

You can also retrieve this data using a script, below a simple example in python

import urllib2
url = 'http://rest.kegg.jp/link/hsa/pathway'
data = urllib2.urlopen(url, timeout=20).read()
# Parse it!

If your organism is not inside the KEGG database, you first need to annotate it through KAAS, obtain the KO IDs and then do a search like this (note that there is a limit in the number of KO IDs that you can put in a single URL, so maybe you need to perform more than one search).

Hope this helps...

Take a look to that biostar post as well A new REST based API for KEGG: Kyoto Encyclopedia of Genes and Genomes

you can use clusterProfiler in R:

devtools::install_github("guangchuangyu/clusterProfiler")
library(clusterProfiler)
hsa_kegg = download_KEGG('hsa')

You can use GeneSCF to download with simple command (Only retrieves the updated data- real-time),

A: focus on specific pathway

A: Gene ontology in sheep

./prepare_database -db=[GO_all|GO_BP|GO_MF|GO_CC|KEGG|REACTOME|NCG] -org=[see,org_codes_help]

Gene Set Clustering based on Functional annotation (GeneSCF)

http://genescf.kandurilab.org/