Hi,

I am trying to convert a list of KEGG pathway name to corresponding KEGG IDs.

To do that, I am using KEGG.db, Version 3.1.2. It seems that this package is not complete, for example one of the KEGG pathways is " Adrenergic signaling in cardiomyocytes" with ID= 'hsa04261', which there is not available in this package?!

I am using the below code:

    library(KEGG.db)

    keggid2name <- as.list(KEGGPATHID2NAME)

    keggid2name["04261"]

Do you have any idea about where can I find complete list of pathway names and IDs?

The KEGGREST package vignette suggests

> library(KEGGREST)
> keggGet("hsa04261")[[1]]$NAME
[1] "Adrenergic signaling in cardiomyocytes - Homo sapiens (human)"
> ids = "hsa04261"                     # alternative -- vector of ids
> sapply(keggGet(ids), "[[", "NAME")
[1] "Adrenergic signaling in cardiomyocytes - Homo sapiens (human)"

Is that what you are looking for?

Hi there,

When I load the KEGG.db package with

library(KEGG.db)

I get the following text:

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

Ben