list.organisms: Client-side interface to obtain the names of organisms...
In kozo2/keggapi: Client-side REST access KEGG

Description Usage Arguments Details Value Author(s) References Examples

View source: R/KEGGREST.R

These functions provides an R interface to allow users to get the names/ids of organisms, databases, pathways that are available through KEGG REST services.

1 2	list.organisms() list.pathways(org)

org

org a character string for the id used by KEGG for organisms. The organism ids are normally three-letter codes with the first letter being the first letter of the genus name and the rest being the first two letters of the species name of the scientic name of the organism of concern

Some queries agsinst the KEGG databases require abbreviations of organisms supported by KEGG. Although the abbreviations normally consist of three letters by truncating the first letter of the genus name and the first two letters of the species name (e. g. hsp for Homo sapiens), list.organisms obtains the abbreviations using the service provided by KEGG REST to make sure the abbreviations are correct and the organisms are indeed supported by KEGG databases.

list.organisms returns a named vector with names of the vector being the scientific names and the values of the vector being the abbreviations used by KEGG for the organisms supported by the databases.

list.pathways returns a named vector with names of the vector being textual descriptions of KEGG pathways and the values of the vector being the ids used by KEGG to represent pathways.

Kozo Nishida

http://www.kegg.jp/kegg/docs/keggapi.html