get.kegg.all: Download current KEGG REACTION and KEGG COMPOUND database...

In RbioRXN: Process Rhea, KEGG, MetaCyc, Unipathway Biochemical Reaction Data

Description

By implementing KEGGREST package in Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/KEGGREST.html), gather all KEGG REACTION and KEGG COMPOUND datain data.frame() object.

Usage

get.kegg.all()

Value

R list object. The list contains two data.frame() objects (reaction and comopund) where data fields include,

ENTRY	KEGG ID (R number)
NAME	Enzyme name
DEFINITION	Reaction equation with standard compound name
EQUATION	Reaction equation with KEGG ID
ENZYME	E.C number
COMMENT	Comment
RPAIR	KEGG RPAIR is a collection of substrate-product pairs (reactant pairs) defined for each reaction in KEGG REACTION
PATHWAY	KEGG PATHWAY that this reaction participates
ORTHOLOGY	Cross-link to KEGG ORTHOLOGY database
REMARK	Usually this column indicates glycan reaction-chemical reaction pair
REFERENCE	Publication info with PMID, title, and journal name

KEGG COMPOUND,

ENTRY	KEGG ID (C number)
NAME	Compound name
FORMULA	Molecular formula
EXACT_MASS	Molecular mass
MOL_WEIGHT	Molecular weight
REMARK
REACTION	KEGG REACTION entries where the compound particiaptes
PATHWAY	KEGG PATHWAY entries where the compound participates
ENZYME	KEGG ENZYME entries where the compound is related
ATOM
BOND
CAS	Cross-link to CAS database
PubChem	Cross-link to PubChem database
ChEBI	Cross-link to ChEBI database
PDB.CCD	Cross-link to Chemical Component Dictionary
X3DMET
NIKKAJI
BRITE
KNApSAcK
COMMENT
BRACKET
LIPIDMAPS
LipidBank
SEQUENCE
REFERENCE

Note

Because 'KEGGREST' package has not been deposited in CRAN, you need to manually install this package by typing:

> source("http://bioconductor.org/biocLite.R")
> biocLite("KEGGREST")

For details,
http://www.bioconductor.org/packages/release/bioc/html/KEGGREST.html

Author(s)

Byoungnam Min <[e-mail]>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol Choi

References

KEGGREST package: http://www.bioconductor.org/packages/release/bioc/html/KEGGREST.html
KEGG API: http://www.kegg.jp/kegg/docs/keggapi.html

See Also

get.kegg.byId

Examples

# Not run: (it will take 30-40 minutes)

##  keggAll = get.kegg.all()
##  head(keggAll$reaction)
##  head(keggAll$comound)

RbioRXN documentation built on May 29, 2017, 10:56 a.m.