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

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()

Arguments

Value

R list object. The list contains two data.frame() objects (reaction and comopund) where data fields include,
ENTRYKEGG ID (R number)
NAMEEnzyme name
DEFINITIONReaction equation with standard compound name
EQUATIONReaction equation with KEGG ID
ENZYMEE.C number
COMMENTComment
RPAIRKEGG RPAIR is a collection of substrate-product pairs (reactant pairs) defined for each reaction in KEGG REACTION
PATHWAYKEGG PATHWAY that this reaction participates
ORTHOLOGYCross-link to KEGG ORTHOLOGY database
REMARKUsually this column indicates glycan reaction-chemical reaction pair
REFERENCEPublication info with PMID, title, and journal name
KEGG COMPOUND,
ENTRYKEGG ID (C number)
NAMECompound name
FORMULAMolecular formula
EXACT_MASSMolecular mass
MOL_WEIGHTMolecular weight
REMARK
REACTIONKEGG REACTION entries where the compound particiaptes
PATHWAYKEGG PATHWAY entries where the compound participates
ENZYMEKEGG ENZYME entries where the compound is related
ATOM
BOND
CASCross-link to CAS database
PubChemCross-link to PubChem database
ChEBICross-link to ChEBI database
PDB.CCDCross-link to Chemical Component Dictionary
X3DMET
NIKKAJI
BRITE
KNApSAcK
COMMENT
BRACKET
LIPIDMAPS
LipidBank
SEQUENCE
REFERENCE

References

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

Examples

Run this code

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

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