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

Description Usage Value Note Author(s) References See Also Examples

View source: R/get.kegg.all.R

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

1

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 <[email protected]>, 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

1
2
3
4
5
# 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.