get.unipathway.all: Download current Unipathway

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

Description

Download Unipathway in OBO, then parse and generate data.frame() object

Usage

get.unipathway.all(oboPath = "")

Arguments

oboPath

Unipathway in OBO from http://www.grenoble.prabi.fr/obiwarehouse/unipathway. If you don't provide the file, the function tries to download from web

Value

R list object. The list() contains two data.frame() objects (reaction and compound) where data fields of each data.frame() include,
reaction includes

id	Unipathway ID
enzName	It usually indicates substrate and product in the reaction
equation	Reaction equation with compound standard name
KEGG	Cross-link to KEGG
RHEA	Cross-link to Rhea
METACYC	Cross-link to MetaCyc
EC	EC number each reaction assigned
GO	GO term
UNIPROT	Cross-link to UniProt
compoundId	Compound ID of each reaction participant
compoundName	Compound standard name of each reaction participant

compound includes

id	Unipathway ID
type	Compound type
name	Compound name
KEGG	Cross-link to KEGG
CHEBI	Cross-link to ChEBI
formula	Molecular formula
inchi	InChI code
synonym.kegg	Synonyms to KEGG

Author(s)

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

References

UniPathway: http://www.grenoble.prabi.fr/obiwarehouse/unipathway

Examples

# Not run:

##  unipathway = get.unipathway.all()
##  dim(unipathway)                   # The number of downloaded reaction entries

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