get.chebi.all: Download and parse current ChEBI

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

Description

Download all ChEBI in BioPAX level 2 (ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl) and parse to generate data.frame() object

Usage

get.chebi.all()

Value

data.frame() object where data fields include

ChEBI	Unique ChEBI identifier
name	Chemical standard name
synonyms	If entity has multiple synonyms, they are separated by "///"
smiles	SMILES representation of chemical structure
inchi	InChI representation of chemical structure
kegg	Cross-link to KEGG COMPOUND database
parent	Parent compound if available
formula	Chemical formula

Author(s)

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

References

ChEBI web address: http://www.ebi.ac.uk/chebi/ \ BioPAX.org: http://www.biopax.org

Examples

# Not run: it will take several minutes (5-7 mins)

##  chebi = get.chebi.all()
##  head(chebi)

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