get.chebi.all: Download and parse current ChEBI

Description Usage Value Author(s) References Examples

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

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

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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 <[email protected]>

References

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

Examples

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# 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.