RbioRXN (version 1.3.1)

get.chebi.all: Download and parse current ChEBI

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

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)