RbioRXN (version 1.3.1)

get.unipathway.all: Download current Unipathway

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

References

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

Examples

# Not run:

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