RbioRXN (version 1.5.1)

get.metacyc.all: Download current MetaCyc via BioCyc Web Services

Description

This function first retrieves all MetaCyc reaction IDs and download BioPAX level 3 for each reaction, then parse to generate data.frame() object. Note that because this function interacts with BioCyc web service for every reaction, it will take many hours depending on your network speed. Thus, we strongly recommend to use parse.metacyc.reaction() and parse.metacyc.compound() functions in this package after manually downloading MetaCyc from http://biocyc.org/download.shtml

NOTE: The MetaCyc server is occasionally unavailable, so this function accesses our own server as additional resource after trying original server. Our server may not contain latest data.

Usage

get.metacyc.all()

Value

R data.frame() object where data fields indclude

MetaCyc

MetaCyc ID

name

Reaction equation with chemical standard name

ec_number

E.C number

name_id

Reaction equation with MetaCyc compound ID

References

MetaCyc download page: http://biocyc.org/download.shtml MetaCyc web services: http://biocyc.org/web-services.shtml

See Also

parse.metacyc.reaction parse.metacyc.compound

Examples

# Not run:

##  metacycAll = get.metacyc.all()
##  head(metacycAll)