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

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

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

Note

We strongly recommend using parse.metacyc.reaction() and parse.metacyc.reaction() functions because of long running process. These two functions need "dat" files downloaded from MetaCyc. See http://biocyc.org/download.shtml

Author(s)

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

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)

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