Package ‘RbioRXN’
May 19, 2015
Type Package
Title Process Rhea, KEGG, MetaCyc, Unipathway Biochemical Reaction
Data
Version 1.5.1
Date 2015-05-19
Author Byoungnam Min, Byeonghyeok Park, Kyoung Heon Kim and In-Geol Choi
Maintainer Byoungnam Min <mbnmbn00@gmail.com>
Description To facilitate retrieving and processing biochemical reaction data such as Rhea, MetaCyc, KEGG and Unipathway, the package provides the functions to download and parse data, instantiate generic reaction and check mass-balance. The package aims to construct an integrated metabolic network and genome-scale metabolic model.
License GPL (>= 2)
Depends R (>= 3.0.3), fmcsR, ChemmineR
Imports plyr, RCurl, gdata, KEGGREST, data.table, stringr
NeedsCompilation no
Repository CRAN
Date/Publication 2015-05-19 13:07:25
R topics documented:
RbioRXN-package . . .
build.subtable . . . . . .
check.mass.balance . . .
example . . . . . . . . .
get.chebi.all . . . . . . .
get.kegg.all . . . . . . .
get.kegg.byId . . . . . .
get.metacyc.all . . . . .
get.metacyc.reaction.byId
get.rhea.all . . . . . . . .
get.rhea.byCompound . .
get.rhea.byId . . . . . .
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2
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8
9
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13
14
2
build.subtable
get.unipathway.all . . . .
instantiate.metacyc . . .
instantiate.rhea . . . . .
is.generic.metacyc . . . .
is.generic.rhea . . . . . .
parse.metacyc.compound
parse.metacyc.reaction .
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Index
RbioRXN-package
15
17
18
19
21
22
24
27
RbioRXN - Process Rhea, KEGG, MetaCyc, Unipathway Biochemical
Reaction Data
Description
To facilitate gaining and processing biochemical reaction such as Rhea, MetaCyc, KEGG and UniPathway, the package provides the functions to download and parse raw data, instantiate generic
reaction, and check mass balance. The package aims to construct an integrated metabolic network
and genome-scale metabolic model.
Details
Package:
Type:
Version:
Date:
License:
RbioRXN
Package
1.5.1
2015-05-19
GPL (>=2)
Author(s)
Byoungnam Min, Byeonghyeok Park, Kyoung Heon Kim and In-Geol Choi
Maintainer: Byoungnam Min <mbnmbn00@gmail.com>
References
http://compbio.korea.ac.kr
build.subtable
Build sub-table for the entries with multiple values
check.mass.balance
3
Description
When you download biochemical reaction data with functions such as get.kegg.all(), get.metacyc.all(),
get.rhea.all(), etc, some entries have multiple values such as "synonyms". This function allows to
build sub-table that separates multiple values in different rows.
Usage
build.subtable(table, column1, column2, separator = "///")
Arguments
table
data.frame object where multiple entries exist
column1
It is usually first column name for unique ID
column2
The column name where the column contains multiple values (e.g., synonyms)
separator
Separator symbol (default is "///")
Value
data.frame() object
Author(s)
Byoungnam Min <mbnmbn00@gmail.com>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol
Choi
Examples
data(example) # load example data
chebi = example$chebi # sample ChEBI
chebi.sub = build.subtable(table = chebi, column1 = "chebi", column2 = "synonyms", separator="///")
head(chebi.sub)
check.mass.balance
Check given biochemical reaction is mass-balanced
Description
Using molecular formula of reaction participants, check given reaction equation is mass-balanced.
Note that some reaction participants don’t have molecular formula (e.g., polymer or generic compound), so these reactions cannot be checked.
Usage
check.mass.balance(equation, chemical_table, id_col="chebi", formula_col="formula",
direction_type=c(" <=> ", " => ", " <\\?> "))
4
example
Arguments
equation
Reaction equation usually from get.rhea.all() or get.metacyc.all() function.
chemical_table Chemial table (data.frame) containing molecular formula
id_col
In chemical table, choose the column name which contains chemical ID (usually
first column)
formula_col
In chemical table, choose the column name which contains molecular formula
direction_type In reaction equation, provide reaction direction symbols. Default value is c("
<=> ", " => ", " <\\?> ")
Value
Character values (not logical)
TRUE
FALSE
Not available
Author(s)
Byoungnam Min <mbnmbn00@gmail.com>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol
Choi
Examples
data(example)
chebi = example$chebi # sample ChEBI
## Check mass balance for example reactions
Rm = example$rhea_massbal # sample Rhea data
check.mass.balance(Rm, chebi, "chebi", "formula", c(" <\\?> ", " <=> ", " => "))
example
Description
Example data for Rbiorxn
Usage
data(example)
Rbiorxn example data
get.chebi.all
get.chebi.all
5
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
Author(s)
Byoungnam Min, Byeonghyuk Park, Kyoung Heon Kim and In-Geol Choi <mbnmbn00@gmail.com>
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)
6
get.kegg.all
get.kegg.all
Download current KEGG REACTION and KEGG COMPOUND
database using KEGGREST package
Description
By implementing KEGGREST package in Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/KEGGRE
gather all KEGG REACTION and KEGG COMPOUND datain data.frame() object.
Usage
get.kegg.all()
Value
R list object. The list contains two data.frame() objects (reaction and comopund) where data fields
include,
ENTRY
KEGG ID (R number)
NAME
Enzyme name
DEFINITION
Reaction equation with standard compound name
EQUATION
Reaction equation with KEGG ID
ENZYME
E.C number
COMMENT
Comment
RPAIR
KEGG RPAIR is a collection of substrate-product pairs (reactant pairs) defined
for each reaction in KEGG REACTION
PATHWAY
KEGG PATHWAY that this reaction participates
ORTHOLOGY
Cross-link to KEGG ORTHOLOGY database
REMARK
Usually this column indicates glycan reaction-chemical reaction pair
REFERENCE
Publication info with PMID, title, and journal name
KEGG COMPOUND,
ENTRY
KEGG ID (C number)
NAME
Compound name
FORMULA
Molecular formula
EXACT_MASS
Molecular mass
MOL_WEIGHT
Molecular weight
REMARK
REACTION
KEGG REACTION entries where the compound particiaptes
PATHWAY
KEGG PATHWAY entries where the compound participates
get.kegg.all
ENZYME
7
KEGG ENZYME entries where the compound is related
ATOM
BOND
CAS
Cross-link to CAS database
PubChem
Cross-link to PubChem database
ChEBI
Cross-link to ChEBI database
PDB.CCD
Cross-link to Chemical Component Dictionary
X3DMET
NIKKAJI
BRITE
KNApSAcK
COMMENT
BRACKET
LIPIDMAPS
LipidBank
SEQUENCE
REFERENCE
Note
Because ’KEGGREST’ package has not been deposited in CRAN, you need to manually install this
package by typing:
> source("http://bioconductor.org/biocLite.R")
> biocLite("KEGGREST")
For details,
http://www.bioconductor.org/packages/release/bioc/html/KEGGREST.html
Author(s)
Byoungnam Min <mbnmbn00@gmail.com>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol
Choi
References
KEGGREST package: http://www.bioconductor.org/packages/release/bioc/html/KEGGREST.html
KEGG API: http://www.kegg.jp/kegg/docs/keggapi.html
See Also
get.kegg.byId
8
get.kegg.byId
Examples
# Not run: (it will take 30-40 minutes)
##
##
##
keggAll = get.kegg.all()
head(keggAll$reaction)
head(keggAll$comound)
get.kegg.byId
Download given KEGG REACTION entry using KEGGREST package
Description
By implementing KEGGREST package in Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/KEGGRE
retrieve given KEGG REACTION in data.frame() object.
Usage
get.kegg.byId(keggId)
Arguments
keggId
single KEGG REACTION ID (R number) or multiple IDs in vector
Value
data.frame() object where data fields include,
ENTRY
KEGG ID
NAME
Enzyme name
DEFINITION
Reaction equation with standard compound name
EQUATION
Reaction equation with KEGG ID
ENZYME
E.C number
COMMENT
Comment
RPAIR
KEGG RPAIR is a collection of substrate-product pairs (reactant pairs) defined
for each reaction in KEGG REACTION
PATHWAY
KEGG PATHWAY that this reaction participates
ORTHOLOGY
Cross-link to KEGG ORTHOLOGY database
REMARK
Usually this column indicates glycan reaction-chemical reaction pair
REFERENCE
Publication with PMID, title, and journal name
get.metacyc.all
9
Note
Because "KEGGREST" package has not been deposited in CRAN, you need to manually install
this package by typing:
> source("http://bioconductor.org/biocLite.R")
> biocLite("KEGGREST")
For details,
http://www.bioconductor.org/packages/release/bioc/html/KEGGREST.html
Author(s)
Byoungnam Min <mbnmbn00@gmail.com>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol
Choi
References
KEGGREST package: http://www.bioconductor.org/packages/release/bioc/html/KEGGREST.html
KEGG API: http://www.kegg.jp/kegg/docs/keggapi.html
See Also
get.kegg.all
Examples
# Not run:
##
##
get.kegg.byId("R00001")
# single KEGG ID
get.kegg.byId(c("R00001", "R00002", "R00005", "R00006")) # mutiple KEGG IDs
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()
10
get.metacyc.reaction.byId
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 <mbnmbn00@gmail.com>, 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)
get.metacyc.reaction.byId
Download given MetaCyc reaction via BioCyc web services
Description
This function downloads and parses given MetaCyc reaction in BioPAX level 3 via MetaCyc web
services (http://biocyc.org/web-services.shtml), and generate data.frame() object
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.
get.rhea.all
11
Usage
get.metacyc.reaction.byId(metacycId)
Arguments
metacycId
MetaCyc ID: single or multiple entries in vector
Value
data.frame() object where data fields include
MetaCyc
MetaCyc ID
name
Reaction equation with chemical standard name
ec_number
E.C. number
name_id
Reaction equation with MetaCyc compound ID
Author(s)
Byoungnam Min <mbnmbn00@gmail.com>, 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
Examples
# Not run:
##
##
##
##
##
##
get.metacyc.reaction.byId("RXN-13970")
get.metacyc.reaction.byId("SERINE--PYRUVATE-AMINOTRANSFERASE-RXN")
get.metacyc.reaction.byId("RXN-13759")
get.metacyc.reaction.byId("RXN-14352")
get.metacyc.reaction.byId("TRANS-RXN-220")
get.metacyc.reaction.byId("RXN-12549")
get.rhea.all
Download current Rhea in data.frame() object
Description
Download current Rhea in BioPAX level 2 and parse to generate data.frame() object
Usage
get.rhea.all()
12
get.rhea.all
Value
data.frame() object where data fields include
rheaId
Rhea ID
reactionType
BiochemicalReaction or transportReaction
equationWithCommonName
Textual reaction equation (compound standard names)
sameParticipant
Reactions with the same reactants and products, but different directionalities
mapped
formuled
polymerization
chemicallyBalanced
status
transport
direction
classOfReactions
At least one reaction participant is class compound described in ChEBI
equationWithChebi
Reaction equation with ChEBI
equationParticipant
crossLinks
If reaction has cross-link to other databases, new columns are generated such as
"MetaCyc", "KEGG" etc
Author(s)
Byoungnam Min <mbnmbn00@gmail.com>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol
Choi
References
Rhea database: http://www.ebi.ac.uk/rhea/home.xhtml
Examples
# Not run: it takes about 20 minutes
##
##
##
rhea = get.rhea.all()
dim(rhea)
# The number of downloaded reactions
head(rhea)
get.rhea.byCompound
13
get.rhea.byCompound
Download Rhea reaction by compound
Description
Download and parse Rhea database with given keyword
Usage
get.rhea.byCompound(rheaCompound)
Arguments
rheaCompound
e.g., caffeine
Value
data.frame() object where data fields include
rheaId
Rhea ID
reactionType
BiochemicalReaction or transportReaction
equationWithCommonName
Textual reaction equation (compound standard names)
sameParticipant
Reactions with same reactants and products, but different directionalities
mapped
formuled
polymerization
chemicallyBalanced
status
transport
direction
classOfReactions
At least one reaction participant is class compound described in ChEBI
equationWithChebi
Reaction equation with ChEBI
equationParticipant
crossLinks
if reaction has cross-link to other databases, new columns are generated such as
"MetaCyc", "KEGG" etc
14
get.rhea.byId
Author(s)
Byoungnam Min <mbnmbn00@gmail.com>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol
Choi
References
Rhea database: http://www.ebi.ac.uk/rhea/home.xhtml
Examples
# Not run:
##
get.rhea.byCompound("caffeine")
get.rhea.byId
Download Rhea by Rhea ID
Description
Download and parse Rhea with given Rhea ID
Usage
get.rhea.byId(rheaId)
Arguments
rheaId
Single Rhea ID or multiple Rhea IDs in vector
Value
data.frame() object where data fields include
rheaId
Rhea ID
reactionType
BiochemicalReaction or transportReaction
equationWithCommonName
Textual reaction equation (compound standard names)
sameParticipant
Reactions with same reactants and products, but different directionalities
mapped
formuled
polymerization
chemicallyBalanced
status
get.unipathway.all
15
transport
direction
classOfReactions
At least one participant is class compounds described in ChEBI
equationWithChebi
Reaction equation with ChEBI
equationParticipant
crossLinks
If the reaction has cross-link to other databases, new columns are generated such
as "MetaCyc", "KEGG" etc
Author(s)
Byoungnam Min <mbnmbn00@gmail.com>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol
Choi
References
Rhea database: http://www.ebi.ac.uk/rhea/home.xhtml
Examples
# Not run:
##
get.rhea.byId(c('10000', '10377'))
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
16
get.unipathway.all
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
Author(s)
Byoungnam Min <mbnmbn00@gmail.com>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol
Choi
References
UniPathway: http://www.grenoble.prabi.fr/obiwarehouse/unipathway
Examples
# Not run:
##
##
unipathway = get.unipathway.all()
dim(unipathway)
# The number of downloaded reaction entries
instantiate.metacyc
17
instantiate.metacyc
Instantiate MetaCyc generic reaction
Description
Generic reaction is a reaction with at least one compound class. This function gains instance reactions from given generic reaction
Usage
instantiate.metacyc(equation, chemical_table, id_col = "UNIQUE.ID",
parent_col = "TYPES", formula_col = "CHEMICAL.FORMULA", smiles_col
= "SMILES", inchi_col = "INCHI", direction_type = c(" => ", " <=> "))
Arguments
equation
MetaCyc generic reaction equation with MetaCyc ID (not compound name)
chemical_table Chemical table containing UNIQUE.ID, TYPES, CEHEMICAL.FORMULA,
SMILES and InChI columns. This table can be generated by parse.metacyc.compound()
function
id_col
In chemical table, choose the column name which contains chemical ID (usually
first column)
parent_col
In chemical table, choose the column name which contains parent compound
("TYPES" in MetaCyc)
formula_col
In chemical table, choose the column name which contains molecular formula
smiles_col
In chemical table, choose the column name which contains SMILES code
inchi_col
In chemical table, choose the column name which contains InChI code
direction_type In reaction equation, provide reaction direction charaters. Default is c(" <=> ",
" => ")
Value
List object containing instance reactions
Author(s)
Byoungnam Min <mbnmbn00@gmail.com>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol
Choi
References
Bioinformatics (Oxford, England) 2012, 28(3):388-396. Construction and completion of flux balance models from pathway databases
O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: An
open chemical toolbox. J Cheminform. 2011 Oct 7;3:33. doi: 10.1186/1758-2946-3-33. PubMed
PMID: 21982300; PubMed Central PMCID: PMC3198950.
18
instantiate.rhea
See Also
parse.metacyc.compound
Examples
# You need to load 'ChemmineOB' package before running this function.
data(example) # Load example rdata
Mc = example$metacyc.c
Mg = example$metacyc_generic$equation
names(Mc)
# Check chemical table columns
# Instantiate: Not run
#instanceM = instantiate.metacyc(Mg, Mc, id_col = "UNIQUE.ID",
# parent_col = "TYPES", formula_col = "CHEMICAL.FORMULA", smiles_col
# = "SMILES", inchi_col = "INCHI", direction_type = c(" => ", " <=> "))
#print(instanceM)
instantiate.rhea
Instantiate Rhea generic reaction
Description
Generic reaction is a reaction with at least one compound class. This function gains instance reactions from given generic reaction
Usage
instantiate.rhea(equation, chemical_table, id_col='chebi',
parent_col='parent', formula_col='formula', smiles_col='smiles',
inchi_col='inchi', direction_type=c(' <\\?> ', ' <=> ', ' => '))
Arguments
equation
Rhea generic reaction equation with ChEBI ID (not compound name)
chemical_table Chemical table containing chebi, parent, formula, smiles and inchi columns.
This table can be generated by get.chebi.all() function
id_col
In chemical table, choose the column name which contains chemical id (usually
first column)
parent_col
In chemical table, choose the column name which contains parent compound
("TYPES" in MetaCyc)
formula_col
In chemical table, choose the column name which contains molecular formula
smiles_col
In chemical table, choose the column name which contains SMILES code
is.generic.metacyc
inchi_col
19
In chemical table, choose the column name which contains InChI code
direction_type In reaction equation, provide reaction direction charaters. Default is c(’ <\\?> ’,
’ <=> ’, ’ => ’)
Value
List object containing instance reactions
Author(s)
Byoungnam Min <mbnmbn00@gmail.com>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol
Choi
References
Rhea: http://www.ebi.ac.uk/rhea
ChEBI: http://www.ebi.ac.uk/chebi
Open babel: O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open
Babel: An open chemical toolbox. J Cheminform. 2011 Oct 7;3:33. doi: 10.1186/1758-2946-3-33.
PubMed PMID: 21982300; PubMed Central PMCID: PMC3198950.
See Also
get.chebi.all
Examples
# You need to load 'ChemmineOB' package before running this function.
data(example) # Load example data
chebi = example$chebi # Sample ChEBI
Rg = example$rhea_generic$equationWithChebi # Sample Rhea generic reaction
## Instantiate: Not run
#instanceR = instantiate.rhea(Rg, chebi, id_col = "chebi", parent_col="parent",
# formula_col="formula", smiles_col="smiles", inchi_col="inchi",
# direction_type=c(" <\\?> ", " <=> ", " => "))
#print(instanceR)
is.generic.metacyc
Check given reaction is generic reaction
Description
Generic reaction is a reaction with at least one compound class as reaction participant (e.g., a primary alcohol + NADP -> an aldehyde + H(+) + NADPH). This function check if given reaction is
generic reaction
20
is.generic.metacyc
Usage
is.generic.metacyc(equation,compound_df,id_col,smiles_col,parent_col,direction_type)
Arguments
equation
Reaction equation usually from get.metacyc.all() function.
compound_df
Chemial table (data.frame) containing SMILES code of each compound in reaction equation
id_col
In chemical table, choose the column name which contains chemical id (usually
first column)
smiles_col
In chemical table, choose the column name which contains SMILES code
parent_col
In chemical table, choose the column name which contains TYPES
direction_type In reaction equation, provide reaction direction charaters. Default is c(" <=> ",
" => ")
Value
Logical TRUE/FALSE
Author(s)
Byoungnam Min <mbnmbn00@gmail.com>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol
Choi
References
MetaCyc: http://metacyc.org
Examples
data(example) # Load sample data
metacyc.c =
metacyc.r.1
metacyc.r.2
metacyc.r =
example$metacyc.c
= example$metacyc_generic$equation
= example$metacyc_massbal
c(metacyc.r.1, metacyc.r.2)
names(metacyc.c) # Print column names
# Check generic reaction
is.generic.metacyc(metacyc.r,metacyc.c,'UNIQUE.ID','SMILES','TYPES',c(' <=> ', ' => '))
is.generic.rhea
21
is.generic.rhea
Check given reaction is generic reaction
Description
Generic reaction is a reaction with at least one compound class as reaction participant (e.g., a primary alcohol + NADP -> an aldehyde + H(+) + NADPH). This function checks if given reaction is
generic reaction
Usage
is.generic.rhea(equation,chebi_df,id_col,parent_col,formula_col,direction_type)
Arguments
equation
Reaction equation usually generated by get.rhea.all() function.
chebi_df
Chemial table data.frame() containing molecular formula and parent compound
id_col
In chemical table, choose the column name which contains chemical id (usually
first column)
parent_col
In chemical table, choose the column name which contains parent compound
("parent" in chebi)
formula_col
In chemical table, choose the column name which contains molecular formula
direction_type In reaction equation, provide reaction direction symbols. Default is c(’ <\\?> ’,
’ <=> ’, ’ => ’)
Value
Logical TRUE/FALSE
Author(s)
Byoungnam Min <mbnmbn00@gmail.com>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol
Choi
References
Rhea: http://www.ebi.ac.uk/rhea
ChEBI: http://www.ebi.ac.uk/chebi
Examples
data(example) # Load example
chebi = example$chebi
rhea_generic = example$rhea_generic$equationWithChebi
rhea_massbal = example$rhea_massbal
rhea = c(rhea_generic, rhea_massbal)
22
parse.metacyc.compound
# Check generic reaction
is.generic.rhea(rhea, chebi, id_col='chebi', parent_col='parent',
formula_col='formula', direction_type=c(' <=> ', ' <\\?> ', ' => '))
parse.metacyc.compound
Parse MetaCyc compound data (compounds.dat in attribute-value format)
Description
Parse MetaCyc compounds.dat file in attribute-value format. The output includes compound name,
synonyms, ChEBI ID, PubChem ID, KEGG ID, CAS ID, types, molecular formula, SMILES code
and InChI
Usage
parse.metacyc.compound(datPath)
Arguments
datPath
Path to compounds.dat file from MetaCyc (BioCyc and EcoCyc also applicable)
Value
data.frame() object where data fields include
UNIQUE.ID
TYPES
COMMON.NAME
CHEMICAL.FORMULA
INCHI
MOLECULAR.WEIGHT
MONOISOTOPIC.MW
NON.STANDARD.INCHI
SMILES
ATOM.CHARGES
SYNONYMS
CREDITS
SUPERATOMS
parse.metacyc.compound
REGULATES
CITATIONS
COMMENT.INTERNAL
COMMENT
SYSTEMATIC.NAME
HAS.NO.STRUCTURE.
COMPONENT.OF
ABBREV.NAME
TAUTOMERS
PKA1
COFACTORS.OF
PKA2
PKA3
N.1.NAME.1
N.NAME
N.1.NAME
SPECIES
IN.MIXTURE
INTERNALS.OF.GROUP
COMPONENTS
GROUP.COORDS.2D
STRUCTURE.GROUPS
STRUCTURE.LINKS
RADICAL.ATOMS
CFG.ICON.COLOR
GROUP.INTERNALS
COFACTORS.OR.PROSTHETIC.GROUPS.OFCHEMSPIDER
PUBCHEM
CHEBI
LIGAND.CPD
NCI
CAS
23
24
parse.metacyc.reaction
X.Wikipedia.
UM.BBD.CPD
KNAPSACK
BRENDA.COMPOUND
LIPID_MAPS
LIGAND
Note
BioCyc and EcoCyc also applicable
Author(s)
Byoungnam Min <mbnmbn00@gmail.com>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol
Choi
References
MetaCyc: http://metacyc.org/
Examples
## parse.metacyc.compound: Not run
#url = 'http://bioinformatics.ai.sri.com/ptools/flatfile-samples/compounds.dat'
#tmpdest = tempfile(pattern = "compounds")
#download.file(url, destfile=tmpdest)
#sample.compounds = parse.metacyc.compound(datPath=tmpdest)
parse.metacyc.reaction
Parse MetaCyc reaction data (reactions.dat in attribute-value format)
Description
Parse MetaCyc reactions.dat file in attribute-value format. The output includes reaction ID, enzyme,
EC number, pathway and equation
Usage
parse.metacyc.reaction(datPath)
Arguments
datPath
Path to reactions.dat from MetaCyc (BioCyc or EcoCyc data also applicable)
parse.metacyc.reaction
Value
data.frame() object where data fields include
UNIQUE.ID
TYPES
ATOM.MAPPINGS
CITATIONS
COMMENT
CREDITS
DBLINKS
IN.PATHWAY
LEFT
PHYSIOLOGICALLY.RELEVANT.
REACTION.DIRECTION
RIGHT
CANNOT.BALANCE.
ENZYMATIC.REACTION
ORPHAN.
SPONTANEOUS.
RXN.LOCATIONS
EC.NUMBER
COMMON.NAME
TEMPLATE.FILE
SYNONYMS
SYSTEMATIC.NAME
DELTAG0
COMMENT.INTERNAL
ENZYMES.NOT.USED
REACTION.LIST
MEMBER.SORT.FN
STD.REDUCTION.POTENTIAL
PREDECESSORS
PRIMARIES
25
26
parse.metacyc.reaction
SIGNAL
equation
LIGAND.RXN
PLANTCYC
METACYC
RHEA
UNIPROT
PIR
LIGAND
BRENDA
superNode
Author(s)
Byoungnam Min <mbnmbn00@gmail.com>, Byeonghyuk Park, Kyoung Heon Kim and In-Geol
Choi
Examples
url = "http://bioinformatics.ai.sri.com/ptools/flatfile-samples/reactions.dat"
tmpdest = tempfile(pattern = "reactions")
download.file(url, destfile=tmpdest)
direction = "LEFT-TO-RIGHT" # sample data is old, so don't mind this code.
sample.reactions = parse.metacyc.reaction(datPath=tmpdest)
print(sample.reactions)
Index
∗Topic BioPAX level 3
get.metacyc.all, 9
get.metacyc.reaction.byId, 10
∗Topic BioPAX
get.chebi.all, 5
∗Topic Biochemical reaction database
RbioRXN-package, 2
∗Topic Biochemical reaction mass
∗Topic Metacyc web services
get.metacyc.all, 9
get.metacyc.reaction.byId, 10
∗Topic Rhea
get.rhea.all, 11
get.rhea.byCompound, 13
get.rhea.byId, 14
instantiate.rhea, 18
is.generic.rhea, 21
RbioRXN-package, 2
∗Topic UniPathway
get.unipathway.all, 15
RbioRXN-package, 2
balance
check.mass.balance, 3
∗Topic ChEBI
get.chebi.all, 5
instantiate.rhea, 18
is.generic.rhea, 21
∗Topic Generic reaction
is.generic.metacyc, 19
is.generic.rhea, 21
RbioRXN-package, 2
∗Topic Instantiation
RbioRXN-package, 2
∗Topic KEGG API
get.kegg.all, 6
get.kegg.byId, 8
∗Topic KEGG COMPOUND
get.kegg.all, 6
∗Topic KEGG REACTION
get.kegg.all, 6
get.kegg.byId, 8
∗Topic KEGG REST
get.kegg.all, 6
get.kegg.byId, 8
∗Topic KEGG
RbioRXN-package, 2
∗Topic MetaCyc
instantiate.metacyc, 17
is.generic.metacyc, 19
parse.metacyc.compound, 22
parse.metacyc.reaction, 24
RbioRXN-package, 2
build.subtable, 2
check.mass.balance, 3
example, 4
example (example), 4
get.chebi.all, 5, 19
get.kegg.all, 6, 9
get.kegg.byId, 7, 8
get.metacyc.all, 9
get.metacyc.reaction.byId, 10
get.rhea.all, 11
get.rhea.byCompound, 13
get.rhea.byId, 14
get.unipathway.all, 15
instantiate.metacyc, 17
instantiate.rhea, 18
is.generic.metacyc, 19
is.generic.rhea, 21
parse.metacyc.compound, 10, 18, 22
parse.metacyc.reaction, 10, 24
RbioRXN (RbioRXN-package), 2
RbioRXN-package, 2
27