buildSBMLFromPathways: Build an SBML model for specific pathway(s) in a given...
In hettling/BiGGR: Constraint based modeling in R using metabolic reconstruction databases

Description Usage Arguments Value Note Author(s) References See Also Examples

Creates an SBML model containing all species, reactions and compartments that are part of (a) given pathway(s) in the database document (e.g. Recon2) passed as an argument.

1	buildSBMLFromPathways(query, database, match.exact=TRUE)

`query`	a `character` or a `vector` or `list` of `character` containing the names of the query pathways
`database`	an object of class `SBMLDocument`
`match.exact`	`logical` whether only the exact pathway name should be matched or whether a pathway should match if one keyword is in the pathway description in the database.

a rsbml Model object containing all reactions, species and compartments that are present in the database for the query pathway(s) or NULL if none of the pathways in the database match the query.

If the reactions in the database document provided in the argument database do not contain any "<notes>" with tags with pathway information indicated by the string "SUBSYSTEM", no pathway information can be extracted and thus the SBML model returned will be empty.

Anand Gavai, Hannes Hettling

Thiele, I. et al. Nat Biotech, 2013

extractPathways

data("Recon2")
database <- Recon2

##Get Model for specific pathway
m1 <- buildSBMLFromPathways("Arginine and Proline Metabolism", database)

##Get Model for specific pathway "Metabolism": does not exist!
m2 <- buildSBMLFromPathways("Metabolism", database)

##Get model of all pathways which contain keyword "metabolism"
m3 <- buildSBMLFromPathways("Metabolism", database, match.exact=FALSE)

##Multi-query:
query <- c("Transport, endoplasmic reticular", "Arginine and Proline Metabolism")
m4 = buildSBMLFromPathways(query, database)
m5 = buildSBMLFromPathways(query[1], database)
length(m4@species)
length(m5@species)

##different database
data(H.pylori_ilT341)
database <- H.pylori_ilT341
m7 <- buildSBMLFromPathways("Metabolism", database, match.exact=FALSE)