getPathwaysForSBML: Extract all pathways from a database that are relevant for a...
In BiGGR: Constraint based modeling in R using metabolic reconstruction databases

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

Extracts all pathway information from an rsbml document containing a metabolic reconstruction database (e.g. Recon2) and returns the subset of these pathways that is associated with the reactions in the given model. The pathway information is parsed from the "<notes>" tag of each reaction.

1	getPathwaysForSBML(model, database)

`database`	an rsbml object of class `SBMLDocument`
`model`	an rsbml object of class `Model`

A vector of type character that contains all the pathways relevant for the given model according to the specified database. Note that duplicate pathways do not appear twice in the return value.

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.

Anand Gavai, Hannes Hettling

Thiele, I. et al. Nat Biotech, 2013

buildSBMLFromPathways buildSBMLFromGenes extractPathways

##Build a model from query genes
data("Recon2")
database <- Recon2
query <- c("218.1", "223.1") ##query gene identifiers
m <- buildSBMLFromGenes(query, database)

##extract all pathways for that model
getPathwaysForSBML(m, database)