bp2.create.model: Construct bp2.model based on RDF data
In microbiome/biopax2: BioPAX level 2 S4 object model

Description Usage Arguments Value Author(s) See Also Examples

This function creates BioPAX level 2 object model, bp2.model, based on biopax data given in RDF format. The RDF data is expected to be output from Rredland library. The model has been tested only with Reactome data.

1	my.bp2 <- bp2.create.model(rdf.data)

rdf.data

data.frame containing the BioPAX level 2 data in rdf format. The data consists of three columns: subject, predicate and object. Subjects and objects are symbol names and predicates name the relations between subjects and objects. Object names can be identical to subjects in which case they are references to corresponding objects.

Instance of "bp2.model" class.

Ossi Koivistoinen

"bp2.model", bp2.resume, bp2.find.nodes

# 1. Read BioPAX data in RDF format using Rredland
require(Rredland)
biopax.file.path <- system.file('data/Reactome_69278.owl',package='bp2')
biopax.owl.file.uri <- paste('file://', biopax.file.path, sep='')	
biopax.rdf <- readRDF(biopax.owl.file.uri, storageType="bdb")
biopax.rdf.data.frame <- as(biopax.rdf, "data.frame")
freeRedl(biopax.rdf) 

# 2. Create bp2.model
my.bp2 <- bp2.create.model(biopax.rdf.data.frame)

# 3. Show some objects
my.bp2@all.objects[1:20]