paxtoolsr (version 1.6.3)

getPc: Get Pathway Commons BioPAX elements

Description

This command retrieves full pathway information for a set of elements such as pathway, interaction or physical entity given the RDF IDs.

Usage

getPc(uri, format = "BIOPAX", verbose = FALSE)

Arguments

uri

a vector that includes valid/existing BioPAX element's URI (RDF ID; for utility classes that were "normalized", such as entity refereneces and controlled vocabularies, it is usually a Idntifiers.org URL. Multiple IDs are allowed per query, for example, c("http://identifiers.org/uniprot/Q06609", "http://identifiers.org/uniprot/Q549Z0") See also about MIRIAM and Identifiers.org in details.

format

output format (Default: BIOPAX). Valid options can be found using pcFormats

verbose

a boolean, display the command used to query Pathway Commons

Value

• a XMLInternalDocument object

concept

paxtoolsr

Details

Get commands only retrieve the BioPAX elements that are directly mapped to the ID. Use the "traverse query to traverse BioPAX graph and obtain child/owner elements. Information on MIRIAM and Identifiers.org http://www.pathwaycommons.org/pc2/#miriam

See Also

pcFormats

Examples

uri <- "http://identifiers.org/uniprot/O14503"
#results <- getPc(uri)

uri <- c("http://identifiers.org/uniprot/O14503", "http://identifiers.org/uniprot/Q9P2X7")
#results <- getPc(uri, verbose=TRUE)