getPc: Get Pathway Commons BioPAX elements

In cannin/paxtoolsr: Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

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
...	additional arguments to read* methods that handle data from Pathway Commons

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

Value

a XMLInternalDocument object

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)

cannin/paxtoolsr documentation built on Feb. 2, 2023, 11:44 a.m.