getPc {paxtoolsr} | R Documentation

## 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

### 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)

[Package paxtoolsr version 1.14.0 Index]