traverse: Access Pathway Commons using XPath-type expressions

Description Usage Arguments Details Value References Examples

View source: R/traverse.R


This command provides XPath-like access to the Pathway Commons.


traverse(uri, path, verbose = FALSE)



a BioPAX element URI - specified similarly to the 'GET' command above). Multiple IDs are allowed (uri=...&uri=...&uri=...).


a BioPAX propery path in the form of property1[:type1]/property2[:type2]; see properties, inverse properties, Paxtools, org.biopax.paxtools.controller.PathAccessor.


a boolean, display the command used to query Pathway Commons


With traverse users can explicitly state the paths they would like to access. The format of the path query is in the form: [Initial Class]/[property1]:[classRestriction(optional)]/[property2]... A "*" sign after the property instructs path accessor to transitively traverse that property. For example, the following path accessor will traverse through all physical entity components within a complex: "Complex/component*/entityReference/xref:UnificationXref" The following will list display names of all participants of interactions, which are components (pathwayComponent) of a pathway (note: pathwayOrder property, where same or other interactions can be reached, is not considered here): "Pathway/pathwayComponent:Interaction/participant*/displayName" The optional parameter classRestriction allows to restrict/filter the returned property values to a certain subclass of the range of that property. In the first example above, this is used to get only the Unification Xrefs. Path accessors can use all the official BioPAX properties as well as additional derived classes and parameters in paxtools such as inverse parameters and interfaces that represent anonymous union classes in OWL. (See Paxtools documentation for more details).


an XMLInternalDocument with results


Paxtools Documentation:


uri <- ""
#results <- traverse(uri=uri, path="ProteinReference/organism/displayName")

paxtoolsr documentation built on May 31, 2017, 11:39 a.m.

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