traverse: Access Pathway Commons using XPath-type expressions
Description
This command provides XPath-like access to the Pathway Commons.
Usage
traverse(uri, path, verbose = FALSE)
Arguments
uri
a BioPAX element URI - specified similarly to the 'GET' command
above). Multiple IDs are allowed (uri=...&uri=...&uri=...).
path
a BioPAX propery path in the form of
property1[:type1]/property2[:type2]; see properties, inverse properties,
Paxtools, org.biopax.paxtools.controller.PathAccessor.
verbose
a boolean, display the command used to query Pathway Commons
Value
an XMLInternalDocument with results
concept
paxtoolsr
Details
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).