Supplemental Table 1 Methods implemented in the PathVisioRPC application programming interface (API). These functions can be called from any programming interface included in RPC.  	
addDataNode( pathwayfilepath,  datanodename,  datanodetype,  datanodeid,  datanodesource) 	Adds a DataNode to a pathway GPML file saved on disk and saves it in the result directory 
addDataNodeByURI( uri,  datanodename,  datanodetype,  datanodeid,  datanodesource,  resultdirectory,  reference,  comment) 	Adds a DataNode to a Pathway GPML file downloaded by it's Wikipathwas ID and saves it in the result directory 
addInteraction( pathwayfilepath,  linename,  startdatanode,  enddatanode,  startarrowtype,  endarrowtype) 	Adds an Interaction to a Pathway GPML saved on disk, connecting two DataNodes specified by the names of the two DataNodes and saves the changed pathway GPML file in the result directory 
addInteractionByID( pathwayfilepath,  linename,  startdatanodegraphid,  enddatanodegraphid,  startarrowtype,  endarrowtype) 	Adds a Line to a Pathway GPML saved on disk, connecting two DataNodes specified by the unique Graph IDs of the two DataNodes and saves the changed pathway GPML file in the result directory 
addInteractionByIDByURI( uri,  linename,  startdatanodegraphid,  enddatanodegraphid,  startarrowtype,  endarrowtype,  lineid,  linesource,  resultdirectory) 	Adds a Line to a Pathway GPML downloaded from Wikipathways by it's Wikipathways ID, connecting two DataNodes specified by the unique Graph IDs of the two DataNodes and saves the changed pathway GPML file in the result directory 
addInteractionByURI( uri,  linename,  startdatanode,  enddatanode,  startarrowtype,  endarrowtype,  lineid,  linesource,  resultdirectory) 	Adds a Line to a Pathway GPML downloaded from Wikipathways by it's Wikipathways ID, connecting two DataNodes specified by the names of the two DataNodes and saves the changed pathway GPML file in the result directory 
addMappers( dbFile) 	Function to add loaded id mappers 
annotateElement( pathwayfilepath,  elementname,  elementid,  elementsource) 	Annotates DataNodes in a pathway GPML file saved on disk, with an identifier and data source and saves the pathway GPML file in the result directory Annotation can also be added while adding DataNodes and Lines 
annotateElementByURI( uri,  elementname,  elementid,  elementsource,  resultdirectory)	 Annotates DataNodes in a Wikipathways pathway downloaded by it's Wikipathways ID, with an identifier and data source and saves the pathway GPML file in the result directory. 
calculatePathwayStatistics( gexfilepath,  dbdirectory,  pathwaydirectory,  criteria,  resultdirectory) 	Calculate Pathway statistics - over representation analysis And exports results as a hyperlinked html page containing a list of all the pathways ranked according to their z score, a folder of images and a folder containing backpages 
createPathway( pathwayname,  pathwayauthor,  organism,  resultdirectory) 	Creates a new empty pathway GPML file and saves it in the result directory 
createVisualization( gexfilepath,  gsample,  gcolors,  gvalues,  rexpressions,  rcolors) 	Create a Visualization XML file for DataNodes Contains color gradients and rules 
exportPathway( pathwayfilepath,  exportfiletype,  resultdirectory) 	Exports the image of a pathway GPML saved on disk and saves it in the result directory 
exportPathwayByte( pathwayfilepath,  filetype) 	Exports a byte array of the image of a pathway GPML file saved on disk 
exportPathwayByteFromURI( uri,  exportfiletype) 	Exports a byte array of the image of a Wikipathways pathway downloaded by it's Wikipathways ID 
exportPathwayFromURI( uri,  exportfiletype,  resultdirectory)	 Exports a pathway image of a Wikipathways pathway, provided it's WikiPathways ID in png, svg or pdf formats 
exportPathwayHtml( pathwayfilepath,  dbdirectory,  resultdirectory) 	Exports a pathway GPML file along with backpages in html format 
exportPathwayHtmlFromURI( uri,  dbdirectory,  resultdirectory) 	Exports a Wikipathways pathway file along with backpages in html format, provided it's WikiPathways ID 
getAllFunctions() 	Function to display all PathVisioRPC functions that can be called by the client 
getDataNodeTypes() 	Function to display the different types of DataNodes that can be drawn using PathVisio 
getGraphIDs( pathwayfilepath,  elementname) 	Function to display GpraphIDs for the element in the pathway 
getInteractionTypes() 	Function to display the types of basic interactions that can be drawn using PathVisio 
getMIMInteractionTypes() 	Functions to display the types of MIM interactions that can be drawn using PathVisio 
getPathwayStatList( pathwaydirectory,  gexfilepath,  dbdirectory,  criteria,  resultdirectory) 	Exports a list of Pathways ranked according to Z score 
importData( inputfilepath,  IdColNum,  SysCode,  SysColNum,  gexFileName,  dbDirectory,  resultdirectorypath) 	Imports tab delimited data and creates a PGEX file 
listMappers() 	Function to display all loaded id mappers 
removeElement( pathwayfilepath,  elementname) 	Removes a DataNode or Line by it's name from a pathway GPML saved on disk and saves it in the result directory. 
removeElementById( pathwayfilepath,  elementgraphid) 	Removes a DataNode or Line by it's unique Graph ID from a pathway GPML file saved on disk and saves it in the result directory 
removeElementByIdByURI( uri,  elementgraphid,  resultdirectory) 	Removes a DataNode or Line by it's unique Graph ID from a pathway GPML file downloaded from Wikipathways using it's Wikipathways ID and saves it in the result directory 
removeElementByURI( uri,  elementname,  resultdirectory) 	Removes a DataNode or Line by it's name from a Wikipathways pathway GPML file downloaded using it's Wikipathways ID and saves it in the result directory. 
removeMappers() 	Function to delete all loaded idmappers 
setDefaultColours( Colour1,  colour2)	Function to set default colors (no rule matched, no data found)
test() 	Test the server client connection 
visualizeData( pathwayfilepath,  gexfilepath,  dbdirectory,  resultdirectory) 	Data is visualized on the pathway GPML file saved on disk and the results are saved on the result directory 
visualizeDataByURI( uri,  gexfilepath,  dbdirectory,  resultdirectory) 	Data is visualized on the pathway GPML downloaded from Wikipathways using it's Wikipathways ID and the results and saved in the result directory