Cytoscape Metadata

cyMetadata is a module which given a Pathway Pommons URI, will pull SBGN graph data from Pathway Commons 2 and map it with metadata from corresponding biopax files.

Required software

• Node.js >=6.3.0

Basic Usage

Including cyMetadata

const cytoscapeJson = require(cytoscapeJson)

Requesting Mapped Metadata

let mappedData = cytoscapeJson.getCytoscapeJson(uri, parserType) 

• parserType indicates the method for parsing data and the source for reteriving the data.
  • (Default) "jsonld" - Loads information from JSON-LD and uses tree-traversal on node objects
  • (Slow) "biopax" - Fetches the full xml biopax file and produces a tree based on teh graph data, which is traversed for the required metadata. This method is typical quite slow and should only be used as a fallback for all other methods.
  • (Fast) "pc2" - This method off-loads biopax traversal onto the Pathway Commons 2 service instead of attempting to handle the file locally. It is the fastest, but requires a stable connection with PC2.
• Note : Mapped metadata will be returned in the form of cytoscape json object

Requesting Pathway Metadata

let pathwayMetadata = cytoscapeJson.getPathwayLevelMetadata(uri)