Package org.biopax.paxtools.examples
package org.biopax.paxtools.examples
This package contains several examples that uses Paxtools to demonstrate basic functionality.
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ClassesClassDescriptionUser: Emek Demir Date: Jan 18, 2007 Time: 4:56:53 PM In this example we get all the unification xrefs in the model and check if they point to the Gene Ontology.Created with IntelliJ IDEA.This example shows how to list all components of a pathway.Prints all the genes (aka proteins) in the L2 pathway and sub-pathways (*conditions apply), and also - trace where they come from.This example class processes all the Level2 BioPAX OWL files in the input directory to find all the protein names Notes: - recent fix: it doesn't traverse into the NEXT-STEP property, as it may lead beyond the boundaries of the pathway of interest! - one may prefer using the Paxtools' jenaIO instead of the simpleIO: import org.biopax.paxtools.io.jena.JenaIOHandler; JenaIOHandler handler = new JenaIOHandler(null, BioPAXLevel.L2);A simple method that prints the publication statistics.This is a class I wrote for fixing the unification xref problem in Reactome entity sets.This example exports A BioPAX model to SIF.A basic example that shows the basic IO operations.This class used for a Paxtools Tutorial during Harmony 2010.A basic example that shows how to list all unification xrefs.Examples on how to use Paxtools BioPAX property editors and accessors API (based on java reflection).