All Classes and Interfaces
Class
Description
Simple (example) BioPAX Validator client
to upload and check BioPAX OWL files.
User: 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.
PaxtoolsMain console application
(very useful BioPAX utilities).
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.
Various console utility functions
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).