See: Description
| Class | Description |
|---|---|
| GOUnificationXREFtoRelationshipXREFConverter |
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.
|
| Macros |
Created with IntelliJ IDEA.
|
| PathwayComponentLister |
This example shows how to list all components of a pathway.
|
| PathwayGenesExtractor |
Prints all the genes (aka proteins) in the L2 pathway
and sub-pathways (*conditions apply), and also - trace
where they come from.
|
| ProteinNameLister |
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);
|
| PublicationStatisticsAnalyzer |
A simple method that prints the publication statistics.
|
| ReactomeEntitySetUnificationXrefFix |
This is a class I wrote for fixing the unification xref problem in Reactome entity sets.
|
| SifnxExportExample |
This example exports A BioPAX model to SIF.
|
| SimpleIOExample |
A basic example that shows the basic IO operations.
|
| Tutorial |
This class used for a Paxtools Tutorial during Harmony 2010.
|
| UnificationIDtoRDFIDLister |
A basic example that shows how to list all unification xrefs.
|
| UseOfReflection |
Examples on how to use Paxtools BioPAX property editors and accessors API
(based on java reflection).
|
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