|
Class Summary |
| 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. |
| 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); |
| ReactomeEntitySetUnificationXrefFix |
This is a class I wrote for fixing the unification xref problem in Reactome entity sets. |
| SifnxExportExample |
|
| SimpleIOExample |
|
| Tutorial |
|
| UnificationIDtoRDFIDLister |
User: root Date: Jan 18, 2007 Time: 4:56:53 PM |