If you are familiar with Java and maven environment, you can try using the biopax-pattern software to convert the reactome BioPAX (level 3) file into SIF with uniprot IDs. It is in the link below.

http://code.google.com/p/biopax-pattern

Once you have the library running, you can convert the owl with the following code:

String dir = "/dir/to/owl/";
SimpleIOHandler h = new SimpleIOHandler();
Model model = h.convertFromOWL(new FileInputStream(dir + "sample-reactome-file.owl"));

CommonIDFetcher idFetcher = new CommonIDFetcher();
idFetcher.setUseUniprotIDs(true);
SIFSearcher s = new SIFSearcher(idFetcher, SIFEnum.IN_COMPLEX_WITH);
s.searchSIF(model, new FileOutputStream(dir + "output.sif"), true);

Here, instead of SIFEnum.IN_COMPLEX_WITH, you can say SIFEnum.values() and generate all kinds of SIF interactions.

Hi,

Try the following cool java tool for BioPAX, Paxtools, which is also partially based on Ozgun's biopax-pattern module and can be run from console (terminal).

First, go grab the latest, just updated, (it's paxtools-4.3.1-beta-no-jena.jar) executable paxtools JAR from the BioPAX project, paxtools downloads.

Next, use either toSif (Simple Interaction Format) or toSifnx command (generates a text tab-separated data file, where a single blank line separates two sections: SIF interaction edges and nodes), e.g., toSif:

$JAVA_HOME/bin/java -Xmx2g -jar paxtools.jar toSif 5957113.owl 5957113.sif.txt uniprot

Note that you'd use uniprot as the last parameter, because there are no HGNC Symbol xrefs in that particular data file.

PS:

Run java paxtools.jar without arguments to see all available command; though, the Paxtools library allows much more if you can code in Java.