How to extract protein interactions from a reactome biopax file?
2
2
Entering edit mode
7.5 years ago
lovetl2002 ▴ 40

Hello,

I'm currently working with Reactome database. I want to get the protein interaction pairs of mouse. However, the file Reactome provided for download is not up to date. A lot of the pairs showed in the browser are missing. So I decide to extract these pairs from the BioPax file they provided.

So the question comes. I can import the file to cytoscape and export it to sif format. For example:

http://www.reactome.org/PathwayBrowser/#SPECIES=48892&DIAGRAM=5957113&ID=5957111&PATH=5956939&DTAB=DT

However, in the exported file, the name of the node is protein name. What I want is uniprot ID. So is there a way to export pairs of uniprot ids rather than protein names in cytoscape? Or is there any ease-to-use tool instead of cytoscape to do this?

Biopax Reactome Network • 3.1k views
0
Entering edit mode

change toSif to toSIF

3
Entering edit mode
7.5 years ago
ozgunbabur ▴ 30

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.

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.

0
Entering edit mode

Thank you. The problem is that I'm not familiar with Java. I'm familiar with R and Python though.

3
Entering edit mode
7.5 years ago
rodche ▴ 60

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.

0
Entering edit mode
Exception in thread "main"
java.lang.IllegalArgumentException: No enum constant org.biopax.paxtools.Main.Command.toSif