Question: How to extract protein interactions from a reactome biopax file?
2
gravatar for lovetl2002
4.9 years ago by
lovetl200240
United States
lovetl200240 wrote:

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 • 2.4k views
ADD COMMENTlink modified 3 months ago by 7876858560 • written 4.9 years ago by lovetl200240

change 'toSif ' to 'toSIF'

ADD REPLYlink written 3 months ago by 7876858560
3
gravatar for ozgunbabur
4.9 years ago by
ozgunbabur30
United States
ozgunbabur30 wrote:

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.

ADD COMMENTlink written 4.9 years ago by ozgunbabur30

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

ADD REPLYlink written 4.9 years ago by lovetl200240
3
gravatar for rodche
4.8 years ago by
rodche60
United States
rodche60 wrote:

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.

ADD COMMENTlink modified 7 weeks ago by RamRS25k • written 4.8 years ago by rodche60
Exception in thread "main" 
    java.lang.IllegalArgumentException: No enum constant org.biopax.paxtools.Main.Command.toSif
ADD REPLYlink modified 7 weeks ago by RamRS25k • written 6 months ago by O.rka130
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