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Contents

Paxtools Quickstart

Download Setups

Installation

  • Install IntelliJ with installer; install Java if prompted.
  • Protege can be run by clicking on the “run.command” file inside the downloaded archive
  • Maven
$ tar -xvf apache-maven-3.2.5-bin.tar.gz
$ sudo mv apache-maven-3.2.5 /usr/local/apache-maven

$ nano ~/.bash_profile

#Add below lines in the .bash_profile
export M2_HOME=/usr/local/apache-maven
export PATH=$PATH:$M2_HOME/bin
# ON OSX, THIS MAY BE NECESSARY: export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk/Contents/Home
#Save and quit

$ source .bash_profile 

If it worked you should have output with the following:

$ mvn --version

Make template Paxtools project.

The project outputs members of all reactions in a pathway and any external database references for them to screen and a file. NOTE: Several files will be downloaded:

mvn archetype:generate -DarchetypeRepository=http://www.biopax.org/m2repo/snapshots/ -DarchetypeGroupId=org.biopax.paxtools -DarchetypeArtifactId=paxtools-archetype -DarchetypeVersion=4.3.1-SNAPSHOT -DgroupId=com.example.test -DartifactId=test -Dversion=1.0-SNAPSHOT

Build Project

Project will be in folder "test". Build the project with following commands:

$ cd test

Install missing dependencies and compile/build project

$ mvn clean install

Run example project

$ java -jar ./target/example-exec.jar

Additional Projects for Writing BioPAX

A collection of database converters written by B. Arman Aksoy

Protege

Examine OWL file using Protege

Sample BioPAX OWL files are located in the src/main/resources/ of example project. After loading an OWL file, click the "Entities" tab at the top, and in the bottom left panel, click on "Individuals by type". You'll be able to see the classes of objects that exist in the BioPAX ontology schema. The panel to the top right will show you definitions for a BioPAX class. The bottom right panel will show you properties (and the values) for a given BioPAX entity instance.

ChiBE: Chisio BioPAX Editor Quickstart

Installation

Unzip and in the command line (in the unzipped directory), run:

./ChiBE.sh

Usage

You can open up the sample OWL files (in resources/) from the the example Paxtools project using ChiBE. Clicking on nodes or edges gives you additional information.

Multiple Files/Pathways in the Same Session

When multiple files/pathways (models) are loaded they are merged. If the model is saved (Model -> Save (as)) the merged network is exported. The currently loaded model can be discarded (Model -> Close).

Visualizing

If you have multiple pathways exist in the file or loaded in the session, you will be asked to "Select pathways to display", just select whatever you would like to see and click "OK".

Getting Additional Pathways

ChiBE has access to an aggregated dataset known as Pathway Commons and can query Pathway Commons for specific content:

Query -> Pathway Commons (Level 3) -> Pathways with Keyword -> Enter "Glycolysis" (for example)

Select your pathway of interest.

BioPAX Web Console: Paxtools Playground

The BioPAX Web Console is an environment to try out Paxtools

Pathway Commons Interactive API

The Pathway Commons Interactive API is an environment to try out Pathway Commons API functions

Links