Contents
- Paxtools Quickstart
- Protege
- ChiBE: Chisio BioPAX Editor Quickstart
- BioPAX Web Console: Paxtools Playground
- Pathway Commons Interactive API
- Links
- IntelliJ Community Edition (Java Editor): https://www.jetbrains.com/idea/download/
- Maven (Java Dependency Major): http://maven.apache.org/download.cgi
- Protege (OWL Viewer, BioPAX is in OWL-formatted): http://protege.stanford.edu/products.php#desktop-protege
- ChiBE: Chisio BioPAX Editor: https://code.google.com/p/chibe/
- 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
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
Project will be in folder "test". Build the project with following commands:
$ cd test
$ mvn clean install
$ java -jar ./target/example-exec.jar
A collection of database converters written by B. Arman Aksoy
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.
Unzip and in the command line (in the unzipped directory), run:
./ChiBE.sh
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.
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).
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".
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.
The BioPAX Web Console is an environment to try out Paxtools
- Code Repository: https://github.com/cannin/biopaxWebConsole
- Live Version: http://pk0iye.appspot.com/
The Pathway Commons Interactive API is an environment to try out Pathway Commons API functions
