From BiopaxWiki
Jump to: navigation, search

About Paxtools

Paxtools is a Java library specially designed for accessing and manipulating data in BioPAX[1] format. Paxtools is developed at Computational Biology Centre at MSKCC [2]; the persistency layer has been initially developed by INOH group [3]; Bader Lab (BBMDR, TDCCBR, University of Toronto) [4] is an active contributor.




A complete and consistent implementation of BioPAX specification 
BioPAX elements in Paxtools are plain Java beans which provide methods to access the properties described in BioPAX, and a model, acting as a container for all BioPAX elements, provides querying facilities for them. Users can either read a BioPAX model from a file or create an empty one from the scratch. Methods to add new elements to a model and to remove elements from a model are also provided.
Support for OWL properties and additional inverse links
Owl properties can be symmetric, transient or subtyped into other properties. These semantics can not be represented directly in an object oriented programming language. Paxtools implements these additional semantics and automatically update the fields of objects. For example, since property “standardName” is a subproperty of “name”, updating the standardName of a protein will also update its list of names. Similarly since “component” is a transient property, a query for the components of a complex will not only list its immediate components but also the components of the subcomplexes inside this complex. In the BioPAX specification properties are unidirectional for brevity. For example, “participant” property links interactions to physical entities. Paxtools provides additional “inverse” links that allows efficient navigation from a physical entity to the all interactions that it participates.
Syntactic validation
Each operation that modifies the model is internally validated by Paxtools to comply with BioPAX syntax, including RDF well-formedness, domain and range restrictions, bidirectional links, and redundancies.(BioPAX Validator project provides a much more detailed validation and also checks for best practices.)
Seamless handling of different BioPAX levels
Recently released BioPAX Level 3 introduced significant improvements to the naming and structure of the BioPAX at some cost of backwards compatibility. Paxtools supports all three BioPAX levels and provides facilities for upgrading older BioPAX models to Level 3, reducing the burden of working with different BioPAX levels for developers.
Converting to and from different formats
Paxtools can convert PSI-MI models to BioPAX Level 3. In addition, BioPAX models can be exported back to OWL and several other useful formats, including SIF (Simple Interaction Format) and GSEA gene sets.
Efficient traversal and editing via reflection
Paxtools implements the Property Editor design pattern to allow tools to manipulate BioPAX models without actually hard coding property and class names. This pattern considerably simplifies development of BioPAX exporters and other tools and makes it easier to extend and update them to support future changes in the BioPAX specification.
Modular and lightweight structure
Paxtools is currently distributed as a Maven project in a modular structure which allows developers to easily select just the parts of PaxTools they need in their application.
A platform for development of BioPAX software infrastructure
Some projects built on top of Paxtools include: a state-of-the-art persistence system using Java Persistence API integrated with the querying facilities, an advanced validator that allows checking complex rules and the best practices using an extensible framework, an integrator that detects and merges interactions that are equivalent based on their participants, and a graph theoretic query engine for finding biologically relevant connections and subnetworks. These software tools are available as a part of Pathway Commons project. Software that uses Paxtools can natively interact with these tools.


The latest official release of Paxtools is v4.3.0. It is available as a "fat" JAR (with dependencies included) at and also through the BioPAX Maven2 repository at (Watch for the recent posts in this topic for future updates.)

If you want to utilize the features that are currently under development, you can always get a local copy of the latest source code from our Mercurial repository [5]

hg clone biopax-paxtools

(Core developers might also want to look at Deploying Paxtools wiki page.)


Paxtools provides, beyond the core and converters API, a console application (paxtools-console modules) that can execute several useful commands. If you have downloaded one of the JAR distribution files, you can access to this console interface with the following command:

java -jar paxtools.jar

And then, - for example:

java -Xmx1g -jar paxtools.jar toLevel3 input_l2.owl output_l3.owl

(- upgrades BioPAX Level 1 or 2, or converts PSI-MI 2.5 (since v4.3.0), to BioPAX Level 3)

java -Xmx1g -jar paxtools.jar toSif input.owl output.tsv

(converts to the Simple binary Interactions Format)

java -Xmx1g -jar paxtools.jar fetch input.owl uri1,uri2,..,uriN output.owl

(extracts a sub-model)

java -Xmx1g -jar paxtools.jar validate input.owl output.html

(calls the online validator); etc.