Paxtools

About Paxtools
Paxtools is a Java library specially designed for accessing and manipulating data in BioPAX format. Paxtools is developed at Computational Biology Centre at MSKCC and Bader Lab (The Donnelly Centre, University of Toronto.

News

 * 22 Sep 2015 - Paxtools 4.3.1 was released
 * 05 Nov 2014 - Paxtools 4.3.0 released
 * 04 Nov 2013 - Paxtools 4.2.1 released
 * 19 Sep 2013 - the Paxtools paper published (PLOS, Open Access)
 * 16 Sep 2013 - Pattern search in BioPAX models paper published (Bioinformatics, Open Access)
 * 19 May 2013 - Paxtools 4.2.0 released
 * 26 June 2013 - Paxtools paper accepted (PLOS)
 * 2005 - 2011 - early Paxtools versions (unpublished)

Resources

 * Announcements
 * Paxtools project pages on Github (including javadoc and other project reports)
 * Maven2 repositories:
 * The latest stable Paxtools modules are available in Maven Central
 * https://oss.sonatype.org/content/groups/public/ - OSSRH public repository (snapshots, since 4.3.1-SNAPSHOT)
 * http://www.biopax.org/m2repo/snapshots/ - older BioPAX snapshots m2 repository
 * http://www.biopax.org/m2repo/releases/ - older BioPAX releases m2 repository
 * Source code: https://github.com/BioPAX/Paxtools
 * Downloads: http://www.biopax.org/downloads/paxtools/ (there are Paxtools JARs with dependencies and the User's Guide in PDF format).
 * Core developers might want to look at Deploying Paxtools wiki page

Features

 * 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: Several projects are built on top of Core Paxtools: a 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 and pattern search for finding biologically relevant connections and sub-networks. These software tools are available as a part of Pathway Commons project. Software that uses Paxtools can natively interact with these tools.

Use
Paxtools provides, beyond the core and converters API, a console application that can execute several useful commands. If you have downloaded one of the "fat" JAR files (with built-in dependencies), then you can access to the console interface description with the following command:

java -jar paxtools.jar