The BioPAX Object Model, API and utilities implemented in Java. Paxtools is developed at Computational Biology Centre at MSKCC and Bader Lab, Donnelly Centre, University of Toronto.
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.
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 (e.g., xrefOf, entityReferenceOf).
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.)
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. (Note: BioPAX Level1 is not supported starting from Paxtools version 5.0.0-SNAPSHOT.)
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), SBGN-ML, and GSEA (GMT) gene sets.
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.
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.
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.
Paxtools provides, beyond the core and converters API, a console application that can execute several useful commands. If you have downloaded the "fat" JAR (with built-in dependencies), then you can access to the console interface description with the following command:
java -jar paxtools.jar (add -Xmx option when processing large data files).
Paxtools can be build and run with JDK-17 or newer, e.g. Temurin-21. Add these JVM options or set
JDK_JAVA_OPTIONS="--add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.lang.reflect=ALL-UNNAMED"
-Dpaxtools.CollectionProvider=org.biopax.paxtools.trove.TProviderto use a high-performance collections provider for BioPAX elements Map or Set (recommended).-Dpaxtools.normalizer.use-latest-registry=true(if using Normalizer/Resolver) to use the latest registry.json from bioregistry.io.-Dpaxtools.core.use-latest-genenames=truefor the HGNC utility class use id mapping data from genenames.org instead of built-in older file.-Dpaxtools.pattern.blacklist=<path>path to "ubique molecules blacklist" file to use with SIF searcher.
If you have homebrew installed on your system (Mac OS X), you can install the latest release of Paxtools via the following brew command (could be old version):
$ brew install homebrew/science/paxtools
$ paxtools help- Maven Central repository (only releases)
- OSSRH public repository (snapshots since 4.3.1, releases)
- old BioPAX snapshots and old BioPAX releases repositories
- BioPAX Downloads
More information about Paxtools can be found in the publication, wiki archive, and BioPAX forum.