Paxtools Guide

Preface
BioPAX project provides a standard, community developed language for representing Pathway Data. If you are a software developer, by using BioPAX you can maximize your applicaton’s access to pathway data from different sources. If you have a pathway database, your BioPAX formatted pathways can reach a greater number of users.

BioPAX covers a large spectrum of data including signaling and metabolic pathways as well as genetic and protein protein interactions. Developing software that produces or consumes BioPAX can be a daunting task at first because of the large number of classes and properties that BioPAX contains and the OWL format it is represented in. Paxtools offers a Java API that maps OWL classes and properties to Java beans and methods that can significantly reduce software development time.

Historically, Paxtools was developed to provide this OWL-Java mapping but today it offers much more. There are utilities for quickly traversing or manipulating objects, fixing common problems or converting your models to different BioPAX levels or other formats such as SIF and GSEA. There are BioPAX JPA mappings for persisting large BioPAX models into a database or advanced graph queries for finding biologically relevant paths between molecules. All of these are organized in a lightweight modular structure to help you embed only the portions you need into your application with minimum footprint.

If you are developing BioPAX exporters, visualization tools, editors or algorithms Paxtools can do most of the BioPAX related plumbing to help you focus on your application. Even if you currently need only a small portion of the information embedded in a BioPAX model, developing your application on top of Paxtools offers future flexibility and extensibility.


 * Some terminology:*
 * OWL : Ontology Web Language

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