Paxtools

Paxtools is an open-source Java library designed for working with BioPAX data, the standard for sharing biological pathway information. It provides a comprehensive programmatic API to read, create, manipulate, validate, and serialize BioPAX models. The library implements the BioPAX ontology and offers Java classes for core elements such as Pathway, PhysicalEntity, Interaction, and Route, enabling developers to build, traverse, and query pathway networks in a type-safe way.

Key features include a model representation (Model) that stores BioPAX entities, a loader to parse BioPAX OWL/RDF documents, and a writer to export models back to BioPAX formats. It also includes a validation engine that checks models against the BioPAX schema, and utilities for querying, transforming, and integrating BioPAX data into analysis pipelines. Paxtools emphasizes interoperability, with adapters and exporters that support common workflows, including exporting to formats used by visualization tools and downstream analyses.

Paxtools originated within the BioPAX community to support programmatic handling of pathway data and has been maintained as an open-source project. It is widely used by researchers and developers to integrate pathway information into computational analyses, validate data integrity, and convert BioPAX models for visualization and data integration. The project is hosted on a public version-control platform, inviting contributions from researchers and software developers participating in the BioPAX ecosystem.