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
Paxtools originated within the BioPAX community to support programmatic handling of pathway data and has been