Paxtools Core (BioPAX object model, I/O API, implementation and extras) · Paxtools core library includes the BioPAX object model and interfaces, the default implementation and extras: reflection-based class factories and property editors/accessors, some inverse properties (e.g., xrefOf, componentOf), traversal and file (I/O) utilities.
Paxtools-Trove · A Trove4j based java collections provider for the paxtools-core BioPAX model.
BioPAX Pattern Search · The BioPAX Pattern Search library; also, e.g., converts BioPAX model to SIF (simple binary interactions) text format.
BioPAX Normalizer and MiriamLink · A BioPAX Normalizer and modified off-line MiriamLink (MIRIAM, EBI, OLS)
BioPAX to SIF Converter (deprecated) · Converts a BioPAX model to binary SIF (simple interaction format) or extended binary SIF by inferring the interactions in the model and describing them in terms of simple interactions. This includes a set of BioPAX-specific inference rules implemented on top of paxtools-core.
BioPAX to SBGN-ML Converter · To convert a BioPAX L3 model to SBGN-ML (SBGN PD), and optionally align.
PSI-MI/MITAB to BioPAX Converter · To Convert PSI-MI or MITAB v2.5 files to BioPAX.
BioPAX Full-text Search · BioPAX full-text indexing and searching (Lucene based)
Graph-Theoretic Querying · BioPAX graph-theoretic querying - for finding paths between molecules, or identifying molecules that are reachable through specific paths, using the BioPAX pathway data model.
Jena based IO · Provides an additional I/O support for BioPAX OWL models using Jena library.
Paxtools Console Application · Paxtools Console Application and Examples
Paxtools Maven Archetype · Paxtools Maven archetype - sample Java project to quickly start using Paxtools library and BioPAX data.
Paxtools · Paxtools is a Java library that allows software to read, write, analyze and manipulate BioPAX models. Paxtools provide a consistent, fully implemented, validating BioPAX API that significantly reduces development time of oftware that require programmatic access to BioPAX. Paxtools is modular, lightweight and platform independent to be easily embedded into applications.
BioPAX to/from JSON Converter · BioPAX to/from JSON Converters
BioPAX to GSEA (.gmt) Converter · Converts data to the GESA (.gmt) format.
