Project Modules

This project has declared the following modules:

Name Description
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.
BioPAX to GSEA (.gmt) Converter Converts data to the GESA (.gmt) format.
PSI-MI/MITAB to BioPAX Converter To Convert PSI-MI or MITAB v2.5 files to BioPAX.
BioPAX to SBGN-ML Converter To convert a BioPAX L3 model to SBGN-ML (SBGN PD), and optionally align.
Paxtools Console Application Paxtools Console Application and Examples
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.
Paxtools-Trove A Trove4j based java collections provider for the paxtools-core BioPAX model.
Paxtools Maven Archetype Paxtools Maven archetype - sample Java project to quickly start using Paxtools library and BioPAX data.
BioPAX to/from JSON Converter BioPAX to/from JSON Converters
BioPAX Full-text Search BioPAX full-text indexing and searching (Lucene based)
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)