Project Group: org.biopax.paxtools

Paxtools Core (BioPAX object model, I/O API, implementation and extras)

org.biopax.paxtools : paxtools-core

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.

Last Version: 5.1.0

Release Date: Sep 12, 2018

Paxtools-Trove

org.biopax.paxtools : paxtools-trove

A Trove4j based java collections provider for the paxtools-core BioPAX model.

Last Version: 5.1.0

Release Date: Sep 12, 2018

BioPAX Normalizer and MiriamLink

org.biopax.paxtools : normalizer

A BioPAX Normalizer and modified off-line MiriamLink (MIRIAM, EBI, OLS)

Last Version: 5.1.0

Release Date: Sep 12, 2018

BioPAX Pattern Search

org.biopax.paxtools : pattern

The BioPAX Pattern Search library; also, e.g., converts BioPAX model to SIF (simple binary interactions) text format.

Last Version: 5.1.0

Release Date: Sep 12, 2018

Graph-Theoretic Querying

org.biopax.paxtools : paxtools-query

BioPAX graph-theoretic querying - for finding paths between molecules, or identifying molecules that are reachable through specific paths, using the BioPAX pathway data model.

Last Version: 5.1.0

Release Date: Sep 12, 2018

BioPAX to SBGN-ML Converter

org.biopax.paxtools : sbgn-converter

To convert a BioPAX L3 model to SBGN-ML (SBGN PD), and optionally align.

Last Version: 5.1.0

Release Date: Sep 12, 2018

BioPAX to GSEA (.gmt) Converter

org.biopax.paxtools : gsea-converter

Converts data to the GESA (.gmt) format.

Last Version: 5.1.0

Release Date: Sep 12, 2018

PSI-MI/MITAB to BioPAX Converter

org.biopax.paxtools : psimi-converter

To Convert PSI-MI or MITAB v2.5 files to BioPAX.

Last Version: 5.1.0

Release Date: Sep 12, 2018

BioPAX to/from JSON Converter

org.biopax.paxtools : json-converter

BioPAX to/from JSON Converters

Last Version: 5.1.0

Release Date: Sep 12, 2018

Paxtools

org.biopax.paxtools : 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.

Last Version: 5.1.0

Release Date: Sep 12, 2018

Paxtools Maven Archetype

org.biopax.paxtools : paxtools-archetype

Paxtools Maven archetype - sample Java project to quickly start using Paxtools library and BioPAX data.

Last Version: 5.1.0

Release Date: Sep 12, 2018

BioPAX Full-text Search

org.biopax.paxtools : paxtools-search

BioPAX full-text indexing and searching (Lucene based)

Last Version: 5.1.0

Release Date: Sep 12, 2018

Paxtools Console Application

org.biopax.paxtools : paxtools-console

Paxtools Console Application and Examples

Last Version: 5.1.0

Release Date: Sep 12, 2018

BioPAX to SIF Converter (deprecated)

org.biopax.paxtools : sif-converter

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.

Last Version: 4.3.1

Release Date: Sep 22, 2015

Jena based IO

org.biopax.paxtools : paxtools-jena-io

Provides an additional I/O support for BioPAX OWL models using Jena library.

Last Version: 4.3.1

Release Date: Sep 22, 2015