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) |