Package org.biopax.paxtools.io.sif

Deprecated.

please use Paxtools pattern module for exporting to the SIF and extended SIF formats.

This package contains methods and algorithms for reducing BioPAX to Simple Interaction Format.

See: Description

Interface Summary

Interface	Description
InteractionRule	This interface defines a rule which can be run on BioPAX model to derive simple interactions.

Class Summary

Class	Description
InteractionSet	This is a set of binary interactions.
SimpleInteraction	This class implements a directed binary interaction between two entities.
SimpleInteractionConverter	Deprecated use the pattern (new Paxtools' module) api instead

Enum Summary

Enum	Description
BinaryInteractionType	This class holds the description, tag (used in SIF file), the information if the interaction is directed for the relevant binary interaction types.

Exception Summary

Exception	Description
MaximumInteractionThresholdExceedException	This exception is thrown when there are more than a maximum number of interactions generated.

Package org.biopax.paxtools.io.sif Description

This package contains methods and algorithms for reducing BioPAX to Simple Interaction Format. Simple Interaction Format (SIF) was originally created for use with Cytoscape, the open source bioinformatics software platform for visualizing molecular interaction networks. SIF is simple to parse, and easy to load into Cytoscape and other third-party applications. Relations in a SIF file are formatted as: source relationship type target where source and target are a valid primary id and relationship type is one of the interaction inference rules. As its name suggests SIF, is a substantially simpler format compared to BioPAX. A BioPAX formatted network is capable of storing rich biological semantics, including multi-participant relationships, states and locations of entities, complexes and complex control relationships. A SIF network, on the other hand, is only capable of storing pairwise interactions between entity references.