Package org.biopax.paxtools.pattern.miner

Package for pattern miner utility.

See: Description

Interface Summary

Interface	Description
IDFetcher
Miner	A miner provides a pattern to mine, and knows how to use the result set to prepare the text output.
SIFMiner	This interface tells that the miner supports SIF output.
SIFToText	An interface for converting a SIF interaction to text.
SIFType

Class Summary

Class	Description
AbstractSIFMiner	Base class for SIF Miners.
BlacklistGenerator	This class generates a blacklist for the given model.
BlacklistGenerator2	This class generates a blacklist for the given model.
BlacklistGenerator3	This class generates a blacklist for the given model.
CatalysisPrecedesMiner	Miner for the catalysis-precedes pattern.
ChemicalAffectsThroughBindingMiner	Miner for the chemical-affects-protein pattern.
ChemicalAffectsThroughControlMiner	Miner for the chemical-affects-protein pattern.
CommonIDFetcher	Tries to get Gene Symbols or UniProt IDs for genes and - display names for small molecules; This id-fetcher is mainly to use with the BioPAX pathway data from Pathway Commons (PC2) db (normalized and enriched with xrefs).
ConfigurableIDFetcher	Tries to get preferred type IDs of an entity reference.
ConsumptionControlledByMiner	Miner for the consumption-controlled-by pattern.
ControlsDegradationIndirectMiner	Yet another miner for the controls-degradation pattern.
ControlsExpressionMiner	Miner for the transcriptional regulation pattern.
ControlsExpressionWithConvMiner	Miner for the transcriptional regulation pattern, modeled using Conversion.
ControlsPhosphorylationMiner	Miner for the controls-phosphorylation pattern.
ControlsProductionOfMiner	Miner for the controls-production-of pattern.
ControlsStateChangeDetailedMiner	Miner for the controls-state-change-detailed pattern.
ControlsStateChangeOfMiner	Miner for the controls-state-change pattern.
ControlsTransportMiner	Miner for the controls-transport pattern.
ControlsTransportOfChemicalMiner	Miner for the controls-transport-of-chemical pattern.
CSCOBothControllerAndParticipantMiner	Miner for the controls-state-change pattern.
CSCOButIsParticipantMiner	Miner for the controls-state-change pattern.
CSCOThroughBindingSmallMoleculeMiner	Miner for the controls-state-change pattern.
CSCOThroughControllingSmallMoleculeMiner	Miner for the controls-state-change pattern.
CSCOThroughDegradationMiner	Miner for the degradation pattern.
CustomFormat	Used for customizing the columns in the SIF text output.
Dialog	This is the user interface with GUI for selecting a model, a pattern miner, and an output file.
DirectedRelationMiner	Miner for the directed relations between proteins.
ExtendedSIFWriter	This class is used for writing the binary interactions to a text output stream in the so called Pathway Commons EXTENDED_BINARY_SIF format.
InComplexWithMiner	Miner for the degradation pattern.
InteractsWithMiner	Miner for the "interacts-with" relation.
MinerAdapter	Adapter class for a miner.
NeighborOfMiner	Miner for the "neighbor-of" relation.
OutputColumn	This class is used for defining a custom column in the te
ReactsWithMiner	Miner for the "reacts-with" relation.
RelatedGenesOfInteractionsMiner	Miner for the related genes (participant or controller) of interactions.
SIFInteraction
SIFSearcher	Searches a model and generates SIF network using the pattern matches.
SimpleIDFetcher	Simple gets the URI (of an entity reference);
UbiquitousIDMiner	Miner for getting ubiquitous small molecules in a model.
UsedToProduceMiner	Miner for the "used-for-production-of" relation.

Enum Summary

Enum	Description
OutputColumn.Type	Type of the output column.
SIFEnum	Enum for representing supported SIF edge types.

Package org.biopax.paxtools.pattern.miner Description

Package for pattern miner utility. This package is not an essential part of the framework, but an example implementation of pattern search software using the framework. Each miner class is capable of creating the pattern and writing the result to a text output. The Dialog class is a GUI that executes the selected miner class on a selected model and writes output to the given file.