Package | Description |
---|---|
org.biopax.paxtools.controller |
This package contains various methods and algorithms for traversing and manipulating the model.
|
org.biopax.paxtools.examples |
This package contains several examples that uses Paxtools to demonstrate basic functionality.
|
org.biopax.paxtools.io.sif |
This package contains methods and algorithms for reducing BioPAX to Simple Interaction Format.
|
org.biopax.paxtools.io.sif.level2 | |
org.biopax.paxtools.model.level2 |
This package contains the interfaces that maps to the BioPAX level 2 specification.
|
Class and Description |
---|
conversion |
physicalEntityParticipant |
Class and Description |
---|
pathway |
Class and Description |
---|
XReferrable |
Class and Description |
---|
physicalEntity |
Class and Description |
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biochemicalReaction
A conversion interaction in which one or more entities (substrates) undergo
ovalent changes to become one or more other entities (products).
|
bioSource
The biological source of an entity (e.g.
|
chemicalStructure
Describes a small molecule structure.
|
complex
A physical entity whose structure is comprised of other physical entities
bound to each other non-covalently, at least one of which is a macromolecule
(e.g.
|
confidence
Confidence that the containing instance actually occurs or exists in vivo,
usually a statistical measure.
|
control |
ControlType
User: root Date: Aug 1, 2006 Time: 5:37:34 PM_DOT
|
conversion |
dataSource
XREF Should be only unification and publication xrefs
|
deltaGprimeO |
Direction
Catalysis direction controlled vocabulary
|
entity
This class represents a discrete biological unit used when describing
pathways.
|
evidence |
experimentalForm |
externalReferenceUtilityClass |
interaction |
InteractionParticipant
marker interface for entities and PEPs
|
kPrime |
Level2Element
Created by IntelliJ IDEA.
|
openControlledVocabulary |
pathway |
pathwayComponent
Interface for pathway steps and processes
|
pathwayStep
This represents a set of pathway events.
|
physicalEntity |
physicalEntityParticipant |
physicalInteraction |
PositionStatusType |
process
Tagging interface for entities that needs evidence and can be targeted by a
control : Pathway and Interaction
|
publicationXref |
relationshipXref |
sequenceEntity
User: root Date: Aug 7, 2006 Time: 4:51:19 PM_DOT
|
sequenceFeature |
sequenceLocation |
sequenceSite |
SpontaneousType |
transport |
unificationXref |
utilityClass |
xref |
XReferrable |
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