| Package | Description |
|---|---|
| org.biopax.paxtools.controller |
This package contains various methods and algorithms for traversing and manipulating the model.
|
| 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 |
|---|
| 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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