Package | Description |
---|---|
org.biopax.paxtools.io.sif |
This package contains methods and algorithms for reducing BioPAX to Simple Interaction Format.
|
org.biopax.paxtools.model.level2 |
This package contains the interfaces that maps to the BioPAX level 2 specification.
|
Modifier and Type | Method and Description |
---|---|
String |
SimpleInteraction.getRelatedEntrezGeneID(XReferrable obj)
Searches for the Entrez Gene ID in the references.
|
Modifier and Type | Interface and Description |
---|---|
interface |
biochemicalReaction
A conversion interaction in which one or more entities (substrates) undergo
ovalent changes to become one or more other entities (products).
|
interface |
catalysis
A control interaction in which a physical entity (a catalyst) increases the
rate of a conversion interaction by lowering its activation energy.
|
interface |
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.
|
interface |
complexAssembly
A conversion interaction in which a set of physical entities, at least one
being a macromolecule (e.g.
|
interface |
confidence
Confidence that the containing instance actually occurs or exists in vivo,
usually a statistical measure.
|
interface |
control |
interface |
conversion |
interface |
dataSource
XREF Should be only unification and publication xrefs
|
interface |
dna |
interface |
entity
This class represents a discrete biological unit used when describing
pathways.
|
interface |
evidence |
interface |
interaction |
interface |
modulation
get controlled should be catalysis
|
interface |
openControlledVocabulary |
interface |
pathway |
interface |
physicalEntity |
interface |
physicalInteraction |
interface |
process
Tagging interface for entities that needs evidence and can be targeted by a
control : Pathway and Interaction
|
interface |
protein |
interface |
rna |
interface |
sequenceEntity
User: root Date: Aug 7, 2006 Time: 4:51:19 PM_DOT
|
interface |
sequenceFeature |
interface |
smallMolecule |
interface |
transport |
interface |
transportWithBiochemicalReaction |
Modifier and Type | Method and Description |
---|---|
Set<XReferrable> |
xref.isXREFof() |
Modifier and Type | Method and Description |
---|---|
Set<publicationXref> |
XReferrable.findCommonPublications(XReferrable that) |
Set<relationshipXref> |
XReferrable.findCommonRelationships(XReferrable that) |
Set<unificationXref> |
XReferrable.findCommonUnifications(XReferrable that) |
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