Package | Description |
---|---|
org.biopax.paxtools.impl.level3 |
This package contains the default implementation for BioPAX Level 3.
|
org.biopax.paxtools.io.sif.level3 |
This package contains the SIF rules for BioPAX Level 3.
|
org.biopax.paxtools.model.level3 |
This package contains the interfaces that maps classes defined in the BioPAX Level 3 specification.
|
org.biopax.paxtools.query.wrapperL3 |
This package contains TODO annotate!
|
Modifier and Type | Class and Description |
---|---|
class |
Group
This class represents a grouping of EntityReferences strictly used by SIF rules for handling generics and complexes.
|
Modifier and Type | Interface and Description |
---|---|
interface |
BindingFeature |
interface |
BiochemicalPathwayStep
Definition: Imposes ordering on a step in a biochemical pathway.
|
interface |
BiochemicalReaction
Definition: A conversion interaction in which one or more entities (substrates) undergo covalent
changes to become one or more other entities (products).
|
interface |
BioSource
Definition: The biological source of an entity (e.g.
|
interface |
Catalysis
Definition: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion
interaction by lowering its activation energy.
|
interface |
CellularLocationVocabulary
Definition: A reference to the Gene Ontology Cellular Component (GO CC) ontology.
|
interface |
CellVocabulary
Definition: A reference to the Cell Type Ontology (CL).
|
interface |
ChemicalConstant |
interface |
ChemicalStructure
Definition: The chemical structure of a small molecule.
|
interface |
Complex
Definition: 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
Definition: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g.
|
interface |
Control
Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity,
i.e.
|
interface |
ControlledVocabulary
Definition: This class represents a term from an external controlled vocabulary (CV).
|
interface |
Controller
This is a role interface for pathway elements that can control processes, namely
Pathway and PhysicalEntity . |
interface |
Conversion
Definition: An interaction in which molecules of one or more
PhysicalEntity pools are physically
transformed and become a member of one or more other PhysicalEntity pools. |
interface |
CovalentBindingFeature
Definition: An entity feature that represent the covalently bound state of a physical entity.
|
interface |
Degradation
Definition: A conversion in which a pool of macromolecules are degraded into their elementary
units.
|
interface |
DeltaG
Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants
(sums of species), delta-G'o.
|
interface |
Dna
Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic
acid.
|
interface |
DnaReference
A DNA reference is a grouping of several DNA entities that are common in
sequence and genomic position.
|
interface |
DnaRegion
Definition: A region on a DNA molecule.
|
interface |
DnaRegionReference
Definition: A DNARegionReference is a grouping of several DNARegion entities that are common in sequence and
genomic position.
|
interface |
Entity
This class represents a discrete biological unit used when describing
pathways.
|
interface |
EntityFeature
Description: A characteristic of a physical entity that can change while the entity still retains its biological
identity.
|
interface |
EntityReference
Definition: An entity reference is a grouping of several physical entities across different
contexts and molecular states, that share common physical properties and often named and treated
as a single entity with multiple states by biologists.
|
interface |
EntityReferenceTypeVocabulary
Definiiton: A reference to a term from an entity reference group ontology.
|
interface |
Evidence
Definition: The support for a particular assertion, such as the existence of an interaction or pathway.
|
interface |
EvidenceCodeVocabulary
Definition: A reference to the PSI Molecular Interaction ontology
experimental method types, including "interaction detection method", "participant identification method",
"feature detection method".
|
interface |
ExperimentalForm
Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of
experimental design.
|
interface |
ExperimentalFormVocabulary
Definition: A term that describes the form of the physical entity in the context of the experiment.
|
interface |
FragmentFeature
Definition: An entity feature that represents the resulting physical entity subsequent to a cleavage or
degradation event.
|
interface |
Gene
Definition: A continuant that encodes information that can be inherited through replication.
|
interface |
GeneticInteraction
Definition : Genetic interactions between genes occur when two genetic perturbations (e.g.
|
interface |
Interaction
Definition: A biological relationship between two or more entities.
|
interface |
InteractionVocabulary
A reference to the PSI Molecular Interaction ontology (MI) interaction type.
|
interface |
KPrime
The apparent equilibrium constant, K', and associated values.
|
interface |
ModificationFeature
Definition: A covalently modified feature on a sequence, relevant to an interaction,
such as a post-translational modification.
|
interface |
Modulation
Definition: An interaction in which one entity regulates, modifies, or otherwise influences another.
|
interface |
MolecularInteraction
Definition: An interaction in which at least one participant is a physical entity, e.g.
|
interface |
Named
Interface for all classes that can have names in BioPAX.
|
interface |
NucleicAcid
Tagger interface for DNA and RNA
|
interface |
NucleicAcidReference
Role interface for NucleicAcidReferences, namely DNA and RNA.
|
interface |
NucleicAcidRegionReference |
interface |
Observable
User: demir Date: Aug 17, 2007 Time: 5:47:27 PM
|
interface |
Pathway |
interface |
PathwayStep
This represents a set of pathway events.
|
interface |
PhenotypeVocabulary |
interface |
PhysicalEntity |
interface |
Process
Tagging interface for entities that can participate in a pathway
and can be targeted by a control : Pathway and Interaction
|
interface |
Protein |
interface |
ProteinReference
Description: A protein reference is a grouping of several protein entities that are encoded by the same
genetic sequence.
|
interface |
Provenance
Definition: The direct source of a pathway data or score.
|
interface |
PublicationXref |
interface |
RelationshipTypeVocabulary
Vocabulary for defining relationship Xref types.
|
interface |
RelationshipXref
Definition: An xref that defines a reference to an entity in an external resource that
does not have the same biological identity as the referring entity.
|
interface |
Rna |
interface |
RnaReference |
interface |
RnaRegion
Definition: A region on a RNA molecule.
|
interface |
RnaRegionReference
A RNA region reference
|
interface |
Score
Definition: A score associated with a publication reference describing how the score was
determined, the name of the method and a comment briefly describing the method.
|
interface |
SequenceEntity
Tagger interface for macromolecules that are related to a genetic sequence: DNA, RNA, Protein.
|
interface |
SequenceEntityReference
Tagger interface for protein, dna and rna entities
|
interface |
SequenceInterval |
interface |
SequenceLocation
Definition: A location on a nucleotide or amino acid sequence.
|
interface |
SequenceModificationVocabulary
Definition: A term that describes the covalent modifications to an amino
acid or nucleic acid chain.
|
interface |
SequenceRegionVocabulary
Definition: A reference to a controlled vocabulary of sequence regions, such as InterPro or Sequence Ontology (SO)
Homepage at http://www.sequenceontology.org.
|
interface |
SequenceSite |
interface |
SimplePhysicalEntity
Tagger interface for non-complex physical entities
|
interface |
SmallMolecule |
interface |
SmallMoleculeReference |
interface |
Stoichiometry
Stoichiometric coefficient of a physical entity in the context of a conversion or complex.
|
interface |
TemplateReaction |
interface |
TemplateReactionRegulation |
interface |
TissueVocabulary
Definition: A reference to the BRENDA
|
interface |
Transport |
interface |
TransportWithBiochemicalReaction |
interface |
UnificationXref
Definition: A unification xref defines a reference to an entity in an external resource that has the same
biological identity as the referring entity Rationale: Unification xrefs are critically important for data
integration.
|
interface |
UtilityClass |
interface |
Xref |
interface |
XReferrable |
Modifier and Type | Method and Description |
---|---|
boolean |
UbiqueFilter.okToTraverse(Level3Element ele)
Checks if the ID of the given element is in the black list.
|
boolean |
StringFieldFilter.okToTraverse(Level3Element ele)
Checks if the related values of the object are among valid values.
|
abstract boolean |
Filter.okToTraverse(Level3Element ele)
Checks if it is ok to traverse the given level 3 element.
|
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