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.impl.level3 |
This package contains the default implementation for BioPAX Level 3.
|
org.biopax.paxtools.io.gsea |
This package contains a simple GSEA converter.
|
org.biopax.paxtools.io.sbgn |
This package contains a BioPAX to SBGN-PD converter and associated classes.
|
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.pattern |
Main package.
|
org.biopax.paxtools.pattern.constraint |
Package for constraints.
|
org.biopax.paxtools.pattern.miner |
Package for pattern miner utility.
|
org.biopax.paxtools.pattern.util |
Package for several utility classes.
|
org.biopax.paxtools.query |
Graph-theoretic querying module in Paxtools is used for identifying paths between molecules or identifying other
molecules that is reachable through some specific paths using the BioPAX data model.
|
org.biopax.paxtools.query.wrapperL3 |
This package contains TODO annotate!
|
org.biopax.paxtools.query.wrapperL3undirected |
This package contains TODO annotate!
|
Class and Description |
---|
BioSource
Definition: The biological source of an entity (e.g.
|
EntityFeature
Description: A characteristic of a physical entity that can change while the entity still retains its biological
identity.
|
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.
|
Named
Interface for all classes that can have names in BioPAX.
|
Pathway |
PhysicalEntity |
Provenance
Definition: The direct source of a pathway data or score.
|
Class and Description |
---|
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.
|
PhysicalEntity |
Class and Description |
---|
BindingFeature |
BiochemicalPathwayStep
Definition: Imposes ordering on a step in a biochemical pathway.
|
BiochemicalReaction
Definition: A conversion interaction in which one or more entities (substrates) undergo covalent
changes to become one or more other entities (products).
|
BioSource
Definition: The biological source of an entity (e.g.
|
Catalysis
Definition: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion
interaction by lowering its activation energy.
|
CatalysisDirectionType
This enum represents the direction of a catalysis under all physiological conditions if there is one.
|
CellularLocationVocabulary
Definition: A reference to the Gene Ontology Cellular Component (GO CC) ontology.
|
CellVocabulary
Definition: A reference to the Cell Type Ontology (CL).
|
ChemicalConstant |
ChemicalStructure
Definition: The chemical structure of a small molecule.
|
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.
|
ComplexAssembly
Definition: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g.
|
Control
Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity,
i.e.
|
ControlledVocabulary
Definition: This class represents a term from an external controlled vocabulary (CV).
|
Controller
This is a role interface for pathway elements that can control processes, namely
Pathway and PhysicalEntity . |
ControlType
Defines the nature of the control relationship between the controller and the controlled entities.
|
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. |
ConversionDirectionType
This enum is used for specifying the direction of a Conversion.
|
CovalentBindingFeature
Definition: An entity feature that represent the covalently bound state of a physical entity.
|
Degradation
Definition: A conversion in which a pool of macromolecules are degraded into their elementary
units.
|
DeltaG
Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants
(sums of species), delta-G'o.
|
Dna
Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic
acid.
|
DnaReference
A DNA reference is a grouping of several DNA entities that are common in
sequence and genomic position.
|
DnaRegion
Definition: A region on a DNA molecule.
|
DnaRegionReference
Definition: A DNARegionReference is a grouping of several DNARegion entities that are common in sequence and
genomic position.
|
Entity
This class represents a discrete biological unit used when describing
pathways.
|
EntityFeature
Description: A characteristic of a physical entity that can change while the entity still retains its biological
identity.
|
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.
|
EntityReferenceTypeVocabulary
Definiiton: A reference to a term from an entity reference group ontology.
|
Evidence
Definition: The support for a particular assertion, such as the existence of an interaction or pathway.
|
EvidenceCodeVocabulary
Definition: A reference to the PSI Molecular Interaction ontology
experimental method types, including "interaction detection method", "participant identification method",
"feature detection method".
|
ExperimentalForm
Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of
experimental design.
|
ExperimentalFormVocabulary
Definition: A term that describes the form of the physical entity in the context of the experiment.
|
FragmentFeature
Definition: An entity feature that represents the resulting physical entity subsequent to a cleavage or
degradation event.
|
Gene
Definition: A continuant that encodes information that can be inherited through replication.
|
GeneticInteraction
Definition : Genetic interactions between genes occur when two genetic perturbations (e.g.
|
Interaction
Definition: A biological relationship between two or more entities.
|
InteractionVocabulary
A reference to the PSI Molecular Interaction ontology (MI) interaction type.
|
KPrime
The apparent equilibrium constant, K', and associated values.
|
Level3Element
A Level 3 specific element.
|
ModificationFeature
Definition: A covalently modified feature on a sequence, relevant to an interaction,
such as a post-translational modification.
|
Modulation
Definition: An interaction in which one entity regulates, modifies, or otherwise influences another.
|
MolecularInteraction
Definition: An interaction in which at least one participant is a physical entity, e.g.
|
Named
Interface for all classes that can have names in BioPAX.
|
NucleicAcid
Tagger interface for DNA and RNA
|
NucleicAcidReference
Role interface for NucleicAcidReferences, namely DNA and RNA.
|
NucleicAcidRegionReference |
Observable
User: demir Date: Aug 17, 2007 Time: 5:47:27 PM
|
Pathway |
PathwayStep
This represents a set of pathway events.
|
PhenotypeVocabulary |
PhysicalEntity |
PositionStatusType |
Process
Tagging interface for entities that can participate in a pathway
and can be targeted by a control : Pathway and Interaction
|
Protein |
ProteinReference
Description: A protein reference is a grouping of several protein entities that are encoded by the same
genetic sequence.
|
Provenance
Definition: The direct source of a pathway data or score.
|
PublicationXref |
RelationshipTypeVocabulary
Vocabulary for defining relationship Xref types.
|
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.
|
Rna |
RnaReference |
RnaRegion
Definition: A region on a RNA molecule.
|
RnaRegionReference
A RNA region reference
|
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.
|
SequenceEntity
Tagger interface for macromolecules that are related to a genetic sequence: DNA, RNA, Protein.
|
SequenceEntityReference
Tagger interface for protein, dna and rna entities
|
SequenceInterval |
SequenceLocation
Definition: A location on a nucleotide or amino acid sequence.
|
SequenceModificationVocabulary
Definition: A term that describes the covalent modifications to an amino
acid or nucleic acid chain.
|
SequenceRegionVocabulary
Definition: A reference to a controlled vocabulary of sequence regions, such as InterPro or Sequence Ontology (SO)
Homepage at http://www.sequenceontology.org.
|
SequenceSite |
SimplePhysicalEntity
Tagger interface for non-complex physical entities
|
SmallMolecule |
SmallMoleculeReference |
StepDirection
Catalysis direction controlled vocabulary
|
Stoichiometry
Stoichiometric coefficient of a physical entity in the context of a conversion or complex.
|
StructureFormatType |
TemplateDirectionType
TODO:Class description User: demir Date: Aug 7, 2009 Time: 10:39:36 AM
|
TemplateReaction |
TemplateReactionRegulation |
TissueVocabulary
Definition: A reference to the BRENDA
|
Transport |
TransportWithBiochemicalReaction |
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.
|
UtilityClass |
Xref |
XReferrable |
Class and Description |
---|
Provenance
Definition: The direct source of a pathway data or score.
|
Class and Description |
---|
EntityFeature
Description: A characteristic of a physical entity that can change while the entity still retains its biological
identity.
|
PhysicalEntity |
Class and Description |
---|
BindingFeature |
Control
Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity,
i.e.
|
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. |
EntityFeature
Description: A characteristic of a physical entity that can change while the entity still retains its biological
identity.
|
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.
|
Level3Element
A Level 3 specific element.
|
Named
Interface for all classes that can have names in BioPAX.
|
Observable
User: demir Date: Aug 17, 2007 Time: 5:47:27 PM
|
PhysicalEntity |
SimplePhysicalEntity
Tagger interface for non-complex physical entities
|
UtilityClass |
XReferrable |
Class and Description |
---|
BindingFeature |
BiochemicalReaction
Definition: A conversion interaction in which one or more entities (substrates) undergo covalent
changes to become one or more other entities (products).
|
BioSource
Definition: The biological source of an entity (e.g.
|
CatalysisDirectionType
This enum represents the direction of a catalysis under all physiological conditions if there is one.
|
CellularLocationVocabulary
Definition: A reference to the Gene Ontology Cellular Component (GO CC) ontology.
|
CellVocabulary
Definition: A reference to the Cell Type Ontology (CL).
|
ChemicalConstant |
ChemicalStructure
Definition: The chemical structure of a small molecule.
|
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.
|
Control
Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity,
i.e.
|
ControlledVocabulary
Definition: This class represents a term from an external controlled vocabulary (CV).
|
Controller
This is a role interface for pathway elements that can control processes, namely
Pathway and PhysicalEntity . |
ControlType
Defines the nature of the control relationship between the controller and the controlled entities.
|
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. |
ConversionDirectionType
This enum is used for specifying the direction of a Conversion.
|
DeltaG
Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants
(sums of species), delta-G'o.
|
Entity
This class represents a discrete biological unit used when describing
pathways.
|
EntityFeature
Description: A characteristic of a physical entity that can change while the entity still retains its biological
identity.
|
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.
|
EntityReferenceTypeVocabulary
Definiiton: A reference to a term from an entity reference group ontology.
|
Evidence
Definition: The support for a particular assertion, such as the existence of an interaction or pathway.
|
EvidenceCodeVocabulary
Definition: A reference to the PSI Molecular Interaction ontology
experimental method types, including "interaction detection method", "participant identification method",
"feature detection method".
|
ExperimentalForm
Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of
experimental design.
|
ExperimentalFormVocabulary
Definition: A term that describes the form of the physical entity in the context of the experiment.
|
Interaction
Definition: A biological relationship between two or more entities.
|
InteractionVocabulary
A reference to the PSI Molecular Interaction ontology (MI) interaction type.
|
KPrime
The apparent equilibrium constant, K', and associated values.
|
Level3Element
A Level 3 specific element.
|
ModificationFeature
Definition: A covalently modified feature on a sequence, relevant to an interaction,
such as a post-translational modification.
|
Named
Interface for all classes that can have names in BioPAX.
|
NucleicAcid
Tagger interface for DNA and RNA
|
NucleicAcidReference
Role interface for NucleicAcidReferences, namely DNA and RNA.
|
NucleicAcidRegionReference |
Observable
User: demir Date: Aug 17, 2007 Time: 5:47:27 PM
|
Pathway |
PathwayStep
This represents a set of pathway events.
|
PhenotypeVocabulary |
PhysicalEntity |
PositionStatusType |
Process
Tagging interface for entities that can participate in a pathway
and can be targeted by a control : Pathway and Interaction
|
Provenance
Definition: The direct source of a pathway data or score.
|
RelationshipTypeVocabulary
Vocabulary for defining relationship Xref types.
|
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.
|
SequenceEntity
Tagger interface for macromolecules that are related to a genetic sequence: DNA, RNA, Protein.
|
SequenceEntityReference
Tagger interface for protein, dna and rna entities
|
SequenceLocation
Definition: A location on a nucleotide or amino acid sequence.
|
SequenceModificationVocabulary
Definition: A term that describes the covalent modifications to an amino
acid or nucleic acid chain.
|
SequenceRegionVocabulary
Definition: A reference to a controlled vocabulary of sequence regions, such as InterPro or Sequence Ontology (SO)
Homepage at http://www.sequenceontology.org.
|
SequenceSite |
SimplePhysicalEntity
Tagger interface for non-complex physical entities
|
StepDirection
Catalysis direction controlled vocabulary
|
Stoichiometry
Stoichiometric coefficient of a physical entity in the context of a conversion or complex.
|
StructureFormatType |
TemplateDirectionType
TODO:Class description User: demir Date: Aug 7, 2009 Time: 10:39:36 AM
|
TissueVocabulary
Definition: A reference to the BRENDA
|
Transport |
UtilityClass |
Xref |
XReferrable |
Class and Description |
---|
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.
|
ModificationFeature
Definition: A covalently modified feature on a sequence, relevant to an interaction,
such as a post-translational modification.
|
Class and Description |
---|
Control
Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity,
i.e.
|
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. |
ConversionDirectionType
This enum is used for specifying the direction of a Conversion.
|
Entity
This class represents a discrete biological unit used when describing
pathways.
|
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.
|
Interaction
Definition: A biological relationship between two or more entities.
|
ModificationFeature
Definition: A covalently modified feature on a sequence, relevant to an interaction,
such as a post-translational modification.
|
Pathway |
PhysicalEntity |
StepDirection
Catalysis direction controlled vocabulary
|
Class and Description |
---|
Control
Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity,
i.e.
|
ModificationFeature
Definition: A covalently modified feature on a sequence, relevant to an interaction,
such as a post-translational modification.
|
Pathway |
ProteinReference
Description: A protein reference is a grouping of several protein entities that are encoded by the same
genetic sequence.
|
SmallMoleculeReference |
Class and Description |
---|
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. |
ConversionDirectionType
This enum is used for specifying the direction of a Conversion.
|
ModificationFeature
Definition: A covalently modified feature on a sequence, relevant to an interaction,
such as a post-translational modification.
|
PhysicalEntity |
SmallMolecule |
SmallMoleculeReference |
Class and Description |
---|
PhysicalEntity |
Class and Description |
---|
Control
Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity,
i.e.
|
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. |
Interaction
Definition: A biological relationship between two or more entities.
|
Level3Element
A Level 3 specific element.
|
PhysicalEntity |
TemplateReaction |
Class and Description |
---|
Interaction
Definition: A biological relationship between two or more entities.
|
Copyright © 2015 BioPAX. All rights reserved.