Package org.biopax.paxtools.model.level3

Interface Entity

All Superinterfaces:
BioPAXElement, Cloneable, Level3Element, Named, Observable, Serializable, XReferrable
All Known Subinterfaces:
BiochemicalReaction, Catalysis, Complex, ComplexAssembly, Control, Controller, Conversion, Degradation, Dna, DnaRegion, Gene, GeneticInteraction, Interaction, Modulation, MolecularInteraction, NucleicAcid, Pathway, PhysicalEntity, Process, Protein, Rna, RnaRegion, SequenceEntity, SimplePhysicalEntity, SmallMolecule, TemplateReaction, TemplateReactionRegulation, Transport, TransportWithBiochemicalReaction
All Known Implementing Classes:
BiochemicalReactionImpl, CatalysisImpl, ComplexAssemblyImpl, ComplexImpl, ControlImpl, ConversionImpl, DegradationImpl, DnaImpl, DnaRegionImpl, EntityImpl, GeneImpl, GeneticInteractionImpl, InteractionImpl, ModulationImpl, MolecularInteractionImpl, NucleicAcidImpl, PathwayImpl, PhysicalEntityImpl, ProcessImpl, ProteinImpl, RnaImpl, RnaRegionImpl, SimplePhysicalEntityImpl, SmallMoleculeImpl, TemplateReactionImpl, TemplateReactionRegulationImpl, TransportImpl, TransportWithBiochemicalReactionImpl
public interface Entity extends Level3Element, Observable, Named
This class represents a discrete biological unit used when describing pathways. This is the root class for all biological concepts in the ontology, which include pathways, interactions and physical entities. As the most abstract class in the ontology, instances of the entity class should never be created. Instead, more specific classes should be used. Synonyms: thing, object, bioentity.

  • Method Details

    • getAvailability

      Set<String> getAvailability()
      The contents of this set can be modified but semantic consistency is not guaranteed. Using addAvailability(String) and removeAvailability(String) is recommended.
      Returns:
      a set of strings describing the availability of this data (e.g. a copyright statement).

    • addAvailability

      void addAvailability(String availability)
      This method adds the given text to the avaialability set.
      Parameters:
      availability - a string describing the availability of this data (e.g. a copyright statement).

    • removeAvailability

      void removeAvailability(String availability)
      This method removes the given text from the avaialability set.
      Parameters:
      availability - a string describing the availability of this data (e.g. a copyright statement).

    • getDataSource

      Set<Provenance> getDataSource()
      This method returns a set of free text descriptions of the source of this data, e.g. a database or person name. This property should be used to describe the source of the data. This is meant to be used by databases that export their data to the BioPAX format or by systems that are integrating data from multiple sources. The granularity of use (specifying the data source in many or few instances) is up to the user. It is intended that this property report the last data source, not all data sources that the data has passed through from creation. The contents of this set can be modified but semantic consistency is not guaranteed. Using addDataSource(Provenance) and removeDataSource(Provenance) is recommended.
      Returns:
      a set of free text descriptions of the source of this data, e.g. a database or person name.

    • addDataSource

      void addDataSource(Provenance dataSource)
      This method adds the given value to the DATA_SOURCE set.
      Parameters:
      dataSource - a free text description of the source of this data, e.g. a database or person name.

    • removeDataSource

      void removeDataSource(Provenance dataSource)
      This method removes the given value from the DATA_SOURCE set.
      Parameters:
      dataSource - a free text description of the source of this data, e.g. a database or person name.

    • getParticipantOf

      Set<Interaction> getParticipantOf()
      This method returns the interaction that this entity/pep takes part in. Contents of this set should not be modified. Reverse of Interaction.getParticipant()
      Returns:
      a set of interactions that