Package org.biopax.paxtools.model.level2

Interface entity

All Superinterfaces:
BioPAXElement, Cloneable, InteractionParticipant, Level2Element, Serializable, XReferrable
All Known Subinterfaces:
biochemicalReaction, catalysis, complex, complexAssembly, control, conversion, dna, interaction, modulation, pathway, physicalEntity, physicalInteraction, process, protein, rna, sequenceEntity, smallMolecule, transport, transportWithBiochemicalReaction
public interface entity extends Level2Element, XReferrable, InteractionParticipant
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

    • addAVAILABILITY

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

    • addDATA_SOURCE

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

    • addSYNONYMS

      void addSYNONYMS(String SYNONYMS_TEXT)
      This method adds the given value to the SYNONYMS set.
      Parameters:
      SYNONYMS_TEXT - a new name to be added

    • 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).

    • getDATA_SOURCE

      Set<dataSource> getDATA_SOURCE()
      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 addDATA_SOURCE(org.biopax.paxtools.model.level2.dataSource) and removeDATA_SOURCE(org.biopax.paxtools.model.level2.dataSource) is recommended.
      Returns:
      a set of free text descriptions of the source of this data, e.g. a database or person name.

    • getNAME

      String getNAME()
      This method returns the preferred full name for this entity.
      Returns:
      preferred full name for this entity

    • getSHORT_NAME

      String getSHORT_NAME()
      This method sets an abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity. If no short name is available, an xref may be used for this purpose by the visualization application.
      Returns:
      an abbreviated name suitable for display.

    • getSYNONYMS

      Set<String> getSYNONYMS()
      The contents of this set can be modified but semantic consistency is not guaranteed. Using addSYNONYMS(java.lang.String) and removeSYNONYMS(java.lang.String) is recommended.
      Returns:
      a set of synonyms for the name of this entity. This should include the values of the NAME and SHORT-NAME property so that it is easy to find all known names in one place.

    • removeAVAILABILITY

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

    • removeDATA_SOURCE

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

    • removeSYNONYMS

      void removeSYNONYMS(String SYNONYMS_TEXT)
      This method removes the given value from the SYNONYMS set.
      Parameters:
      SYNONYMS_TEXT - a new name to be added

    • setAVAILABILITY

      void setAVAILABILITY(Set<String> AVAILABILITY_TEXT)
      This method overrides existing set with the new set. If you want to append to the existing set, use addAVAILABILITY(java.lang.String) instead.
      Parameters:
      AVAILABILITY_TEXT - a set of strings describing the availability of this data (e.g. a copyright statement).

    • setDATA_SOURCE

      void setDATA_SOURCE(Set<dataSource> DATA_SOURCE)
      This method overrides existing set with the new set. If you want to append to the existing set, use addDATA_SOURCE(org.biopax.paxtools.model.level2.dataSource) instead.
      Parameters:
      DATA_SOURCE - a set of free text descriptions of the source of this data, e.g. a database or person name.

    • setNAME

      void setNAME(String NAME)
      This method sets the preferred full name for this entity to the given value.
      Parameters:
      NAME - The preferred full name for this entity.

    • setSHORT_NAME

      void setSHORT_NAME(String SHORT_NAME)
      An abbreviated name for this entity, preferably a name that is short enough to be used in a visualization application to label a graphical element that represents this entity. If no short name is available, an xref may be used for this purpose by the visualization application.
      Parameters:
      SHORT_NAME - new short name

    • setSYNONYMS

      void setSYNONYMS(Set<String> SYNONYMS)
      This method overrides existing set with the new set. If you want to append to the existing set, use addSYNONYMS(java.lang.String) instead.
      Parameters:
      SYNONYMS - a set of names for this entity.