| Definition: An entity with a physical structure.
Comment: This class serves as the super-class for all physical entities, although its current set of subclasses is limited to molecules. This list may be expanded to include photon, environment, cell and cellular component in later levels of BioPAX, depending on community need. As a highly abstract class in the ontology, instances of the physicalEntity class should be created rarely, if ever.
Synonyms: part, interactor, object
Naming rationale: It’s difficult to find a name that encompasses all of the subclasses of this class without being too general. E.g. PSI-MI uses ‘interactor’, BIND uses ‘object’, BioCyc uses ‘chemicals’. physicalEntity seems to be a good name for this specialization of entity.
Examples: protein, small molecule, RNA |