| GOterm | representation of GO terms |
| InterProTerm | Implementation of InterProI term interface |
| Ontology | standard implementation of an Ontology |
| OntologyEngineI | Interface a minimal Ontology implementation should satisfy |
| OntologyI | Interface for an ontology implementation |
| OntologyStore | A repository of ontologies |
| Path | a path for an ontology term graph |
| PathI | Interface for a path between ontology terms |
| Relationship | a relationship for an ontology |
| RelationshipFactory | Instantiates a new Bio::Ontology::RelationshipI (or derived class) through a factory |
| RelationshipI | Interface for a relationship between ontology terms |
| RelationshipType | a relationship type for an ontology |
| SimpleGOEngine | a Ontology Engine for GO implementing OntologyEngineI |
| SimpleOntologyEngine | Implementation of OntologyEngineI interface |
| Term | interface for ontology terms |
| TermFactory | Instantiates a new Bio::Ontology::TermI (or derived class) through a factory |
| TermI | interface for ontology terms |