Systems and methods for annotating conversations between a user and an electronic assistant in a hierarchical manner are disclosed. An example system includes a data store of hierarchical annotation records. The hierarchical annotation records include root records and non-root records. Each root record has a conversation identifier and an annotation identifier. Each non-root record includes an annotation identifier and a parent identifier, the parent identifier being an annotation identifier of another record. At least some of the non-root records further include an annotation tag. The system generates a first new root record and first non-root records for an input dialog act and generates a second new root record and second non-root records for an output dialog act that is responsive to the input dialog act. At least one of the second non-root records includes an annotation tag linking back to a record of the first non-root records.