The present invention generally provides methods, systems, and articles of manufacture for managing an annotation system that includes storing annotations for a document family, i.e., a series of versions of a data source. Annotations created for one version of the data source may be viewed in context from both subsequent and prior versions of the same data source. Embodiments of the invention associate annotations with both a data source “family identifier” as well as a “version identifier.” Other than adding a family ID to the data source, the data source remains unchanged. The family ID is maintained across different versions of the data source, whereas version IDs are determined for a specific version of the data source. Version IDs can be constructed from each data source directly, and do not need to be stored.