A system, method, and medium supports analyzing intellectual property documents by linking and annotating patents, copyrights, trademarks, license agreements, and other intellectual property documents. It can be used by intellectual property professionals in memorializing thought processes, work products, and reasoning, in preliminary or final form, and can support development and use of a rich linked set representing complex relationships in an intellectual property portfolio. Optionally, marked up, linked documents are divided into data streams; one contains the original document for mark-up, and one contains annotation data. The marked-up document may be further revised and/or annotated even by multiple users. The same document such as a patent may be centrally stored but independently marked-up by different users (or groups of users). The system extracts from a marked-up document annotation data with any changes, and provides one or more data streams, containing the annotation data for storage and or later use.