1. A pen-based computing system for digitally capturing content from a printed document comprising one or more pages of printed data, the printed document associated with a document identifier, the system comprising: a digital bookclip comprising a physical material encoded with a pattern, the physical material distinct from the printed document; a smart pen device comprising: an imaging system configured to capture an interaction of the smart pen device with the digital bookclip by reading the encoded pattern of the digital bookclip, the smart pen device capturing a beginning location on the digital bookclip corresponding to a beginning of the interaction and an end location on the digital bookclip corresponding to an end of the interaction; a database storing a digital representation of the printed document; and a memory storing computer program code configured to be executed by a processor coupled to the smart pen device, the computer program code including instructions for: accessing the digital representation of the printed document from the database using the document identifier, determining a vertical or horizontal orientation of the digital bookclip with respect to the printed document; receiving the captured beginning and end locations corresponding to the interaction of the smart pen with the digital bookclip; identifying a selected first portion of the digital representation of the printed document based on the determined orientation of the digital bookclip with respect to the printed document and the beginning location and the end location of the digital bookclip captured when the digital bookclip is aligned with the printed document; and retrieving the portion of the digital representation of the printed document.