The markup process implemented by the 1641 Depositions primarily aims to capture the knowledge of the seventeenth century historians involved in the transcription of the source materials. This includes recording information such as the people and places involved in each deposition, the dates in which the alleged crimes took place and the nature of these crimes. This process of describing the content of each deposition in a structured fashion allows more detailed searches to be performed across the depositions as a collection.

While the Digital Humanities is a vibrant area of innovative and multi-disciplinary research, over the course of the past decade, DH projects have tended to generate individual repositories of digital data in a variety of formats (databases, plain text, xml etc). These repositories have formed isolated islands of information which has restricted the possibility of combining data and searching for information across numerous resources.

The Text Encoding Initiative (TEI) Guidelines for Electronic Text Encoding and Interchange is an international and interdisciplinary standard that is widely used by libraries, museums, publishers, and individual scholars to represent all kinds of literary material for online publication. The use of TEI to describe content in a standard, structured fashion promotes the interoperability of content collections. As such, TEI has been adopted as the markup standard used in the 1641 Depositions project.

The use of TEI to describe the depositions facilitates the integation of numerous related digital resources with the 1641 Depositions. The combination of these digital sources of historical data underpins the creation of new knowledge.  Research continues to be shaped by the primary materials but the fact that these materials can now be linked and queried simultaneously allows the Humanities researcher to ask new and more complex questions.