While adherence to clinical guidelines improves the quality and consistency of care, personalized healthcare also requires a deep understanding of individual disease models and treatment plans. The structured preparation of medical routine data in a certain clinical context, e.g. a treatment pathway outlined in a medical guideline, is currently a challenging task. Medical data is often stored in diverse formats and systems, and the relevant clinical knowledge defining the context is not available in machine-readable formats. We present an approach to extract information from medical free text documentation by using structured clinical knowledge to guide information extraction into a structured and encoded format, overcoming the known challenges for natural language processing algorithms. Preliminary results have been encouraging, as one of our methods managed to extract 100% of all data-points with 85% accuracy in details. These advancements show the potential of our approach to effectively use unstructured clinical data to elevate the quality of patient care and reduce the workload of medical personnel.