Vast amounts of data in healthcare are available in unstructured text format, usually in the local language of the countries. These documents contain valuable information. Secondary use of clinical narratives and information extraction of key facts and relations from them about the patient disease history can foster preventive medicine and improve healthcare. In this paper, we propose a hybrid method for the automatic transformation of clinical text into a structured format. The documents are automatically sectioned into the following parts: diagnosis, patient history, patient status, lab results. For the “Diagnosis” section a deep learning text-based encoding into ICD-10 codes is applied using MBG-ClinicalBERT - a fine-tuned ClinicalBERT model for Bulgarian medical text. From the “Patient History” section, we identify patient symptoms using a rule-based approach enhanced with similarity search based on MBG-ClinicalBERT word embeddings. We also identify symptom relations like negation. For the “Patient Status” description, binary classification is used to determine the status of each anatomic organ. In this paper, we demonstrate different methods for adapting NLP tools for English and other languages to a low resource language like Bulgarian.