A NLP pipeline for the automatic extraction of microorganisms names from microbiological notes

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Abstract

According to the 'Istituto Superiore di Sanita (ISS), hospital infections are the most frequent and serious complication of health care. This constitutes a real health emergency which requires incisive and joint action at all levels of the local and national health organization. Most of the valuable information related to the presence of a specific microorganism in the blood are written into the notes field of the laboratory exams results. The main objective of this work is to build a Natural Language Processing (NLP) pipeline for the automatic extraction of the names of microorganisms present in the clinical texts. A sample of 499 microbiological notes have been analysed with the developed system and all the microorganisms names have been extracted correctly, according to the labels given by the expert.

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APA

Mora, S., Attene, J., Gazzarata, R., Parruti, G., & Giacomini, M. (2021). A NLP pipeline for the automatic extraction of microorganisms names from microbiological notes. In Studies in Health Technology and Informatics (Vol. 285, pp. 153–158). IOS Press BV. https://doi.org/10.3233/SHTI210589

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