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arXiv · 2104.00975

Use of 'off-the-shelf' information extraction algorithms in clinical informatics: a feasibility study of MetaMap annotation of Italian medical notes

Emma Chiaramello·Francesco Pinciroli·Alberico Bonalumi·Angelo Caroli·Gabriella Tognola
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Abstract

Information extraction from narrative clinical notes is useful for patient care, as well as for secondary use of medical data, for research or clinical purposes. Many studies focused on information extraction from English clinical texts, but less dealt with clinical notes in languages other than English. This study tested the feasibility of using 'off the shelf' information extraction algorithms to identify medical concepts from Italian clinical notes. We used MetaMap to map medical concepts to the Unified Medical Language System (UMLS). The study addressed two questions: (Q1) to understand if it would be possible to properly map medical terms found in clinical notes and related to the semantic group of 'Disorders' to the Italian UMLS resources; (Q2) to investigate if it would be feasible to use MetaMap as it is to extract these medical concepts from Italian clinical notes. Results in EXP1 showed that the Italian UMLS Metathesaurus sources covered 91% of the medical terms of the 'Disorders' semantic group, as found in the studied dataset. Even if MetaMap was built to analyze texts written in English, it worked properly also with texts written in Italian. MetaMap identified correctly about half of the concepts in the Italian clinical notes. Using MetaMap's annotation on Italian clinical notes instead of a simple text search improved our results of about 15 percentage points. MetaMap showed recall, precision and F-measure of 0.53, 0.98 and 0.69, respectively. Most of the failures were due to the impossibility for MetaMap to generate Italian meaningful variants. MetaMap's performance in annotating automatically translated English clinical notes was in line with findings in the literature, with similar recall (0.75), F-measure (0.83) and even higher precision (0.95).

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Emma Chiaramello, Francesco Pinciroli, Alberico Bonalumi, Angelo Caroli, Gabriella Tognola. 2021-04-02. Use of 'off-the-shelf' information extraction algorithms in clinical informatics: a feasibility study of MetaMap annotation of Italian medical notes. https://doi.org/10.1016/j.jbi.2016.07.017

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