From narrative descriptions to MedDRA: automagically encoding adverse drug reactions

TL;DR

This paper introduces MagiCoder, an NLP algorithm that automatically encodes free-text adverse drug reaction reports into MedDRA terms, significantly reducing manual effort and improving data processing efficiency in pharmacovigilance.

Contribution

The paper presents MagiCoder, a novel NLP-based method for automatic MedDRA encoding of ADR reports, demonstrating high accuracy and efficiency across different report lengths.

Findings

Average recall of 86% on short descriptions

Average precision of 88% on short descriptions

Reduces manual encoding time for pharmacologists

Abstract

The collection of narrative spontaneous reports is an irreplaceable source for the prompt detection of suspected adverse drug reactions (ADRs): qualified domain experts manually revise a huge amount of narrative descriptions and then encode texts according to MedDRA standard terminology. The manual annotation of narrative documents with medical terminology is a subtle and expensive task, since the number of reports is growing up day-by-day. MagiCoder, a Natural Language Processing algorithm, is proposed for the automatic encoding of free-text descriptions into MedDRA terms. MagiCoder procedure is efficient in terms of computational complexity (in particular, it is linear in the size of the narrative input and the terminology). We tested it on a large dataset of about 4500 manually revised reports, by performing an automated comparison between human and MagiCoder revisions. For the current base version of MagiCoder, we measured: on short descriptions, an average recall of $86\%$ and an average precision of $88\%$; on medium-long descriptions (up to 255 characters), an average recall of $64\%$ and an average precision of $63\%$. From a practical point of view, MagiCoder reduces the time required for encoding ADR reports. Pharmacologists have simply to review and validate the MagiCoder terms proposed by the application, instead of choosing the right terms among the 70K low level terms of MedDRA. Such improvement in the efficiency of pharmacologists' work has a relevant impact also on the quality of the subsequent data analysis. We developed MagiCoder for the Italian pharmacovigilance language. However, our proposal is based on a general approach, not depending on the considered language nor the term dictionary.