From narrative descriptions to MedDRA: automagically encoding adverse drug reactions
This reduces time and cost for pharmacologists in pharmacovigilance by automating a tedious manual task, though it is incremental as it applies existing NLP methods to a specific domain.
The paper tackles the problem of manually encoding adverse drug reaction reports into MedDRA terminology by proposing MagiCoder, an NLP algorithm that automates this process, achieving up to 88% precision and 86% recall on short descriptions.
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.