Launching into clinical space with medspaCy: a new clinical text processing toolkit in Python.
Hannah Eyre, Alec B. Chapman, Kelly Peterson, Jianlin Shi, Patrick R. Alba, Makoto Jones, Tamára L. Box, Scott L. DuVall, Olga V. Patterson
Abstract
Despite impressive success of machine learning algorithms in clinical natural language processing (cNLP), rule-based approaches still have a prominent role. In this paper, we introduce medspaCy, an extensible, open-source cNLP library based on spaCy framework that allows flexible integration of rule-based and machine learning-based algorithms adapted to clinical text. MedspaCy includes a variety of components that meet common cNLP needs such as context analysis and mapping to standard terminologies. By utilizing spaCy's clear and easy-to-use conventions, medspaCy enables development of custom pipelines that integrate easily with other spaCy-based modules. Our toolkit includes several core components and facilitates rapid development of pipelines for clinical text.