preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology

Abstract

MotivationIn precision oncology, clinicians are aiming to find the best treatment for any patient based on their molecular characterization. A major bottleneck is the annotation and evaluation of individual variants, for which usually a range of knowledge bases are manually screened. To incorporate and integrate the vast information of different databases, fast and accurate methods for harmonization are necessary. Summarypreon is a fast and accurate library for the normalization of drug names and cancer types in large-scale data integration. Availability and Implementationpreon is implemented in Python and freely available via the PyPI repository. Source code and gold standard data sets are available at https://github.com/ermshaua/preon/. Contactmanuela.benary@bih-charite.de Supplementary informationSupplementary data are available online.