BENNERD: A Neural Named Entity Linking System for COVID-19 Mohammad Golam Sohraby,∗, Khoa N. A. Duongy,∗, Makoto Miway, z , Goran Topic´y, Masami Ikeday, and Hiroya Takamuray yArtificial Intelligence Research Center (AIRC) National Institute of Advanced Industrial Science and Technology (AIST), Japan zToyota Technological Institute, Japan fsohrab.mohammad, khoa.duong,
[email protected], fikeda-masami,
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[email protected] Abstract in text mining system, Xuan et al.(2020b) created CORD-NER dataset with comprehensive NE an- We present a biomedical entity linking (EL) system BENNERD that detects named enti- notations. The annotations are based on distant ties in text and links them to the unified or weak supervision. The dataset includes 29,500 medical language system (UMLS) knowledge documents from the CORD-19 corpus. The CORD- base (KB) entries to facilitate the corona virus NER dataset gives a shed on NER, but they do not disease 2019 (COVID-19) research. BEN- address linking task which is important to address NERD mainly covers biomedical domain, es- COVID-19 research. For example, in the example pecially new entity types (e.g., coronavirus, vi- sentence in Figure1, the mention SARS-CoV-2 ral proteins, immune responses) by address- ing CORD-NER dataset. It includes several needs to be disambiguated. Since the term SARS- NLP tools to process biomedical texts includ- CoV-2 in this sentence refers to a virus, it should ing tokenization, flat and nested entity recog- be linked to an entry of a virus in the knowledge nition, and candidate generation and rank- base, not to an entry of ‘SARS-CoV-2 vaccination’, ing for EL that have been pre-trained using which corresponds to therapeutic or preventive pro- the CORD-NER corpus.