PT - JOURNAL ARTICLE AU - Ghadeer Mobasher AU - Lukrécia Mertová AU - Sucheta Ghosh AU - Olga Krebs AU - Bettina Heinlein AU - Wolfgang Müller TI - Combining dictionary- and rule-based approximate entity linking with tuned BioBERT AID - 10.1101/2021.11.09.467905 DP - 2021 Jan 01 TA - bioRxiv PG - 2021.11.09.467905 4099 - http://biorxiv.org/content/early/2021/11/11/2021.11.09.467905.short 4100 - http://biorxiv.org/content/early/2021/11/11/2021.11.09.467905.full AB - Chemical named entity recognition (NER) is a significant step for many downstream applications like entity linking for the chemical text-mining pipeline. However, the identification of chemical entities in a biomedical text is a challenging task due to the diverse morphology of chemical entities and the different types of chemical nomenclature. In this work, we describe our approach that was submitted for BioCreative version 7 challenge Track 2, focusing on the ‘Chemical Identification’ task for identifying chemical entities and entity linking, using MeSH. For this purpose, we have applied a two-stage approach as follows (a) usage of fine-tuned BioBERT for identification of chemical entities (b) semantic approximate search in MeSH and PubChem databases for entity linking. There was some friction between the two approaches, as our rule-based approach did not harmonise optimally with partially recognized words forwarded by the BERT component. For our future work, we aim to resolve the issue of the artefacts arising from BERT tokenizers and develop joint learning of chemical named entity recognition and entity linking using pre-trained transformer-based models and compare their performance with our preliminary approach. Next, we will improve the efficiency of our approximate search in reference databases during entity linking. This task is non-trivial as it entails determining similarity scores of large sets of trees with respect to a query tree. Ideally, this will enable flexible parametrization and rule selection for the entity linking search.Competing Interest StatementGhadeer Mobasher is part of the PoLiMeR-ITN (http://polimer-itn.eu/). Her project is supported by European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement PoLiMeR, No 81261. The work was supported by the Klaus Tschira Foundation, KTS.