Web Interface of NER and RE with BERT for Biomedical Text Mining

Abstract

The BioBERT Named Entity Recognition (NER) model is a high-performance model designed to identify both known and unknown entities. It surpasses previous NER models utilized by text-mining tools, such as tmTool and ezTag, in effectively discovering novel entities. In previous studies, the Biomedical Entity Recognition and Multi-Type Normalization Tool (BERN) employed this model to identify words that represent specific names, discern the type of the word, and implement it on a web page to offer NER service. However, we aimed to offer a web service that includes Relation Extraction (RE), a task determining the relation between entity pairs within a sentence. First, just like BERN, we fine-tuned the BioBERT NER model within the biomedical domain to recognize new entities. We identified two categories: diseases and genes/proteins. Additionally, we fine-tuned the BioBERT RE model to determine the presence or absence of a relation between the identified gene–disease entity pairs. The NER and RE results are displayed on a web page using the Django web framework. NER results are presented in distinct colors, and RE results are visualized as graphs in NetworkX and Cytoscape, allowing users to interact with the graphs.