Cited By
View all- Youn JLi FSimmons GKim STagkopoulos I(2024)FoodAtlasComputers in Biology and Medicine10.1016/j.compbiomed.2024.109072181:COnline publication date: 21-Nov-2024
Applying BioBERT to Extract Germline Gene-Disease Associations for Building a Knowledge Graph from the Biomedical Literature
Pages 37 - 42
Abstract
Published biomedical information has and continues to rapidly increase. The recent advancements in Natural Language Processing (NLP), have generated considerable interest in automating the extraction, normalization, and representation of biomedical knowledge about entities such as genes and diseases. Our study analyzes germline abstracts in the construction of knowledge graphs of the immense work that has been done in this area for genes and diseases. This paper presents SimpleGermKG, an automatic knowledge graph construction approach that connects germline genes and diseases. For the extraction of genes and diseases, we employ BioBERT, a pre-trained BERT model on biomedical corpora. We propose an ontology-based and rule-based algorithm to standardize and disambiguate medical terms. For semantic relationships between articles, genes, and diseases, we implemented a part-whole relation approach to connect each entity with its data source and visualize them in a graph-based knowledge representation. Lastly, we discuss the knowledge graph applications, limitations, and challenges to inspire the future research of germline corpora. Our knowledge graph contains 297 genes, 130 diseases, and 46,747 triples. Graph-based visualizations are used to show the results.
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Index Terms
- Applying BioBERT to Extract Germline Gene-Disease Associations for Building a Knowledge Graph from the Biomedical Literature
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May 2023
109 pages
ISBN:9798400700637
DOI:10.1145/3603765
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Published: 17 October 2023
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ICISDM 2023: 2023 the 7th International Conference on Information System and Data Mining
May 10 - 12, 2023
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View all- Youn JLi FSimmons GKim STagkopoulos I(2024)FoodAtlasComputers in Biology and Medicine10.1016/j.compbiomed.2024.109072181:COnline publication date: 21-Nov-2024
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