Sean T. Hayes

Armando D. Diaz Gonzalez, Kevin S. Hughes, Songhui Yue et al.

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 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.

Songhui Yue, Yang Shao, Sean Hayes

Query optimization has been studied using machine learning, reinforcement learning, and, more recently, graph-based convolutional networks. Ontology, as a structured, information-rich knowledge representation, can provide context, particularly in learning problems. This paper presents OntoTune, an ontology-based platform for enhancing learning for query optimization. By connecting SQL queries, database metadata, and statistics, the ontology developed in this research is promising in capturing relationships and important determinants of query performance. This research also develops a method to embed ontologies while preserving as much of the relationships and key information as possible, before feeding it into learning algorithms such as tree-based and graph-based convolutional networks. A case study shows how OntoTune's ontology-driven learning delivers performance gains compared with database system default query execution.