KSDKG: construction and application of knowledge graph for kidney stone disease based on biomedical literature and public databases.

Abstract

Kidney stone disease (KSD) is a common urological disorder with an increasing incidence worldwide. The extensive knowledge about KSD is dispersed across multiple databases, challenging the visualization and representation of its hierarchy and connections. This paper aims at constructing a disease-specific knowledge graph for KSD to enhance the effective utilization of knowledge by medical professionals and promote clinical research and discovery. Text parsing and semantic analysis were conducted on literature related to KSD from PubMed, with concept annotation based on biomedical ontology being utilized to generate semantic data in RDF format. Moreover, public databases were integrated to construct a large-scale knowledge graph for KSD. Additionally, case studies were carried out to demonstrate the practical utility of the developed knowledge graph. We proposed and implemented a Kidney Stone Disease Knowledge Graph (KSDKG), covering more than 90 million triples. This graph comprised semantic data extracted from 29,174 articles, integrating available data from UMLS, SNOMED CT, MeSH, DrugBank and Microbe-Disease Knowledge Graph. Through the application of three cases, we retrieved and discovered information on microbes, drugs and diseases associated with KSD. The results illustrated that the KSDKG can integrate diverse medical knowledge and provide new clinical insights for identifying the underlying mechanisms of KSD. The KSDKG efficiently utilizes knowledge graph to reveal hidden knowledge associations, facilitating semantic search and response. As a blueprint for developing disease-specific knowledge graphs, it offers valuable contributions to medical research.