Publication date: Oct 11, 2024

Target discovery is a crucial step in drug development, as it directly affects the success rate of clinical trials. Knowledge graphs (KGs) offer unique advantages in processing complex biological data and inferring new relationships. Existing biomedical KGs primarily focus on tasks such as drug repositioning and drug-target interactions, leaving a gap in the construction of KGs tailored for target discovery. We established a comprehensive biomedical KG focusing on target discovery, termed TarKG, by integrating seven existing biomedical KGs, nine public databases, and traditional Chinese medicine knowledge databases. TarKG consists of 1,143,313 entities and 32,806,467 relations across 15 entity categories and 171 relation types, all centered around three core entity types: Disease, Gene, Compound. TarKG provides specialized knowledges for the core entities including chemical structures, protein sequences or text descriptions. By using different KG embedding algorithms, we assessed the knowledge completion capabilities of TarKG, particularly for disease-target link prediction. In case studies, we further examined TarKG’s ability to predict potential protein targets for Alzheimer’s disease (AD) and to identify diseases potentially associated with the metallo-deubiquitinase CSN5, using literature analysis for validation. Furthermore, we provided a user-friendly web server (https://tarkg. ddtmlab. org) that enables users to perform knowledge retrieval and relation inference using TarKG. TarKG is accessible at https://tarkg. ddtmlab. org. Supplementary data are available at Bioinformatics online.

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