Authors
Nguyen, T. T. D., Nguyen-Phuong, T., Nguyen, Q.-H., Abbasi, A. M., Le Phan, H.-D., Nguyen, L. B.-A., Phan, N.-T., Curabaz, N. N., Hauser, A. S., Tanoli, Z., Nguyen, D. T., Kooistra, A. J.
Abstract
Biomedical knowledge evolves rapidly, yet most disease-centered knowledge graphs remain unchanged after publication. We present PrimeKG-Plus, an extension of PrimeKG that updates all 20 original data resources to releases available as of Dec 2025 and incorporates additional resources, including OpenTargets, RepurposeDrugs, and nSIDES. The graph is further expanded with relations extracted from 637 PubMed abstracts and PMC full-text articles using a large-language-model-assisted curation workflow. Extracted relations were refined through normalization, UMLS-based synonym mapping, SapBERT embedding based similarity ranking, and human expert review to ensure data quality. This literature-driven expansion focuses on rare neurological disorders, including Canavan disease, Niemann-Pick disease type C, Tay-Sachs disease and Batten disease. Network topology analyses indicate that the expanded graph improves indirect drug-disease connectivity of 3-6 hops through the graph while adding 447,288 Drug-Protein-Disease paths linking drug-disease pairs that were previously unreachable. Temporal FDA validation captured 55 new molecular entities after the June 2021 PrimeKG data cut-off as drug nodes, 46 absent from the original PrimeKG. By integrating newly incorporated and updated resources with systematically curated literature-derived associations, PrimeKG-Plus provides an up-to-date knowledge graph for network-based drug repurposing and precision medicine applications. Data and code are publicly available.
Preprint server:
bioRxiv
The authors list and abstract were imported from bioRxiv on 20 Jul 2026.
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