PloverDB: a high-performance platform for serving biomedical knowledge graphs as standards-compliant web APIs.

Abstract

Knowledge graphs are increasingly being used to integrate heterogeneous biomedical knowledge and data. General-purpose graph database management systems such as Neo4j are often used to host and search knowledge graphs, but such tools come with overhead and leave biomedical-specific standards compliance and reasoning to the user. Interoperability across biomedical knowledge bases and reasoning systems necessitates the use of standards such as those adopted by the Biomedical Data Translator consortium. We present PloverDB, a comprehensive software platform for hosting and efficiently serving biomedical knowledge graphs as standards-compliant web application programming interfaces. In addition to fundamental back-end knowledge reasoning tasks, PloverDB automatically handles entity resolution, exposure of standardized metadata and test data, and multiplexing of knowledge graphs, all in a single platform designed specifically for efficient query answering and ease of deployment. PloverDB increases data accessibility and utility by allowing data providers to quickly serve their biomedical knowledge graphs as standards-compliant web services. PloverDB's source code and technical documentation are publicly available under an MIT License at github:RTXteam/PloverDB, archived on Zenodo at doi:10.5281/zenodo.15454600.