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Updated: May 17, 2025

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports

Published on: October 13, 2023

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

Amy K Glen¹, Eric W Deutsch², Stephen A Ramsey^1,3

¹School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon, USA.

Biorxiv : the Preprint Server for Biology

|March 31, 2025

Summary

This summary is machine-generated.

PloverDB offers a specialized platform for biomedical knowledge graphs, simplifying data integration and accessibility. It ensures standards compliance and efficient querying, enhancing data utility for researchers.

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Area of Science:

Biomedical Informatics
Data Science
Knowledge Representation

Background:

Knowledge graphs are vital for integrating diverse biomedical data.
General graph databases lack biomedical standards compliance and reasoning capabilities.
Interoperability requires adherence to standards like those from the Biomedical Data Translator consortium.

Purpose of the Study:

To present PloverDB, a software platform for hosting and serving biomedical knowledge graphs.
To provide standards-compliant web APIs for biomedical knowledge graphs.
To streamline data accessibility and utility for biomedical data providers.

Main Methods:

Developed PloverDB as a comprehensive software platform.
Integrated back-end knowledge reasoning, entity resolution, and metadata exposure.
Designed for efficient query answering and ease of deployment.
Ensured automatic handling of standardized metadata and test data.

Main Results:

PloverDB efficiently serves biomedical knowledge graphs as standards-compliant web APIs.
The platform automates entity resolution and metadata exposure.
It simplifies the deployment and multiplexing of knowledge graphs.
PloverDB enhances data accessibility and utility for data providers.

Conclusions:

PloverDB is a specialized platform that addresses the limitations of general-purpose graph databases for biomedical knowledge.
It facilitates standards compliance and efficient data serving through web APIs.
The platform empowers data providers to make their knowledge graphs more accessible and useful.