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

Title:
PloverDB: a high-performance platform for serving biomedical knowledge graphs as standards-compliant web APIs.
Authors:
Glen AK; School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, United States., Deutsch EW; Institute for Systems Biology, Seattle, WA 98109, United States., Ramsey SA; School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, United States.; Department of Biomedical Sciences, Oregon State University, Corvallis, OR 97331, United States.
Source:
Bioinformatics (Oxford, England) [Bioinformatics] 2025 Jul 01; Vol. 41 (7).
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
Imprint Name(s):
Original Publication: Oxford : Oxford University Press, c1998-
MeSH Terms:
Software* , Internet* , Computational Biology*/methods , Computer Graphics* , Database Management Systems*, User-Computer Interface ; Databases, Factual
Comments:
Update of: bioRxiv. 2025 May 29:2025.03.09.642156. doi: 10.1101/2025.03.09.642156.. (PMID: 40161641)
References:
BMC Bioinformatics. 2022 Sep 29;23(1):400. (PMID: 36175836)
Bioinformatics. 2019 Dec 15;35(24):5382-5384. (PMID: 31410449)
Front Syst Biol. 2025 Aug 29;5:1544432. (PMID: 40951793)
Bioinformatics. 2023 Mar 1;39(3):. (PMID: 36752514)
Bioinformatics. 2023 Sep 2;39(9):. (PMID: 37707514)
Clin Transl Sci. 2022 Aug;15(8):1848-1855. (PMID: 36125173)
Bioinformatics. 2022 Mar 28;38(7):2077-2079. (PMID: 35020801)
Clin Transl Sci. 2022 Aug;15(8):1838-1847. (PMID: 35611543)
Grant Information:
OT2TR002520 United States TR NCATS NIH HHS; OT2 TR002520 United States TR NCATS NIH HHS; OT2 TR003428 United States TR NCATS NIH HHS; United States NH NIH HHS; OT2TR003428 United States TR NCATS NIH HHS
Entry Date(s):
Date Created: 20250628 Date Completed: 20250713 Latest Revision: 20250921
Update Code:
20250921
PubMed Central ID:
PMC12255876
DOI:
10.1093/bioinformatics/btaf380
PMID:
40580448
Database:
MEDLINE

Weitere Informationen

Summary: 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.
Availability and Implementation: 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.
(© The Author(s) 2025. Published by Oxford University Press.)