CoxBase meets Wikibase: creating sustainability for genomic Q Fever data
Creators: name: Scharf, Vanessa
name: Andrea, Helbich
name: Förstner, Konrad U.
name: Frangoulidis, Dimitrios
Publisher: name: Zenodo
Year: 2025
Subjects: Linked Open Data, Knowledge Graph, Q Fever, Wikibase, CoxBase

description: What is CoxBase?

CoxBase is a specialized relational database dedicated to aggregating and organizing comprehensive pheno- and genotypic data on Coxiella burnetii, the bacteriumresponsible for Q fever [1]. Serving as a central resource for researchers studying Coxiella burnetii, CoxBase compiles genomic, proteomic, and transcriptomicinformation, along with data on virulence factors, host interactions, and antibiotic resistance. By integrating this information in a single, searchable platform, CoxBasestreamlines access to valuable data, enabling researchers to explore the bacterium’s molecular mechanisms, pathogenesis, and potential treatment targets moreefficiently. Designed to support and accelerate Coxiella burnetii research, CoxBase fosters collaboration and knowledge sharing, promoting deeper understanding andadvancements in combating Q fever. CoxBase can be found at https://coxbase.q-gaps.de.

Why using QFeverBase for CoxBase data?

Data from scientific research projects and publications often suffer from the fact that they are not easily accessible for further scientific research and applications at the end of the projects. Due to the enormous increase in scientific data worldwide, sustainable and barrier-free access to scientific data and information is one of the current and future key challenges for the scientific community. Using Wikibase as the backend for CoxBase offers significant advantages by transforming it into a collaborative,extendable, and interconnected platform. With Wikibase, researchers across institutions can collaboratively contribute, edit, and validate the Coxiella burnetii data, ensuring it stays comprehensive and up-to-date with the latest findings. Additionally, Wikibase’s RDF (Resource Description Framework) support allows CoxBase to be seamlessly connected with other RDF-based resources, such as public health databases, genomic repositories, and biological ontologies. This connectivity enables broader data integration and comparison, enhancing the context and relevance of CoxBase data. Unlike traditional relational databases, which rely on predefined schema and rigid table structures, graph databases excel at capturing complex, multidimensional relationships between entities, such as pathogen strains, host interactions, epidemiological data, and antimicrobial resistance profiles. Furthermore, with SPARQL query support, users can execute complex, flexible searches across interconnected datasets, making it easier to identify patterns, relationships, and insights across various data dimensions—streamlining research into Coxiella burnetii and advancing Q fever understanding. Data from QFeverBase has been integrated into the NFDI4Microbiota Knowledge Graph Query Service [2]. The integration further strengthens this knowledge network, ensuring that CoxBase contributes to a broader ecosystem of microbiological research.

What is Wikibase and Wikidata?

Wikibase and Wikidata are powerful, collaborative platforms that serve as essential tools for organizing, structuring, and sharing knowledge as linked open data. Wikidata, a centralized knowledge base, provides freely accessible, multilingual, and machine-readable data on a wide range of topics, from historical events to scientific concepts. Technically building upon MediaWiki, the same software underlying Wikipedia, Wikidata is powered by Wikibase, a flexible open-source extension that enables users and organizations to collaboratively build and manage structured data in a graph database. This data can then be easily integrated into other projects, like Wikipedia, or used to enhance data-driven research and applications. The created item “revision needed” helps the community to exchange information and ideas in a pinpointed fashion.

References

[1] Fasemore AM, Helbich A, Walter MC, Dandekar T, Vergnaud G, Förstner KU, Frangoulidis D, 2021. CoxBase: an Online Platform for Epidemiological Surveillance,Visualization, Analysis, and Typing of Coxiella burnetii Genomic Sequences. mSystems 6:e00403-21. https://doi.org/10.1128/mSystems.00403-21