MetaboSERV——一个用于选择、交换和可视化代谢组学数据并具有可控数据访问权限的平台。

MetaboSERV-a platform for selecting, exchanging, and visualizing metabolomics data with controlled data access.

作者信息

Tucholski Tim, Maennel Angela, Njipouombe Nsangou Yacoub Abelard, Schuchardt Sven, Gruber Matthias, Kellermeier Fabian, Dettmer Katja, Oefner Peter J, Gronwald Wolfram, Altenbuchinger Michael, Dönitz Jürgen, Zacharias Helena U

机构信息

Department of Medical Bioinformatics, University Medical Center Göttingen, 37077 Göttingen, Germany.

Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Hannover Medical School, 30625 Hannover, Germany.

出版信息

Gigascience. 2025 Jan 6;14. doi: 10.1093/gigascience/giaf075.

DOI:10.1093/gigascience/giaf075

PMID:40748655

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12315529/

Abstract

BACKGROUND

The growing number of metabolomics studies, based on high-dimensional data measured by hyphenated mass spectrometry (MS) and/or nuclear magnetic resonance (NMR) spectroscopy, has sparked the creation of several public metabolomics data repositories. Each repository emphasizes different aspects regarding data selection and representation, but most offer only limited options for privacy-preserving data sharing.

RESULTS

We present MetaboSERV, an open-source, browser-based metabolomics platform dedicated to the selection, integration, and sharing of quantitative metabolomics data and metadata with controlled data access. MetaboSERV aims to aid researchers in analyzing their results by facilitating means to browse, visualize, and compare data across available datasets. It provides different access control functionalities, creating an environment in which data can be shared safely in a privacy-preserving manner to support collaborative and interdisciplinary research. Furthermore, it is designed to be extensible and adaptable to existing data management infrastructures through the creation of self-managed MetaboSERV instances, for which we provide the source code and a set of configurable Docker images.

CONCLUSIONS

The public MetaboSERV instance is available at https://metaboserv.ckdn.app, and the source code can be found at https://gitlab.gwdg.de/MedBioinf/metabolomics/metaboserv. The Research Resource Identifier (RRID) for MetaboSERV is SCR_025496.

摘要

背景

基于联用质谱（MS）和/或核磁共振（NMR）光谱测量的高维数据，代谢组学研究数量不断增加，催生了多个公共代谢组学数据存储库。每个存储库在数据选择和表示方面强调不同的方面，但大多数在隐私保护数据共享方面提供的选择有限。

结果

我们展示了MetaboSERV，这是一个基于浏览器的开源代谢组学平台，致力于定量代谢组学数据和元数据的选择、整合与共享，并具有可控的数据访问权限。MetaboSERV旨在通过促进跨可用数据集浏览、可视化和比较数据的方式，帮助研究人员分析其结果。它提供了不同的访问控制功能，营造了一个能够以隐私保护方式安全共享数据的环境，以支持协作和跨学科研究。此外，它的设计具有可扩展性，可通过创建自我管理的MetaboSERV实例来适应现有的数据管理基础设施，我们为此提供了源代码和一组可配置的Docker镜像。