Advancing microbiome research through standardized data and metadata collection: introducing the Microbiome Research Data Toolkit-Reference-Cited by-同舟云学术

Advancing microbiome research through standardized data and metadata collection: introducing the Microbiome Research Data Toolkit

Published:2024 Issue: Volume:2024 Page:
ISSN:1758-0463
Container-title:Database
language:en
Short-container-title:

Author:

Zass Lyndon¹,Mwapagha Lamech M²,Louis-Jacques Adetola F³,Allali Imane⁴,Mulindwa Julius⁵,Kiran Anmol⁶⁷,Hanachi Mariem⁸,Souiai Oussama⁸^ORCID,Mulder Nicola¹,Oduaran Ovokeraye H⁹^ORCID

Affiliation:

1. Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, University of Cape Town , Rondebosch, Cape Town 7701, South Africa

2. Department of Biology, Chemistry and Physics, Faculty of Health, Natural Resources and Applied Sciences, Namibia University of Science and Technology , Private Bag 13388, 13 Jackson Kaujeua Street, Windhoek, Namibia

3. Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, University of Florida , 1600 SW Archer Road, Gainesville, FL 32610, USA

4. Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat , Rabat, Morocco

5. Department of Biochemistry and Sports Sciences, College of Natural Sciences, Makerere University , P.O. Box 7062, Kampala, Uganda

6. Malawi-Liverpool-Wellcome Trust , P.O. Box 30096, Blantyre 3, Malawi

7. Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool CH64 7TE, UK

8. Laboratory of Bioinformatics, Biomathematics and Biostatistics (LR16IPT09), Institute Pasteur of Tunis, University Tunis El Manar , 13, Place Pasteur, B.P. 74, Tunis 1002, Tunisia

9. Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand , 9 Jubilee Road, Parktown 2193, Johannesburg, Johannesburg, South Africa

Abstract

Abstract Microbiome research has made significant gains with the evolution of sequencing technologies. Ensuring comparability between studies and enhancing the findability, accessibility, interoperability and reproducibility of microbiome data are crucial for maximizing the value of this growing body of research. Addressing the challenges of standardized metadata reporting, collection and curation, the Microbiome Working Group of the Human Hereditary and Health in Africa (H3Africa) consortium aimed to develop a comprehensive solution. In this paper, we present the Microbiome Research Data Toolkit, a versatile tool designed to standardize microbiome research metadata, facilitate MIxS-MIMS and PhenX reporting, standardize prospective collection of participant biological and lifestyle data, and retrospectively harmonize such data. This toolkit enables past, present and future microbiome research endeavors to collaborate effectively, fostering novel collaborations and accelerating knowledge discovery in the field. Database URL: https://doi.org/10.25375/uct.24218999.v2

Funder

National Institutes of Health

Publisher

Oxford University Press (OUP)

Link

https://academic.oup.com/database/article-pdf/doi/10.1093/database/baae062/58937573/baae062.pdf

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