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Journal Article

HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes

Authors

Kasmanas,  Jonas Coelho
External Organizations;

/persons/resource/abartho

Bartholomäus,  Alexander
3.7 Geomicrobiology, 3.0 Geochemistry, Departments, GFZ Publication Database, Deutsches GeoForschungsZentrum;

Corrêa,  Felipe Borim
External Organizations;

Tal,  Tamara
External Organizations;

Jehmlich,  Nico
External Organizations;

Herberth,  Gunda
External Organizations;

von Bergen,  Martin
External Organizations;

Stadler,  Peter F
External Organizations;

de Carvalho,  André Carlos Ponce Leon Ferreira
External Organizations;

Nunes da Rocha,  Ulisses
External Organizations;

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Fulltext (public)

5005731.pdf
(Publisher version), 2MB

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There is no public supplementary material available
Citation

Kasmanas, J. C., Bartholomäus, A., Corrêa, F. B., Tal, T., Jehmlich, N., Herberth, G., von Bergen, M., Stadler, P. F., de Carvalho, A. C. P. L. F., Nunes da Rocha, U. (2021): HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes. - Nucleic Acids Research, 49, D1, D743-D750.
https://doi.org/10.1093/nar/gkaa1031


Cite as: https://gfzpublic.gfz-potsdam.de/pubman/item/item_5005731
Abstract
Metagenomics became a standard strategy to comprehend the functional potential of microbial communities, including the human microbiome. Currently, the number of metagenomes in public repositories is increasing exponentially. The Sequence Read Archive (SRA) and the MG-RAST are the two main repositories for metagenomic data. These databases allow scientists to reanalyze samples and explore new hypotheses. However, mining samples from them can be a limiting factor, since the metadata available in these repositories is often misannotated, misleading, and decentralized, creating an overly complex environment for sample reanalysis. The main goal of the HumanMetagenomeDB is to simplify the identification and use of public human metagenomes of interest. HumanMetagenomeDB version 1.0 contains metadata of 69 822 metagenomes. We standardized 203 attributes, based on standardized ontologies, describing host characteristics (e.g. sex, age and body mass index), diagnosis information (e.g. cancer, Crohn's disease and Parkinson), location (e.g. country, longitude and latitude), sampling site (e.g. gut, lung and skin) and sequencing attributes (e.g. sequencing platform, average length and sequence quality). Further, HumanMetagenomeDB version 1.0 metagenomes encompass 58 countries, 9 main sample sites (i.e. body parts), 58 diagnoses and multiple ages, ranging from just born to 91 years old. The HumanMetagenomeDB is publicly available at https://webapp.ufz.de/hmgdb/.