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

Autor(es)

Kasmanas, Jonas Coelho ^{[1, 2, 3]} ; Bartholomaeus, Alexander ^[4] ; Correa, Felipe Borim ^{[2, 3]} ; Tal, Tamara ^[5] ; Jehmlich, Nico ^[6] ; Herberth, Gunda ^[7] ; von Bergen, Martin ^{[6, 8]} ; Stadler, Peter F. ^[3] ; de Leon Ferreira de Carvalho, Andre Carlos Ponce ^[1] ; da Rocha, Ulisses Nunes ^[2]

Afiliação do(s) autor(es)

^[1] Univ Sao Paulo, Inst Math & Comp Sci, Sao Carlos - Brazil

^[2] Helmholtz Ctr Environm Res UFZ GmbH, Dept Environm Microbiol, D-04318 Leipzig, Saxony - Germany

^[3] Univ Leipzig, Dept Comp Sci & Interdisciplinary Ctr Bioinformat, D-04107 Leipzig, Saxony - Germany

^[4] GFZ German Res Ctr Geosci, Sect Geomicrobiol 3 7, D-14473 Potsdam - Germany

^[5] Helmholtz Ctr Environm Res UFZ GmbH, Dept Bioanalyt Ecotoxicol, D-04318 Leipzig, Saxony - Germany

^[6] Helmholtz Ctr Environm Res UFZ GmbH, Dept Mol Syst Biol, D-04318 Leipzig, Saxony - Germany

^[7] Helmholtz Ctr Environm Res UFZ GmbH, Dept Environm Immunol, D-04318 Leipzig, Saxony - Germany

^[8] Univ Leipzig, Fac Life Sci, Inst Biochem, D-04107 Leipzig, Saxony - Germany

• Tipo de documento: Artigo Científico
• Fonte: Nucleic Acids Research; v. 49, n. D1, p. D743-D750, JAN 8 2021.
• Citações Web of Science: 1

Resumo

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. Human-MetagenomeDB 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. (AU)

• Processo FAPESP: 13/07375-0 - CeMEAI - Centro de Ciências Matemáticas Aplicadas à Indústria
• Beneficiário: Francisco Louzada Neto
• Modalidade de apoio: Auxílio à Pesquisa - Centros de Pesquisa, Inovação e Difusão - CEPIDs
• Processo FAPESP: 19/03396-9 - Análise e classificação de microbiomas humanos: detecção de bioindicadores e otimização por meio de aprendizado de máquina
• Beneficiário: Jonas Coelho Kasmanas
• Modalidade de apoio: Bolsas no Brasil - Doutorado Direto