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/.

中文翻译：

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HumanMetagenomeDB：人类元基因组的精选和标准化元数据的公共存储库

摘要

元基因组学成为理解包括人类微生物组在内的微生物群落功能潜力的标准策略。当前，公共存储库中的元基因组数量呈指数增长。序列读取档案（SRA）和MG-RAST是宏基因组数据的两个主要存储库。这些数据库使科学家可以重新分析样本并探索新的假设。但是，从这些样本中提取样本可能是一个限制因素，因为这些存储库中可用的元数据通常会被误解，误导和分散，从而为样本重新分析创建了一个过于复杂的环境。HumanMetagenomeDB的主要目标是简化目标人类公共基因组的识别和使用。HumanMetagenomeDB版本1.0包含69 822个元基因组的元数据。我们标准化了203个属性，基于标准化的本体论，描述宿主特征（例如性别，年龄和体重指数），诊断信息（例如癌症，克罗恩病和帕金森病），位置（例如国家/地区，经度和纬度），采样地点（例如肠道，肺和皮肤） ）和测序属性（例如测序平台，平均长度和序列质量）。此外，HumanMetagenomeDB版本1.0元基因组涵盖58个国家/地区，9个主要样本位点（即身体部位），58个诊断结果和多个年龄段，从出生到91岁。HumanMetagenomeDB可在https://webapp.ufz.de/hmgdb/上公开获得。G。肠，肺和皮肤）和测序属性（例如测序平台，平均长度和序列质量）。此外，HumanMetagenomeDB版本1.0元基因组涵盖58个国家/地区，9个主要样本位点（即身体部位），58个诊断结果和多个年龄段，从出生到91岁。HumanMetagenomeDB可在https://webapp.ufz.de/hmgdb/上公开获得。G。肠，肺和皮肤）和测序属性（例如测序平台，平均长度和序列质量）。此外，HumanMetagenomeDB版本1.0元基因组涵盖58个国家/地区，9个主要样本位点（即身体部位），58个诊断结果和多个年龄段，从出生到91岁。HumanMetagenomeDB可在https://webapp.ufz.de/hmgdb/上公开获得。