HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes.
HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes.
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DOI：
10.1093/nar/gkaa1031
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发表时间：
2021-01-08
影响因子：
14.9
通讯作者：
Nunes da Rocha U
中科院分区：
文献类型：
--
作者：
Kasmanas JC;Bartholomäus A;Corrêa FB;Tal T;Jehmlich N;Herberth G;von Bergen M;Stadler PF;Carvalho ACPLF;Nunes da Rocha U
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。目前，公共存储库中的元基因组数量呈指数级增长。序列读取档案库(SRA)和MG-RAST是两个主要的元基因组数据存储库。这些数据库允许科学家重新分析样本并探索新的假设。然而，从这些存储库中挖掘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经常被错误注释、误导和分散，从而为样本重新分析创造了一个过于复杂的环境。HumanMetagenomeDB的主要目标是简化对感兴趣的公共人类元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。我们基于标准化的本体对203个属性进行了标准化，描述了宿主特征(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、经度和纬度)、采样地点(例如肠道、肺部和皮肤)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元基因组包括58个国家、9个主要样本部位(即身体部位)、58种诊断和多个年龄，从刚出生到91岁不等。HumanMetagenomeDB可在https://webapp.ufz.de/hmgdb/.上公开获得
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/.
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粪便宏基因组的荟萃分析揭示了针对大肠癌的全球微生物特征。
影响因子：
82.9
作者：
Wirbel J;Pyl PT;Kartal E;Zych K;Kashani A;Milanese A;Fleck JS;Voigt AY;Palleja A;Ponnudurai R;Sunagawa S;Coelho LP;Schrotz-King P;Vogtmann E;Habermann N;Niméus E;Thomas AM;Manghi P;Gandini S;Serrano D;Mizutani S;Shiroma H;Shiba S;Shibata T;Yachida S;Yamada T;Waldron L;Naccarati A;Segata N;Sinha R;Ulrich CM;Brenner H;Arumugam M;Bork P;Zeller G
通讯作者：
Zeller G
影响因子：
14.9
作者：
Kodama Y;Shumway M;Leinonen R;International Nucleotide Sequence Database Collaboration
通讯作者：
International Nucleotide Sequence Database Collaboration
影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
14.9
作者：
Harrison PW;Alako B;Amid C;Cerdeño-Tárraga A;Cleland I;Holt S;Hussein A;Jayathilaka S;Kay S;Keane T;Leinonen R;Liu X;Martínez-Villacorta J;Milano A;Pakseresht N;Rajan J;Reddy K;Richards E;Rosello M;Silvester N;Smirnov D;Toribio AL;Vijayaraja S;Cochrane G
通讯作者：
Cochrane G
影响因子：
14.9
作者：
Correa, Felipe Borim;Saraiva, Joao Pedro;da Rocha, Ulisses Nunes
通讯作者：
da Rocha, Ulisses Nunes