TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes
TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes
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DOI：
10.1093/nar/gkz994
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发表时间：
2020-01-08
影响因子：
14.9
通讯作者：
da Rocha, Ulisses Nunes
中科院分区：
文献类型：
--
作者：
Correa, Felipe Borim;Saraiva, Joao Pedro;da Rocha, Ulisses Nunes
专注于微生物群落遗传潜力（宏基因组学）的微生物组研究成为微生物生态学的标准。 MG-RAST 和 Sequence Read Archive (SRA) 是两个主要的宏基因组存储库，包含超过 202 858 个公共可用的宏基因组，并且这个数字呈指数级增长。然而，由于数据的错误注释、误导性和分散性，挖掘数据库可能具有挑战性。 TerrescialMetagenomeDB 的主要目标是让科学家更容易找到感兴趣的陆地宏基因组，这些宏基因组可以与荟萃分析中的新数据集进行比较。我们将陆地宏基因组定义为不属于海洋环境的宏基因组。此外，我们使用文本挖掘来管理数据库，以分配潜在的描述性关键字，以更好地了解陆地宏基因组的环境方面，例如生物群落和材料。 TerrescialMetagenomeDB 1.0 版包含来自 SRA 和 MG-RAST 的 15 022 个陆地宏基因组。可下载的数据总计达 68 Tbp。总共 199 个陆地术语分为 14 类。这些宏基因组跨越 83 个国家、30 个生物群落和 7 个主要来源材料。
Microbiome studies focused on the genetic potential of microbial communities (metagenomics) became standard within microbial ecology. MG-RAST and the Sequence Read Archive (SRA), the two main metagenome repositories, contain over 202 858 public available metagenomes and this number has increased exponentially. However, mining databases can be challenging due to misannotated, misleading and decentralized data. The main goal of TerrestrialMetagenomeDB is to make it easier for scientists to find terrestrial metagenomes of interest that could be compared with novel datasets in meta-analyses. We defined terrestrial metagenomes as those that do not belong to marine environments. Further, we curated the database using text mining to assign potential descriptive keywords that better contextualize environmental aspects of terrestrial metagenomes, such as biomes and materials. TerrestrialMetagenomeDB release 1.0 includes 15 022 terrestrial metagenomes from SRA and MG-RAST. Together, the downloadable data amounts to 68 Tbp. In total, 199 terrestrial terms were divided into 14 categories. These metagenomes span 83 countries, 30 biomes and 7 main source materials.