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Title (Primary) TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes
Author Borim CorrĂȘa, F.; Saraiva, J.P.; Stadler, P.F.; Nunes da Rocha, U.;
Journal Nucleic Acids Research
Year 2020
Department UMB;
Volume 48
Issue D1
Language englisch;
POF III (all) T41;
Supplements https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkz994#supplementary-data
Abstract 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. The TerrestrialMetagenomeDB is publicly available at https://webapp.ufz.de/tmdb.
ID 22777
Persistent UFZ Identifier https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=22777
Borim CorrĂȘa, F., Saraiva, J.P., Stadler, P.F., Nunes da Rocha, U. (2020):
TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes
Nucleic Acids Res. 48 (D1), D626 - D632