Filters








5 Hits in 1.2 sec

TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes

2019 Nucleic Acids Research  
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.  ...  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.  ...  ACKNOWLEDGEMENTS We thank Natascha Menezes Bergo for testing the Terres-trialMetagenomeDB web application and Rodolfo Brizola Toscan for creating the script to download the sequencing data.  ... 
doi:10.1093/nar/gkz994 pmid:31728526 pmcid:PMC7145636 fatcat:lb642kyrsjcwpmqsir3nwanldq

TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes [article]

Felipe Borim Corrêa, Joao Pedro Saraiva, Peter F. Stadler, Ulisses Nunes da Rocha
2019 bioRxiv   pre-print
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.  ...  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.  ...  The other 12 terrestrial categories defined in this work appeared in a lower frequency. 10%), and all the others were available in less than 5% of the metagenomes metadata.  ... 
doi:10.1101/796441 fatcat:ba7yokvegfgnnmyxf5i5hgfzc4

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

Jonas Coelho Kasmanas, Alexander Bartholomäus, Felipe Borim Corrêa, Tamara Tal, Nico Jehmlich, Gunda Herberth, Martin von Bergen, Peter F Stadler, André Carlos Ponce de Leon Ferreira de Carvalho, Ulisses Nunes da Rocha
2020 Nucleic Acids Research  
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.  ...  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 are grateful to Sandra Cristina Godinho Pires da Silva for the valuable insights during the metadata collection. We have gratitude to Camila Lima Zanini for her view on the development  ... 
doi:10.1093/nar/gkaa1031 pmid:33221926 fatcat:fifchpf4wvek3gle54egzwsaxi

Planet Microbe: a platform for marine microbiology to discover and analyze interconnected 'omics and environmental data

Alise J Ponsero, Matthew Bomhoff, Kai Blumberg, Ken Youens-Clark, Nina M Herz, Elisha M Wood-Charlson, Edward F Delong, Bonnie L Hurwitz
2020 Nucleic Acids Research  
This work highlights the need for curated aggregation efforts that can enable new insights into high-quality metagenomic datasets.  ...  In recent years, large-scale oceanic sequencing efforts have provided a deeper understanding of marine microbial communities and their dynamics.  ...  ACKNOWLEDGEMENTS We thank the members of the Hurwitz Lab for comments on the Planet Microbe interface and feedback on the manuscript.  ... 
doi:10.1093/nar/gkaa637 pmid:32735679 fatcat:tq5xr4bzmnhvlorrsuh3n43qpa

Planet Microbe: a platform for marine microbiology to discover and analyze interconnected 'omics and environmental data [article]

Alise J. Ponsero, Matthew Bomhoff, Kai Blumberg, Ken Youens-Clark, Nina M. Herz, Elisha M. Wood-Charlson, Edward F. Delong, Bonnie L. Hurwitz, UNESCO/IOC
2020
This work highlights the need for curated aggregation efforts that can enable new insights into high-quality metagenomic datasets.  ...  In recent years, large-scale oceanic sequencing efforts have provided a deeper understanding of marine microbial communities and their dynamics.  ...  ACKNOWLEDGEMENTS We thank the members of the Hurwitz Lab for comments on the Planet Microbe interface and feedback on the manuscript.  ... 
doi:10.25607/obp-961 fatcat:ljd4pf5yergwrfby2dy5gfaewa