Literature DB >> 32735679

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

Alise J Ponsero1,2, Matthew Bomhoff1,2, Kai Blumberg1,2, Ken Youens-Clark1,2, Nina M Herz1, Elisha M Wood-Charlson3, Edward F Delong4, Bonnie L Hurwitz1,2.   

Abstract

In recent years, large-scale oceanic sequencing efforts have provided a deeper understanding of marine microbial communities and their dynamics. These research endeavors require the acquisition of complex and varied datasets through large, interdisciplinary and collaborative efforts. However, no unifying framework currently exists for the marine science community to integrate sequencing data with physical, geological, and geochemical datasets. Planet Microbe is a web-based platform that enables data discovery from curated historical and on-going oceanographic sequencing efforts. In Planet Microbe, each 'omics sample is linked with other biological and physiochemical measurements collected for the same water samples or during the same sample collection event, to provide a broader environmental context. This work highlights the need for curated aggregation efforts that can enable new insights into high-quality metagenomic datasets. Planet Microbe is freely accessible from https://www.planetmicrobe.org/.
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

Entities:  

Year:  2020        PMID: 32735679     DOI: 10.1093/nar/gkaa637

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  5 in total

1.  The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes.

Authors:  Caroline Vernette; Julien Lecubin; Pablo Sánchez; Shinichi Sunagawa; Tom O Delmont; Silvia G Acinas; Eric Pelletier; Pascal Hingamp; Magali Lescot
Journal:  Nucleic Acids Res       Date:  2022-06-10       Impact factor: 19.160

2.  SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata.

Authors:  Giulia Agostinetto; Davide Bozzi; Danilo Porro; Maurizio Casiraghi; Massimo Labra; Antonia Bruno
Journal:  Database (Oxford)       Date:  2022-05-16       Impact factor: 4.462

3.  The 2021 Nucleic Acids Research database issue and the online molecular biology database collection.

Authors:  Daniel J Rigden; Xosé M Fernández
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

4.  A database of animal metagenomes.

Authors:  Ruirui Hu; Rui Yao; Lei Li; Yueren Xu; Bingbing Lei; Guohao Tang; Haowei Liang; Yunjiao Lei; Cunyuan Li; Xiaoyue Li; Kaiping Liu; Limin Wang; Yunfeng Zhang; Yue Wang; Yuying Cui; Jihong Dai; Wei Ni; Ping Zhou; Baohua Yu; Shengwei Hu
Journal:  Sci Data       Date:  2022-06-16       Impact factor: 8.501

5.  Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems.

Authors:  Kai L Blumberg; Alise J Ponsero; Matthew Bomhoff; Elisha M Wood-Charlson; Edward F DeLong; Bonnie L Hurwitz
Journal:  Front Microbiol       Date:  2021-12-08       Impact factor: 5.640

  5 in total

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