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Title: The National Microbiome Data Collaborative Data Portal: an integrated multi-omics microbiome data resource

Journal Article · · Nucleic Acids Research
DOI:https://doi.org/10.1093/nar/gkab990· OSTI ID:1843943
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  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Kitware, Clifton Park, NY (United States)
  3. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  4. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  5. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  6. Joint Genome Institute
  7. Polyneme LLC, New York, NY (United States)
+ Show Author Affiliations

The National Microbiome Data Collaborative (NMDC) Data Portal supports microbiome multi-omics data exploration and access through an integrated, distributed data framework aligned with the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. The NMDC Data Portal currently hosts 10.2 terabytes of multi-omics microbiome data, spanning five data types (metagenomes, metatranscriptomes, metaproteomes, metabolomes, and natural organic matter characterizations), generated at two Department of Energy User Facilities, the Joint Genome Institute (JGI) at Lawrence Berkeley National Laboratory (LBNL) and the Environmental Molecular Systems Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL). A flexible data schema leveraging community-driven standards underpins how data is managed and integrated. Annotated multi-omic data products are produced by the NMDC workflows and linked through common biosamples to enable search capabilities based on environmental context, instrumentation, and functional attributes. As a pilot system, the NMDC Data Portal offers download capabilities and several search components, including interactive geographic visualization of samples; environmental classification distribution visualized through an interactive Sankey diagram; time-series slider to select longitudinal samples of interest; and an upset plot displaying the number of multi-omics data generated from the same biosample within a study.

Research Organization:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Contributing Organization:
National Microbiome Data Collaborative
Grant/Contract Number:
AC05-76RL01830; AC02-05CH11231: 89233218CNA000001; AC05-00OR22725
OSTI ID:
1843943
Alternate ID(s):
OSTI ID: 1862112
Report Number(s):
PNNL-SA-165796
Journal Information:
Nucleic Acids Research, Vol. 50, Issue D1; ISSN 0305-1048
Publisher:
Oxford University PressCopyright Statement
Country of Publication:
United States
Language:
English

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Expression of DREB-Like Genes in Coffea canephora and C. arabica Subjected to Various Types of Abiotic Stress journal March 2019
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iDNA6mA-Rice: A Computational Tool for Detecting N6-Methyladenine Sites in Rice journal September 2019
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DeepMiR2GO: Inferring Functions of Human MicroRNAs Using a Deep Multi-Label Classification Model journal November 2019
Investigation of the Antifungal Activity and Mode of Action of Thymus vulgaris, Citrus limonum, Pelargonium graveolens, Cinnamomum cassia, Ocimum basilicum, and Eugenia caryophyllus Essential Oils journal May 2018
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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
microbiome
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microbial ecology
ontology