Portals of Discovery: The NMDC Infrastructure and Products for Microbiome Research
Authors:
Montana Smith1* (montana.smith@pnnl.gov), Alicia Clum3, Anastasiya Prymolenna1, Antonio Camargo3, Bin Hu2, Cameron Giberson1, Chien-chi Lo2, Chris Mungall3, Donny Winston5, Elais Player Jackson2, Francie Rodriguez2, Grant Fujimoto1, Ingrid Ockert3, Jeff Baumes4, Julia Kelliher2, Kjiersten Fagnan3, Lee Ann McCue1, Marcel Huntemann3, Mark Flynn2, Mark Miller3, Michal Babinski2, Migun Shakya2, Mike Nagler4, Patrick Chain2, Patrick Kalita3, Paul Piehowski1, Po-E (Paul) Li2, Samuel Purvine1, Set Sarrafan3, Shane Canon3, Shreyas Cholia3, Simon Roux3, Sujay Patil3, Yan Xu2, Yuri Corilo1, and Emiley Eloe-Fadrosh3
Institutions:
1Pacific Northwest National Laboratory; 2Los Alamos National Laboratory; 3Lawrence Berkeley National Laboratory; 4Kitware Inc, New York; and 5Polyneme LLC, New York
URLs:
Goals
The vision of the National Microbiome Data Collaborative (NMDC) is to connect data, people, and ideas to advance microbiome innovation and discovery. The team is committed to creating the needed infrastructure to answer tomorrow’s research questions. With this vision in mind, the NMDC seeks to support a Findable, Accessible, Interoperable, and Reusable (FAIR) microbiome data sharing network—through infrastructure, data standards, and community building—that addresses pressing challenges in environmental sciences. The infrastructure and portals that the NMDC has developed provide the research community with a platform to share their microbiome research and data in accordance with the FAIR principles, thereby promoting data reuse and accelerating scientific discoveries.
Abstract
The NMDC is committed to FAIR multiomics microbiome data. The NMDC infrastructure supports a collaborative, integrative science ecosystem that empowers the research community to contribute, explore and investigate microbiome data. This is accomplished through the three key NMDC products that are openly available to the research community: (1) the Submission Portal, (2) the Data Portal, and (3) NMDC EDGE. The NMDC Submission Portal provides users a place to contribute sample metadata in a standardized manner with in-sheet validation to ensure machine readability and findability. The Data Portal consumes this metadata and presents search tools to find and access information about the research studies and data generated from the samples. The Data Portal also provides links to the associated omics data processed through the NMDC’s standardized bioinformatics workflows. NMDC EDGE is an user-friendly interface for the NMDC standardized bioinformatics workflows. These three NMDC products are built specifically with the BER research community in mind and refined through a process of continual collaboration that is based on user-focused feedback. Leveraging each of the NMDC products enables environmental microbiome researchers to adhere to FAIR data principles, thus expanding potential research questions, comparisons, and scientific discovery.
References
Eloe-Fadrosh, E. A. et al. 2022. “The National Microbiome Data Collaborative Data Portal: An Integrated Multi-omics Microbiome Data Resource,” Nucleic Acids Res. 7(60), (D1):D828–D836. DOI:10.1093/nar/gkab990.
Wood-Charlson, E. M. et al. 2020. “The National Microbiome Data Collaborative: Enabling Microbiome Science,” Nat Rev Microbiol 18, 313–314. DOI:10.1038/s41579-020-0377-0.
Funding Information
This work is supported by the U.S. Department of Energy Office of Science, through the Genomic Science Program in the Office of Biological and Environmental Research (BER). The national laboratory partners are operated under contract numbers DE-AC02-05CH11231 (LBNL), 89233218CNA000001 (LANL), and DE-AC05-76RL01830 (PNNL).