Focuses of the National Microbiome Data Collaborative

Authors

Alicia Clum¹* (aclum@lbl.gov), Anastasiya Prymolenna², Antonio Camargo¹, Bin Hu², Cameron Giberson², Chien-Chi Lo³, Chris Mungall¹, Donny Winston⁵, Elais Player Jackson³, Francie Rodriguez³, Grant Fujimoto², Ingrid Ockert¹, Jeff Baumes⁴, Julia Kelliher³, Kjiersten Fagnan¹, Lee Ann McCue², Marcel Huntemann¹, Mark Flynn³, Mark Miller¹, Michal Babinski³, Migun Shakya³, Mike Nagler⁴, Montana Smith², Patrick Chain³, Patrick Kalita¹, Paul Piehowski², Po-E (Paul) Li³, Samuel Purvine², Set Sarrafan¹, Shane Canon¹, Shreyas Cholia¹, Simon Roux¹, Sujay Patil¹, Yan Xu³, Yuri Corilo², Emiley Eloe-Fadrosh¹

Institutions

¹Lawrence Berkeley National Laboratory, Berkeley, California; ²Pacific Northwest National Laboratory, Richland, Washington; ³Los Alamos National Laboratory, Los Alamos, New Mexico; ⁴Kitware Inc., Clifton Park, NY; ⁵Polyneme LLC, New York, NY

URLs

• https://microbiomedata.org/

Abstract

The National Microbiome Data Collaborative (NMDC) is committed to providing findable, accessible, interoperable, and reusable (FAIR) multiomics microbiome data. This is accomplished through the three key NMDC products that are openly available to the research community: the submission portal (https://data.microbiomedata.org/submission/home), the data portal (https://data.microbiomedata.org/; Eloe-Fadrosh et al. 2022), and NMDC EDGE (https://nmdc-edge.org/home). 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 NMDC’s standardized bioinformatics workflows. NMDC EDGE is a user-friendly interface for 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 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 Multiomics Microbiome Data Resource,” Nucleic Acids Research 50(D1), D828–D836. DOI:10.1093/nar/gkab990.

Funding Information

This work is supported by the DOE Office of Science, through the Genomic Science Program in BER. The national laboratory partners are operated under contract numbers DE- AC02-05CH11231 (LBNL), 89233218CNA000001 (LANL), and DE-AC05-76RL01830 (PNNL).