Supporting Continental Scale Research in the National Microbiome Data Collaborative Data Portal

Authors:

Alicia Clum¹* ([email protected]), Anastasiya Prymolenna², Antonio Camargo¹, Bea Meluch², Bin Hu³, Brynn Zalmanek²,
Cameron Giberson², Camilo Posso², Chien-Chi Lo³, Chris Mungall¹, Donny Winston⁵, Eric Cavanna¹, Francie Rodriguez³, Grant Fujimoto², James Tessmer², Jeff Baumes⁴, Jing Cao⁵, Julia Kelliher³, Kaitlyn Li³, Katherine Heal², Kaylee Kudish³, Kevin Fox², Kjiersten Fagnan¹, Leah Johnson³, Lee Ann McCue², Mark Flynn³, Mark Miller¹, Mary Salvi⁴, Michael Thornton¹, Michal Babinski³, Migun Shakya³, Mike Nagler⁴, Montana Smith², Patrick Chain³, Patrick Kalita¹, Paul Piehowski², Po-E (Paul) Li³, Samuel Purvine², Set Sarrafan¹, Shalki Shrivastava¹, Shane Canon¹, Shreyas Cholia¹, Sierra Moxon¹, Simon Roux¹, Sujay Patil¹, Wendi Lynch¹, Yan Xu³, Yuri Corilo², Emiley Eloe-Fadrosh¹ (PI)

Institutions:

¹Lawrence Berkeley National Laboratory; ²Pacific Northwest National Laboratory; ³Los Alamos National Laboratory; ⁴Kitware Inc; ⁵Polyneme LLC

Abstract

Continental scale research is important to understand global processes such as climate change and ecosystem dynamics and can be used to identify patterns and trends including spatial variations and temporal trends. The National Microbiome Data Collaborative (NMDC) Data Portal (Eloe-Fadrosh et al. 2022) has sample and processing information as well as standardized workflow results for several continental scale datasets of high value to the research community. To support a continental-scale understanding of terrestrial ecosystems, the NMDC hosts soil data from National Ecological Observatory Network (NEON) sites, Environmental Molecular Sciences Laboratory’s (EMSL) 1,000 Soils Research Campaign, and the Earth Microbiome Project 500 (EMP500). To enable continental- scale research of aquatic ecosystems, the NMDC hosts freshwater and benthic data from NEON sites and freshwater samples used to generate the Genome Resolved Open Watershed (GROW) database. These efforts all leverage standardized and documented sampling protocols, enabling comparisons of datasets across sites.

The Data Portal is focused on making multiomics datasets more findable to enable data reuse. It provides search tools to find information by principal investigator or study name, by sample information like geographic location, collection date, and depth, or by information about how the omics data was generated. Additionally, data can be searched by Kyoto Encyclopedia of Genes and Genomes (KEGG) terms to identify samples by molecular function. Once datasets have been identified, standardized workflow results can be downloaded in bulk via the website.

References

Eloe-Fadrosh, E. A., et al. 2022. “The National Microbiome Data Collaborative Data Portal: An Integrated Multi-Omics Microbiome Data Resource,” Nucleic Acids Research 50(D1), D828–36. DOI:10.1093/nar/gkab990.