The National Microbiome Data Collaborative: A Community-Driven Data Infrastructure

Authors

Mark Andrew Miller¹* (MAM@lbl.gov), Michal Babinski¹, Patrick Chain¹, Mark Flynn¹, Bin Hu¹, Leah Johnson¹, Julia Kelliher¹, Kaitlyn Li¹, Po-E (Paul) Li¹, Chien-chi Lo¹, Francie Rodriguez¹, Migun Shakya¹, Yan Xu¹, Antonio Camargo², Shane Canon², Eric Cavanna², Shreyas Cholia², Alicia Clum², Emiley Eloe-Fadrosh², Kjiersten Fagnan², Patrick Kalita², Wendi Lynch², Nigel Mouncey², Sierra Moxon², Sujay Patil², Simon Roux², Setareh Sarrafan², Shalki Shrivastava², Michael Thornton², Yuri Corilo³, Kevin Fox³, Grant Fujimoto³, Cameron Giberson³, Katherine Heal³, Douglas Mans³, Lee Ann McCue³, Bea Meluch³, Paul Piehowski³, Camilo Posso³, Anastasiya Prymolenna³, Sam Purvine³, Montana Smith³, James Tessmer³, Brynn Zalmanek³, Jeff Baumes⁴, Mike Nagler⁴, Mary Salvi⁴, Jing Cao⁵, Donny Winston⁵, Chris Mungall²

Institutions

¹Los Alamos National Laboratory, Los Alamos, NM; ²Lawrence Berkeley National Laboratory, Berkeley, CA; ³Pacific Northwest National Laboratory, Richland, WA; ⁴Kitware Inc, NY; ⁵Polyneme LLC, NY

URLs

https://microbiomedata.org/

Abstract

Microbes play a key role in many environmental processes. Microbiome data is multi-faceted, encompassing molecular/omics data (sequence, metabolic, proteomic, natural organic matter) as well as biogeochemical. Organizing and integrating this data presents many technological and organizational challenges. The DOE National Microbiome Data Collaborative (NMDC) was created to tackle interdisciplinary environmental microbiome science by connecting data, people, and ideas.

The NMDC provides three core products for microbiome scientists: A user-friendly web interface for submitting data and metadata about collected samples, a platform for analyzing sample omics data, and a web portal that allows members of the community to explore and collate datasets, using either a web interface or Application Programming Interfaces (APIs).

NMDC is committed to the “FAIR” principles to make data Findable, Accessible, Interoperable, and Reusable. Each piece of information in the NMDC database, from the source sample through to processed data objects, is assigned a unique, persistent, resolvable identifier. Sample metadata follows the Genomic Standards Consortium standards, and terms from the Environment Ontology (ENVO) are used to annotate sample environments. The unified data model weaves together these standards, organized around core concepts (e.g., studies, samples, analytes, computational workflows, data objects, gene functions), as well as different properties (e.g., soil moisture content, pH, metabolite concentration, etc.). Researchers are developing a Field Notes mobile application that allows for real-time sample collection.

The NMDC has a number of partnerships with other organizations. An example is the partnership with the NSF National Ecological Observatory Network (NEON) to provide access to paired metagenome and environmental data. Using NMDC APIs it is possible to explore relationships between metagenome features such as taxonomic community and NEON environmental variables, or to combine with other datasets to perform larger meta-analyses.

Together, the NMDC is advancing how scientists create, use, and reuse microbiome data.