The National Microbiome Data Collaborative (NMDC) is a new US-based pilot initiative launched in June 2019 to support microbiome data exploration and discovery through a collaborative, integrative data science ecosystem. The primary goal is to democratize microbiome data science by providing access to multi-omics microbiome data to support reproducible, cross-study analyses aligned with the FAIR data principles. To demonstrate the utility of linking across multi-omics microbiome data, the NMDC team has initially focused on projects funded through the Facilities Integrating Collaborations for User Science (FICUS) Program, a partnership between two DOE User Facilities, the JGI at LBNL and EMSL at PNNL. These projects span diverse terrestrial and aquatic environments, and address questions related to microbially-mediated carbon transformations, biogeochemical cycling, and plant-microbiome interactions. Currently, metagenome and metatranscriptome data are made available through maintained resources at the JGI, including the JGI Genome Portal, the Genomes OnLine Database (GOLD), and the Integrated Microbial Genomes and Microbiomes (IMG/M). Metaproteome, metabolome and natural organic characterization data generated at EMSL are made available through the MyEMSL/NEXUS system. While the primary research teams are aware of data generated for their own projects across these two User Facilities, challenges exist for the broader research community to search associated data and link complementary data derived from the same biosample or project. Further, publications resulting from data generated at the JGI and EMSL reference a suite of repositories (e.g., PRIDE, MetaboLights, INSDC) where data is dispersed across resources that renders meta-analyses difficult for multi-omics data.
About our documentation
Our documentation is based on the Diátaxis framework.