Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities

Abstract

Microbiome samples are inherently defined by the environment in which they are found. Therefore, data that provide context and enable interpretation of measurements produced from biological samples, often referred to as metadata, are critical. Important contributions have been made in the development of community-driven metadata standards; however, these standards have not been uniformly embraced by the microbiome research community. To understand how these standards are being adopted, or the barriers to adoption, across research domains, institutions, and funding agencies, the National Microbiome Data Collaborative (NMDC) hosted a workshop in October 2019. This report provides a summary of discussions that took place throughout the workshop, as well as outcomes of the working groups initiated at the workshop.

MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways

“…Finally, we also provide metadata about the mapping containing among others mapping time, used experimental data, and pathways. It fulfills the FAIR (findable, accessible, interoperable, and reusable) principles [24] and highlights the importance of emerging metadata standards [25]. Finally, we tested the performance of the 'Pathway-Calculator' by uploading experimental data with different file sizes (10,000 proteins, 100,000 proteins, and 1,000,000 proteins with 44 samples per test) and a different number of pathways on a local desktop computer (AMD Ryzen 5 3600, 16 GB DDR4 RAM 3000 MHz, Chrome Browser version 89.0.4389.90).…”

Integrating the human microbiome in the forensic toolkit: Current bottlenecks and future solutions

“…Finally, although not specific only to human microbiome research, another aspect that we would like to point out is the high variability in metadata between studies, especially when publicly available microbiome data are used in future forensic research. Currently available metadata is often misannotated, misleading and non-standardized, which makes sample reanalysis overly complex [128]. Importantly, metadata does not only refer to sample attributes, but also to sample preparation and processing [128].…”

SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata

“…It is The copyright holder for this preprint this version posted August 18, 2021. ; https://doi.org/10.1101/2021.08.17.456635 doi: bioRxiv preprint for example the "Minimum Information about any (x) Sequence" (MIxS) packages (71) or the incorporation of DOIs for datasets (72). Unfortunately, some work is still needed to establish standard procedures and a universal set of ontologies that are easily accessible by the entire community (45,73).…”

“…Inconsistency and uncontrolled metadata filling were demonstrated by Gonçalves and Musen (46), revealing the necessity of standardized metadata compilation (47). (23,45) to promote data discovery and reuse in the microbiome field, and allow for broader dissemination of knowledge and compliance for both humans and machines.…”

“…Inconsistency and uncontrolled metadata filling were demonstrated by Gonçalves and Musen (46), revealing the necessity of standardized metadata compilation (47). FAIR (Findable, Accessible, Interoperable, and Reusable) principles are supported within the National Microbiome Data Collaborative and FAIR Microbiome community (https://www.go-fair.org/implementation-networks/overview/fair-microbiome ) (23,45) to promote data discovery and reuse in the microbiome field, and allow for broader dissemination of knowledge and compliance for both humans and machines.…”