Reducing the technical burden on publishing standardized metadata for microbiome studies

Authors

• M Quiñones
• D Liou
• C Shyu
• L Kim
• J Kehr
• N Weber
• D Hurt

Abstract

There is increasing interest in understanding the role of the microbiome in health outcomes. Studies across the world are each publishing sequencing datasets for hundreds of samples, presenting researchers with a great opportunity for integrating data to facilitate discovery. It is widely understood that the benefits of cross-study comparisons can only be realized if samples are annotated with sufficient metadata and controlled vocabularies, but researchers still find conventional annotation and metadata publishing processes very cumbersome. To overcome these challenges, our team – in collaboration with the NIAID Microbiome Project – has developed METAGENOTE, a system that offers: a) an excel-like web table for annotation of biological samples with integrated ontologies and anatomy diagrams for intuitive retrieval of vocabulary terms; and b) an engine for automation of metadata submission to NCBI's Sequence Read Archive (SRA) repository consisting of a 5-step wizard that greatly reduces the technical burden of publishing metadata with associated sequence files. METAGENOTE has adopted the standards created by the Genomics Standards Consortium, including the Minimal Information about a Marker Gene Sequence (MIMARKS), which is used to describe the “what, when, and how” of 16S rRNA gene survey data and its source. To meet the need for a streamlined process for study creation in NCBI repositories, METAGENOTE simplifies the annotation process and mediates batch transfer of sequencing files to SRA. The ultimate goal of this effort is to provide a powerful yet simple system that will encourage more researchers to share the detailed metadata needed for discovery through comparative analyses.

Scientific Focus Area: Microbiology and Infectious Diseases

This page was last updated on Friday, March 26, 2021