A Practical Approach to Using the Genomic Standards Consortium MIxS Reporting Standard for Comparative Genomics and Metagenomics

Emiley A Eloe-Fadrosh; Christopher J Mungall; Mark Andrew Miller; Montana Smith; Sujay Sanjeev Patil; Julia M Kelliher; Leah Y D Johnson; Francisca E Rodriguez; Patrick S G Chain; Bin Hu; Michael B Thornton; Lee Ann McCue; Alice Carolyn McHardy; Nomi L Harris; T B K Reddy; Supratim Mukherjee; Christopher I Hunter; Ramona Walls; Lynn M Schriml

doi:10.1007/978-1-0716-3838-5_20

A Practical Approach to Using the Genomic Standards Consortium MIxS Reporting Standard for Comparative Genomics and Metagenomics

Methods Mol Biol. 2024:2802:587-609. doi: 10.1007/978-1-0716-3838-5_20.

Authors

Emiley A Eloe-Fadrosh¹, Christopher J Mungall², Mark Andrew Miller², Montana Smith³, Sujay Sanjeev Patil², Julia M Kelliher⁴, Leah Y D Johnson⁴, Francisca E Rodriguez⁴, Patrick S G Chain⁴, Bin Hu⁴, Michael B Thornton², Lee Ann McCue³, Alice Carolyn McHardy⁵, Nomi L Harris², T B K Reddy⁶, Supratim Mukherjee⁶, Christopher I Hunter⁷, Ramona Walls⁸, Lynn M Schriml⁹

Affiliations

¹ Environmental Genomics and System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [email protected].
² Environmental Genomics and System Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
³ Pacific Northwest National Laboratory, Richland, WA, USA.
⁴ Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
⁵ Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.
⁶ DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
⁷ GigaScience Press, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong.
⁸ Critical Path Institute, Tucson, AZ, USA.
⁹ University of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA.

PMID: 38819573
DOI: 10.1007/978-1-0716-3838-5_20

Abstract

Comparative analysis of (meta)genomes necessitates aggregation, integration, and synthesis of well-annotated data using standards. The Genomic Standards Consortium (GSC) collaborates with the research community to develop and maintain the Minimum Information about any (x) Sequence (MIxS) reporting standard for genomic data. To facilitate the use of the GSC's MIxS reporting standard, we provide a description of the structure and terminology, how to navigate ontologies for required terms in MIxS, and demonstrate practical usage through a soil metagenome example.

Keywords: Genome; Metadata; Metagenome; Schema; Validation; Standards.

MeSH terms

Databases, Genetic
Genomics* / methods
Genomics* / standards
Metagenome* / genetics
Metagenomics* / methods
Metagenomics* / standards
Soil Microbiology