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. 2024:2802:587-609.
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

Emiley A Eloe-Fadrosh  1 , Christopher J Mungall  2 , Mark Andrew Miller  2 , Montana Smith  3 , Sujay Sanjeev Patil  2 , Julia M Kelliher  4 , Leah Y D Johnson  4 , Francisca E Rodriguez  4 , Patrick S G Chain  4 , Bin Hu  4 , Michael B Thornton  2 , Lee Ann McCue  3 , Alice Carolyn McHardy  5 , Nomi L Harris  2 , T B K Reddy  6 , Supratim Mukherjee  6 , Christopher I Hunter  7 , Ramona Walls  8 , Lynn M Schriml  9
Affiliations

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

Emiley A Eloe-Fadrosh et al. Methods Mol Biol. 2024.

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.

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References

    1. Wilkinson MD, Dumontier M, Aalbersberg IJJ et al (2016) The FAIR guiding principles for scientific data management and stewardship. Sci Data 3:160018. https://doi.org/10.1038/sdata.2016.18 - DOI
    1. Field D, Amaral-Zettler L, Cochrane G et al (2011) The genomic standards consortium. PLoS Biol 9:e1001088. https://doi.org/10.1371/journal.pbio.1001088 - DOI
    1. Yilmaz P, Kottmann R, Field D et al (2011) Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol 29:415–420. https://doi.org/10.1038/nbt.1823 - DOI
    1. Buttigieg PL, Pafilis E, Lewis SE et al (2016) The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation. J Biomed Semant 7:57. https://doi.org/10.1186/s13326-016-0097-6 - DOI
    1. Mungall CJ, Torniai C, Gkoutos GV et al (2012) Uberon, an integrative multi-species anatomy ontology. Genome Biol 13:R5. https://doi.org/10.1186/gb-2012-13-1-r5 - DOI

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