Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

By Pelin Yilmaz, R. Kottmann, Dawn Field, Rob Knight, James R. Cole, L. Amaral-Zettler, Jack A. Gilbert, Ilene Karsch-Mizrachi, Anjanette Johnston, Guy Cochrane and 88 more. Nature Biotechnology, 2011

745 citations recorded by the source corpus.

Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmental packages' apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9100ab1ecd945852d5abac75becc92dc71ededd6

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Citations in the corpus

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification (2014, methodology): “The Genomic Standards Consortium (GSC) mandates the Minimum Information about any (x) Sequence (MIxS) specifications to be used when making sequence data available in public repositories (11,12).”
Metagenomics - a guide from sampling to data analysis (2012, methodology): “MIxS is an umbrella term to describe MIGS (the Minimum Information about a Genome Sequence), MIMS (the Minimum Information about a Metagenome Sequence) and MIMARKS (Minimum Information about a MARKer Sequence)[87] and contains standard formats for recording environmental and experimental data.”
The environment ontology: contextualising biological and biomedical entities (2013, methodology): “The omics community has been an early-adopter of ENVO, which is a recommended ontology in the core component of the Minimal Information about any (x) Sequence (MIxS) specification [39], a project of the Genomic Standards Consortium (GSC; [40]).”
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome (2012, background): “A standard file format for representing sample by observation contingency tables could compliment these existing standards by providing a means for associating MIxS-compliant metadata provided in ISA-TAB format with samples and observations.”
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata (2011, positive): “These include the implementation of GOLD-‐ specific Controlled Vocabularies (CVs) for the representation of the associated data, in coordination with the Genomics Standards Consortium (GSC) (8) complying wit”
The MG-RAST metagenomics database and portal in 2015 (2015, methodology): “In addition, MG-RAST maintains provenance data: both metadata compliant with Genomics Standards Consortium standards (4) and user-extendible metadata.”