1. Background - GenomicsStandardsConsortium/mixs GitHub Wiki
Without specific guidelines, most genomic, metagenomic and marker gene sequences in databases are sparsely annotated with the information required to guide data integration, comparative studies and knowledge generation. Even with complex keyword searches, it is currently impossible to reliably retrieve sequences that have originated from certain environments or particular locations on Earth—for example, all sequences from "soil" or "freshwater lakes" in a certain region of the world. Because public sequence repositories (INSDC, MG-RAST, GOLD...) depend on author-submitted information to enrich the value of sequence data sets, we argue that the only way to change the current practice is to establish a standard of reporting that requires contextual (meta)data to be deposited at the time of sequence submission. The adoption of such a standard would elevate the quality, accessibility and utility of information that can be collected from INSDC or any other data repository.
The GSC has defined a set of core descriptors for genomes and metagenomes in the form of MIGS/MIMS specification. MIGS/MIMS extends the minimum information already captured by the INSDC. More recently introduced MIMARKS captures information about marker genes. Additionally, we also introduced "environmental packages" that standardize sets of measurements and observations describing particular habitats that are applicable across all GSC checklists and beyond. We define ‘environment’ as any location in which a sample or organism is found, e.g., soil, air, water, human-associated, plant-associated or laboratory. The environmental packages are relevant to any sequence of known origin and are designed to be used in combination with MIGS, MIMS and MIMARKS checklists.
To create a single entry point to all minimum information checklists from the GSC and to the environmental packages, we created an overarching framework, the MIxS standard. MIxS includes the technology-specific checklists from the previous MIGS and MIMS standards, provides a way of introducing additional checklists such as MIMARKS, and also allows annotation of sample data using environmental packages.