THE LINKS IN THIS PAGE TO ALL THE CURRENT CHECKLIST VERSIONS NEEDS TO BE MADE FUTRUE PROOF- i.e. links to relevant github repo locations

MIxS

The GSC family of minimum information standards (checklists) – Minimum Information about any (x) Sequence (MIxS)

MIxS currently consists of three separate checklists; MIGS for genomes, MIMS for metagenomes, and MIMARKS for marker genes.

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 (publication in Nature Biotechnology). 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.

The three checklists that are currently under MIxS share the same central set of core descriptors, but have checklist specific descriptors as well. Additionally, they enable a detailed description of environment through the use of optional environmental packages.

Download MIxS Checklist v5.0: mixs_v5

or from the MIxS GitHub here

Download MIxS Checklist v4.0 here

Environmental packages

The core MIxS team developed the following environmental packages These packages are available as separate spreadsheets:

Air (download MIxS-air only)
Built-environment (download MIxS-built environment only)
Host-associated (download MIxS-host associated only)
Human-associated (download MIxS-human associated only)
Human-gut (download MIxS-human gut only)
Human-oral (download MIxS-human oral only)
Human-skin (download MIxS-human skin only)
Human-vaginal (download MIxS-human vaginal only)
Microbial mat/biofilm (download MIxS-microbial mat/biofilm only)
Miscellaneous natural or artificial environment (download MIxS-misc. natural or artificial environment only)
Plant-associated (download MIxS-plant associated only)
Sediment (download MIxS-sediment only)
Soil (download MIxS-soil only)
Wastewater/sludge (download MIxS-wastewater/sludge only)
Water (download MIxS-water only)
Hydrocarbon resources-cores (download from GitHub)
Hydrocarbon resources-fluids/swabs (download from GitHub)

Newly Published MIxS Packages:

18. Minimum Information About a Single Amplified Genome (MISAG) (download from GitHub)

19. Minimum Information About a Metagenome-Assembled Genome (MIMAG) (download from GitHub)

20. Minimum Information About an Uncultivated Virus Genome (MIUViG) (download from GitHub)

In-Progress MIxS Standards

21. Parasite Microbiome MIxS (MIxS-PMP)

22. Agricultural Microbiome MIxS (MIxS-Ag)

The environmental packages are certainly not limited to these initial 14, and new packages as requested by the community will be added to this list. Further details about the extensions to the current MIxS checklist can be found here.

The entire checklist for all sequence types can be downloaded above, but please note that if you only need the spreadsheet for a survey of marker genes, or for a metagenome sequence, reduced spreadsheets are available via relevant project pages of MIGS/MIMS and MIMARKS.

The excel document is structured as below:

Sheet1 – README

Sheet2 – The “MIxS” checklist sheet

Column 1 – structured comment name: name of a checklist item as it will appear in GenBank structured comments

Column 2 – item: full name of item as it appears in the publication

Column 3 – definition: a description of the item, including links to ontologies and other resources that can be used to fill in values for the item

Column 4 – example: examples of values for an item

Column 5 – expected value: short description and/or expected value of an item

Column 6 – section: the section of an item

Columns 7,8,9,10,11,12,13,14-eu,ba,pl,vi,org,me,mimarks_survey,mimarks_specimen: information about whether an item is mandatory (M), conditional mandatory (C), optional (X), environment-dependent (E) or not applicable (-) for a given checklist type

Column 15 – value syntax: the proper syntax for writing the value for a given item

Column 16 – occurrence: indicates whether a given item can be used only once (1), multiple times (m), or none (0)

Column 17 – position: position of item as it appears in the publication

Column 18 – preferred units: a unit suggestion if a measurement value is given

Sheet3 – The “Environmental Packages” sheet

Column 1 – environmental package: name of package

Column 2 – structured comment name: name of a package item as it will appear in GenBank structured comments

Column 3 – package item: full name of an item

Column 4 – definition: definition of the item

Column 5 – requirement: certain package items are mandatory for some packages, for example ‘depth’ is mandatory when using packages water, sediment or soil

Column 6 – expected value: short description and/or expected value of an item

Column 7 – value syntax: the proper syntax for writing the value for a given item

Column 8 – occurrence: indicates whether a given item can be used only once (1), multiple times (m), or none (0)

Column 9 – position: position of item within a package as requested by the respective community/consortium that developed the package

Column 10 – preferred units: a unit suggestion if a measurement value is given

A few important notes:

All dates, times, durations and intervals should be written in ISO 8601 formats
Units – Strict units are not defined for items in the MIxS checklists, but suggestions are made under “preferred units”, wherever applicable the unit of choice should accompany the value of an item. The units should be in accordance with the The International System of Units (SI)
If a value is missing, please consider using the INSDC missing value vocabulary:
- Not applicable - information is inappropriate to report, can indicate that the standard itself fails to model or represent the information appropriately
- Not collected - information of an expected format was not given because it has not been collected
- Not provided - information of an expected format was not given, a value may be given at the later stage
- Restricted access - information exists but can not be released openly because of privacy concerns
- Missing - its unknown if the data was collected or not

If you require further information about MIxS checklists, please visit the compliance and implementation pages, and MIxS extensions pages.