Checklists

Since release 5.0, the following checklists are under the MIxS umbrella:

MIGS: Minimum information about a genome sequence. see publication
MIMS: Minimum information about a metagenome sequence. see publication
MIMARKS: Minimum information about a marker gene sequence. see publication
MISAG: Minimum information about a single amplified genome sequence. see publication
MIMAG: Minimum information about a metagenome-assembled genome sequence. see publication
MIUViG: Minimum Information about an Uncultivated Virus Genome, see publication

MIGS and MIMARKS are further divided into additional subchecklists, based on the genome sequence in question, or the sequencing type.

MIGS-EU: MIGS for eukaryotic genome sequences
MIGS-BA: MIGS for bacterial and archaeal genome sequences
MIGS-PL: MIGS for plasmid sequences
MIGS-VI: MIGS for viral genome sequences
MIGS-ORG: MIGS for organelle sequences
MIMARKS-SP: MIMARKS-survey for marker gene sequences obtained directly from the environment
MIMARKS-SU: MIMARKS-specimen for marker gene sequences from cultured or voucher-identifiable specimens

Core and type-specific descriptors

All checklists share the same central set of core (Minimum) descriptors, which are:

Project name
Sample name
Taxonomy ID of DNA sample
Geographic location (latitude and longitude)
Geographic location (country and/or sea,region)
Collection date
Environment (biome, feature, and material)
Sequencing method

Each checklist is then defined by additional type-specific descriptors. These specific descriptors are summarized below for each checklist and subchecklist. Please note that this summary only includes minimum information for each sequence type, meaning that other conditional and optional descriptors are not included here.

MIGS-EU

isolation and growth condition
assembly quality
assembly software
number of contigs

MIGS-BA

number of replicons
reference for biomaterial
isolation and growth condition
assembly quality
assembly software
number of contigs

MIGS-PL

propagation
isolation and growth condition
assembly software

MIGS-VI

propagation
isolation and growth condition
assembly software

MIGS-ORG

isolation and growth condition
assembly software

MIMS

MIMARKS-S

target gene

MIMARKS-C

isolation and growth condition
target gene

MISAG

taxonomic identity marker
assembly quality
assembly software
completeness score
completeness software
contamination score
sorting technology
single cell lysis approach
WGA amplification approach

MIMAG

taxonomic identity marker
assembly quality
assembly software
completeness score
completeness software
contamination score
binning parameters
binning software

MIUViG

source of UViGs
virus enrichment approach

Environmental packages

The core MIxS team have developed a series environmental packages which expand on the basic set of mandatory terms to help flesh out metadata expectations for more specific environmental samples. These packages are described more on their individual pages.

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
Notes on using the ENVO terms in the MIxS context are provided here.

MIxS terms

Here we list all possible terms defined within the GSC MIxS checklists.

There are autogenerated read-the-docs pages for all Checklist and packages that can be found here.