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-SU: MIMARKS-survey for marker gene sequences obtained directly from the environment
MIMARKS-SP: 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-SU

target gene

MIMARKS-SP

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:

Date & Time

All dates, times, durations and intervals should be written in ISO 8601 formats

Units

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)

Missing value reporting

If a value is missing, please consider using the INSDC missing value vocabulary. This list of values is designed to give reasons for the missing value which can be very useful when interpreting the related data. The valid missing values are summarised below:

missing: control sample - Information is not applicable as the sample represents a negative control sample collected in a lab.
missing: sample group - Information is not applicable as the sample represents a group of samples that do not have a single origin. E.g. for co-assembly or transcriptome assembly.
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: synthetic construct - Information does not exist as the sample represents an ab-initio synthetic construct.
missing: lab stock - Information was not collected as the sample represents a cultured cell line or model organism under long-term lab control.
missing: third party data - Information does not exist as the metadata was not collected or reported in records predating the 2023 agreement. For use in Third Party data submissions.
missing: endangered species - Information can not be reported as the target organism is endangered e.g. on the IUCN red-list.
missing: human-identifiable - Information can not be reported as the metadata would make the sample human-identifiable.

If none of the above are appropriate, it may indicate that the standard is not the correct one to model or represent the information, consider using other checklist(s), or adjusting the template to remove terms that are not appropriate (be careful to not remove mandatory terms!).

ENVO term usage

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.