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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. The minimal set of specific descriptors for each checklist and subchecklist are summarized below. Please note that this summary only includes the mandatory descriptors for each sequence type, meaning that other conditional and optional descriptors are not included here.

Click to show MIGS-EU (eukaryotes) mandatory terms.

* isolation and growth condition
* assembly quality
* assembly software
* number of contigs

Click to show MIGS-BA (bacteria) mandatory terms.

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

Click to show MIGS-PL (plasmids) mandatory terms.

* propagation
* isolation and growth condition
* assembly software

Click to show MIGS-VI (viruses) mandatory terms.

* propagation
* isolation and growth condition
* assembly software

Click to show MIGS-ORG (organelles) mandatory terms.

* isolation and growth condition
* assembly software

There are no MIMS specific mandatory terms.

Click to show MIMARKS-SP (specimen) mandatory terms.

* target gene

Click to show MIMARKS-C (survey) mandatory terms.

* isolation and growth condition
* target gene

Click to show MISAG mandatory terms.

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

Click to show MIMAG mandatory terms.

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

Click to show MIUVIG mandatory terms.

* source of UViGs
* virus enrichment approach

Extensions

See the extensions page for more details on available extensions.

MIxS descriptors (terms)

Here we list all possible descriptors defined within the GSC MIxS checklists and extensions.

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

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.