5. MIxS checklists - GenomicsStandardsConsortium/mixs GitHub Wiki

Checklists

As of release 5.0, the following checklists are under the MIxS umbrella:

  • MIGS: Minimum information about a genome sequence
  • MIMS: Minimum information about a metagenome sequence
  • MIMARKS: Minimum information about a marker gene sequence
  • MISAG: Minimum information about a single amplified genome sequence
  • MIMAG: Minimum information about a metagenome-assembled genome sequence

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 specific descriptors

The five checklists that are currently under MIxS share the same central set of core descriptors, which are:

  • investigation type
  • project name
  • 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, sequence type-specific descriptors. Users of MIxS should first determine the type of genome or marker gene sequence that they have, and then proceed to complement the core descriptors with the checklist specific mandatory descriptors to achieve MIxS compliant metadata. 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.

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

Legend (accessory elements)

Each descriptor in MIxS checklists is complemented by accessory information that assists in correct usage and parsing of a descriptor.

  1. structured comment name: short name of a checklist descriptor. Consists of small case letters and underscores, and no spaces, desirable length no more than 30 characters.

  2. item: full name of a checklist descriptor; should be short but also illustrative of the descriptor's purpose

  3. description: an extended definition of the descriptor; including links to ontologies and other resources that can be used to fill in values for the descriptor

  4. example: examples of values for a descriptor

  5. expected value: short definition and/or expected value of a descriptor; expressed in simple terms, such as boolean, date and time, measurement value, or ontology name where applicable

  6. section: indicates which section (should be one of: investigation, environment, mixs extension, nucleic acid sequence source, sequencing) a descriptor belongs to

  7. checklist requirement (EU,BA,PL,VI,ORG,MIMARKS-SU,MIMARKS-SP,MISAG,MIMAG): information about whether a descriptor is:

  • mandatory (M): descriptor must be present for compliance with the checklist_
  • conditional mandatory (C): descriptor must be present for compliance with the checklist, but only when applicable to the study, i.e. if this item is not applicable for the study the metadata data will still be checklist compliant even if it is left out
  • optional (X): descriptor may be present, not mandatory for compliance with checklist
  • environment-dependent (E): descriptor must be present depending on the environment the original sample was obtained from
  • not applicable (-): descriptor is not applicable for a given checklist type

  1. value syntax: a pseudo-code representation of the expected value of a given descriptor, for parsing purposes. if descriptor is of type enumeration, then the associated controlled vocabulary is also given here

  2. occurrence: indicates if a given descriptor may be used only once (1), multiple times (m), or none (0)

  3. position: position/pseudo-id of descriptor as it appears in ordered-lists of checklists descriptors

  4. preferred units: a unit suggestion if a descriptor is for a measurement value