Enum: InsdcMissingValueEnum

Permissible values recommended by INSDC for reporting missing metadata values.

Permissible Values

Value	Description
not applicable	Information is inappropriate to report, can indicate that the standard itsel...
missing
not collected	Information of an expected format was not given because it has not been colle...
not provided	Information of an expected format was not given, a value may be given at the ...
restricted access	Information exists but can not be released openly because of privacy concerns
missing: control sample	Information is not applicable as the sample represents a negative control sam...
missing: sample group	Information is not applicable as the sample represents a group of samples tha...
missing: synthetic construct	Information does not exist as the sample represents an ab-initio synthetic co...
missing: lab stock	Information was not collected as the sample represents a cultured cell line o...
missing: third party data	Information does not exist as the metadata was not collected or reported in r...
missing: data agreement established pre-2023	Data agreements were established before the 2023 INSDC standard and metadata ...
missing: endangered species	Information can not be reported as the target organism is endangered e
missing: human-identifiable	Information can not be reported as the metadata would make the sample human-i...

Examples

Value
geographic location (country and/or sea): missing: data agreement-established pre-2023
collection date: missing: control sample
geographic location (country and/or sea): missing: human-identifiable

LinkML Source

name: InsdcMissingValueEnum
description: Permissible values recommended by INSDC for reporting missing metadata
  values.
comments:
- The International Nucleotide Database Collaboration (INSDC) have a standardised
  missing/null value reporting language to be used where a value of an expected format
  for sample metadata reporting can not be provided.
- The controlled vocabulary takes into account different type of constraints. Submitters
  are strongly encouraged to always provide true values. However, if missing/null
  value reporting is required, submitters are asked to use a term with the finest
  granularity for their situation. See the table below for accepted missing value
  reporting terms.
- Please use the above standardised missing value vocabulary only if a true value
  of an expected format for a mandatory field is missing. If a true value is missing
  for a recommended or an optional field, then these fields should not be used for
  reporting at all. When reporting a missing mandatory field, the eight granular 'reporting
  level' terms need to be preceded with the term "missing:" to declare both the absence
  of a true value as well as the reason.
examples:
- value: 'geographic location (country and/or sea): missing: data agreement-established
    pre-2023'
- value: 'collection date: missing: control sample'
- value: 'geographic location (country and/or sea): missing: human-identifiable'
from_schema: https://w3id.org/mixs
see_also:
- https://www.insdc.org/technical-specifications/missing-value-reporting/
permissible_values:
  not applicable:
    text: not applicable
    description: 'Information is inappropriate to report,  can indicate that the standard
      itself fails to model or represent the information appropriately

      '
    aliases:
    - n/a
    - na
  missing:
    text: missing
    aliases:
    - no data
    - not available
    - unavailable
    - unknown
    - unspecified
  not collected:
    text: not collected
    description: Information of an expected format was not given because it has not
      been collected
    aliases:
    - not determined
    - not recorded
  not provided:
    text: not provided
    description: Information of an expected format was not given, a value may be given
      at the later stage
    aliases:
    - not reported
  restricted access:
    text: restricted access
    description: Information exists but can not be released openly because of privacy
      concerns
    aliases:
    - restricted
  'missing: control sample':
    text: 'missing: control sample'
    description: Information is not applicable as the sample represents a negative
      control sample collected in a lab.
  'missing: sample group':
    text: 'missing: sample group'
    description: '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.

      '
  'missing: synthetic construct':
    text: 'missing: synthetic construct'
    description: Information does not exist as the sample represents an ab-initio
      synthetic construct.
  'missing: lab stock':
    text: 'missing: lab stock'
    description: 'Information was not collected as the sample represents a cultured
      cell line or model organism  under long-term lab control.

      '
  'missing: third party data':
    text: 'missing: third party data'
    description: '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: data agreement established pre-2023':
    text: 'missing: data agreement established pre-2023'
    description: 'Data agreements were established before the 2023 INSDC standard
      and metadata can not be provided.  A value may be given at a later stage.

      '
  'missing: endangered species':
    text: 'missing: endangered species'
    description: Information can not be reported as the target organism is endangered
      e.g. on the IUCN red-list.
  'missing: human-identifiable':
    text: 'missing: human-identifiable'
    description: Information can not be reported as the metadata would make the sample
      human-identifiable.

Enum: InsdcMissingValueEnum

Permissible Values

Examples

See Also

LinkML Source