Class: IsotopologAddition

name: IsotopologAddition
description: One isotopolog, or one heterogeneous material with no compound identifier,
  added during an isotope labeling process, with the isotope it carries, whether it
  was isotopically labeled or at natural abundance, the atom fraction and position
  of the label, and the dose.
from_schema: https://w3id.org/nmdc/nmdc
slots:
- isotope_atom_fractions
- isotopolog
- hetero_isotopolog
- isotopolog_label
- isotopolog_atom_pos
- isotopolog_dose
- type
class_uri: nmdc:IsotopologAddition
rules:
- preconditions:
    slot_conditions:
      isotopolog:
        name: isotopolog
        value_presence: ABSENT
  postconditions:
    slot_conditions:
      hetero_isotopolog:
        name: hetero_isotopolog
        required: true
  description: If isotopolog is absent, then hetero_isotopolog is required, so that
    every entry names the input in one of the two ways.
  title: hetero_isotopolog_required_when_isotopolog_absent
- preconditions:
    slot_conditions:
      isotopolog:
        name: isotopolog
        value_presence: PRESENT
  postconditions:
    slot_conditions:
      hetero_isotopolog:
        name: hetero_isotopolog
        value_presence: ABSENT
  description: If isotopolog is present, then hetero_isotopolog must be absent, so
    that no entry names the input in both ways.
  title: hetero_isotopolog_absent_when_isotopolog_present
- preconditions:
    slot_conditions:
      isotopolog_label:
        name: isotopolog_label
        equals_string: natural abundance
  postconditions:
    slot_conditions:
      isotopolog_atom_pos:
        name: isotopolog_atom_pos
        value_presence: ABSENT
  description: If isotopolog_label is natural abundance, then isotopolog_atom_pos
    must be absent, because an InChI isotope layer can only describe enrichment.
  title: isotopolog_atom_pos_absent_at_natural_abundance

name: IsotopologAddition
description: One isotopolog, or one heterogeneous material with no compound identifier,
  added during an isotope labeling process, with the isotope it carries, whether it
  was isotopically labeled or at natural abundance, the atom fraction and position
  of the label, and the dose.
from_schema: https://w3id.org/nmdc/nmdc
attributes:
  isotope_atom_fractions:
    name: isotope_atom_fractions
    description: Contains the isotopes used and at what fraction, for an isotopolog
      added during an isotope labeling process.
    title: isotope atom fractions
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    owner: IsotopologAddition
    domain_of:
    - IsotopologAddition
    range: IsotopologComposition
    multivalued: true
    inlined: true
    inlined_as_list: true
  isotopolog:
    name: isotopolog
    description: Isotopolog (isotope source/substrate/molecule) added to the biological
      sample.
    title: isotopolog
    comments:
    - Inputs such as root exudates or cells, goes in hetero_isotopolog instead; NMDC
      does not use a sentinel identifier for that case.
    examples:
    - value: water
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: MIXS:0001339
    owner: IsotopologAddition
    domain_of:
    - IsotopologAddition
    range: ChemicalEntityEnum
    recommended: true
    multivalued: false
  hetero_isotopolog:
    name: hetero_isotopolog
    description: 'An input to the labeling that has no ChEBI identifier, described
      in free text: an undefined mixture such as root exudates or plant litter, or
      cells or biomass such as T4 phages. A defined compound with a ChEBI identifier
      goes in isotopolog instead.'
    title: heterogeneous isotopolog
    comments:
    - Exactly one of isotopolog and hetero_isotopolog is given on each IsotopologAddition
      entry; the rules on that class enforce it.
    - hetero_isotopolog is a column of the MISIP supplementary tables (Simpson et
      al. 2024, https://doi.org/10.1093/gigascience/giae071) and is not yet a MIxS
      slot.
    examples:
    - value: root exudates
    - value: T4 phages
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://github.com/GenomicsStandardsConsortium/mixs/issues/1409
    rank: 1000
    owner: IsotopologAddition
    domain_of:
    - IsotopologAddition
    range: string
  isotopolog_label:
    name: isotopolog_label
    description: List whether the isotopolog added to this biological sample was heavy-labelled
      or natural abundance
    title: isotopolog label status
    examples:
    - value: natural abundance
    - value: isotopically labeled
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: MIXS:0001340
    owner: IsotopologAddition
    domain_of:
    - IsotopologAddition
    range: IsotopologLabelEnum
    required: true
  isotopolog_atom_pos:
    name: isotopolog_atom_pos
    description: InChI label designating set of all isotopically enriched atoms in
      isotopolog. This slot should be omitted for natural abundance samples
    title: set of labeled atoms in isotopolog
    examples:
    - value: InChI=1S/C7H8/c1-7-5-3-2-4-6-7/h2-6H,1H3/i1+1,2+1,3+1,4+1,5+1,6+1,7+1
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: MIXS:0001347
    owner: IsotopologAddition
    domain_of:
    - IsotopologAddition
    range: string
    recommended: true
    pattern: ^InChI=1S?/[^\s/]+(?:/[^\s/i][^\s/]*)*/i(?=[^\s/]*(?:[0-9][+-][0-9]|[0-9][DT])|/h[^\s/]*[DT])[^\s/]*(?:/[^\s/]+)*$
  isotopolog_dose:
    name: isotopolog_dose
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: ppm
      storage_units:
        tag: storage_units
        value: '[ppm]'
    description: The concentration (in ppm) of isotopolog added to environmental matrix
      as a total mass per volume.
    title: dose of isotopolog
    comments:
    - isotopolog mass / total volume soil; ppm of isotopolog in total container volume
    examples:
    - object:
        type: nmdc:QuantityValue
        has_raw_value: 10 [ppm]
        has_numeric_value: 10
        has_unit: '[ppm]'
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: MIXS:0001348
    owner: IsotopologAddition
    domain_of:
    - IsotopologAddition
    range: QuantityValue
    recommended: true
  type:
    name: type
    description: the class_uri of the class that has been instantiated
    title: Type
    notes:
    - makes it easier to read example data files
    - required for polymorphic MongoDB collections
    comments:
    - 'Deprecating this slot was proposed and rejected: without it, a document read
      back from a polymorphic MongoDB collection cannot be resolved to the class it
      instantiates. It is required on every class for that reason, rather than as
      a convention inherited from LinkML.'
    examples:
    - value: nmdc:Biosample
    - value: nmdc:Study
    from_schema: https://w3id.org/nmdc/nmdc
    structured_aliases:
    - literal_form: workflow_execution_class
      predicate: NARROW_SYNONYM
      notes:
      - JGI Analysis Tracker (JAT) macro nmdc_metadata.yaml, in an access-restricted
        Bitbucket repository (https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml);
        source is the public NMDC page describing how JAT is used.
      source: https://github.com/microbiomedata/nmdc_automation/blob/main/data_management/README.md
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    owner: IsotopologAddition
    domain_of:
    - Agent
    - EukEval
    - FunctionalAnnotationAggMember
    - IsotopologAddition
    - IsotopologComposition
    - PeptideQuantification
    - ProteinQuantification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - OntologyRelation
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    - ProvenanceMetadata
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    range: uriorcurie
    required: true
class_uri: nmdc:IsotopologAddition
rules:
- preconditions:
    slot_conditions:
      isotopolog:
        name: isotopolog
        value_presence: ABSENT
  postconditions:
    slot_conditions:
      hetero_isotopolog:
        name: hetero_isotopolog
        required: true
  description: If isotopolog is absent, then hetero_isotopolog is required, so that
    every entry names the input in one of the two ways.
  title: hetero_isotopolog_required_when_isotopolog_absent
- preconditions:
    slot_conditions:
      isotopolog:
        name: isotopolog
        value_presence: PRESENT
  postconditions:
    slot_conditions:
      hetero_isotopolog:
        name: hetero_isotopolog
        value_presence: ABSENT
  description: If isotopolog is present, then hetero_isotopolog must be absent, so
    that no entry names the input in both ways.
  title: hetero_isotopolog_absent_when_isotopolog_present
- preconditions:
    slot_conditions:
      isotopolog_label:
        name: isotopolog_label
        equals_string: natural abundance
  postconditions:
    slot_conditions:
      isotopolog_atom_pos:
        name: isotopolog_atom_pos
        value_presence: ABSENT
  description: If isotopolog_label is natural abundance, then isotopolog_atom_pos
    must be absent, because an InChI isotope layer can only describe enrichment.
  title: isotopolog_atom_pos_absent_at_natural_abundance