Class: IsotopologComposition

Contains the isotopes used and at what fraction.

classDiagram class IsotopologComposition click IsotopologComposition href "../IsotopologComposition" IsotopologComposition : isotope IsotopologComposition --> "1" IsotopeEnum : isotope click IsotopeEnum href "../IsotopeEnum" IsotopologComposition : isotopolog_atom_frac IsotopologComposition --> "0..1 _recommended_" QuantityValue : isotopolog_atom_frac click QuantityValue href "../QuantityValue" IsotopologComposition : type

Slots

Name	Cardinality and Range	Description	Inheritance
isotope	1 IsotopeEnum	The element and mass number of the stable isotope used in isotopolog labeling.	direct
isotopolog_atom_frac	0..1 recommended QuantityValue	The fraction of heavy-labelled atoms out of all atoms of a given element in...	direct
type	1 Uriorcurie	the class_uri of the class that has been instantiated	direct

Usages

used by	used in	type	used
IsotopologAddition	isotope_atom_fractions	range	IsotopologComposition

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/nmdc/nmdc

Mappings

Mapping Type	Mapped Value

LinkML Source

Direct

name: IsotopologComposition
description: Contains the isotopes used and at what fraction.
from_schema: https://w3id.org/nmdc/nmdc
slots:
- isotope
- isotopolog_atom_frac
- type
class_uri: nmdc:IsotopologComposition

Induced

name: IsotopologComposition
description: Contains the isotopes used and at what fraction.
from_schema: https://w3id.org/nmdc/nmdc
attributes:
  isotope:
    name: isotope
    description: The element and mass number of the stable isotope used in isotopolog
      labeling.
    title: isotope
    examples:
    - value: 13C
    - value: 15N
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: MIXS:0001338
    owner: IsotopologComposition
    domain_of:
    - IsotopologComposition
    range: IsotopeEnum
    required: true
    multivalued: false
  isotopolog_atom_frac:
    name: isotopolog_atom_frac
    annotations:
      storage_units:
        tag: storage_units
        value: '1'
    description: The fraction of heavy-labelled atoms out of all atoms of a given
      element in the isotopolog.
    title: atom fraction of isotopolog
    examples:
    - object:
        type: nmdc:QuantityValue
        has_raw_value: '0.95'
        has_numeric_value: 0.95
        has_unit: '1'
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: MIXS:0001346
    owner: IsotopologComposition
    domain_of:
    - IsotopologComposition
    range: QuantityValue
    range_expression:
      slot_conditions:
        has_numeric_value:
          name: has_numeric_value
          minimum_value: 0
          maximum_value: 1
    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: IsotopologComposition
    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:IsotopologComposition