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Class: thermodynamic estimate (ThermodynamicEstimate)

A reified thermodynamic quantity for a reaction, bundled with the aqueous conditions it holds at, its uncertainty, and the method and source it came from. Transformed ("primed") quantities are only interpretable together with pH, ionic strength, pMg and temperature, because the transform aggregates each reactant's microspecies into a single pseudoisomer group at those conditions. A reaction may therefore carry several estimates, one per condition set.

URI: chemrof:ThermodynamicEstimate

 classDiagram
    class ThermodynamicEstimate
    click ThermodynamicEstimate href "../ThermodynamicEstimate/"
      ChemicalRelationship <|-- ThermodynamicEstimate
        click ChemicalRelationship href "../ChemicalRelationship/"

      ThermodynamicEstimate : electrical_potential_difference

      ThermodynamicEstimate : estimation_method





        ThermodynamicEstimate --> "0..1" ThermodynamicEstimationMethodEnum : estimation_method
        click ThermodynamicEstimationMethodEnum href "../ThermodynamicEstimationMethodEnum/"



      ThermodynamicEstimate : ionic_strength

      ThermodynamicEstimate : owl_subclass_of





        ThermodynamicEstimate --> "0..1" OwlClass : owl_subclass_of
        click OwlClass href "../OwlClass/"



      ThermodynamicEstimate : p_h

      ThermodynamicEstimate : p_mg

      ThermodynamicEstimate : quantity_type





        ThermodynamicEstimate --> "1" ThermodynamicQuantityTypeEnum : quantity_type
        click ThermodynamicQuantityTypeEnum href "../ThermodynamicQuantityTypeEnum/"



      ThermodynamicEstimate : source

      ThermodynamicEstimate : standard_error

      ThermodynamicEstimate : temperature

      ThermodynamicEstimate : unit





        ThermodynamicEstimate --> "0..1" ThermodynamicUnitEnum : unit
        click ThermodynamicUnitEnum href "../ThermodynamicUnitEnum/"



      ThermodynamicEstimate : unresolved_participants





        ThermodynamicEstimate --> "*" ChemicalEntity : unresolved_participants
        click ChemicalEntity href "../ChemicalEntity/"



      ThermodynamicEstimate : value

Inheritance

Slots

Name Cardinality and Range Description Inheritance
quantity_type 1
ThermodynamicQuantityTypeEnum		 Which thermodynamic quantity this estimate reports direct
value 1
Float		 The numeric value of the estimate, in the stated unit direct
standard_error 0..1
Float		 One standard deviation of the estimate, in the same unit as value direct
unit 0..1
ThermodynamicUnitEnum		 The unit of value direct
p_h 0..1
Float		 The pH at which this estimate holds direct
ionic_strength 0..1
Float		 Ionic strength at which this estimate holds direct
p_mg 0..1
Float		 The negative logarithm of the free magnesium ion activity direct
temperature 0..1
Float		 Temperature at which this estimate holds direct
electrical_potential_difference 0..1
Float		 Membrane potential across the compartment boundary, for transport reactions direct
estimation_method 0..1
ThermodynamicEstimationMethodEnum		 How the value was arrived at direct
source 0..1
String		 The tool, database or publication the estimate came from, including a version... direct
unresolved_participants *
ChemicalEntity		 Reaction participants that could not be resolved to a structure, and so contr... direct
owl_subclass_of 0..1
OwlClass		 Holds between C and P if C owl:subClassOf P OwlClass

Usages

used by used in type used
Reaction has_thermodynamic_estimate range ThermodynamicEstimate
IsomeraseReaction has_thermodynamic_estimate range ThermodynamicEstimate

See Also

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/chemrof

Mappings

Mapping Type Mapped Value
self chemrof:ThermodynamicEstimate
native chemrof:ThermodynamicEstimate

LinkML Source

Direct

name: ThermodynamicEstimate
description: A reified thermodynamic quantity for a reaction, bundled with the aqueous
  conditions it holds at, its uncertainty, and the method and source it came from.
  Transformed ("primed") quantities are only interpretable together with pH, ionic
  strength, pMg and temperature, because the transform aggregates each reactant's
  microspecies into a single pseudoisomer group at those conditions. A reaction may
  therefore carry several estimates, one per condition set.
title: thermodynamic estimate
from_schema: https://w3id.org/chemrof
see_also:
- https://equilibrator.readthedocs.io/
is_a: ChemicalRelationship
attributes:
  quantity_type:
    name: quantity_type
    description: Which thermodynamic quantity this estimate reports.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain_of:
    - ThermodynamicEstimate
    range: ThermodynamicQuantityTypeEnum
    required: true
  value:
    name: value
    description: The numeric value of the estimate, in the stated unit.
    from_schema: https://w3id.org/chemrof
    domain_of:
    - GroupingByGenusAndPropertyValue
    - Concentration
    - ThermodynamicEstimate
    range: float
    required: true
  standard_error:
    name: standard_error
    description: One standard deviation of the estimate, in the same unit as value.
    comments:
    - For component contribution estimates this is the square root of the corresponding
      diagonal element of the covariance matrix. Errors are correlated between reactions,
      so they must not be combined as if independent when summing over a pathway.
    - Omit rather than guess when the source reports no uncertainty.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain_of:
    - ThermodynamicEstimate
    range: float
  unit:
    name: unit
    description: The unit of value. Expected for energy-valued and potential-valued
      quantities, and omitted for dimensionless ones such as the reversibility index.
    from_schema: https://w3id.org/chemrof
    domain_of:
    - Concentration
    - ThermodynamicEstimate
    range: ThermodynamicUnitEnum
  p_h:
    name: p_h
    description: The pH at which this estimate holds.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain_of:
    - ThermodynamicEstimate
    range: float
    minimum_value: 0.0
    maximum_value: 14.0
  ionic_strength:
    name: ionic_strength
    description: Ionic strength at which this estimate holds.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain_of:
    - ThermodynamicEstimate
    range: float
    unit:
      ucum_code: mol/L
  p_mg:
    name: p_mg
    description: The negative logarithm of the free magnesium ion activity. Affects
      any reactant that forms magnesium complexes, notably nucleotides and polyphosphates.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain_of:
    - ThermodynamicEstimate
    range: float
  temperature:
    name: temperature
    description: Temperature at which this estimate holds.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain_of:
    - ThermodynamicEstimate
    range: float
    unit:
      ucum_code: K
  electrical_potential_difference:
    name: electrical_potential_difference
    description: Membrane potential across the compartment boundary, for transport
      reactions. The sign convention is that of the source.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain_of:
    - ThermodynamicEstimate
    range: float
    unit:
      ucum_code: V
  estimation_method:
    name: estimation_method
    description: How the value was arrived at.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain_of:
    - ThermodynamicEstimate
    range: ThermodynamicEstimationMethodEnum
  source:
    name: source
    description: The tool, database or publication the estimate came from, including
      a version where available.
    examples:
    - value: eQuilibrator 3.0
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain_of:
    - ThermodynamicEstimate
    range: string
  unresolved_participants:
    name: unresolved_participants
    description: Reaction participants that could not be resolved to a structure,
      and so contributed neither a group decomposition nor a microspecies ladder.
      An estimate that lists any of these should be treated as unreliable.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain_of:
    - ThermodynamicEstimate
    range: ChemicalEntity
    multivalued: true

Induced

name: ThermodynamicEstimate
description: A reified thermodynamic quantity for a reaction, bundled with the aqueous
  conditions it holds at, its uncertainty, and the method and source it came from.
  Transformed ("primed") quantities are only interpretable together with pH, ionic
  strength, pMg and temperature, because the transform aggregates each reactant's
  microspecies into a single pseudoisomer group at those conditions. A reaction may
  therefore carry several estimates, one per condition set.
title: thermodynamic estimate
from_schema: https://w3id.org/chemrof
see_also:
- https://equilibrator.readthedocs.io/
is_a: ChemicalRelationship
attributes:
  quantity_type:
    name: quantity_type
    description: Which thermodynamic quantity this estimate reports.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: quantity_type
    owner: ThermodynamicEstimate
    domain_of:
    - ThermodynamicEstimate
    range: ThermodynamicQuantityTypeEnum
    required: true
  value:
    name: value
    description: The numeric value of the estimate, in the stated unit.
    from_schema: https://w3id.org/chemrof
    alias: value
    owner: ThermodynamicEstimate
    domain_of:
    - GroupingByGenusAndPropertyValue
    - Concentration
    - ThermodynamicEstimate
    range: float
    required: true
  standard_error:
    name: standard_error
    description: One standard deviation of the estimate, in the same unit as value.
    comments:
    - For component contribution estimates this is the square root of the corresponding
      diagonal element of the covariance matrix. Errors are correlated between reactions,
      so they must not be combined as if independent when summing over a pathway.
    - Omit rather than guess when the source reports no uncertainty.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: standard_error
    owner: ThermodynamicEstimate
    domain_of:
    - ThermodynamicEstimate
    range: float
  unit:
    name: unit
    description: The unit of value. Expected for energy-valued and potential-valued
      quantities, and omitted for dimensionless ones such as the reversibility index.
    from_schema: https://w3id.org/chemrof
    alias: unit
    owner: ThermodynamicEstimate
    domain_of:
    - Concentration
    - ThermodynamicEstimate
    range: ThermodynamicUnitEnum
  p_h:
    name: p_h
    description: The pH at which this estimate holds.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: p_h
    owner: ThermodynamicEstimate
    domain_of:
    - ThermodynamicEstimate
    range: float
    minimum_value: 0.0
    maximum_value: 14.0
  ionic_strength:
    name: ionic_strength
    description: Ionic strength at which this estimate holds.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: ionic_strength
    owner: ThermodynamicEstimate
    domain_of:
    - ThermodynamicEstimate
    range: float
    unit:
      ucum_code: mol/L
  p_mg:
    name: p_mg
    description: The negative logarithm of the free magnesium ion activity. Affects
      any reactant that forms magnesium complexes, notably nucleotides and polyphosphates.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: p_mg
    owner: ThermodynamicEstimate
    domain_of:
    - ThermodynamicEstimate
    range: float
  temperature:
    name: temperature
    description: Temperature at which this estimate holds.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: temperature
    owner: ThermodynamicEstimate
    domain_of:
    - ThermodynamicEstimate
    range: float
    unit:
      ucum_code: K
  electrical_potential_difference:
    name: electrical_potential_difference
    description: Membrane potential across the compartment boundary, for transport
      reactions. The sign convention is that of the source.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: electrical_potential_difference
    owner: ThermodynamicEstimate
    domain_of:
    - ThermodynamicEstimate
    range: float
    unit:
      ucum_code: V
  estimation_method:
    name: estimation_method
    description: How the value was arrived at.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: estimation_method
    owner: ThermodynamicEstimate
    domain_of:
    - ThermodynamicEstimate
    range: ThermodynamicEstimationMethodEnum
  source:
    name: source
    description: The tool, database or publication the estimate came from, including
      a version where available.
    examples:
    - value: eQuilibrator 3.0
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: source
    owner: ThermodynamicEstimate
    domain_of:
    - ThermodynamicEstimate
    range: string
  unresolved_participants:
    name: unresolved_participants
    description: Reaction participants that could not be resolved to a structure,
      and so contributed neither a group decomposition nor a microspecies ladder.
      An estimate that lists any of these should be treated as unreliable.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: unresolved_participants
    owner: ThermodynamicEstimate
    domain_of:
    - ThermodynamicEstimate
    range: ChemicalEntity
    multivalued: true
  owl_subclass_of:
    name: owl_subclass_of
    annotations:
      owl:
        tag: owl
        value: SubClassOf
    description: 'Holds between C and P if C owl:subClassOf P. Note that in this model,
      most classes are metaclasses (see ''owl class''), where these metaclasses may
      represent *groupings* or specific countable elements or species. We provide
      two different sub-properties of subclass of for two cases: (1) subtype_of, which
      connects grouping classes (e.g. alkane is_a hydrocarbon; alpha-amino-acid is_a
      amino-acid), (2) classified_by, which connects a specific element to a grouping
      class (e.g. methane is_a hydrocarbon; iron is_a metal; serine is_a amino-acid)'
    title: owl subclass of
    from_schema: https://w3id.org/chemrof
    aliases:
    - is a
    exact_mappings:
    - rdfs:subClassOf
    narrow_mappings:
    - bo:family
    rank: 1000
    is_a: classification_relationship
    mixin: true
    domain: OwlClass
    alias: owl_subclass_of
    owner: ThermodynamicEstimate
    domain_of:
    - OwlClass
    range: OwlClass