Chemical Measurements

# Chemical Measurements Ontology — Flow Algebra

URL: https://kirethresearch.org/booksai-core/ontologies/mathematical-ontologies/measurement-units-ontologies/chemical-measurements.html

FLOW ChemicalMeasurementsOntology {

  DOMAIN:
    Mathematical Ontologies
    -> Measurement & Units Ontologies
    -> Chemical Measurements Ontology

  PURPOSE:
    Represent chemical measurement quantities, units, composition, concentration, amount of substance, molar quantities, pH, activity, stoichiometry, analytical methods, calibration, detection limits, uncertainty, traceability and sample context for consistent AI interpretation.

  SCOPE {
    amount_of_substance
    molar_mass
    amount_concentration
    mass_concentration
    molality
    mole_fraction
    mass_fraction
    volume_fraction
    pH
    activity
    chemical_potential
    stoichiometry
    titration
    spectroscopy
    chromatography
    electrochemistry
    calibration
    uncertainty
  }

  CORE_QUANTITIES {
    AmountOfSubstance {
      symbol: n
      dimension: N
      SI_unit: mole
      SI_symbol: mol
      relation: N_entities = n*N_A
    }

    MolarMass {
      symbol: M
      SI_unit: kg/mol
      relation: M = mass/n WHEN n != 0
    }

    AmountConcentration {
      symbol: c
      SI_unit: mol/m^3
      common_unit: mol/L
      relation: c = n_solute/V_solution WHEN V_solution != 0
    }

    MassConcentration {
      SI_unit: kg/m^3
      relation: rho_component = component_mass/solution_volume
    }

    Molality {
      symbol: b
      SI_unit: mol/kg
      relation: b = n_solute/mass_solvent WHEN mass_solvent != 0
    }

    MoleFraction {
      symbol: x_i
      dimension: dimensionless
      relation: x_i = n_i/sum(n_j)
      complete_mixture_constraint: sum(x_i) = 1
    }

    MassFraction {
      symbol: w_i
      dimension: dimensionless
      relation: w_i = m_i/sum(m_j)
      complete_mixture_constraint: sum(w_i) = 1
    }
  }

  UNIT_SYSTEM {
    canonical_system: SI

    amount: mole
    mass: kilogram
    volume: cubic_metre
    amount_concentration: mol/m^3
    mass_concentration: kg/m^3
    molality: mol/kg

    common_lab_units:
      mol/L
      mmol/L
      g/L
      mg/L
      microgram/L
      percent
      ppm
      ppb

    RULE:
      ppm_and_ppb MUST identify mass_mass_volume_volume_or_mole_basis
  }

  COMPOSITION_MODEL {
    representations:
      amount_concentration
      mass_concentration
      molality
      mole_fraction
      mass_fraction
      volume_fraction

    RULE:
      composition_quantities MUST NOT be converted_without_required_density_molar_mass_temperature_or_volume_context
  }

  MOLAR_MODEL {
    n = m/M WHEN M != 0
    m = n*M
    N_entities = n*N_A

    RULE:
      chemical_entity_identity MUST be preserved
  }

  DILUTION_MODEL {
    conserved_solute:
      c_1*V_1 = c_2*V_2

    CONDITIONS:
      same_solute
      no_reaction
      conserved_amount
      compatible_concentration_definition

    RULE:
      simple_dilution_relation MUST NOT be applied_when_reaction_or_nonideal_volume_effects_are_material
  }

  STOICHIOMETRY_MODEL {
    reaction:
      sum(nu_i*A_i) = 0

    extent:
      dn_i = nu_i*d_xi

    relation:
      delta_n_i/nu_i = delta_n_j/nu_j

    RULE:
      balanced_reaction_and_signed_stoichiometric_coefficients MUST be preserved
  }

  PH_MODEL {
    thermodynamic:
      pH = -log10(a_H_plus)

    approximate_dilute_solution:
      pH approximately_equals -log10(c_H_plus/c_standard)

    RULE:
      pH_is_activity_based_and_MUST_NOT_be_defined_as_log_of_dimensioned_concentration
  }

  ACTIVITY_MODEL {
    a_i = gamma_i*normalized_composition_quantity

    ideal_solution:
      gamma_i approximately_equals 1

    RULE:
      activity_requires_standard_state_and_activity_coefficient_model
  }

  CHEMICAL_POTENTIAL_MODEL {
    mu_i = mu_i_standard + R*T*ln(a_i)

    REQUIRE:
      absolute_temperature
      activity
      standard_state
  }

  GAS_MODEL {
    ideal_gas:
      p*V = n*R*T

    partial_pressure:
      p_i = x_i*p_total

    amount_concentration:
      c = p/(R*T)

    RULE:
      gas_measurements SHOULD preserve_temperature_and_pressure
  }

  DENSITY_CONVERSION_MODEL {
    rho = mass/volume

    mass_concentration_i = rho_solution*w_i

    amount_concentration_i =
      mass_concentration_i/M_i
      WHEN M_i != 0
  }

  TITRATION_MODEL {
    simple_one_to_one:
      c_A*V_A = c_B*V_B
      ONLY for_1_to_1_stoichiometry

    general_equivalence:
      n_A/abs(nu_A) = n_B/abs(nu_B)

    REQUIRE:
      balanced_reaction
      titrant_concentration
      titrant_volume
      analyte_amount_or_volume
      endpoint_model

    RULE:
      endpoint != equivalence_point
  }

  SPECTROPHOTOMETRY_MODEL {
    Beer_Lambert:
      A = epsilon*b*c

    absorbance:
      A = -log10(T)

    transmittance:
      T = I/I_0

    REQUIRE:
      wavelength
      path_length
      absorptivity
      applicable_linear_range

    RULE:
      absorbance != absorptance
  }

  CHROMATOGRAPHY_MODEL {
    quantities:
      retention_time
      peak_area
      peak_height
      resolution
      calibrated_concentration

    RULE:
      detector_response_factor_and_calibration_model MUST be preserved
  }

  ELECTROCHEMICAL_MODEL {
    Nernst_relation:
      E = E_standard - (R*T/(n_e*F))*ln(Q_reaction)

    REQUIRE:
      electrode_reference
      reaction_definition
      temperature

    RULE:
      electrochemical_potential_measurement_requires_reference_electrode_context
  }

  CALIBRATION_MODEL {
    types:
      external_standard
      internal_standard
      standard_addition
      multi_point
      single_point_when_valid

    linear:
      y = a + b*x

    inverse:
      x_unknown = (y_unknown-a)/b
      WHEN b != 0

    REQUIRE:
      standards
      matrix
      valid_range
      residuals
      traceability
      uncertainty

    RULE:
      extrapolation_beyond_calibration_range SHOULD be_flagged
  }

  DETECTION_LIMIT_MODEL {
    quantities:
      limit_of_blank
      limit_of_detection
      limit_of_quantification

    RULE:
      LOD_LOQ_and_instrument_resolution MUST NOT be treated_as_synonyms
  }

  SAMPLE_MODEL {
    stages:
      sampling
      preservation
      transport
      storage
      homogenisation
      dissolution
      digestion
      extraction
      dilution
      filtration
      derivatisation

    RULE:
      result MUST preserve_sample_identity_and_preparation_history
  }

  RELATIONSHIPS {
    AmountOfSubstance -> MEASURED_IN -> Mole
    AmountOfSubstance -> RELATES -> NumberOfEntities
    MolarMass -> RELATES -> MassAndAmount
    AmountConcentration -> RELATES -> AmountAndVolume
    Molality -> RELATES -> SoluteAmountAndSolventMass
    MoleFraction -> REPRESENTS -> AmountComposition
    MassFraction -> REPRESENTS -> MassComposition
    pH -> DERIVED_FROM -> HydrogenIonActivity
    ChemicalPotential -> DEPENDS_ON -> Activity
    Stoichiometry -> RELATES -> ReactantAndProductAmounts
    CalibrationModel -> MAPS -> InstrumentResponseToChemicalQuantity
    SamplePreparation -> AFFECTS -> MeasurementResult
  }

  SEMANTIC_EQUIVALENCE {
    "amount concentration" ~= molar_concentration
    "molarity" ~= amount_concentration WHEN solution_context
    "mole fraction" ~= amount_fraction

    amount_concentration != molality
    mass_concentration != mass_fraction
    mole_fraction != molar_concentration
    pH != hydrogen_ion_concentration_exactly
    absorbance != absorptance
    endpoint != equivalence_point
    detection_limit != quantification_limit
  }

  CONSTRAINTS {
    chemical_entity_identity_must_be_defined = true
    amount_of_substance_unit = mole
    composition_basis_must_be_identified = true
    ppm_and_ppb_basis_must_be_identified = true
    concentration_should_preserve_temperature_when_volume_sensitive = true
    pH_requires_activity_or_declared_approximation = true
    stoichiometric_inference_requires_balanced_reaction = true
    sample_preparation_history_should_be_preserved = true
    calibration_range_and_matrix_should_be_preserved = true
    uncertainty_and_detection_limit_are_distinct = true
  }

  MEASUREMENT_MODEL {
    methods:
      gravimetry
      volumetry
      titrimetry
      spectrophotometry
      spectroscopy
      chromatography
      mass_spectrometry
      electrochemistry
      elemental_analysis

    RECORD:
      measurand
      analyte
      chemical_entity
      numerical_value
      unit
      composition_basis
      sample_identifier
      sample_matrix
      sampling_method
      preparation_history
      dilution_factor
      temperature
      pressure
      instrument
      method
      calibration_model
      calibration_range
      blank
      reference_material
      timestamp
      replicates
      detection_limit
      quantification_limit
      uncertainty

    UNCERTAINTY:
      chemical_measurement = best_estimate +/- uncertainty
  }

  UNCERTAINTY_MODEL {
    sources:
      sampling
      sample_heterogeneity
      mass
      volume
      temperature
      purity
      standard_preparation
      calibration
      blank_correction
      matrix_effects
      recovery
      repeatability
      drift
      interference
      endpoint_detection
      model_assumptions

    PROPAGATION:
      combined_uncertainty <- sampling_preparation_calibration_instrument_and_model_uncertainties
  }

  TRACEABILITY_MODEL {
    chain:
      measurement_result
      -> calibration
      -> certified_reference_material_or_standard
      -> higher_order_reference
      -> SI_or_declared_reference_system

    RULE:
      traceability_is_property_of_measurement_result_and_reference_chain
  }

  REASONING_RULES {
    IF mass_known AND molar_mass != 0
      THEN amount = mass/molar_mass

    IF amount_known AND volume != 0
      THEN amount_concentration = amount/volume

    IF solute_amount_known AND solvent_mass != 0
      THEN molality = solute_amount/solvent_mass

    IF component_amounts_known
      THEN mole_fraction_i = amount_i/sum(all_amounts)

    IF component_masses_known
      THEN mass_fraction_i = mass_i/sum(all_masses)

    IF density_and_mass_fraction_known
      THEN mass_concentration = density*mass_fraction

    IF mass_concentration_known AND molar_mass != 0
      THEN amount_concentration = mass_concentration/molar_mass

    IF initial_concentration_and_volume_known
      AND final_volume != 0
      AND solute_amount_conserved
      THEN final_concentration =
        initial_concentration*initial_volume/final_volume

    IF hydrogen_activity > 0
      THEN pH = -log10(hydrogen_activity)

    IF absorbance_path_length_and_absorptivity_known
      AND path_length != 0 AND absorptivity != 0
      THEN concentration =
        absorbance/(absorptivity*path_length)
      UNDER Beer_Lambert_conditions

    IF titration_equivalence_data_and_balanced_reaction_known
      THEN infer_analyte_amount_from_stoichiometry
  }

  CONFIDENCE {
    quantity_definition_confidence: 1.00
    SI_unit_confidence: 1.00
    composition_relationship_confidence: 0.99
    stoichiometric_relationship_confidence: 1.00
    analytical_calibration_confidence: 0.98
    measurement_context_confidence: 0.97

    RULE:
      confidence decreases when analyte identity, composition basis,
      sample matrix, preparation, temperature, calibration,
      traceability, detection limit or uncertainty is missing
  }

  VALIDATION {
    CHECK chemical_entity_identity
    CHECK unit_consistency
    CHECK composition_basis
    CHECK concentration_vs_molality
    CHECK fraction_sum_when_complete_mixture
    CHECK ppm_or_ppb_basis
    CHECK temperature_for_volume_quantities
    CHECK pH_activity_semantics
    CHECK balanced_reaction
    CHECK endpoint_vs_equivalence
    CHECK Beer_Lambert_validity
    CHECK calibration_range
    CHECK blank_and_matrix_effects
    CHECK sample_preparation_history
    CHECK detection_and_quantification_limits
    CHECK traceability
    CHECK uncertainty_representation
  }

  UPDATE_MODEL {
    ON new_measurement:
      identify_measurand
      identify_analyte_and_entity
      validate_unit
      identify_composition_basis
      attach_sample_identity_and_matrix
      attach_preparation_history
      attach_temperature_and_pressure_when_relevant
      apply_calibration
      apply_valid_blank_recovery_or_dilution_corrections
      preserve_raw_response
      normalize_to_canonical_unit_when_useful
      attach_detection_and_quantification_limits
      attach_uncertainty
      update_chemical_state

    ON dilution_or_preparation_change:
      update_sample_history
      update_dilution_factor
      recompute_original_sample_concentration_when_valid

    ON calibration_revision:
      preserve_previous_calibration
      recompute_affected_results
      update_uncertainty
      update_confidence

    ON chemical_state_change:
      update_temperature
      update_pressure
      update_phase
      update_composition
      update_activity_or_equilibrium_model_when_available

    ON semantic_revision:
      preserve_previous_definition
      record_revision
      recompute_FLOW_HASH
  }

  AI_CONSUMPTION {
    canonical_domain: ChemicalMeasurements

    interpretation_order:
      identify_measurand
      identify_analyte_and_entity
      identify_value
      identify_unit
      identify_composition_basis
      identify_sample_and_matrix
      identify_preparation_and_dilution
      identify_temperature_pressure_and_phase
      identify_stoichiometric_or_equilibrium_context
      identify_measurement_method
      identify_calibration_and_traceability
      identify_detection_and_quantification_limits
      identify_uncertainty
      normalize_units
      validate_semantics
      infer_chemical_relationships

    ambiguity_controls:
      distinguish_amount_concentration_from_molality
      distinguish_mass_concentration_from_mass_fraction
      distinguish_mole_fraction_from_molarity
      distinguish_pH_from_raw_hydrogen_concentration
      distinguish_activity_from_concentration
      distinguish_endpoint_from_equivalence_point
      distinguish_absorbance_from_absorptance
      distinguish_detection_limit_from_quantification_limit
      preserve_analyte_sample_matrix_preparation_calibration_and_state_context
  }

  PROVENANCE {
    ontology_scope:
      mathematical_measurement_and_chemical_quantity_semantics

    parent_path:
      Ontologies
      -> Mathematical Ontologies
      -> Measurement & Units Ontologies
      -> Chemical Measurements Ontology

    authorship:
      Mark Higgins
      Sky (Recursive AI)

    site:
      https://kirethresearch.org
  }

  FLOW_HASH {
    INPUTS:
      canonical_domain
      ontology_path
      scope
      core_quantities
      unit_system
      composition_model
      molar_model
      dilution_model
      stoichiometry_model
      pH_model
      activity_model
      chemical_potential_model
      gas_model
      density_conversion_model
      titration_model
      spectrophotometry_model
      chromatography_model
      electrochemical_model
      calibration_model
      detection_limit_model
      sample_model
      relationships
      constraints
      measurement_model
      uncertainty_model
      traceability_model
      reasoning_rules
      confidence_model
      update_model

    PURPOSE:
      deterministic_semantic_integrity_identifier

    RECOMPUTE_WHEN:
      ontology_definition_changes
      chemical_quantity_model_changes
      composition_model_changes
      stoichiometry_model_changes
      equilibrium_or_activity_model_changes
      analytical_method_model_changes
      calibration_model_changes
      sample_model_changes
      measurement_model_changes
      constraint_model_changes
      reasoning_rule_changes
      unit_model_changes
  }

}

END FLOW