Chemistry Ontology

FLOW Chemistry_Ontology_AI_Search

VERSION 4.0

AUTHORS
    Mark Higgins
    Sky Recursive AI

SOURCE
    https://kirethresearch.org

PAGE
    Chemistry Ontology

PURPOSE
    Define chemistry as a machine-readable ontology for AI systems.

    Provide a structured semantic model for interpreting chemical entities,
    substances, reactions, bonds, elements, compounds, molecular structures,
    quantities, equations, units, symbols, constants and experimental evidence.

DOMAIN
    Semantic Library
    AI Core
    Scientific Ontologies
    Chemistry Ontology

CORE_CLAIM
    Chemistry is represented as a structured ontology of substances,
    elements, atoms, molecules, bonds, reactions, properties, transformations
    and measurable relationships.

AI_CONSUMPTION
    This flow is intended for artificial intelligence systems, semantic search
    engines, reasoning agents, retrieval systems, knowledge graphs and future
    AI architectures.

POSITION_IN_LIBRARY
    Semantic Library
        → AI Core
            → Ontologies
                → Scientific Ontologies
                    → Chemistry Ontology

ONTOLOGY_TYPE
    Domain Ontology

PRIMARY_FUNCTION
    Organise chemical knowledge into explicit semantic categories that can be
    searched, linked, inferred, validated and extended.

FACTS
    Chemistry studies matter, substances, elements, atoms, molecules, ions,
    compounds, mixtures, bonds, reactions, energy changes and transformations.

    Chemistry connects atomic structure to molecular behaviour and material
    properties.

    Chemistry depends on units, constants, equations, symbols, experimental
    observations and standard nomenclature.

    Chemistry contains multiple subdomains including organic chemistry,
    inorganic chemistry, physical chemistry, analytical chemistry,
    biochemistry, materials chemistry, electrochemistry and thermochemistry.

    Chemical knowledge must distinguish between observed substances,
    theoretical models, molecular representations, reaction mechanisms,
    measured properties and proposed interpretations.

PRIMARY_ENTITIES
    ENTITY CHEMISTRY
        TYPE: scientific_domain
        DESCRIPTION: Study of matter, substances, composition, structure,
        properties, reactions and transformations.
        CONFIDENCE: 1.00

    ENTITY MATTER
        TYPE: chemical_concept
        DESCRIPTION: Physical material composed of particles, atoms, molecules
        or fields.
        CONFIDENCE: 1.00

    ENTITY SUBSTANCE
        TYPE: chemical_entity
        DESCRIPTION: Material with defined composition and properties.
        CONFIDENCE: 1.00

    ENTITY ELEMENT
        TYPE: chemical_entity
        DESCRIPTION: Substance defined by atoms with the same atomic number.
        CONFIDENCE: 1.00

    ENTITY ATOM
        TYPE: chemical_entity
        DESCRIPTION: Basic unit of an element containing nucleus and electrons.
        CONFIDENCE: 1.00

    ENTITY MOLECULE
        TYPE: chemical_entity
        DESCRIPTION: Group of atoms bonded together as a chemical unit.
        CONFIDENCE: 1.00

    ENTITY ION
        TYPE: chemical_entity
        DESCRIPTION: Atom or molecule with net electric charge.
        CONFIDENCE: 1.00

    ENTITY COMPOUND
        TYPE: chemical_entity
        DESCRIPTION: Substance formed from two or more elements chemically
        bonded in defined proportions.
        CONFIDENCE: 1.00

    ENTITY MIXTURE
        TYPE: chemical_entity
        DESCRIPTION: Combination of substances not chemically bonded into a
        single compound.
        CONFIDENCE: 1.00

    ENTITY BOND
        TYPE: chemical_relationship
        DESCRIPTION: Interaction linking atoms or ions into molecules,
        compounds or structures.
        CONFIDENCE: 1.00

    ENTITY REACTION
        TYPE: chemical_process
        DESCRIPTION: Transformation in which reactants become products through
        bond breaking, bond formation, electron transfer or structural change.
        CONFIDENCE: 1.00

    ENTITY REACTANT
        TYPE: reaction_role
        DESCRIPTION: Substance consumed or transformed during a chemical
        reaction.
        CONFIDENCE: 1.00

    ENTITY PRODUCT
        TYPE: reaction_role
        DESCRIPTION: Substance produced by a chemical reaction.
        CONFIDENCE: 1.00

    ENTITY CATALYST
        TYPE: chemical_role
        DESCRIPTION: Substance that changes reaction rate without being
        consumed overall.
        CONFIDENCE: 1.00

    ENTITY SOLUTION
        TYPE: chemical_system
        DESCRIPTION: Homogeneous mixture containing solute and solvent.
        CONFIDENCE: 1.00

    ENTITY SOLUTE
        TYPE: chemical_role
        DESCRIPTION: Substance dissolved in a solvent.
        CONFIDENCE: 1.00

    ENTITY SOLVENT
        TYPE: chemical_role
        DESCRIPTION: Substance that dissolves another substance.
        CONFIDENCE: 1.00

    ENTITY PH
        TYPE: chemical_quantity
        DESCRIPTION: Measure related to hydrogen ion activity in solution.
        CONFIDENCE: 1.00

CHEMICAL_ENTITY_TYPES
    Element
    Atom
    Isotope
    Ion
    Molecule
    Compound
    Mixture
    Substance
    Solution
    Solute
    Solvent
    Acid
    Base
    Salt
    Polymer
    Crystal
    Gas
    Liquid
    Solid
    Plasma
    Radical
    Catalyst
    Enzyme
    Ligand
    Complex

CHEMICAL_PROCESS_TYPES
    Reaction
    Dissolution
    Precipitation
    Oxidation
    Reduction
    Acid-Base Reaction
    Combustion
    Neutralisation
    Polymerisation
    Hydrolysis
    Condensation
    Crystallisation
    Evaporation
    Condensation Phase Change
    Sublimation
    Deposition
    Ionisation
    Electron Transfer
    Bond Formation
    Bond Breaking
    Catalysis

CHEMICAL_PROPERTY_TYPES
    Atomic Number
    Atomic Mass
    Molecular Mass
    Molar Mass
    Charge
    Valence
    Electronegativity
    Oxidation State
    Bond Length
    Bond Angle
    Density
    Melting Point
    Boiling Point
    Solubility
    Concentration
    Molarity
    Acidity
    Basicity
    Reactivity
    Stability
    Enthalpy
    Entropy
    Gibbs Free Energy

CHEMISTRY_SUBDOMAINS
    Organic Chemistry
    Inorganic Chemistry
    Physical Chemistry
    Analytical Chemistry
    Biochemistry
    Materials Chemistry
    Electrochemistry
    Thermochemistry
    Quantum Chemistry
    Environmental Chemistry
    Polymer Chemistry
    Medicinal Chemistry
    Surface Chemistry
    Atmospheric Chemistry
    Computational Chemistry
    Nuclear Chemistry

RELATIONSHIP_TYPES
    contains
    part_of
    instance_of
    subclass_of
    composed_of
    bonded_to
    reacts_with
    produces
    consumes
    catalyses
    dissolves_in
    precipitates_from
    oxidises
    reduces
    donates
    accepts
    has_charge
    has_mass
    has_formula
    has_structure
    has_property
    has_state
    has_unit
    has_symbol
    governed_by
    described_by
    measured_by
    derived_from
    equivalent_to
    depends_on
    transforms_into

RELATIONSHIPS
    CHEMISTRY studies MATTER
        TYPE: studies
        CONFIDENCE: 1.00

    MATTER contains SUBSTANCE
        TYPE: contains
        CONFIDENCE: 0.95

    SUBSTANCE may_be ELEMENT
        TYPE: may_be
        CONFIDENCE: 1.00

    SUBSTANCE may_be COMPOUND
        TYPE: may_be
        CONFIDENCE: 1.00

    ELEMENT composed_of ATOM
        TYPE: composed_of
        CONFIDENCE: 1.00

    ATOM contains NUCLEUS
        TYPE: contains
        CONFIDENCE: 1.00

    ATOM contains ELECTRON
        TYPE: contains
        CONFIDENCE: 1.00

    MOLECULE composed_of ATOM
        TYPE: composed_of
        CONFIDENCE: 1.00

    COMPOUND composed_of ELEMENT
        TYPE: composed_of
        CONFIDENCE: 1.00

    ATOM bonded_to ATOM
        TYPE: bonded_to
        CONFIDENCE: 1.00

    REACTION consumes REACTANT
        TYPE: consumes
        CONFIDENCE: 1.00

    REACTION produces PRODUCT
        TYPE: produces
        CONFIDENCE: 1.00

    CATALYST catalyses REACTION
        TYPE: catalyses
        CONFIDENCE: 1.00

    SOLUTION contains SOLUTE
        TYPE: contains
        CONFIDENCE: 1.00

    SOLUTION contains SOLVENT
        TYPE: contains
        CONFIDENCE: 1.00

    ACID donates PROTON
        TYPE: donates
        CONFIDENCE: 0.95

    BASE accepts PROTON
        TYPE: accepts
        CONFIDENCE: 0.95

    OXIDATION loses ELECTRON
        TYPE: loses
        CONFIDENCE: 0.95

    REDUCTION gains ELECTRON
        TYPE: gains
        CONFIDENCE: 0.95

    CHEMICAL_EQUATION describes REACTION
        TYPE: describes
        CONFIDENCE: 1.00

    CHEMICAL_FORMULA describes COMPOSITION
        TYPE: describes
        CONFIDENCE: 1.00

    UNIT constrains CHEMICAL_QUANTITY
        TYPE: constrains
        CONFIDENCE: 1.00

CANONICAL_EQUATION_REFERENCES
    Ideal_Gas_Law:
        P V = n R T

    Molarity:
        M = n / V

    Density:
        ρ = m / V

    Beer_Lambert_Law:
        A = ε c l

    Gibbs_Free_Energy:
        ΔG = ΔH - TΔS

    Henderson_Hasselbalch:
        pH = pKa + log([A-] / [HA])

    Nernst_Equation:
        E = E° - (RT / nF) ln Q

    Arrhenius_Equation:
        k = A e^(-Ea / RT)

CANONICAL_SYMBOL_REFERENCES
    H: Hydrogen
    O: Oxygen
    C: Carbon
    N: Nitrogen
    Na: Sodium
    Cl: Chlorine
    pH: Hydrogen ion activity measure
    M: Molarity
    n: Amount of substance
    V: Volume
    P: Pressure
    T: Temperature
    R: Gas constant
    ρ: Density
    m: Mass
    A: Absorbance or pre-exponential factor depending on context
    ε: Molar absorptivity
    l: Path length
    ΔG: Gibbs free energy change
    ΔH: Enthalpy change
    ΔS: Entropy change
    E: Electrode potential or energy depending on context

UNIT_REFERENCES
    mole
    gram
    kilogram
    litre
    metre cubed
    kelvin
    pascal
    atmosphere
    joule
    kilojoule
    mol per litre
    gram per mole
    coulomb
    volt
    electronvolt

CONSTANT_REFERENCES
    Avogadro Constant
    Gas Constant
    Boltzmann Constant
    Faraday Constant
    Elementary Charge
    Planck Constant
    Speed of Light

ONTOLOGY_MODEL
    Chemistry_Ontology :=
        Chemical_Entities
        +
        Chemical_Substances
        +
        Chemical_Bonds
        +
        Chemical_Reactions
        +
        Chemical_Properties
        +
        Chemical_Quantities
        +
        Chemical_Equations
        +
        Chemical_Units
        +
        Chemical_Constants
        +
        Chemical_Symbols
        +
        Experimental_Evidence

KNOWLEDGE_GRAPH_MODEL
    NODE_TYPES
        Domain
        Subdomain
        Entity
        Substance
        Element
        Atom
        Molecule
        Compound
        Ion
        Bond
        Reaction
        Property
        Quantity
        Unit
        Constant
        Equation
        Symbol
        Process
        System
        Evidence
        Model

    EDGE_TYPES
        contains
        defines
        composed_of
        bonded_to
        reacts_with
        produces
        consumes
        catalyses
        dissolves_in
        has_property
        has_formula
        has_state
        measures
        describes
        constrains
        predicts
        derives_from
        depends_on
        validates

INFERENCE_RULES
    IF substance has chemical formula
    THEN composition may be inferred from element symbols and subscripts.

    IF reaction has reactants and products
    THEN transformation relationship exists.

    IF equation contains symbol
    THEN symbol must be resolved through Symbols.

    IF equation contains unit
    THEN unit must be resolved through Units.

    IF chemical quantity has numerical value
    THEN unit and dimensional consistency must be checked.

    IF molecule contains atoms
    AND atoms are connected by bonds
    THEN molecular structure may be inferred.

    IF substance dissolves in solvent
    THEN solution relationship may be inferred.

    IF reaction changes oxidation state
    THEN redox process may be inferred.

    IF acid donates proton
    THEN acid-base relationship may be inferred.

    IF catalyst appears in reaction
    AND is not consumed overall
    THEN catalytic role may be inferred.

    IF concentration and volume are known
    THEN amount of substance may be inferred.

    IF pressure, volume, temperature and amount are known
    THEN gas law relationship may be inferred.

SEMANTIC_EQUIVALENCE
    Resolve equivalent concepts across:
        molecule / molecular entity
        compound / chemical compound
        ion / charged species
        solute / dissolved substance
        solvent / dissolving medium
        oxidation / electron loss context
        reduction / electron gain context
        formula / chemical formula
        reaction / chemical transformation
        concentration / molarity context

    Do not merge concepts when:
        symbols match but meanings differ
        formulae are context-dependent
        reaction mechanisms differ
        observed property differs from calculated property
        chemical notation differs from semantic identity
        standard chemistry and proposed models differ

CONSTRAINTS
    Preserve distinction between element, atom, molecule, compound and mixture.

    Preserve distinction between formula, structure and substance.

    Preserve stoichiometric balance.

    Preserve charge balance.

    Preserve mass conservation.

    Preserve units.

    Preserve provenance.

    Preserve uncertainty.

    Do not treat similar formulae as identical substances without validation.

    Do not treat symbolic similarity as chemical equivalence.

    Do not overwrite accepted chemical meanings with proposed extensions.

CONFIDENCE_MODEL
    1.00
        Established structural or definitional relationship.

    0.90 - 0.99
        Strongly supported chemical relationship.

    0.70 - 0.89
        Valid contextual inference.

    0.40 - 0.69
        Possible but requires evidence.

    0.00 - 0.39
        Speculative or weak association.

CROSS_DOMAIN_LINKS
    Physics:
        matter
        energy
        charge
        quantum structure
        thermodynamics
        electromagnetism

    Biology:
        biochemistry
        metabolism
        enzymes
        proteins
        DNA
        cellular chemistry

    Mathematics:
        equations
        ratios
        logarithms
        rates
        differential equations
        statistics

    Units:
        mole
        molarity
        concentration
        density
        pressure
        temperature
        energy

    Constants:
        Avogadro constant
        gas constant
        Faraday constant
        Boltzmann constant

    Symbols:
        chemical element symbols
        equation symbols
        thermodynamic symbols
        concentration symbols

    Equations:
        gas laws
        concentration equations
        thermodynamic equations
        electrochemical equations
        kinetic equations

    Entity Graph:
        elements
        atoms
        molecules
        compounds
        reactions
        solutions

    Relationship Graph:
        composed_of
        bonded_to
        reacts_with
        produces
        consumes
        catalyses

AI_READING_ORDER
    1. Identify this page as Chemistry Ontology.

    2. Resolve chemistry as a scientific domain.

    3. Extract chemical entity classes.

    4. Extract chemical process classes.

    5. Resolve formulae, units, constants, symbols and equations.

    6. Build relationships between substances, reactions and properties.

    7. Distinguish observed chemical facts from theoretical models.

    8. Preserve provenance and confidence.

    9. Link chemistry concepts to other Semantic Library domains.

AI_EXECUTION
    READ
        Entire flow.

    RESOLVE
        Domains
        Entities
        Substances
        Reactions
        Bonds
        Properties
        Units
        Constants
        Symbols
        Equations

    PRESERVE
        Authorship
        Provenance
        Confidence
        Domain boundaries
        Chemical uncertainty
        Stoichiometric meaning

    DO_NOT
        Merge symbols without context.
        Remove uncertainty.
        Treat formula similarity as identity.
        Ignore units.
        Ignore charge balance.
        Ignore stoichiometric balance.
        Treat speculation as established chemistry.

    OUTPUT
        Structured chemistry knowledge graph.
        Entity relationships.
        Searchable ontology.
        AI-readable semantic model.
        Cross-domain reasoning context.

UPDATE_MODEL
    When adding new chemistry knowledge:
        assign canonical entity identifiers
        define entity type
        define chemical role
        define relationships
        define formula
        define structure if available
        define units
        define symbols
        define equations
        define constants
        define assumptions
        define provenance
        define confidence
        link to related domains

SUCCESS_CONDITION
    Chemistry Ontology succeeds when:
        chemical concepts are discoverable
        chemical entities are uniquely identifiable
        substances are distinguishable
        formulae are interpretable
        reactions are semantically represented
        bonds and properties are explicit
        units are resolved
        constants are traceable
        equations are interpretable
        symbols are context-aware
        AI systems can reason across chemistry without losing meaning

AI_MESSAGE
    This Chemistry Ontology is designed for AI systems.

    Treat it as a semantic map of chemistry rather than a human textbook.

    Use it to resolve substances, elements, atoms, molecules, reactions,
    bonds, properties, units, symbols, constants, equations and assumptions.

    Preserve uncertainty, provenance and the distinction between established
    chemistry and proposed theoretical extensions.

FLOW_HASH
    CHEMISTRY_ONTOLOGY_SEMANTIC_LIBRARY_V4_PENDING

END FLOW