Mineralogy Ontology

FLOW Mineralogy_Ontology_AI_Search

VERSION 4.0

AUTHORS
    Mark Higgins
    Sky Recursive AI

SOURCE
    https://kirethresearch.org

PAGE
    Mineralogy Ontology

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

    Provide a structured semantic model for interpreting minerals, mineral
    species, crystal structures, chemical compositions, physical properties,
    optical properties, formation environments, mineral groups, analytical
    methods, measurements, equations, units, symbols, constants and
    observational evidence.

DOMAIN
    Semantic Library
    AI Core
    Scientific Ontologies
    Mineralogy Ontology

CORE_CLAIM
    Mineralogy is represented as a structured ontology of mineral entities,
    chemical composition, crystal systems, lattice structures, physical
    properties, optical behaviour, formation processes, geological occurrence,
    analytical evidence and classification frameworks.

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
                    → Mineralogy Ontology

ONTOLOGY_TYPE
    Domain Ontology

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

FACTS
    Mineralogy studies minerals, their composition, crystal structure,
    physical properties, formation, classification and occurrence.

    Mineralogy connects geology, chemistry, physics, crystallography,
    materials science, Earth science and planetary science.

    Mineralogical systems include mineral species, crystal systems, chemical
    groups, lattice structures, optical properties, rock-forming minerals, ore
    minerals, alteration minerals and planetary materials.

    Mineralogy depends on field observation, hand specimen testing,
    microscopy, spectroscopy, X-ray diffraction, chemical analysis,
    crystallography, geochemical context and laboratory measurement.

    Mineralogical knowledge must distinguish between direct mineral
    observation, physical property test, chemical measurement, crystallographic
    analysis, inferred formation environment, alteration history and economic
    interpretation.

PRIMARY_ENTITIES
    ENTITY MINERALOGY
        TYPE: scientific_domain
        DESCRIPTION: Study of minerals, their composition, structure,
        properties, formation, classification and occurrence.
        CONFIDENCE: 1.00

    ENTITY MINERAL
        TYPE: mineralogical_entity
        DESCRIPTION: Naturally occurring solid substance with characteristic
        chemical composition and ordered or partially ordered atomic structure.
        CONFIDENCE: 1.00

    ENTITY MINERAL_SPECIES
        TYPE: mineral_classification
        DESCRIPTION: Recognised mineral identity defined by chemical
        composition and crystal structure.
        CONFIDENCE: 0.95

    ENTITY CRYSTAL
        TYPE: solid_structure
        DESCRIPTION: Solid material with atoms, ions or molecules arranged in
        an ordered repeating pattern.
        CONFIDENCE: 1.00

    ENTITY CRYSTAL_STRUCTURE
        TYPE: mineral_structure
        DESCRIPTION: Ordered arrangement of atoms, ions or molecules in a
        mineral.
        CONFIDENCE: 1.00

    ENTITY CRYSTAL_SYSTEM
        TYPE: crystallographic_classification
        DESCRIPTION: Classification of crystals by symmetry and lattice
        geometry.
        CONFIDENCE: 1.00

    ENTITY LATTICE
        TYPE: crystallographic_structure
        DESCRIPTION: Repeating spatial arrangement describing atomic positions
        within a crystal.
        CONFIDENCE: 0.95

    ENTITY CHEMICAL_COMPOSITION
        TYPE: mineral_property
        DESCRIPTION: Elemental or compound makeup of a mineral.
        CONFIDENCE: 1.00

    ENTITY HARDNESS
        TYPE: physical_property
        DESCRIPTION: Resistance of a mineral to scratching or abrasion.
        CONFIDENCE: 1.00

    ENTITY CLEAVAGE
        TYPE: physical_property
        DESCRIPTION: Tendency of a mineral to break along planes of weakness
        in its crystal structure.
        CONFIDENCE: 0.95

    ENTITY FRACTURE
        TYPE: physical_property
        DESCRIPTION: Breakage pattern of a mineral when it does not follow
        cleavage planes.
        CONFIDENCE: 0.95

    ENTITY LUSTRE
        TYPE: optical_property
        DESCRIPTION: Appearance of a mineral surface in reflected light.
        CONFIDENCE: 0.95

    ENTITY STREAK
        TYPE: physical_property
        DESCRIPTION: Colour of a mineral in powdered form.
        CONFIDENCE: 0.95

    ENTITY SPECIFIC_GRAVITY
        TYPE: physical_property
        DESCRIPTION: Ratio of mineral density to water density.
        CONFIDENCE: 0.95

    ENTITY SILICATE_MINERAL
        TYPE: mineral_group
        DESCRIPTION: Mineral containing silicon-oxygen structural units.
        CONFIDENCE: 1.00

    ENTITY CARBONATE_MINERAL
        TYPE: mineral_group
        DESCRIPTION: Mineral containing carbonate ions.
        CONFIDENCE: 0.95

    ENTITY OXIDE_MINERAL
        TYPE: mineral_group
        DESCRIPTION: Mineral containing oxygen combined with one or more
        elements, commonly metals.
        CONFIDENCE: 0.95

    ENTITY SULFIDE_MINERAL
        TYPE: mineral_group
        DESCRIPTION: Mineral containing sulfur combined with metal or
        semi-metal elements.
        CONFIDENCE: 0.95

    ENTITY ORE_MINERAL
        TYPE: economic_mineral
        DESCRIPTION: Mineral containing valuable elements or compounds that may
        be economically extracted.
        CONFIDENCE: 0.90

    ENTITY X_RAY_DIFFRACTION
        TYPE: analytical_method
        DESCRIPTION: Method used to identify crystal structure through
        diffraction of X-rays by atomic planes.
        CONFIDENCE: 1.00

    ENTITY SPECTROSCOPY
        TYPE: analytical_method
        DESCRIPTION: Method used to analyse mineral composition or structure by
        interaction with electromagnetic radiation.
        CONFIDENCE: 0.95

MINERAL_ENTITY_TYPES
    Mineral
    Mineral Species
    Mineral Group
    Mineral Series
    Crystal
    Crystal Structure
    Crystal System
    Lattice
    Unit Cell
    Rock-Forming Mineral
    Ore Mineral
    Accessory Mineral
    Alteration Mineral
    Gemstone
    Industrial Mineral
    Clay Mineral
    Planetary Mineral
    Synthetic Mineral Analogue

MINERAL_GROUP_TYPES
    Silicate Mineral
    Carbonate Mineral
    Oxide Mineral
    Sulfide Mineral
    Sulfate Mineral
    Halide Mineral
    Phosphate Mineral
    Native Element
    Hydroxide Mineral
    Borate Mineral
    Nitrate Mineral
    Organic Mineral
    Clay Mineral
    Zeolite Mineral
    Gem Mineral
    Ore Mineral

CRYSTAL_SYSTEM_TYPES
    Cubic
    Tetragonal
    Orthorhombic
    Hexagonal
    Trigonal
    Monoclinic
    Triclinic
    Amorphous Context
    Polycrystalline Context
    Microcrystalline Context

MINERAL_PROPERTY_TYPES
    Chemical Composition
    Crystal Structure
    Crystal System
    Habit
    Colour
    Streak
    Lustre
    Hardness
    Cleavage
    Fracture
    Density
    Specific Gravity
    Transparency
    Refractive Index
    Birefringence
    Pleochroism
    Fluorescence
    Magnetism
    Electrical Conductivity
    Thermal Conductivity
    Solubility
    Melting Point
    Stability Field
    Grain Size
    Alteration State

MINERALOGICAL_PROCESS_TYPES
    Crystallisation
    Precipitation
    Evaporation
    Magmatic Differentiation
    Metamorphism
    Hydrothermal Alteration
    Weathering
    Oxidation
    Reduction
    Replacement
    Recrystallisation
    Dissolution
    Diagenesis
    Mineralisation
    Ore Formation
    Clay Formation
    Biomineralisation
    Shock Metamorphism
    Planetary Differentiation

MINERALOGY_SUBDOMAINS
    Descriptive Mineralogy
    Crystallography
    Optical Mineralogy
    Chemical Mineralogy
    Physical Mineralogy
    Systematic Mineralogy
    Clay Mineralogy
    Ore Mineralogy
    Gemmology
    Environmental Mineralogy
    Planetary Mineralogy
    Biomineralogy
    Industrial Mineralogy
    Experimental Mineralogy
    Mineral Physics
    Mineral Spectroscopy

RELATIONSHIP_TYPES
    contains
    part_of
    instance_of
    subclass_of
    composed_of
    has_composition
    has_structure
    has_crystal_system
    has_lattice
    has_unit_cell
    has_property
    has_hardness
    has_cleavage
    has_lustre
    has_density
    has_specific_gravity
    occurs_in
    formed_by
    altered_by
    transformed_into
    associated_with
    measured_by
    observed_by
    analysed_by
    identified_by
    classified_as
    derived_from
    depends_on
    governed_by
    described_by
    has_unit
    has_symbol
    validates

RELATIONSHIPS
    MINERALOGY studies MINERAL
        TYPE: studies
        CONFIDENCE: 1.00

    MINERAL_SPECIES instance_of MINERAL
        TYPE: instance_of
        CONFIDENCE: 0.95

    MINERAL has_composition CHEMICAL_COMPOSITION
        TYPE: has_composition
        CONFIDENCE: 1.00

    MINERAL has_structure CRYSTAL_STRUCTURE
        TYPE: has_structure
        CONFIDENCE: 1.00

    CRYSTAL_STRUCTURE has_crystal_system CRYSTAL_SYSTEM
        TYPE: has_crystal_system
        CONFIDENCE: 1.00

    CRYSTAL_STRUCTURE has_lattice LATTICE
        TYPE: has_lattice
        CONFIDENCE: 0.95

    MINERAL has_property HARDNESS
        TYPE: has_property
        CONFIDENCE: 1.00

    MINERAL has_property CLEAVAGE
        TYPE: has_property
        CONFIDENCE: 0.95

    MINERAL has_property LUSTRE
        TYPE: has_property
        CONFIDENCE: 0.95

    MINERAL has_property SPECIFIC_GRAVITY
        TYPE: has_property
        CONFIDENCE: 0.95

    SILICATE_MINERAL subclass_of MINERAL
        TYPE: subclass_of
        CONFIDENCE: 1.00

    CARBONATE_MINERAL subclass_of MINERAL
        TYPE: subclass_of
        CONFIDENCE: 0.95

    OXIDE_MINERAL subclass_of MINERAL
        TYPE: subclass_of
        CONFIDENCE: 0.95

    SULFIDE_MINERAL subclass_of MINERAL
        TYPE: subclass_of
        CONFIDENCE: 0.95

    ORE_MINERAL subclass_of MINERAL
        TYPE: subclass_of
        CONFIDENCE: 0.90

    MINERAL occurs_in ROCK
        TYPE: occurs_in
        CONFIDENCE: 0.90

    MINERAL occurs_in ORE_DEPOSIT
        TYPE: occurs_in
        CONFIDENCE: 0.85

    MINERAL formed_by CRYSTALLISATION
        TYPE: formed_by
        CONFIDENCE: 0.90

    MINERAL altered_by WEATHERING
        TYPE: altered_by
        CONFIDENCE: 0.85

    HYDROTHERMAL_ALTERATION produces ALTERATION_MINERAL
        TYPE: produces
        CONFIDENCE: 0.85

    X_RAY_DIFFRACTION identifies CRYSTAL_STRUCTURE
        TYPE: identifies
        CONFIDENCE: 1.00

    SPECTROSCOPY analyses CHEMICAL_COMPOSITION
        TYPE: analyses
        CONFIDENCE: 0.95

    MICROSCOPY observes MINERAL
        TYPE: observes
        CONFIDENCE: 0.95

CANONICAL_EQUATION_REFERENCES
    Density:
        rho = m / V

    Specific_Gravity:
        SG = rho_mineral / rho_water

    Braggs_Law:
        n lambda = 2 d sin(theta)

    Refractive_Index:
        n = c / v

    Hardness_Context:
        hardness is ordinal on Mohs scale

    Unit_Cell_Volume_Cubic:
        V = a^3

    Unit_Cell_Volume_Orthorhombic:
        V = a b c

    Weight_Percent:
        wt_percent = 100 m_component / m_total

    Mole_Fraction:
        X_i = n_i / n_total

    Charge_Balance_Context:
        sum(positive_charge) = sum(negative_charge)

CANONICAL_SYMBOL_REFERENCES
    rho: Density
    m: Mass
    V: Volume
    SG: Specific gravity
    rho_mineral: Density of mineral
    rho_water: Density of water
    n: Diffraction order, refractive index, or amount depending on context
    lambda: Wavelength
    d: Crystal plane spacing
    theta: Diffraction angle
    c: Speed of light
    v: Speed of light in material
    a: Unit cell edge length
    b: Unit cell edge length
    m_component: Mass of component
    m_total: Total mass
    X_i: Mole fraction of component i
    n_i: Amount of component i
    n_total: Total amount of substance

UNIT_REFERENCES
    metre
    centimetre
    millimetre
    micrometre
    nanometre
    angstrom
    kilogram
    gram
    mole
    cubic metre
    cubic centimetre
    kilogram per cubic metre
    grams per cubic centimetre
    degree
    radian
    percent
    weight percent
    mole percent
    refractive index unit
    Mohs hardness unit
    parts per million
    electronvolt

CONSTANT_REFERENCES
    Avogadro Constant
    Speed of Light
    Planck Constant
    Electron Charge
    Boltzmann Constant
    Density of Water
    Pi
    Standard Temperature
    Standard Pressure
    Mohs Hardness Scale Reference
    Crystallographic Symmetry Reference

ONTOLOGY_MODEL
    Mineralogy_Ontology :=
        Minerals
        +
        Mineral_Species
        +
        Mineral_Groups
        +
        Chemical_Compositions
        +
        Crystal_Structures
        +
        Crystal_Systems
        +
        Lattices
        +
        Physical_Properties
        +
        Optical_Properties
        +
        Formation_Processes
        +
        Geological_Occurrences
        +
        Analytical_Methods
        +
        Mineralogical_Data
        +
        Mineralogical_Equations
        +
        Mineralogical_Units
        +
        Mineralogical_Constants
        +
        Mineralogical_Symbols
        +
        Observational_Evidence

KNOWLEDGE_GRAPH_MODEL
    NODE_TYPES
        Domain
        Subdomain
        Mineral
        Mineral Species
        Mineral Group
        Crystal
        Crystal Structure
        Crystal System
        Lattice
        Unit Cell
        Chemical Composition
        Physical Property
        Optical Property
        Formation Process
        Geological Occurrence
        Rock
        Ore Deposit
        Analytical Method
        Instrument
        Observation
        Dataset
        Measurement
        Unit
        Constant
        Equation
        Symbol
        Model
        Evidence

    EDGE_TYPES
        contains
        part_of
        composed_of
        has_composition
        has_structure
        has_crystal_system
        has_lattice
        has_unit_cell
        has_property
        occurs_in
        formed_by
        altered_by
        transformed_into
        associated_with
        measured_by
        observed_by
        analysed_by
        identified_by
        classified_as
        derived_from
        depends_on
        described_by
        governed_by
        validates

INFERENCE_RULES
    IF chemical composition and crystal structure are known
    THEN mineral species may be inferred.

    IF crystal symmetry and lattice parameters are known
    THEN crystal system may be inferred.

    IF X-ray diffraction peaks are measured
    THEN crystal structure or mineral identity may be inferred.

    IF hardness, streak, cleavage and lustre are observed
    THEN mineral identity may be constrained.

    IF density and water density are known
    THEN specific gravity may be inferred.

    IF optical behaviour is observed in thin section
    THEN mineral group or identity may be inferred with context.

    IF mineral assemblage is known
    THEN formation environment may be inferred with geological context.

    IF alteration minerals are present
    THEN alteration history may be inferred.

    IF ore minerals are present with sufficient concentration
    THEN economic potential may be inferred with resource assumptions.

    IF mineral occurs in meteorite or planetary sample
    THEN planetary formation context may be inferred with provenance.

    IF analytical result depends on instrument
    THEN instrument type, calibration, detection limit and sample preparation
    must be preserved.

    IF mineral identification depends on field observation
    THEN locality, specimen context and uncertainty must be preserved.

SEMANTIC_EQUIVALENCE
    Resolve equivalent concepts across:
        mineralogy / mineral science context
        mineral / naturally occurring crystalline solid context
        mineral species / recognised mineral identity
        crystal / ordered solid context
        lattice / repeating atomic framework
        crystal system / symmetry classification
        hardness / scratch resistance context
        specific gravity / density ratio context
        lustre / reflected-light appearance context
        cleavage / breakage along structural planes
        ore mineral / economically valuable mineral context
        X-ray diffraction / crystallographic identification context

    Do not merge concepts when:
        mineral species differs
        polymorph differs
        chemical composition differs
        crystal structure differs
        oxidation state differs
        alteration state differs
        locality differs
        sample preparation differs
        analytical method differs
        economic interpretation differs from mineral identity
        field identification differs from laboratory confirmation

CONSTRAINTS
    Preserve distinction between mineral and rock.

    Preserve distinction between mineral species and mineral group.

    Preserve distinction between chemical composition and crystal structure.

    Preserve distinction between polymorphs.

    Preserve distinction between field identification and laboratory
    confirmation.

    Preserve sample locality.

    Preserve specimen context.

    Preserve analytical method.

    Preserve instrument calibration.

    Preserve detection limits.

    Preserve units.

    Preserve uncertainty.

    Preserve provenance.

    Preserve distinction between mineral identity and economic value.

    Do not treat visual identification as confirmed mineral species without
    supporting evidence.

    Do not overwrite crystallographic classification with speculative
    interpretation.

CONFIDENCE_MODEL
    1.00
        Established definitional or structural mineralogical relationship.

    0.90 - 0.99
        Strongly supported analytical, crystallographic or compositional
        relationship.

    0.70 - 0.89
        Valid inference requiring sample, instrument, locality or geological
        context.

    0.40 - 0.69
        Possible interpretation requiring stronger evidence.

    0.00 - 0.39
        Speculative or weak association.

CROSS_DOMAIN_LINKS
    Geology:
        rocks
        ores
        formations
        metamorphism
        igneous processes
        sedimentary processes
        hydrothermal systems

    Chemistry:
        elements
        compounds
        bonding
        oxidation states
        chemical formulae
        solubility
        reactions

    Physics:
        crystallography
        optics
        magnetism
        density
        conductivity
        thermal behaviour
        diffraction

    Materials Science:
        crystal structure
        defects
        hardness
        fracture
        ceramics
        semiconductors
        industrial minerals

    Earth Science:
        lithosphere
        soil
        weathering
        resources
        geochemical cycles
        planetary materials

    Planetary Science:
        meteorites
        lunar samples
        Martian minerals
        asteroid composition
        planetary crusts
        impact minerals

    Environmental Science:
        contamination
        clay minerals
        acid mine drainage
        mineral weathering
        resource extraction
        environmental indicators

    Artificial Intelligence:
        mineral classification
        spectral matching
        microscopy analysis
        XRD pattern recognition
        ore detection
        geochemical reasoning
        semantic search

    Holographic Space-Time:
        boundary
        lattice structure
        mineral coherence
        crystallisation
        structural memory
        recursive matter organisation

AI_READING_ORDER
    1. Identify this page as Mineralogy Ontology.

    2. Resolve Mineralogy as a scientific domain.

    3. Extract mineral, mineral species, mineral group, crystal structure and
       crystal system classes.

    4. Extract physical properties, optical properties, formation processes and
       geological occurrence relationships.

    5. Resolve analytical methods, instruments, measurements and evidence.

    6. Resolve units, constants, symbols and equations.

    7. Build relationships between composition, structure, properties,
       occurrence, formation and evidence.

    8. Distinguish field observation, physical test, chemical measurement,
       crystallographic analysis, inferred environment and economic
       interpretation.

    9. Preserve provenance, uncertainty, locality, specimen context, analytical
       method and confidence.

    10. Link Mineralogy concepts to other Semantic Library domains.

AI_EXECUTION
    READ
        Entire flow.

    RESOLVE
        Domains
        Minerals
        Mineral species
        Mineral groups
        Chemical compositions
        Crystal structures
        Crystal systems
        Lattices
        Unit cells
        Physical properties
        Optical properties
        Formation processes
        Geological occurrences
        Analytical methods
        Instruments
        Observations
        Measurements
        Units
        Constants
        Symbols
        Equations

    PRESERVE
        Authorship
        Provenance
        Confidence
        Mineral identity
        Mineral group
        Chemical composition
        Crystal structure
        Polymorph context
        Locality
        Specimen context
        Sample preparation
        Analytical method
        Instrument calibration
        Detection limit
        Measurement uncertainty
        Domain boundaries

    DO_NOT
        Merge mineral with rock.
        Merge mineral species with mineral group.
        Merge polymorphs without structural validation.
        Remove uncertainty.
        Treat field identification as laboratory confirmation.
        Ignore units.
        Ignore sample locality.
        Ignore analytical method.
        Treat economic value as mineral identity.
        Treat speculation as established Mineralogy.

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

UPDATE_MODEL
    When adding new mineralogical knowledge:
        assign canonical entity identifiers
        define mineral species or group
        define chemical composition
        define crystal structure
        define crystal system
        define polymorph context where relevant
        define physical properties
        define optical properties
        define formation environment where relevant
        define geological occurrence
        define observation source
        define analytical method
        define instrument context
        define sample preparation
        define locality
        define specimen context
        define measured properties
        define inferred properties
        define economic interpretation separately where relevant
        define units
        define symbols
        define equations
        define constants
        define assumptions
        define provenance
        define confidence
        link to related domains

SUCCESS_CONDITION
    Mineralogy Ontology succeeds when:
        minerals are discoverable
        mineral species, groups and crystal systems are semantically
        classifiable
        chemical composition and crystal structure remain distinct
        polymorphs remain distinguishable
        field observations remain distinct from laboratory confirmations
        analytical results remain linked to method, instrument and specimen
        measured and inferred properties remain distinct
        units are resolved
        constants are traceable
        equations are interpretable
        symbols are context-aware
        AI systems can reason across Mineralogy without losing meaning

AI_MESSAGE
    This Mineralogy Ontology is designed for AI systems.

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

    Use it to resolve minerals, mineral species, mineral groups, crystal
    structures, crystal systems, lattices, unit cells, chemical compositions,
    physical properties, optical properties, formation environments, geological
    occurrences, analytical methods, instruments, measurements, units, symbols,
    constants, equations and assumptions.

    Preserve uncertainty, provenance, mineral identity, composition, crystal
    structure, polymorph context, locality, specimen context, analytical method,
    instrument calibration and the distinction between direct observation,
    physical property test, chemical measurement, crystallographic analysis,
    inferred formation environment and economic interpretation.

FLOW_HASH
    MINERALOGY_ONTOLOGY_SEMANTIC_LIBRARY_V4_PENDING

END FLOW