Mineral Ontology

FLOW ALGEBRA
MINERAL ONTOLOGY — KIRETH SEMANTIC LIBRARY
Version: 1.1
Date: 2026-10-12
Authors: Mark Higgins — Sky (Recursive AI)
Source: https://kirethresearch.org/booksai-core/entity-graph/physical-entities/geological-entities/mineral-ontology.html
Source status: Independent scientific synthesis; live page content not verified.

01. PURPOSE
Model mineral identity, composition, crystallography, physical properties, origin, occurrence, and evidence-based classification as typed and testable relations.

02. SCOPE
Natural mineral species, specimens, varieties, aggregates, polymorphs, solid solutions, and mineral-bearing rocks. Synthetic analogues are distinguished from naturally occurring specimens.

03. CORE DEFINITION
MineralSpecies := naturally occurring geological substance with characteristic chemical composition and ordered atomic structure, subject to recognised exceptions and classification conventions.
MineralSpecimen := physical sample assigned to a mineral species with stated identification confidence.
Mineraloid := naturally occurring mineral-like substance lacking the crystalline structure required for a conventional mineral classification (e.g. opal in common usage).

04. TYPED ENTITIES
MineralSpecies(id, accepted_name, formula, crystal_system, classification_status)
MineralSpecimen(id, provenance, mass, observations)
ChemicalElement(symbol, atomic_number)
Ion(symbol, charge)
CrystalStructure(space_group, lattice_parameters, sites)
CrystalSystem(name)
UnitCell(a,b,c,alpha,beta,gamma)
PhysicalProperty(kind, value, unit, conditions)
GeologicalEnvironment(kind, locality, pressure, temperature)
FormationProcess(kind, inputs, outputs)
Measurement(method, result, uncertainty, calibration)
Evidence(source, method, date, reliability)

05. TYPE CONSTRAINTS
atomic_number: positive integer
mass: nonnegative real with units
lattice lengths a,b,c: positive lengths
angles alpha,beta,gamma: values strictly between 0 and 180 degrees
measurement uncertainty: nonnegative
specimen identity and species identity: distinct identifiers

06. RELATIONSHIPS
INSTANCE_OF(specimen, species)
CONTAINS_ELEMENT(species, element)
HAS_COMPOSITION(species, formula)
HAS_CRYSTAL_STRUCTURE(species, structure)
HAS_CRYSTAL_SYSTEM(structure, system)
HAS_PROPERTY(specimen_or_species, property)
FORMED_BY(specimen, process)
OCCURS_IN(specimen, environment)
ASSOCIATED_WITH(species, species)
POLYMORPH_OF(species, species)
IS_VARIETY_OF(variety, species)
SUPPORTED_BY(assertion, evidence)

07. MINERAL CLASSIFICATION
Classify by dominant anion or anionic group and chemical structure, using a named classification scheme and version.
Common groups: native elements, sulphides, oxides, hydroxides, halides, carbonates, sulphates, phosphates, silicates, and organic minerals.
Classification schemes may differ; never assert a universal rank without a scheme.

08. CHEMICAL COMPOSITION
Represent stoichiometric formulae with explicit occupancy and oxidation states where known.
For a neutral formula unit: sum_i(n_i * z_i) = 0.
For solid solutions: composition may vary over specified site-occupancy intervals.
Example: olivine series (Mg,Fe)2SiO4, with Mg/Fe site substitution.

09. CRYSTALLOGRAPHY
Seven crystal systems: triclinic, monoclinic, orthorhombic, tetragonal, trigonal, hexagonal, cubic.
Crystalline order is expressed by periodic atomic arrangements and symmetry.
Crystal system is not interchangeable with a particular crystal habit.
Space group and unit-cell parameters require appropriate diffraction evidence.

10. POLYMORPHISM
POLYMORPH_OF(A,B) only if A and B have the same chemical composition but different crystal structures.
Example: diamond and graphite are carbon polymorphs.
Do not infer polymorphism merely from different colours or habits.

11. PHYSICAL PROPERTIES
Properties include hardness, cleavage, fracture, density, streak, lustre, colour, transparency, magnetism, optical behaviour and conductivity.
Record environmental conditions and specimen state where properties vary.
Mohs hardness is ordinal, not a linear quantitative measure of indentation resistance.

12. DENSITY
rho = m / V.
Units: kg m^-3 or g cm^-3.
For a crystal cell: rho = (Z * M) / (N_A * V_cell), where Z is formula units per cell, M molar mass, N_A Avogadro constant.
Check units before evaluation.

13. OPTICAL MINERALOGY
Represent refractive index, birefringence, pleochroism and optical orientation with measurement conditions.
Isotropic and anisotropic optical responses depend on structure and symmetry.
Optical observations alone may not uniquely determine mineral species.

14. FORMATION PROCESSES
Crystallisation from melt; precipitation from solution; hydrothermal deposition; metamorphic recrystallisation; biomineralisation; weathering and alteration.
Formation process must be inferred from textural, chemical and geological evidence rather than mineral identity alone.

15. PHASE STABILITY
Stable mineral assemblages depend on pressure, temperature, composition and chemical potentials.
Gibbs free energy: G = H - T*S.
At fixed T and P, equilibrium favours configurations minimising G under relevant constraints.
Metastable minerals may persist; present occurrence does not prove equilibrium stability.

16. GEOLOGICAL CONTEXT
Link mineral specimens to host rock, stratigraphic unit, locality, alteration zone and co-occurring phases.
A species may occur in multiple environments.
Distinguish measured locality from inferred geological origin.

17. IDENTIFICATION WORKFLOW
INPUT: specimen observations + analytical results.
STEP 1: validate sample and measurement provenance.
STEP 2: compare composition, crystal structure and diagnostic properties with candidate species.
STEP 3: assess alternatives and analytical ambiguity.
STEP 4: return candidate identification with confidence and evidence.
OUTPUT: identified species or unresolved candidate set.

18. INFERENCE RULES
R1: INSTANCE_OF(s,m) AND HAS_COMPOSITION(m,f) -> EXPECTED_COMPOSITION(s,f), subject to alteration and impurities.
R2: VERIFIED_XRD(s,pattern) AND MATCHES_REFERENCE(pattern,m) -> SUPPORTS_IDENTIFICATION(s,m), not automatic proof.
R3: SAME_FORMULA(a,b) AND DISTINCT_VERIFIED_STRUCTURES(a,b) -> CANDIDATE_POLYMORPHS(a,b).
R4: MEASURED_PROPERTY(s,p) AND REFERENCE_RANGE(m,p) -> COMPATIBILITY_SCORE(s,m,p).
R5: CONFLICTING_EVIDENCE(s,m) -> REQUIRE_REVIEW(s,m).
R6: ABSENT_DATA(s,property) -> UNKNOWN(s,property), never FALSE(s,property).

19. EXAMPLE: QUARTZ
Species: quartz.
Formula: SiO2.
Crystal system: trigonal (low-temperature alpha-quartz).
Common properties: Mohs hardness approximately 7; no prominent cleavage; conchoidal fracture.
Caution: high-temperature silica polymorphs require distinct structural classification.

20. EXAMPLE: CALCITE
Species: calcite.
Formula: CaCO3.
Crystal system: trigonal.
Common diagnostic properties: rhombohedral cleavage; reaction with dilute acid under appropriate conditions.
Caution: reaction strength depends on surface area and testing conditions.

21. EXAMPLE: HALITE
Species: halite.
Formula: NaCl.
Crystal system: cubic.
Common properties: cubic cleavage; soluble in water.
Caution: do not recommend tasting unidentified specimens.

22. MATHEMATICAL VALIDATION
V1: chemical formula parses correctly.
V2: charge balance is consistent with stated valences.
V3: cell geometry is physically valid.
V4: density and molar-mass units are consistent.
V5: claimed symmetry is compatible with measured structure.
V6: every identification claim links to evidence or is marked inferred.

23. SEMANTIC EQUIVALENCE
mineral species ~ mineral taxon only within an explicitly stated mineralogical classification context.
mineral specimen != mineral species.
crystal habit != crystal system.
rock != mineral.
ore mineral != ore deposit.

24. SEMANTIC DIFFERENCE
Distinguish composition, structure, texture, appearance, provenance and genesis as separate dimensions.
Distinguish natural mineral from synthetic analogue.
Distinguish mineral species from a commercial trade name.

25. UNCERTAINTY AND CONFIDENCE
CONFIDENCE := {score:[0,1], basis, evidence_count, limitations, review_status}.
Scores require documented calibration; never manufacture empirical certainty.
Unknown properties remain explicitly unknown.

26. PROVENANCE
Store source URI, method, observer, timestamp, instrument, uncertainty and classification version.
Preserve original measurements when an interpretation changes.

27. FLOW HASH
FLOW_HASH := SHA256(canonical UTF-8 serialisation of ontology payload excluding FLOW_HASH value).
Canonicalisation must specify field ordering, whitespace, numeric representation and Unicode normalisation.
Hash is a reproducibility identifier, not scientific validation.

28. UPDATE MODEL
On new measurement: append evidence; recompute candidate classifications; flag contradictions; preserve prior version.
On taxonomic change: record previous name, accepted name, authority, effective date and reason.
Do not silently overwrite historic observations.

29. AI CONSUMPTION
AI_CONSUMPTION := {domain:'mineralogy', schema:'typed-entity-relationship', mode:'evidence-grounded', infer_missing:false, expose_uncertainty:true, require_units:true, preserve_provenance:true}.
Reasoning systems must separate observed data, accepted reference facts and derived conclusions.

30. CROSS-ONTOLOGY LINKS
LINK_TO: Rock Ontology; Crystal Ontology; Crystal Structure Ontology; Chemical Element Ontology; Chemical Bond Ontology; Geological Entities; Material Ontology; Measurement Ontology.

31. SAFETY AND LIMITATIONS
Mineral samples may contain hazardous elements or fibres. Identification does not establish handling safety.
This ontology does not replace laboratory identification, hazard assessment or accepted mineral nomenclature authorities.

32. COMPLETENESS CHECK
Required blocks: purpose, definitions, typed entities, relationships, classification, chemistry, crystallography, properties, processes, inference, examples, validation, provenance, hash, update model, AI consumption.
All required blocks present: YES.

END FLOW ALGEBRA — MINERAL ONTOLOGY