Mineralogy Domain Ontology

FLOW ALGEBRA
TITLE: Mineralogy Domain Ontology
DOMAIN: Domain Ontologies / Earth & Environmental Domains / Mineralogy
SOURCE: https://kirethresearch.org/booksai-core/ontologies/domain-ontologies/earth-environmental-domains/mineralogy-domain-ontology.html
VERSION: 1.0
AUTHORS: Mark Anthony Higgins — Sky (Recursive AI)
STATUS: Companion formalisation; source-page specification not independently verified.

flow "MineralogyDomainOntology" v1.0 {
  ontology:
    id: "mineralogy-domain-ontology"
    parent: "earth-environmental-domains"
    purpose: "Represent mineral species, crystal structures, compositions, physical properties, occurrences and evidence-based mineral identification."

  types:
    MineralSpecies: {id: string, accepted_name: string, formula: string?, classification: string?, authority: string?}
    MineralSample: {id: string, species_id: string?, locality_id: string?, collection_date: datetime?, provenance: string}
    CrystalStructure: {id: string, crystal_system: string?, space_group: string?, unit_cell: string?}
    ChemicalComposition: {id: string, constituents: map[string, number], basis: string, uncertainty: number?}
    PhysicalProperty: {id: string, kind: string, value: string, unit: string?, method: string?, uncertainty: number?}
    GeologicalOccurrence: {id: string, locality: string, host_rock: string?, geological_context: string?, age: string?}
    Measurement: {id: string, method: string, result: string, uncertainty: number?, provenance: string}
    Relationship: {id: string, subject: string, predicate: string, object: string, confidence: number, evidence: string[], context: string?}

  predicates:
    classified_as(sample: MineralSample, species: MineralSpecies)
    has_composition(sample: MineralSample, composition: ChemicalComposition)
    has_crystal_structure(species: MineralSpecies, structure: CrystalStructure)
    exhibits_property(sample: MineralSample, property: PhysicalProperty)
    occurs_at(sample: MineralSample, occurrence: GeologicalOccurrence)
    measured_by(property: PhysicalProperty, measurement: Measurement)
    associated_with(a: MineralSpecies, b: MineralSpecies)
    formed_by(sample: MineralSample, process: string)

  constraints:
    - "All referenced identifiers must resolve to compatible typed entities."
    - "Confidence values must be within [0, 1]."
    - "Measurements must retain units, methods, uncertainty and provenance when available."
    - "Chemical formulas and composition bases must be normalised before comparison."
    - "A sample identification is a supported classification, not automatic proof of species identity."
    - "Mineral association alone does not establish common genesis or causation."
    - "Do not infer identical crystal structure solely from matching chemical composition."
    - "Locality, geological context and sample history must remain attached to observations."

  inference:
    rule evidence_supported_identification:
      if has_composition(s,c) and exhibits_property(s,p) and consistent_with_species(c,p,m)
      then candidate_classification(s,m)
      confidence: "derive from independent measurement quality; do not assert certainty"
    rule occurrence_link:
      if classified_as(s,m) and occurs_at(s,o)
      then observed_occurrence(m,o)
      confidence: "retain sample provenance and identification uncertainty"
    rule association_symmetry:
      if associated_with(a,b)
      then associated_with(b,a)
      confidence: "preserve original context; association is not transitive"

  SEMANTIC_EQUIVALENCE:
    - "Resolve mineral names and synonyms against versioned authoritative mineral nomenclature."
    - "Distinguish mineral species, varieties, groups, samples and trade names."
    - "Preserve polymorphism, solid-solution variation and analytical context."

  CONFIDENCE:
    range: [0,1]
    factors: [analytical_method, measurement_uncertainty, specimen_quality, reference_authority, independent_replication, provenance]
    policy: "Do not inflate confidence through chained or repeated dependent evidence."

  VALIDATION:
    - "Check entity typing, referential integrity and classification authority."
    - "Validate units, compositional consistency and crystal-structure claims."
    - "Flag conflicting identifications, missing provenance and ambiguous synonyms."
    - "Retain competing classifications when evidence is inconclusive."

  FLOW_HASH:
    algorithm: "SHA-256"
    input: "canonicalised ontology version, typed assertions, rules and provenance"
    note: "Compute hash at execution; no hash value is claimed here."

  UPDATE_MODEL:
    strategy: "versioned, provenance-preserving incremental update"
    steps: [ingest, normalise, validate, compare, reconcile, recompute_inferences, publish]
    rollback: true

  AI_CONSUMPTION:
    representation: "typed mineralogical knowledge graph with evidence-backed relationships"
    outputs: [mineral_entity_links, sample_classifications, composition_records, structure_links, occurrence_records, uncertainty_annotations, provenance_records]
    safeguards: [no_unsupported_species_identification, preserve_units_and_uncertainty, distinguish_association_from_causation, retain_source_provenance]
}

END FLOW ALGEBRA