Crystallography Domain Ontology

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

flow "CrystallographyDomainOntology" v1.0 {
  ontology:
    id: "crystallography-domain-ontology"
    parent: "earth-environmental-domains"
    purpose: "Represent crystal structures, symmetry, diffraction observations and evidence-backed crystallographic relationships."

  types:
    Crystal: {id: string, material_id: string, phase_id: string?, provenance: string}
    CrystalStructure: {id: string, lattice_id: string, space_group: string?, atomic_sites: string[], source: string}
    UnitCell: {id: string, a: Quantity, b: Quantity, c: Quantity, alpha: Quantity, beta: Quantity, gamma: Quantity}
    Lattice: {id: string, crystal_system: enum[triclinic, monoclinic, orthorhombic, tetragonal, trigonal, hexagonal, cubic], centring: string}
    SymmetryOperation: {id: string, kind: enum[rotation, reflection, inversion, translation, screw, glide], representation: string}
    AtomicSite: {id: string, element: string, fractional_coordinates: number[3], occupancy: number, displacement_parameter: number?}
    DiffractionObservation: {id: string, method: enum[x_ray, neutron, electron, other], wavelength: Quantity?, timestamp: datetime?, dataset: string, provenance: string}
    Refinement: {id: string, structure_id: string, method: string, residual: number?, uncertainty: number?, evidence: string[]}
    Quantity: {value: number, unit: string, uncertainty: number?}
    Relationship: {id: string, subject: string, predicate: string, object: string, confidence: number, evidence: string[], context: string?}

  predicates:
    has_structure(crystal: Crystal, structure: CrystalStructure)
    has_unit_cell(structure: CrystalStructure, cell: UnitCell)
    uses_lattice(structure: CrystalStructure, lattice: Lattice)
    contains_site(structure: CrystalStructure, site: AtomicSite)
    permits_symmetry(structure: CrystalStructure, operation: SymmetryOperation)
    measured_by(structure: CrystalStructure, observation: DiffractionObservation)
    refined_by(structure: CrystalStructure, refinement: Refinement)
    is_polymorph_of(a: CrystalStructure, b: CrystalStructure)

  constraints:
    - "All relationship endpoints resolve to typed entities."
    - "Confidence is within [0,1] and requires evidence provenance."
    - "Unit-cell lengths are positive and angles lie strictly between 0 and 180 degrees."
    - "The unit-cell metric tensor must be positive definite."
    - "Atomic-site occupancies lie within [0,1]; disorder models require explicit constraints."
    - "Fractional coordinates and symmetry operations use a declared cell setting and origin choice."
    - "Space-group assignments must be consistent with observed symmetry and systematic absences, subject to uncertainty."
    - "Do not infer unique structure solely from chemical composition or diffraction peak matches."
    - "Distinguish crystallographic phase, crystal specimen, lattice and structure."

  inference:
    rule structure_cell:
      if has_structure(c,s) and has_unit_cell(s,u)
      then associated_cell(c,u)
      confidence: "retain evidence and crystallographic setting"
    rule symmetry_site_equivalence:
      if contains_site(s,a) and permits_symmetry(s,op) and valid(op)
      then symmetry_related_positions(s,a,op)
      confidence: "conditional on validated symmetry assignment"
    rule polymorph_symmetry:
      if is_polymorph_of(a,b)
      then is_polymorph_of(b,a)
      confidence: "preserve material identity and phase evidence"

  SEMANTIC_EQUIVALENCE:
    - "Normalise crystal systems, lattice settings, space-group symbols and numbers using versioned crystallographic references."
    - "Do not merge polymorphs, enantiomorphs or alternative structure refinements solely by matching formulae."
    - "Preserve coordinate transformations, origin settings, temperatures and pressures."

  CONFIDENCE:
    range: [0,1]
    factors: [diffraction_quality, refinement_fit, measurement_uncertainty, phase_purity, model_ambiguity, independent_replication]
    policy: "Evidence-backed confidence must not rise automatically through chained inference."

  VALIDATION:
    - "Validate units, cell geometry, site occupancies, symmetry closure and structure consistency."
    - "Record diffraction method, experimental conditions, refinement statistics and provenance."
    - "Flag alternative space groups, twinning, disorder and unresolved structural ambiguity."

  FLOW_HASH:
    algorithm: "SHA-256"
    input: "canonicalised ontology version, structure assertions, evidence, rules and provenance"
    note: "Compute at execution; no precomputed hash is asserted."

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

  AI_CONSUMPTION:
    representation: "typed crystallographic knowledge graph with evidence-backed relationships"
    outputs: [crystal_entities, structure_links, symmetry_assertions, measurement_annotations, inferred_relationships, provenance_records]
    safeguards: [preserve_units_and_settings, distinguish_phases, retain_uncertainty, prohibit_unverified_structure_merges]
}

END FLOW ALGEBRA