Paleontology Domain Ontology

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

flow "PaleontologyDomainOntology" v1.0 {
  ontology:
    id: "paleontology-domain-ontology"
    parent: "earth-environmental-domains"
    purpose: "Represent fossil evidence, extinct organisms, stratigraphic context, geological time, evolutionary hypotheses and reproducible paleontological interpretations."

  types:
    FossilSpecimen: {id: string, accession: string?, preservation: string?, repository: string?, provenance: string}
    Taxon: {id: string, scientific_name: string, rank: string?, authority: string?, status: string?}
    GeologicalUnit: {id: string, name: string, lithology: string?, location: string?, provenance: string}
    GeologicalInterval: {id: string, name: string, timescale_version: string, older_bound_ma: number?, younger_bound_ma: number?}
    Locality: {id: string, coordinates: string?, coordinate_reference_system: string?, spatial_uncertainty: number?, provenance: string}
    Observation: {id: string, method: string, observed_at: datetime?, observer: string?, provenance: string}
    AgeEstimate: {value_ma: number, uncertainty_ma: number?, dating_method: string, calibration: string?, provenance: string}
    Hypothesis: {id: string, statement: string, status: enum[proposed, supported, disputed, rejected], evidence: string[]}
    Relationship: {id: string, subject: string, predicate: string, object: string, context: string?, confidence: number, evidence: string[]}

  predicates:
    assigned_to_taxon(specimen: FossilSpecimen, taxon: Taxon)
    recovered_from(specimen: FossilSpecimen, unit: GeologicalUnit)
    found_at(specimen: FossilSpecimen, locality: Locality)
    dated_to(unit: GeologicalUnit, interval: GeologicalInterval)
    supported_by(hypothesis: Hypothesis, observation: Observation)
    temporally_precedes(a: GeologicalInterval, b: GeologicalInterval)
    shares_character_with(a: Taxon, b: Taxon)
    hypothesised_ancestor_of(a: Taxon, b: Taxon)

  constraints:
    - "All referenced identifiers must resolve to typed entities."
    - "Confidence must be within [0,1]."
    - "Geological ages in Ma must distinguish older from younger bounds and record dating uncertainty."
    - "Taxonomic assignment is a revisable hypothesis, not an immutable identity."
    - "Stratigraphic association alone does not establish direct ancestry."
    - "Absence of fossils is not automatically evidence of taxon absence."
    - "Chronological ordering must use a declared geological timescale version."
    - "Preserve specimen repository, locality precision and source provenance."

  inference:
    rule specimen_context:
      if recovered_from(s,u) and dated_to(u,t)
      then candidate_interval(s,t)
      confidence: "conditional on stratigraphic integrity and dating evidence"
    rule interval_precedence:
      if temporally_precedes(a,b) and temporally_precedes(b,c) and compatible_timescales(a,b,c)
      then temporally_precedes(a,c)
      confidence: "retain uncertainty and boundary evidence"
    rule taxonomic_support:
      if assigned_to_taxon(s,t) and validated_diagnostic_characters(s,t)
      then evidence_for_taxonomic_assignment(s,t)
      confidence: "evaluate diagnostic strength and alternative classifications"

  SEMANTIC_EQUIVALENCE:
    - "Map taxon synonyms to versioned taxonomic authorities without conflating distinct taxon concepts."
    - "Normalise geological interval names against an identified timescale edition."
    - "Keep specimen identifiers distinct from taxon names and locality labels."

  CONFIDENCE:
    range: [0,1]
    factors: [specimen_preservation, stratigraphic_integrity, dating_uncertainty, taxonomic_diagnostics, source_reliability, independent_replication]
    policy: "Propagate uncertainty; never increase certainty merely through inference chaining."

  VALIDATION:
    - "Check identifiers, type compatibility, units, stratigraphic order and provenance."
    - "Flag inconsistent ages, conflicting taxonomic assignments and unverified locality data."
    - "Preserve competing evolutionary interpretations and uncertain placements."

  FLOW_HASH:
    algorithm: "SHA-256"
    input: "canonicalised ontology version, typed assertions, inference rules and provenance"
    note: "Compute 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 paleontological knowledge graph with evidence-backed relationships"
    outputs: [specimen_links, taxon_assignments, stratigraphic_context, temporal_constraints, uncertainty_annotations, provenance_records]
    safeguards: [no_unverified_ancestry_claims, preserve_taxonomic_versions, preserve_dating_uncertainty, distinguish_observation_from_hypothesis]
}

END FLOW ALGEBRA