Pathology Domain Ontology

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

flow "PathologyDomainOntology" v1.0 {
  ontology:
    id: "pathology-domain-ontology"
    parent: "medical-domains"
    purpose: "Represent pathological processes, specimens, findings, diagnoses, evidence and uncertainty while preserving clinical context and provenance."

  types:
    Disease: {id: string, designation: string, classification_system: string?, classification_version: string?}
    PathologicalProcess: {id: string, kind: string, onset: datetime?, progression: string?}
    AnatomicalStructure: {id: string, name: string, ontology_reference: string?}
    Specimen: {id: string, specimen_type: string, collection_time: datetime?, source_site: string?, provenance: string}
    Examination: {id: string, method: string, specimen_id: string?, performed_at: datetime?, provenance: string}
    Finding: {id: string, description: string, result: string?, unit: string?, uncertainty: number?, provenance: string}
    Diagnosis: {id: string, disease_id: string?, status: enum[suspected, provisional, confirmed, excluded, indeterminate], evidence: string[], confidence: number?}
    Evidence: {id: string, source: string, method: string?, timestamp: datetime?, reliability: number?}
    Relationship: {id: string, subject: string, predicate: string, object: string, context: string?, confidence: number, evidence: string[]}

  predicates:
    affects(process: PathologicalProcess, structure: AnatomicalStructure)
    associated_with(disease: Disease, process: PathologicalProcess)
    sampled_from(specimen: Specimen, structure: AnatomicalStructure)
    examined_by(specimen: Specimen, examination: Examination)
    produces_finding(examination: Examination, finding: Finding)
    supports(finding: Finding, diagnosis: Diagnosis)
    contradicts(finding: Finding, diagnosis: Diagnosis)
    evidenced_by(relationship: Relationship, evidence: Evidence)

  constraints:
    - "All relationship endpoints must resolve to typed entities."
    - "Confidence and evidence reliability, when present, must lie within [0, 1]."
    - "Specimen provenance and examination methods must be recorded."
    - "Measurement units and uncertainty must be preserved where applicable."
    - "Association does not by itself establish causation or diagnosis."
    - "Absence of an observed finding does not automatically exclude a disease."
    - "Distinguish suspected, provisional, confirmed, excluded and indeterminate diagnoses."
    - "Protect patient privacy; do not require identifying patient data for ontology assertions."

  inference:
    rule specimen_finding_trace:
      if examined_by(s,e) and produces_finding(e,f)
      then derived_from(f,s)
      confidence: "retain examination and specimen provenance"
    rule diagnostic_support:
      if supports(f,d) and valid(f)
      then evidence_for(d,f)
      confidence: "context and diagnostic-method dependent; no automatic confirmation"
    rule process_location:
      if affects(p,a) and sampled_from(s,a)
      then relevant_anatomical_context(s,p)
      confidence: "contextual association only; not proof of process in specimen"

  SEMANTIC_EQUIVALENCE:
    - "Map disease and finding terms to versioned clinical terminologies when available."
    - "Separate synonyms, related concepts and exact clinical identity."
    - "Preserve specimen site, examination method, disease stage and temporal context."

  CONFIDENCE:
    range: [0,1]
    factors: [specimen_quality, test_performance, observer_agreement, evidence_reliability, clinical_context, independent_confirmation]
    policy: "Do not inflate confidence through repeated or dependent evidence."

  VALIDATION:
    - "Check entity types, identifiers, units, methods, timestamps and provenance."
    - "Flag incompatible classifications, contradictory findings and missing context."
    - "Require documented evidence for diagnostic assertions and maintain alternatives."
    - "Treat this ontology as knowledge representation, not an autonomous diagnostic authority."

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

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

  AI_CONSUMPTION:
    representation: "typed pathology knowledge graph with evidence-backed relationships"
    outputs: [disease_links, specimen_links, finding_relations, diagnostic_evidence, uncertainty_annotations, provenance_records]
    safeguards: [protect_patient_privacy, no_unsupported_diagnoses, preserve_uncertainty, human_clinical_review]
}

END FLOW ALGEBRA