---
# Health Ontology (Tier 2 leaf pack)
#
# A MIF domain ontology for general clinical-record data (HL7 FHIR core
# resources) and functioning classification (WHO ICF). Extends
# clinical-health-base directly (one hop), which supplies the shared
# FHIR-shaped and ICD-11-shaped clinical primitives this pack's own types
# specialize.
#
# Grounded in: HL7 FHIR R5 core resources, WHO ICD-11 (general classification
# shape), WHO ICF (functioning/disability/health classification). See
# health-physics-ontology-domains research session, entity-inventory.json
# (pack=health, 13 rows) and finding-health-coverage-audit.json (survived:
# 2 ICD-11 classes + 4 ICF components + 7 FHIR resources mapped; ICF's
# "Personal Factors" component explicitly excluded since the standard itself
# declines to classify or code it).
#
# Version: 0.1.0
# Last Updated: 2026-07-04

ontology:
  id: health
  version: "0.1.0"
  description: "Health domain ontology: general clinical-record data (HL7 FHIR core resources) and functioning classification (WHO ICF)"
  extends:
    - clinical-health-base

namespaces:
  semantic:
    children:
      health-classification:
        description: "ICD-11 diagnosis classification"
        type_hint: semantic
      health-functioning:
        description: "ICF functioning, disability, and health classification"
        type_hint: semantic
  episodic:
    children:
      health-clinical-record:
        description: "FHIR-shaped clinical record data"
        type_hint: episodic

entity_types:
  - name: patient
    description: "The subject of a health record"
    base: semantic
    traits: [cited, dated, versioned]
    schema:
      required: [patient_id]
      properties:
        patient_id: { type: string }
        name: { type: string }
        birth_date: { type: string, format: date }
        gender: { type: string }
        identifiers: { type: array, items: { type: string } }
    source_vocab: "HL7 FHIR"
    source_class: "Patient resource (R5, Normative since v4.0.0)"
    prior_art: "reuse -- direct clone of FHIR's normative Patient resource; also subtypes clinical-health-base's clinical-record-subject"
    disposition: reuse
    subtype_of: [clinical-record-subject]

  - name: condition
    description: "A clinical condition, problem, diagnosis, or other event"
    base: semantic
    traits: [cited, dated, categorized]
    schema:
      required: [condition_id, code]
      properties:
        condition_id: { type: string }
        code: { type: string }
        clinical_status: { type: string }
        onset_date: { type: string, format: date }
        subject_ref: { type: string }
    source_vocab: "HL7 FHIR"
    source_class: "Condition resource (R5)"
    prior_art: "reuse -- direct clone of FHIR's Condition resource"
    disposition: reuse

  - name: fhir-observation
    description: "A measured or asserted clinical datum. Named fhir-observation, not observation: research.ontology.yaml (an ancestor of this ontology via clinical-health-base) already defines its own, incompatible observation entity type, and the JSON-LD projection uses global ids (mif:entityType/<name>) that would collide"
    base: episodic
    traits: [cited, dated, measured]
    schema:
      required: [observation_id, code, value]
      properties:
        observation_id: { type: string }
        code: { type: string }
        value: { type: string }
        unit: { type: string }
        effective_time: { type: string, format: date-time }
        subject_ref: { type: string }
    source_vocab: "HL7 FHIR"
    source_class: "Observation resource (R5)"
    prior_art: "reuse -- direct clone of FHIR's Observation resource; also subtypes clinical-health-base's clinical-observation (the same shape cardiology's echocardiography-study/ecg-finding and fitness's four Open mHealth types extend from)"
    disposition: reuse
    subtype_of: [clinical-observation]

  - name: encounter
    description: "An interaction between a patient and healthcare provider(s)"
    base: episodic
    traits: [cited, dated, categorized]
    schema:
      required: [encounter_id, status]
      properties:
        encounter_id: { type: string }
        status: { type: string }
        class: { type: string }
        period: { type: string }
        subject_ref: { type: string }
    source_vocab: "HL7 FHIR"
    source_class: "Encounter resource (R5)"
    prior_art: "reuse -- direct clone of FHIR's Encounter resource; also subtypes clinical-health-base's clinical-encounter"
    disposition: reuse
    subtype_of: [clinical-encounter]

  - name: procedure
    description: "An action performed on or for a patient"
    base: episodic
    traits: [cited, dated, categorized]
    schema:
      required: [procedure_id, code]
      properties:
        procedure_id: { type: string }
        code: { type: string }
        status: { type: string }
        performed_date: { type: string, format: date }
        subject_ref: { type: string }
    source_vocab: "HL7 FHIR"
    source_class: "Procedure resource (R5)"
    prior_art: "reuse -- direct clone of FHIR's Procedure resource"
    disposition: reuse

  - name: allergy-intolerance
    description: "An allergy or intolerance record"
    base: semantic
    traits: [cited, dated, categorized]
    schema:
      required: [allergy_id, substance]
      properties:
        allergy_id: { type: string }
        substance: { type: string }
        criticality: { type: string }
        reaction: { type: string }
        subject_ref: { type: string }
    source_vocab: "HL7 FHIR"
    source_class: "AllergyIntolerance resource (R5)"
    prior_art: "reuse -- direct clone of FHIR's AllergyIntolerance resource"
    disposition: reuse

  - name: diagnostic-report
    description: "A report of diagnostic results"
    base: episodic
    traits: [cited, dated, documented]
    schema:
      required: [report_id, status]
      properties:
        report_id: { type: string }
        status: { type: string }
        code: { type: string }
        result_refs: { type: array, items: { type: string } }
        conclusion: { type: string }
    source_vocab: "HL7 FHIR"
    source_class: "DiagnosticReport resource (R5)"
    prior_art: "reuse -- direct clone of FHIR's DiagnosticReport resource; the same resource family cardiology's echocardiography-study and cardiac-catheterization-study instantiate as specialty reports"
    disposition: reuse

  - name: clinical-diagnosis
    description: "The general ICD-11 stem-code / Foundation category diagnosis shape"
    base: semantic
    traits: [cited, dated, versioned, categorized]
    schema:
      required: [stem_code, title]
      properties:
        stem_code: { type: string }
        title: { type: string }
        chapter: { type: string }
        foundation_uri: { type: string, format: uri }
    source_vocab: "WHO ICD-11"
    source_class: "ICD-11-MMS stem code / Foundation category"
    prior_art: "mint -- the general ICD-11 stem-code shape, of which cardiology's 13 circulatory-chapter types are chapter-specific instances; promoted alongside clinical-health-base's diagnostic-classification-entry, which this type subtypes"
    disposition: mint
    subtype_of: [diagnostic-classification-entry]

  - name: diagnosis-extension-qualifier
    description: "An ICD-11 extension or cluster code qualifying a diagnosis stem code"
    base: semantic
    traits: [cited, dated, categorized]
    schema:
      required: [extension_code, stem_code, title]
      properties:
        extension_code: { type: string }
        stem_code: { type: string, description: "Renamed from qualifies_stem to match diagnostic-classification-entry's field name directly: the stem code this qualifier attaches to" }
        dimension_type: { type: string }
        title: { type: string, description: "A human-readable label for this specific qualifier (e.g. 'Severe'), distinct from dimension_type (which axis it qualifies: severity, temporality, etiology, etc.)" }
    source_vocab: "WHO ICD-11"
    source_class: "ICD-11-MMS extension codes (severity, temporality, etiology, anatomy, histopathology, causality)"
    prior_art: "mint -- no MIF equivalent for a diagnosis-qualifying extension/cluster code exists; subtypes clinical-health-base's diagnostic-classification-entry per finding-intermediary-layering-spec.json"
    disposition: mint
    subtype_of: [diagnostic-classification-entry]

  - name: body-function
    description: "A physiological body function classification"
    base: semantic
    traits: [cited, dated, categorized, scored]
    schema:
      required: [chapter_code, title]
      properties:
        chapter_code: { type: string }
        title: { type: string }
        impairment_qualifier: { type: string }
    source_vocab: "WHO ICF"
    source_class: "b1-b8 Body Functions chapters"
    prior_art: "mint -- no MIF equivalent for ICF's physiological-function classification exists"
    disposition: mint

  - name: body-structure
    description: "An anatomical body structure classification"
    base: semantic
    traits: [cited, dated, categorized, scored]
    schema:
      required: [chapter_code, title]
      properties:
        chapter_code: { type: string }
        title: { type: string }
        impairment_qualifier: { type: string }
    source_vocab: "WHO ICF"
    source_class: "s1-s8 Body Structures chapters"
    prior_art: "mint -- no MIF equivalent for ICF's anatomical-structure classification exists"
    disposition: mint

  - name: activity-participation-domain
    description: "A functioning/participation classification domain"
    base: semantic
    traits: [cited, dated, categorized, scored]
    schema:
      required: [domain_code, title]
      properties:
        domain_code: { type: string }
        title: { type: string }
        performance_qualifier: { type: string }
        capacity_qualifier: { type: string }
    source_vocab: "WHO ICF"
    source_class: "d1-d9 Activities and Participation domains"
    prior_art: "mint -- no MIF equivalent for ICF's functioning/participation classification exists"
    disposition: mint

  - name: environmental-factor
    description: "An environmental-context classification factor"
    base: semantic
    traits: [cited, dated, categorized]
    schema:
      required: [chapter_code, title]
      properties:
        chapter_code: { type: string }
        title: { type: string }
        barrier_or_facilitator_qualifier: { type: string }
    source_vocab: "WHO ICF"
    source_class: "e1-e5 Environmental Factors chapters"
    prior_art: "mint -- no MIF equivalent for ICF's environmental-context classification exists"
    disposition: mint

discovery:
  enabled: true
  confidence_threshold: 0.8
  patterns:
    - content_pattern: "\\b(ICD-11|diagnosis code|diagnostic classification)\\b"
      suggest_entity: clinical-diagnosis
      suggest_namespace: _semantic/health-classification
    - content_pattern: "\\b(body function|ICF b[1-8]|impairment of function)\\b"
      suggest_entity: body-function
      suggest_namespace: _semantic/health-functioning
    - content_pattern: "\\b(activities of daily living|ICF d[1-9]|participation restriction)\\b"
      suggest_entity: activity-participation-domain
      suggest_namespace: _semantic/health-functioning
    - content_pattern: "\\b(FHIR Patient|patient record|demographics)\\b"
      suggest_entity: patient
      suggest_namespace: _episodic/health-clinical-record
    - content_pattern: "\\b(FHIR Observation|vital sign|lab result|clinical measurement)\\b"
      suggest_entity: fhir-observation
      suggest_namespace: _episodic/health-clinical-record
    - content_pattern: "\\b(clinical encounter|inpatient admission|outpatient visit)\\b"
      suggest_entity: encounter
      suggest_namespace: _episodic/health-clinical-record