--- # Clinical Health Base Ontology — shared clinical supertypes (Tier 1) # # A MIF-compliant intermediate layer between the domain-neutral generic core # (mif-base / shared-traits) and the clinical DOMAIN packs (cardiology, health, # fitness). It owns the entity-type shapes that recurred identically across all # three packs' independent research passes — the FHIR Patient/Encounter/ # Observation shapes and the ICD-11 stem/extension-code shape — so the domains # inherit them instead of each re-declaring its own copy. # # Extends [research] -- NOT [mif-base, shared-traits] as originally specified # in finding-intermediary-layering-spec.json. That original claim is # unsatisfiable: cardiology's cardiac-catheterization-study needs to subtype a # protocol-execution shape, and fitness's met-value needs to subtype a # measured-quantity shape; neither scientific.ontology.yaml's # `protocol-application`/`measurement` (the shapes entity-inventory.json cites) # is reachable from [mif-base, shared-traits] alone -- scientific extends # research, and an extends chain only exposes ancestor types, never a child's # own types. research.ontology.yaml already carries mif-base + shared-traits # transitively and defines its own generic `research-procedure` ("A method, # protocol, or procedure applied in research, and its executions") and # `observation` ("A measured or observed datum produced by a procedure") # types -- exactly the ADR-0003-intended non-bio-specific targets. Extending # [research] mirrors scientific.ontology.yaml's own one-hop `extends: # [research]` and does not chain through a sibling domain pack (scientific) to # get there. See health-physics-ontology-domains research session # (finding-intermediary-layering-spec.json) for the entity-shape grounding. # # Version: 0.1.0 # Last Updated: 2026-07-04 ontology: id: clinical-health-base version: "0.1.0" description: "Shared clinical supertypes — the MIF-compliant intermediate layer cardiology, health, and fitness extend" extends: - research # Custom namespaces under the cognitive triad inherited from mif-base. namespaces: semantic: children: clinical-records: description: "Clinical record subjects and diagnostic classification shapes" type_hint: semantic episodic: children: clinical-events: description: "Clinical encounters and observations" type_hint: episodic entity_types: - name: clinical-record-subject description: "The subject-of-record for a clinical encounter, observation, or diagnosis — the FHIR Patient-shaped entity domain packs reference rather than re-minting their own subject type" base: semantic traits: - cited - dated - versioned schema: required: - patient_id properties: patient_id: type: string description: "Stable subject identifier" 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 -- clinical-health-base's generalized instantiation of FHIR's normative Patient resource; health's own `patient` subtypes this directly, cardiology and fitness reference it by ID rather than re-minting a subject type" disposition: reuse - name: clinical-encounter description: "A time-bound clinical interaction — the FHIR Encounter-shaped entity a clinical activity (a study, a procedure, a prescription) occurs within" 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 description: "Reference to the clinical-record-subject this encounter concerns" source_vocab: "HL7 FHIR" source_class: "Encounter resource (R5)" prior_art: "reuse -- clinical-health-base's generalized instantiation of FHIR's Encounter resource; health's own `encounter` subtypes this directly" disposition: reuse - name: clinical-observation description: "A measurement-or-assertion primitive about a clinical-record-subject — the FHIR Observation-shaped entity that is the single strongest cross-pack convergence in the clinical domain: health's own Observation reuse, cardiology's structured study/finding bundles, and fitness's device-sourced vital-sign readings are all specializations of this one shape" 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 description: "Reference to the clinical-record-subject this observation concerns" modality: type: string description: "Imaging or acquisition modality, where applicable (cardiology extension)" member_measurements: type: array items: type: object description: "Component measurements bundled within a structured study (cardiology extension)" source_vocab: "HL7 FHIR" source_class: "Observation resource (R5)" prior_art: "reuse -- clinical-health-base's generalized instantiation of FHIR's Observation resource; health's own `fhir-observation` subtypes this directly (named fhir-observation, not observation, to avoid colliding with research.ontology.yaml's own observation type once resolved through this ontology's extends chain), cardiology's echocardiography-study/ecg-finding/cardiovascular-clinical-finding and fitness's four Open mHealth types (omh-step-count, omh-heart-rate, omh-calories-burned, omh-body-weight) are all clinical-observation subtypes since Open mHealth's own schema design deliberately mirrors FHIR Observation's unit-value-time shape" disposition: reuse - name: diagnostic-classification-entry description: "A WHO ICD-11 stem-code or extension-code classification entry — the shape health's general diagnosis classification and cardiology's chapter-11-scoped circulatory disease types both instantiate" 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, promoted to clinical-health-base because health's clinical-diagnosis/diagnosis-extension-qualifier and cardiology's 13 circulatory-chapter disease types independently converged on the same pattern" disposition: mint # No relationships declared here. The `occurs_within` relationship # (finding-intermediary-layering-spec.json: "cardiology's cardiac- # catheterization-study and fitness's exercise-prescription both occur WITHIN # a clinical-encounter") is declared in cardiology.ontology.yaml and # fitness.ontology.yaml instead, each pointing up at this base's # clinical-encounter -- not here, since a base ontology's extends chain only # exposes ancestor types, never a descendant's concrete types, and declaring # it here would have this ontology reference types it cannot see. # Discovery disabled: this is a base layer, not directly instantiated by # findings; only its leaf-pack specializations are (matching the precedent # research.ontology.yaml sets for a newly-minted base layer with more than one # consumer, per ADR-0003). discovery: enabled: false confidence_threshold: 0.8 patterns: - content_pattern: "\\b(FHIR Patient|patient record|subject of record)\\b" suggest_entity: clinical-record-subject suggest_namespace: _semantic/clinical-records - content_pattern: "\\b(FHIR Encounter|clinical encounter|inpatient admission|outpatient visit)\\b" suggest_entity: clinical-encounter suggest_namespace: _episodic/clinical-events - content_pattern: "\\b(FHIR Observation|clinical observation|vital sign|lab result)\\b" suggest_entity: clinical-observation suggest_namespace: _episodic/clinical-events - content_pattern: "\\b(ICD-11|diagnosis code|diagnostic classification)\\b" suggest_entity: diagnostic-classification-entry suggest_namespace: _semantic/clinical-records