@prefix msdo: <http://example.org/msdo#> .
@prefix owl:  <http://www.w3.org/2002/07/owl#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd:  <http://www.w3.org/2001/XMLSchema#> .
@prefix dc:   <http://purl.org/dc/elements/1.1/> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix snomed: <http://snomed.info/id/> .
@prefix rxnorm: <http://rxnav.nlm.nih.gov/REST/rxcui/> .
@prefix atc: <http://www.whocc.no/atc_ddd_index/> .
@prefix meddra: <http://purl.bioontology.org/ontology/MEDDRA/> .
@prefix loinc: <http://loinc.org/rdf/> .
@prefix icps: <http://www.who.int/patientsafety/taxonomy/> .
@prefix umls: <https://uts.nlm.nih.gov/uts/umls/> .

#################################################################
# Ontology Metadata
#################################################################

msdo:MSCDO a owl:Ontology ;
  dc:title "Medication Safety Co-Decision Ontology (MSCDO)" ;
  dc:description "A comprehensive ontology enabling ontology-driven human–AI co-decision-making for preventing medication-related harm, integrating medication knowledge, patient context, risk and safety, explainability, and ICPS-based prevention strategies." ;
  dc:creator "Anonymous (for peer review)" ;
  dc:date "2026" .

#################################################################
# =========================
# FIRST-LEVEL CONCEPTS
# =========================
#################################################################

msdo:MedicationEntity a owl:Class ;
  rdfs:label "Medication Entity" ;
  rdfs:comment "Standardized medicinal product representation aligned with RxNorm and ATC." ;
  skos:exactMatch rxnorm:Concept ;
  skos:closeMatch atc:ATCCode .

msdo:PatientContext a owl:Class ;
  rdfs:label "Patient Context" ;
  rdfs:comment "Patient-specific clinical, demographic, physiological, and genetic factors influencing medication safety." ;
  skos:closeMatch umls:CUI .

msdo:MedicationRelatedRisk a owl:Class ;
  rdfs:label "Medication-Related Risk" ;
  rdfs:comment "Potential or actual harm associated with medication use, including errors and adverse events." ;
  skos:exactMatch meddra:10000000 .

msdo:DecisionArtifact a owl:Class ;
  rdfs:label "Decision Artifact" ;
  rdfs:comment "AI- or clinician-generated recommendations, explanations, and evidence." .

msdo:HumanAIInteraction a owl:Class ;
  rdfs:label "Human–AI Interaction" ;
  rdfs:comment "Collaborative decision-making processes between clinicians and AI systems." .

msdo:PatientSafetyPrevention a owl:Class ;
  rdfs:label "Patient Safety and Prevention" ;
  rdfs:comment "ICPS-aligned prevention, detection, and mitigation mechanisms for medication-related harm." ;
  skos:exactMatch icps:ConceptualFramework .

#################################################################
# =========================
# MEDICATION LAYER
# =========================
#################################################################

msdo:Medication a owl:Class ;
  rdfs:subClassOf msdo:MedicationEntity ;
  rdfs:comment "A clinical drug concept normalized using RxNorm." ;
  owl:equivalentClass rxnorm:ClinicalDrug .

msdo:ActiveIngredient a owl:Class ;
  rdfs:comment "Pharmacologically active substance in a medication." ;
  skos:exactMatch rxnorm:Ingredient .

msdo:TherapeuticClass a owl:Class ;
  rdfs:comment "Pharmacological or therapeutic grouping of medications." ;
  owl:equivalentClass atc:ATCCode .

msdo:Dose a owl:Class ;
  skos:closeMatch rxnorm:DoseForm .

msdo:RouteOfAdministration a owl:Class ;
  skos:closeMatch snomed:284009009 .

msdo:Frequency a owl:Class .
msdo:Duration a owl:Class .
msdo:PolypharmacyContext a owl:Class ;
  rdfs:comment "Concurrent use of multiple medications increasing cumulative risk." .

msdo:MedicationUseContext a owl:Class ;
  rdfs:comment "Stage of medication use (prescribing, dispensing, administration, monitoring)." ;
  skos:closeMatch icps:Process .

#################################################################
# =========================
# PATIENT CONTEXT
# =========================
#################################################################

msdo:Patient a owl:Class ;
  rdfs:subClassOf msdo:PatientContext ;
  skos:exactMatch snomed:116154003 .

msdo:ClinicalCondition a owl:Class ;
  owl:equivalentClass snomed:404684003 .

msdo:LaboratoryParameter a owl:Class ;
  owl:equivalentClass loinc:LP29684-5 .

msdo:OrganFunction a owl:Class ;
  skos:closeMatch snomed:363787002 .

msdo:PharmacogenomicProfile a owl:Class ;
  skos:closeMatch umls:C1704417 .

msdo:RiskProfile a owl:Class ;
  skos:closeMatch icps:PatientCharacteristics .

#################################################################
# =========================
# RISK & SAFETY
# =========================
#################################################################

msdo:AdverseDrugEvent a owl:Class ;
  rdfs:subClassOf msdo:MedicationRelatedRisk ;
  owl:equivalentClass meddra:10002034 .

msdo:AdverseDrugReaction a owl:Class ;
  rdfs:subClassOf msdo:AdverseDrugEvent ;
  skos:exactMatch meddra:10001000 .

msdo:MedicationError a owl:Class ;
  rdfs:subClassOf msdo:MedicationRelatedRisk ;
  owl:equivalentClass icps:MedicationError .

msdo:DrugDrugInteraction a owl:Class ;
  skos:closeMatch umls:C0013227 .

msdo:Contraindication a owl:Class ;
  skos:exactMatch snomed:410684002 .

msdo:Severity a owl:Class ;
  skos:closeMatch meddra:Severity .

msdo:Probability a owl:Class .

#################################################################
# =========================
# DECISION & EXPLAINABILITY
# =========================
#################################################################

msdo:Recommendation a owl:Class ;
  rdfs:subClassOf msdo:DecisionArtifact .

msdo:AlternativeOption a owl:Class .
msdo:Explanation a owl:Class ;
  rdfs:comment "Human-readable justification bridging AI reasoning and clinical understanding." .

msdo:EvidenceStrength a owl:Class ;
  skos:closeMatch umls:CUI .

msdo:Uncertainty a owl:Class .
msdo:Guideline a owl:Class ;
  skos:closeMatch umls:CUI .

#################################################################
# =========================
# HUMAN–AI CO-DECISION
# =========================
#################################################################

msdo:Clinician a owl:Class ;
  skos:exactMatch snomed:158965000 .

msdo:AISystem a owl:Class .

msdo:CoDecision a owl:Class ;
  rdfs:subClassOf msdo:HumanAIInteraction ;
  rdfs:comment "A shared clinical decision resulting from clinician–AI collaboration." .

msdo:Rationale a owl:Class .
msdo:TrustCalibration a owl:Class .

#################################################################
# =========================
# ICPS PREVENTION
# =========================
#################################################################

msdo:ContributingFactor a owl:Class ;
  owl:equivalentClass icps:ContributingFactor .

msdo:Detection a owl:Class ;
  skos:closeMatch icps:Detection .

msdo:NearMiss a owl:Class ;
  owl:equivalentClass icps:NearMiss .

msdo:MitigatingAction a owl:Class ;
  skos:exactMatch icps:MitigatingFactors .

msdo:PreventiveStrategy a owl:Class ;
  skos:exactMatch icps:PreventiveAction .

#################################################################
# =========================
# OBJECT PROPERTIES
# =========================
#################################################################

msdo:hasActiveIngredient a owl:ObjectProperty ;
  rdfs:domain msdo:Medication ;
  rdfs:range msdo:ActiveIngredient .

msdo:hasTherapeuticClass a owl:ObjectProperty ;
  rdfs:domain msdo:Medication ;
  rdfs:range msdo:TherapeuticClass .

msdo:hasClinicalCondition a owl:ObjectProperty ;
  rdfs:domain msdo:Patient ;
  rdfs:range msdo:ClinicalCondition .

msdo:causesAdverseEvent a owl:ObjectProperty ;
  rdfs:domain msdo:Medication ;
  rdfs:range msdo:AdverseDrugEvent .

msdo:hasContributingFactor a owl:ObjectProperty ;
  rdfs:domain msdo:MedicationError ;
  rdfs:range msdo:ContributingFactor .

msdo:mitigatedBy a owl:ObjectProperty ;
  rdfs:domain msdo:MedicationRelatedRisk ;
  rdfs:range msdo:MitigatingAction .

msdo:reviewedBy a owl:ObjectProperty ;
  rdfs:domain msdo:Recommendation ;
  rdfs:range msdo:Clinician .

msdo:overriddenBy a owl:ObjectProperty ;
  rdfs:domain msdo:Recommendation ;
  rdfs:range msdo:Clinician .


################################################################# # ========================= # EXTENDED CLASSES # ========================= ################################################################# msdo:TherapyRegimen a owl:Class ; rdfs:subClassOf msdo:Medication ; rdfs:comment "Structured medication therapy regimen." . msdo:InteractionSeverity a owl:Class ; rdfs:subClassOf msdo:DrugDrugInteraction ; rdfs:comment "Severity level of a drug-drug interaction." . msdo:InteractionMechanism a owl:Class ; rdfs:subClassOf msdo:DrugDrugInteraction ; rdfs:comment "Mechanistic explanation of drug interaction." . msdo:CYP450Interaction a owl:Class ; rdfs:subClassOf msdo:DrugDrugInteraction ; rdfs:comment "Cytochrome-mediated drug interaction." . msdo:GeneticVariability a owl:Class ; rdfs:subClassOf msdo:PharmacogenomicProfile ; rdfs:comment "Genetic variability affecting drug response." . msdo:NarrowTherapeuticWindow a owl:Class ; rdfs:subClassOf msdo:MedicationRelatedRisk ; rdfs:comment "Drugs requiring close therapeutic monitoring." . ################################################################# # PROCESS INTEGRITY ################################################################# msdo:MedicationDiscrepancy a owl:Class ; rdfs:comment "Medication discrepancy identified during reconciliation." . msdo:IntentionalDiscrepancy a owl:Class ; rdfs:subClassOf msdo:MedicationDiscrepancy . msdo:DocumentationError a owl:Class ; rdfs:subClassOf msdo:MedicationDiscrepancy . ################################################################# # HARM LAYER ################################################################# msdo:HarmSeverity a owl:Class . msdo:SeriousHarm a owl:Class ; rdfs:subClassOf msdo:HarmSeverity . ################################################################# # EXPLAINABILITY ################################################################# msdo:EvidenceTransparency a owl:Class ; rdfs:subClassOf msdo:DecisionArtifact . msdo:KnowledgeGap a owl:Class ; rdfs:subClassOf msdo:DecisionArtifact . msdo:CalibratedRecommendation a owl:Class ; rdfs:subClassOf msdo:Recommendation . ################################################################# # GOVERNANCE ################################################################# msdo:DetectionMechanism a owl:Class ; rdfs:subClassOf msdo:PatientSafetyPrevention . msdo:OrganizationalOutcome a owl:Class ; rdfs:subClassOf msdo:PatientSafetyPrevention . msdo:ContinuousLearning a owl:Class ; rdfs:subClassOf msdo:PatientSafetyPrevention . ################################################################# # ========================= # ADDITIONAL OBJECT PROPERTIES # ========================= ################################################################# msdo:interactsWith a owl:ObjectProperty ; rdfs:domain msdo:Medication ; rdfs:range msdo:Medication . msdo:hasSeverity a owl:ObjectProperty ; rdfs:domain msdo:DrugDrugInteraction ; rdfs:range msdo:Severity . msdo:prescribedDrug a owl:ObjectProperty ; rdfs:domain msdo:Patient ; rdfs:range msdo:Medication . msdo:hasGeneticRisk a owl:ObjectProperty ; rdfs:domain msdo:Patient ; rdfs:range msdo:GeneticVariability . msdo:hasDiscrepancyType a owl:ObjectProperty ; rdfs:domain msdo:MedicationDiscrepancy ; rdfs:range msdo:MedicationDiscrepancy . msdo:associatedWith a owl:ObjectProperty ; rdfs:domain msdo:Medication ; rdfs:range msdo:AdverseDrugReaction . msdo:hasEvidenceStrength a owl:ObjectProperty ; rdfs:domain msdo:Recommendation ; rdfs:range msdo:EvidenceStrength . msdo:hasUncertaintyLevel a owl:ObjectProperty ; rdfs:domain msdo:Recommendation ; rdfs:range msdo:Uncertainty . ################################################################# # ========================= # RULES (SWRL ANNOTATION) # ========================= ################################################################# msdo:SWRL_HighRiskCombination a owl:AnnotationProperty ; rdfs:comment """ Medication(?d1) ^ Medication(?d2) ^ interactsWith(?d1, ?d2) -> HighRiskMedicationCombination(?d1) """ . msdo:SWRL_DoseAdjustment a owl:AnnotationProperty ; rdfs:comment """ Patient(?p) ^ hasGeneticRisk(?p, ?g) ^ prescribedDrug(?p, ?d) -> RequiresDoseAdjustment(?p) """ . msdo:SWRL_DiscrepancyReview a owl:AnnotationProperty ; rdfs:comment """ MedicationDiscrepancy(?x) -> TriggerMedicationReview(?x) """ . msdo:SWRL_HumanOverride a owl:AnnotationProperty ; rdfs:comment """ Recommendation(?r) ^ reviewedBy(?r, ?c) -> RequiresHumanOverrideReview(?r) """ . msdo:SWRL_SafetySignal a owl:AnnotationProperty ; rdfs:comment """ Medication(?d) ^ associatedWith(?d, ?adr) -> EmergingSafetySignal(?d) """ . 

#################################################################
# =========================
# EMBEDDED SPARQL QUERIES
# =========================
#################################################################

msdo:SPARQL_HighRisk a owl:AnnotationProperty ;
rdfs:comment """
SELECT ?medication ?event
WHERE {
  ?medication msdo:causesAdverseEvent ?event .
  ?event a msdo:AdverseDrugEvent .
}
""" .

msdo:SPARQL_PreventableErrors a owl:AnnotationProperty ;
rdfs:comment """
SELECT ?error ?factor ?strategy
WHERE {
  ?error a msdo:MedicationError .
  ?error msdo:hasContributingFactor ?factor .
  ?error msdo:mitigatedBy ?strategy .
}
""" .