@prefix bcio: . @prefix chebi: . @prefix cmo: . @prefix dcterms: . @prefix efo: . @prefix fm: . @prefix loinc: . @prefix mesh: . @prefix ncit: . @prefix owl: . @prefix prov: . @prefix rdfs: . @prefix sio: . @prefix snomed: . @prefix sosa: . @prefix time: . @prefix voaf: . @prefix vso: . @prefix xsd: . fm:ApEn a owl:NamedIndividual, fm:NonlinearHRV ; rdfs:label "ApEn" ; rdfs:comment "Approximate entropy of RR series (m=2). Legacy metric retained for comparability; ECG signal-based computation (Čukić et al. method) planned as extension" ; fm:belongsToLayer fm:Layer2_Biomarkers ; fm:computedFrom fm:RRIntervals ; fm:hasParamsRef "https://github.com/cik860/fair-mind-ap/blob/main/hrv_params.json"^^xsd:anyURI ; fm:pipelineStatus "implemented" . fm:BMI a cmo:0000105, owl:NamedIndividual, fm:DemographicVar ; rdfs:label "BMI" ; rdfs:comment "Body mass index (kg/m2). Nearest OMR value to recording_date; filtered 10-80" ; fm:belongsToLayer fm:Layer3_Provenance ; fm:pipelineStatus "implemented" . fm:BPM a ncit:C49673, owl:NamedIndividual, fm:PhysiologicalRate ; rdfs:label "BPM" ; rdfs:comment "Mean heart rate (beats per minute). 60000 / mean(RR_ms); 10-second window" ; fm:belongsToLayer fm:Layer2_Biomarkers ; fm:computedFrom fm:RRIntervals ; fm:hasParamsRef "https://github.com/cik860/fair-mind-ap/blob/main/hrv_params.json"^^xsd:anyURI ; fm:pipelineStatus "implemented" . fm:BR a ncit:C49660, owl:NamedIndividual, fm:PhysiologicalRate ; rdfs:label "BR" ; rdfs:comment "Breathing rate derived from ECG (breaths/min). ECG-derived breathing rate via EDR method (neurokit2); NCIT C49660 preferred over PATO for clinical measurement concept" ; fm:belongsToLayer fm:Layer2_Biomarkers ; fm:computedFrom fm:RRIntervals ; fm:hasParamsRef "https://github.com/cik860/fair-mind-ap/blob/main/hrv_params.json"^^xsd:anyURI ; fm:pipelineStatus "implemented" . fm:DBP a vso:0000015, owl:NamedIndividual, fm:DemographicVar ; rdfs:label "DBP" ; rdfs:comment "Diastolic blood pressure (mmHg). Nearest OMR value to recording_date" ; fm:belongsToLayer fm:Layer3_Provenance ; fm:pipelineStatus "implemented" . fm:DFA a owl:NamedIndividual, fm:NonlinearHRV ; rdfs:label "DFA" ; rdfs:comment "Detrended fluctuation analysis alpha. Short-term scaling exponent; nolds library; ECG signal-based computation (Čukić et al. method) planned as extension" ; fm:belongsToLayer fm:Layer2_Biomarkers ; fm:computedFrom fm:RRIntervals ; fm:hasParamsRef "https://github.com/cik860/fair-mind-ap/blob/main/hrv_params.json"^^xsd:anyURI ; fm:pipelineStatus "implemented" . fm:ECGSignal a owl:Class, owl:NamedIndividual ; rdfs:subClassOf fm:SignalSource . fm:ECG_source a owl:NamedIndividual, prov:Activity, fm:ProvenanceVar ; rdfs:label "ECG_source" ; rdfs:comment "ECG acquisition device/protocol metadata. ECG acquisition event; PROV-O Activity; format: dataset|fs|channels|samples|fmt|adc" ; rdfs:seeAlso ; fm:belongsToLayer fm:Layer3_Provenance ; fm:pipelineStatus "implemented" . fm:HF a owl:NamedIndividual, fm:SpectralHRV ; rdfs:label "HF" ; rdfs:comment "High-frequency HRV power 0.15-0.4 Hz (ms^2). Computed via Lomb-Scargle Periodogram (LSP); more reliable than LF at 10s; parasympathetic marker" ; fm:belongsToLayer fm:Layer2_Biomarkers ; fm:computedFrom fm:RRIntervals ; fm:frequencyBand "0.15-0.4 Hz" ; fm:hasParamsRef "https://github.com/cik860/fair-mind-ap/blob/main/hrv_params.json"^^xsd:anyURI ; fm:pipelineStatus "not_computed" . fm:HFD a owl:NamedIndividual, fm:NonlinearHRV ; rdfs:label "HFD" ; rdfs:comment "Higuchi fractal dimension of RR series. kmax=min(10 or N/2); antropy library; ECG signal-based computation (Čukić et al. method) planned as extension" ; fm:belongsToLayer fm:Layer2_Biomarkers ; fm:computedFrom fm:RRIntervals ; fm:hasParamsRef "https://github.com/cik860/fair-mind-ap/blob/main/hrv_params.json"^^xsd:anyURI ; fm:pipelineStatus "implemented" . fm:LF a owl:NamedIndividual, fm:SpectralHRV ; rdfs:label "LF" ; rdfs:comment "Low-frequency HRV power 0.04-0.15 Hz (ms^2). Computed via Lomb-Scargle Periodogram (LSP); ultra-short-term estimate; NIH supports use for ANS assessment with caveats documented" ; fm:belongsToLayer fm:Layer2_Biomarkers ; fm:computedFrom fm:RRIntervals ; fm:frequencyBand "0.04-0.15 Hz" ; fm:hasParamsRef "https://github.com/cik860/fair-mind-ap/blob/main/hrv_params.json"^^xsd:anyURI ; fm:pipelineStatus "not_computed" . fm:LFnu a owl:NamedIndividual, fm:SpectralHRV ; rdfs:label "LFnu" ; rdfs:comment "Normalized LF power. LF/(LF+HF)*100; normalized LF power; FAIR-MIND extension term" ; fm:belongsToLayer fm:Layer2_Biomarkers ; fm:computedFrom fm:RRIntervals ; fm:frequencyBand "0.04-0.15 Hz (normalized)" ; fm:hasParamsRef "https://github.com/cik860/fair-mind-ap/blob/main/hrv_params.json"^^xsd:anyURI ; fm:pipelineStatus "not_computed" . fm:MAD a owl:NamedIndividual, fm:TimeDomainHRV ; rdfs:label "MAD" ; rdfs:comment "Median absolute deviation of RR intervals (ms). Robust variability index; ontology extension needed" ; fm:belongsToLayer fm:Layer2_Biomarkers ; fm:computedFrom fm:RRIntervals ; fm:hasParamsRef "https://github.com/cik860/fair-mind-ap/blob/main/hrv_params.json"^^xsd:anyURI ; fm:pipelineStatus "implemented" . fm:RMSSD a efo:EFO_0009257, owl:NamedIndividual, fm:TimeDomainHRV ; rdfs:label "RMSSD" ; rdfs:comment "Root mean square of successive RR differences (ms). Parasympathetic marker; artifact filtering via neurokit2" ; fm:belongsToLayer fm:Layer2_Biomarkers ; fm:computedFrom fm:RRIntervals ; fm:hasParamsRef "https://github.com/cik860/fair-mind-ap/blob/main/hrv_params.json"^^xsd:anyURI ; fm:pipelineStatus "implemented" . fm:SBP a vso:0000038, owl:NamedIndividual, fm:DemographicVar ; rdfs:label "SBP" ; rdfs:comment "Systolic blood pressure (mmHg). Nearest OMR value to recording_date" ; fm:belongsToLayer fm:Layer3_Provenance ; fm:pipelineStatus "implemented" . fm:SD1 a owl:NamedIndividual, fm:PoincareHRV ; rdfs:label "SD1" ; rdfs:comment "Poincare plot short-term variability (ms). BMONT missing explicit Poincare terms" ; fm:belongsToLayer fm:Layer2_Biomarkers ; fm:computedFrom fm:RRIntervals ; fm:hasParamsRef "https://github.com/cik860/fair-mind-ap/blob/main/hrv_params.json"^^xsd:anyURI ; fm:pipelineStatus "implemented" . fm:SD2 a owl:NamedIndividual, fm:PoincareHRV ; rdfs:label "SD2" ; rdfs:comment "Poincare plot long-term variability (ms). Requires ontology extension for Poincare metrics" ; fm:belongsToLayer fm:Layer2_Biomarkers ; fm:computedFrom fm:RRIntervals ; fm:hasParamsRef "https://github.com/cik860/fair-mind-ap/blob/main/hrv_params.json"^^xsd:anyURI ; fm:pipelineStatus "implemented" . fm:SDNN a efo:EFO_0009256, owl:NamedIndividual, fm:TimeDomainHRV ; rdfs:label "SDNN" ; rdfs:comment "Standard deviation of NN intervals (ms)" ; fm:belongsToLayer fm:Layer2_Biomarkers ; fm:computedFrom fm:RRIntervals ; fm:hasParamsRef "https://github.com/cik860/fair-mind-ap/blob/main/hrv_params.json"^^xsd:anyURI ; fm:pipelineStatus "implemented" . fm:SampEn a owl:NamedIndividual, fm:NonlinearHRV ; rdfs:label "SampEn" ; rdfs:comment "Sample entropy of RR series (m=2). r=0.2*std; inf replaced with NaN; ECG signal-based computation (Čukić et al. method) planned as extension" ; fm:belongsToLayer fm:Layer2_Biomarkers ; fm:computedFrom fm:RRIntervals ; fm:hasParamsRef "https://github.com/cik860/fair-mind-ap/blob/main/hrv_params.json"^^xsd:anyURI ; fm:pipelineStatus "implemented" . fm:TP a owl:NamedIndividual, fm:SpectralHRV ; rdfs:label "TP" ; rdfs:comment "Total power of HRV (ms^2). Total spectral power (LF+HF+VLF); computed via LSP; reliability limited at 10s; documented in params" ; fm:belongsToLayer fm:Layer2_Biomarkers ; fm:computedFrom fm:RRIntervals ; fm:frequencyBand "0.003-0.4 Hz" ; fm:hasParamsRef "https://github.com/cik860/fair-mind-ap/blob/main/hrv_params.json"^^xsd:anyURI ; fm:pipelineStatus "not_computed" . fm:admittime a loinc:LP185883-8, owl:NamedIndividual, fm:Timestamp ; rdfs:label "admittime" ; rdfs:comment "Admission timestamp" ; rdfs:seeAlso ; fm:belongsToLayer fm:Layer3_Provenance ; fm:pipelineStatus "implemented" . fm:age a owl:NamedIndividual, fm:DemographicVar ; rdfs:label "age" ; rdfs:comment "Age at ECG (years). Derived: anchor_age + (recording_date.year - anchor_year)" ; rdfs:seeAlso sio:SIO_001013 ; fm:belongsToLayer fm:Layer3_Provenance ; fm:pipelineStatus "implemented" . fm:anchor_age a sio:SIO_001013, owl:NamedIndividual, fm:DemographicVar ; rdfs:label "anchor_age" ; rdfs:comment "MIMIC-IV anchor age. Reference point for computing age at ECG" ; fm:belongsToLayer fm:Layer3_Provenance ; fm:pipelineStatus "implemented" . fm:anchor_year a owl:NamedIndividual, fm:DemographicVar ; rdfs:label "anchor_year" ; rdfs:comment "MIMIC-IV anchor year. Used with recording_date to derive age" ; fm:belongsToLayer fm:Layer3_Provenance ; fm:pipelineStatus "implemented" . fm:antidepress a owl:NamedIndividual, fm:MedicationVar ; rdfs:label "antidepress" ; rdfs:comment "Antidepressant medication use (binary). Covers SSRI/SNRI classes; renamed from antidepressant" ; rdfs:seeAlso mesh:D000928 ; fm:belongsToLayer fm:Layer4_Medications ; fm:pipelineStatus "implemented" . fm:belongsToLayer a owl:ObjectProperty ; rdfs:domain fm:Variable ; rdfs:isDefinedBy ; rdfs:range fm:APLayer . fm:computedFrom a owl:ObjectProperty ; rdfs:comment "Source signal from which this variable is computed." ; rdfs:domain fm:ComputedVariable ; rdfs:isDefinedBy ; rdfs:range fm:SignalSource ; rdfs:subPropertyOf prov:wasDerivedFrom . fm:depression a snomed:35489007, owl:NamedIndividual, fm:ClinicalVar ; rdfs:label "depression" ; rdfs:comment "Depression flag (ICD-10 F32, F33). Binary; replaces PHQ-9 (unavailable in MIMIC-IV)" ; fm:belongsToLayer fm:Layer1_Clinical ; fm:pipelineStatus "implemented" . fm:dischtime a loinc:MTHU048209, owl:NamedIndividual, fm:Timestamp ; rdfs:label "dischtime" ; rdfs:comment "Discharge timestamp" ; rdfs:seeAlso ; fm:belongsToLayer fm:Layer3_Provenance ; fm:pipelineStatus "implemented" . fm:dod a ncit:C70810, owl:NamedIndividual, fm:Timestamp ; rdfs:label "dod" ; rdfs:comment "Date of death if known. Mortality endpoint" ; rdfs:seeAlso ; fm:belongsToLayer fm:Layer3_Provenance ; fm:pipelineStatus "implemented" . fm:file_name a owl:NamedIndividual, prov:Location, fm:Identifier ; rdfs:label "file_name" ; rdfs:comment "Relative path to WFDB record (.hea/.dat). Relative path to WFDB waveform files (.hea/.dat); source locator" ; rdfs:seeAlso ; fm:belongsToLayer fm:Layer3_Provenance ; fm:pipelineStatus "implemented" . fm:frequencyBand a owl:DatatypeProperty ; rdfs:comment "Frequency range for spectral HRV analysis." ; rdfs:isDefinedBy ; rdfs:range xsd:string . fm:hadm_id a ncit:C25179, owl:NamedIndividual, fm:Identifier ; rdfs:label "hadm_id" ; rdfs:comment "Hospital admission identifier. Hospital admission episode identifier; links ECG to clinical context" ; rdfs:seeAlso ; fm:belongsToLayer fm:Layer3_Provenance ; fm:pipelineStatus "implemented" . fm:hasParamsRef a owl:DatatypeProperty ; rdfs:comment "URI to computation parameter documentation." ; rdfs:domain fm:ComputedVariable ; rdfs:isDefinedBy ; rdfs:range xsd:anyURI . fm:lithium a owl:NamedIndividual, fm:MedicationVar ; rdfs:label "lithium" ; rdfs:comment "Lithium medication use (binary). BCIO links to CHEBI compound for lithium carbonate" ; rdfs:seeAlso chebi:30145 ; fm:belongsToLayer fm:Layer4_Medications ; fm:pipelineStatus "implemented" . fm:pNN20 a owl:NamedIndividual, fm:TimeDomainHRV ; rdfs:label "pNN20" ; rdfs:comment "Percentage of NN differences > 20ms. BMONT defines pNN50 but not pNN20; extension needed" ; fm:belongsToLayer fm:Layer2_Biomarkers ; fm:computedFrom fm:RRIntervals ; fm:hasParamsRef "https://github.com/cik860/fair-mind-ap/blob/main/hrv_params.json"^^xsd:anyURI ; fm:pipelineStatus "implemented" . fm:pNN50 a owl:NamedIndividual, fm:TimeDomainHRV ; rdfs:label "pNN50" ; rdfs:comment "Percentage of NN differences > 50ms. Percentage of NN intervals >50ms; no verified EFO/CMO term found; FAIR-MIND extension pending EFO submission" ; fm:belongsToLayer fm:Layer2_Biomarkers ; fm:computedFrom fm:RRIntervals ; fm:hasParamsRef "https://github.com/cik860/fair-mind-ap/blob/main/hrv_params.json"^^xsd:anyURI ; fm:pipelineStatus "implemented" . fm:pipelineStatus a owl:DatatypeProperty ; rdfs:comment "Implementation status: implemented, not_computable, planned." ; rdfs:isDefinedBy ; rdfs:range xsd:string . fm:recording_date a owl:NamedIndividual, prov:InstantaneousEvent, fm:ProvenanceVar ; rdfs:label "recording_date" ; rdfs:comment "Date and time of ECG measurement. ISO8601 timestamp; renamed from ecg_time" ; rdfs:seeAlso ; fm:belongsToLayer fm:Layer3_Provenance ; fm:pipelineStatus "implemented" . fm:sex a bcio:BCIO_015105, owl:NamedIndividual, fm:DemographicVar ; rdfs:label "sex" ; rdfs:comment "Biological sex of participant. Values M/F; renamed from gender" ; fm:belongsToLayer fm:Layer3_Provenance ; fm:pipelineStatus "implemented" . fm:study_id a owl:NamedIndividual, prov:Entity, fm:Identifier ; rdfs:label "study_id" ; rdfs:comment "MIMIC-IV-ECG unique ECG study identifier. MIMIC-IV-ECG recording identifier; PROV-O Entity representing one ECG record" ; rdfs:seeAlso ; fm:belongsToLayer fm:Layer3_Provenance ; fm:pipelineStatus "implemented" . fm:subject_id a ncit:C41189, owl:NamedIndividual, fm:Identifier ; rdfs:label "subject_id" ; rdfs:comment "MIMIC-IV unique patient identifier. MIMIC-IV patient identifier; maps to NCIT Study Subject concept" ; rdfs:seeAlso ; fm:belongsToLayer fm:Layer3_Provenance ; fm:pipelineStatus "implemented" . fm:suicidality a owl:NamedIndividual, fm:ClinicalVar ; rdfs:label "suicidality" ; rdfs:comment "Suicidal thoughts or behavior flag. ICD-10 T1491/Z915; ideation vs attempt distinction unclear" ; rdfs:seeAlso snomed:429451000124109 ; fm:belongsToLayer fm:Layer1_Clinical ; fm:pipelineStatus "implemented" . fm:z_BMI a owl:NamedIndividual, fm:DemographicVar ; rdfs:label "z_BMI" ; rdfs:comment "Body mass index (standardized z-score). Standardized z-score of BMI; FAIR-MIND extension" ; fm:belongsToLayer fm:Layer3_Provenance ; fm:pipelineStatus "implemented" . fm:z_age a owl:NamedIndividual, fm:DemographicVar ; rdfs:label "z_age" ; rdfs:comment "Age (standardized z-score). Standardized z-score of age; no exact EFO/NCIT term for z-scored demographic; FAIR-MIND extension" ; fm:belongsToLayer fm:Layer3_Provenance ; fm:pipelineStatus "implemented" . fm:ClinicalVar a owl:Class ; rdfs:comment "Clinical diagnostic variable." ; rdfs:isDefinedBy ; rdfs:subClassOf fm:Variable . fm:Layer1_Clinical a owl:Class, owl:NamedIndividual ; rdfs:subClassOf fm:APLayer . fm:Layer4_Medications a owl:Class, owl:NamedIndividual ; rdfs:subClassOf fm:APLayer . fm:MedicationVar a owl:Class ; rdfs:comment "Medication prescription variable." ; rdfs:isDefinedBy ; rdfs:subClassOf fm:Variable . fm:PhysiologicalRate a owl:Class ; rdfs:isDefinedBy ; rdfs:subClassOf fm:ComputedVariable . fm:PoincareHRV a owl:Class ; rdfs:isDefinedBy ; rdfs:subClassOf fm:HRVFeature . fm:ProvenanceVar a owl:Class ; rdfs:comment "Provenance metadata variable (recording source, parameters)." ; rdfs:isDefinedBy ; rdfs:subClassOf prov:Entity, fm:Variable . fm:SignalSource a owl:Class ; rdfs:isDefinedBy . fm:Timestamp a owl:Class ; rdfs:comment "Temporal instant variable (admission, discharge, recording date)." ; rdfs:isDefinedBy ; rdfs:subClassOf time:Instant, fm:Variable . fm:ComputedVariable a owl:Class ; rdfs:comment "A computed variable derived from physiological signals." ; rdfs:isDefinedBy ; rdfs:subClassOf sosa:ObservableProperty, fm:Variable . fm:HRVFeature a owl:Class ; rdfs:isDefinedBy ; rdfs:subClassOf fm:ComputedVariable . fm:Identifier a owl:Class ; rdfs:comment "Record identifier, traceable as a PROV-O entity." ; rdfs:isDefinedBy ; rdfs:subClassOf prov:Entity, fm:Variable . fm:NonlinearHRV a owl:Class ; rdfs:isDefinedBy ; rdfs:subClassOf fm:HRVFeature . fm:SpectralHRV a owl:Class ; rdfs:isDefinedBy ; rdfs:subClassOf fm:HRVFeature . fm:APLayer a owl:Class ; rdfs:isDefinedBy . fm:TimeDomainHRV a owl:Class ; rdfs:isDefinedBy ; rdfs:subClassOf fm:HRVFeature . fm:Variable a owl:Class ; rdfs:isDefinedBy . fm:DemographicVar a owl:Class ; rdfs:comment "Demographic characteristic variable (age, sex, BMI)." ; rdfs:isDefinedBy ; rdfs:subClassOf ncit:C17357, fm:Variable . fm:Layer2_Biomarkers a owl:Class, owl:NamedIndividual ; rdfs:subClassOf fm:APLayer . fm:RRIntervals a owl:Class, owl:NamedIndividual ; rdfs:subClassOf fm:SignalSource . fm:Layer3_Provenance a owl:Class, owl:NamedIndividual ; rdfs:subClassOf fm:APLayer . a voaf:Vocabulary, owl:Ontology ; dcterms:contributor "Milena Čukić" ; dcterms:created "2026-05-01"^^xsd:date ; dcterms:creator "Inkyung Choi" ; dcterms:description "A variable-level vocabulary for integrating depression clinical data with ECG-derived HRV biomarkers, composing 8 established ontologies across 4 semantic layers. Uses RDFS-level semantics with SHACL validation; OWL declarations maintained for forward compatibility." ; dcterms:license ; dcterms:publisher "Sungkyunkwan University" ; dcterms:source ; dcterms:title "FAIR-MIND Application Profile" ; rdfs:seeAlso ; owl:versionIRI ; owl:versionInfo "v4.0" .