diff --git a/src/valuesets/schema/medical/pain.yaml b/src/valuesets/schema/medical/pain.yaml new file mode 100644 index 0000000..7193e8c --- /dev/null +++ b/src/valuesets/schema/medical/pain.yaml @@ -0,0 +1,602 @@ +name: pain +title: Pain-Related Value Sets +description: 'Value sets for pain assessment and management including intensity scales, + duration categories, anatomical locations, quality descriptors, interference levels, + psychosocial constructs, and quantitative sensory testing modalities. + + Based on OPPERA (Orofacial Pain: Prospective Evaluation and Risk Assessment) + standardized measures with alignment to NIH Pain CDEs, PROMIS, and relevant ontologies. + + ' +id: https://w3id.org/valuesets/medical/pain +imports: +- linkml:types +prefixes: + linkml: https://w3id.org/linkml/ + NCIT: http://purl.obolibrary.org/obo/NCIT_ + UBERON: http://purl.obolibrary.org/obo/UBERON_ + HP: http://purl.obolibrary.org/obo/HP_ + SNOMED: http://snomed.info/id/ + LOINC: http://loinc.org/ + OBI: http://purl.obolibrary.org/obo/OBI_ + valuesets: https://w3id.org/valuesets/ +default_prefix: valuesets +slots: + pain_intensity_nrs: + description: Numeric Rating Scale pain intensity (0-10) + range: PainIntensityNumericRatingScaleEnum + pain_intensity_category: + description: Categorical pain intensity classification + range: PainIntensityCategoryEnum + pain_duration: + description: Pain duration classification + range: PainDurationEnum + pain_location: + description: Anatomical location of pain + range: PainLocationEnum + pain_quality: + description: Qualitative pain descriptors + range: PainQualityEnum + pain_interference_level: + description: Pain-related disability or interference level + range: PainInterferenceLevelEnum + psychosocial_construct: + description: Pain-related psychosocial constructs + range: PsychosocialConstructEnum + qst_modality: + description: Quantitative sensory testing modality + range: QuantitativeSensoryTestingModalityEnum + startle_reflex_response: + description: Startle reflex response category + range: StartleReflexResponseEnum + pain_frequency: + description: Frequency of pain episodes + range: PainFrequencyEnum + pain_onset_pattern: + description: Pattern of pain onset and development + range: PainOnsetPatternEnum +enums: + PainIntensityNumericRatingScaleEnum: + description: 0-10 Numeric Rating Scale for pain intensity + permissible_values: + ZERO: + description: No pain + meaning: LOINC:LA6111-4 + annotations: + numeric_value: 0 + category: none + ONE: + description: Pain level 1 + annotations: + numeric_value: 1 + category: mild + TWO: + description: Pain level 2 + annotations: + numeric_value: 2 + category: mild + THREE: + description: Pain level 3 + annotations: + numeric_value: 3 + category: mild + FOUR: + description: Pain level 4 + annotations: + numeric_value: 4 + category: moderate + FIVE: + description: Pain level 5 + annotations: + numeric_value: 5 + category: moderate + SIX: + description: Pain level 6 + annotations: + numeric_value: 6 + category: moderate + SEVEN: + description: Pain level 7 + annotations: + numeric_value: 7 + category: severe + EIGHT: + description: Pain level 8 + annotations: + numeric_value: 8 + category: severe + NINE: + description: Pain level 9 + annotations: + numeric_value: 9 + category: severe + TEN: + description: Worst possible pain + meaning: LOINC:LA6115-5 + annotations: + numeric_value: 10 + category: severe + PainIntensityCategoryEnum: + description: Categorical classifications of pain intensity + permissible_values: + NONE: + description: No pain present + meaning: LOINC:LA6111-4 + annotations: + nrs_range: 0 + MILD: + description: Mild pain that doesn't interfere with activities + meaning: HP:0012825 + annotations: + nrs_range: 1-3 + interference: minimal + MODERATE: + description: Moderate pain that interferes with some activities + meaning: HP:0012826 + annotations: + nrs_range: 4-6 + interference: some + SEVERE: + description: Severe pain that significantly interferes with activities + meaning: HP:0012828 + annotations: + nrs_range: 7-10 + interference: significant + PainDurationEnum: + description: Temporal categories for pain duration and chronicity + permissible_values: + ACUTE: + description: Pain lasting less than 3 months + meaning: SNOMED:373930000 + annotations: + duration: <3 months + characteristics: typically tissue healing related + SUBACUTE: + description: Pain lasting 3-6 months + annotations: + duration: 3-6 months + characteristics: transition period + CHRONIC: + description: Pain persisting beyond 6 months + meaning: HP:0030813 + annotations: + duration: >6 months + characteristics: persistent beyond expected healing + PERSISTENT: + description: Continuous ongoing pain + annotations: + pattern: continuous + characteristics: unremitting + INTERMITTENT: + description: Pain that comes and goes + annotations: + pattern: episodic + characteristics: periods of relief + RECURRENT: + description: Pain that returns after periods of absence + annotations: + pattern: recurring episodes + characteristics: predictable or unpredictable returns + PainLocationEnum: + description: Anatomical locations where pain occurs + permissible_values: + JAW: + description: Jaw or temporomandibular joint area + meaning: UBERON:0001708 + annotations: + region: orofacial + includes: TMJ, masseter, temporalis + FACE: + description: Facial region + meaning: UBERON:0001456 + annotations: + region: orofacial + includes: cheek, forehead, orbital area + HEAD: + description: Head including cranium + meaning: UBERON:0000033 + annotations: + region: cephalic + includes: scalp, temporal, parietal areas + NECK: + description: Cervical region + meaning: UBERON:0000974 + annotations: + region: cervical + includes: anterior, posterior, lateral neck + BACK: + description: Dorsal spine and paraspinal regions + meaning: UBERON:0001137 + annotations: + region: axial + includes: lumbar, thoracic, cervical spine + CHEST: + description: Thoracic region + meaning: UBERON:0001443 + annotations: + region: thoracic + includes: anterior chest wall, ribs + ABDOMEN: + description: Abdominal region + meaning: UBERON:0000916 + annotations: + region: abdominal + includes: upper, lower, lateral abdomen + UPPER_EXTREMITY: + description: Arms, shoulders, hands + meaning: UBERON:0001460 + annotations: + region: appendicular + includes: shoulder, arm, forearm, hand + LOWER_EXTREMITY: + description: Legs, hips, feet + meaning: UBERON:0001774 + annotations: + region: appendicular + includes: hip, thigh, leg, foot + PELVIS: + description: Pelvic region + meaning: UBERON:0002355 + annotations: + region: pelvic + includes: sacroiliac, pubic areas + SHOULDER: + description: Shoulder joint and surrounding area + meaning: UBERON:0001467 + annotations: + region: appendicular + joint: glenohumeral + HIP: + description: Hip joint and surrounding area + meaning: UBERON:0001464 + annotations: + region: appendicular + joint: coxofemoral + KNEE: + description: Knee joint and surrounding area + meaning: UBERON:0001465 + annotations: + region: appendicular + joint: tibiofemoral + ANKLE: + description: Ankle joint and surrounding area + meaning: UBERON:0002389 + annotations: + region: appendicular + joint: talocrural + WRIST: + description: Wrist joint and surrounding area + meaning: UBERON:0002388 + annotations: + region: appendicular + joint: radiocarpal + GENERALIZED: + description: Widespread or generalized pain + annotations: + region: systemic + pattern: diffuse + PainQualityEnum: + description: Qualitative descriptors of pain sensation (McGill Pain Questionnaire derived) + permissible_values: + THROBBING: + description: Pulsating, beating pain + meaning: HP:0025195 + annotations: + category: temporal + mechanism: vascular + ACHING: + description: Dull, persistent discomfort + annotations: + category: continuous + mechanism: deep tissue + STABBING: + description: Sharp, piercing pain + meaning: HP:0003781 + annotations: + category: punctate + mechanism: neuropathic + BURNING: + description: Hot, searing sensation + meaning: HP:0030827 + annotations: + category: thermal + mechanism: neuropathic + TINGLING: + description: Pins and needles sensation + meaning: HP:0003401 + annotations: + category: paresthetic + mechanism: neuropathic + PRESSURE: + description: Squeezing, compressing sensation + annotations: + category: constrictive + mechanism: mechanical + CRAMPING: + description: Spasmodic, gripping pain + meaning: HP:0003394 + annotations: + category: spasmodic + mechanism: muscular + SHOOTING: + description: Lightning-like, radiating pain + annotations: + category: radiating + mechanism: neuropathic + GNAWING: + description: Persistent, consuming pain + annotations: + category: continuous + mechanism: deep tissue + TEARING: + description: Ripping, pulling apart sensation + annotations: + category: mechanical + mechanism: tissue damage + PIERCING: + description: Sharp, penetrating pain + annotations: + category: punctate + mechanism: acute tissue injury + CRUSHING: + description: Heavy, overwhelming pressure + annotations: + category: constrictive + mechanism: severe compression + POUNDING: + description: Rhythmic, hammering pain + annotations: + category: temporal + mechanism: vascular + ELECTRIC: + description: Shock-like, electrical sensation + annotations: + category: neuralgic + mechanism: nerve discharge + PainInterferenceLevelEnum: + description: Levels of pain-related disability and functional interference + permissible_values: + NO_LIMITATION: + description: No functional limitation due to pain + annotations: + grade: 0 + activities: all normal activities possible + promis_alignment: minimal interference + MILD_LIMITATION: + description: Mild functional limitation, minimal impact on daily activities + meaning: HP:0012825 + annotations: + grade: 1 + activities: slight difficulty with demanding activities + promis_alignment: mild interference + MODERATE_LIMITATION: + description: Moderate functional limitation, some impact on daily activities + meaning: HP:0012826 + annotations: + grade: 2 + activities: difficulty with normal activities + promis_alignment: moderate interference + SEVERE_LIMITATION: + description: Severe functional limitation, significant impact on daily activities + meaning: HP:0012828 + annotations: + grade: 3 + activities: major difficulty with basic activities + promis_alignment: severe interference + COMPLETE_LIMITATION: + description: Unable to perform activities due to pain + annotations: + grade: 4 + activities: unable to perform basic functions + promis_alignment: very severe interference + PsychosocialConstructEnum: + description: Pain-related psychosocial constructs from OPPERA battery + permissible_values: + DEPRESSION: + description: Depressive symptoms and mood disorders + meaning: HP:0000716 + annotations: + instrument: CES-D + domain: mood + ANXIETY: + description: Anxiety symptoms and disorders + meaning: HP:0000739 + annotations: + instrument: STAI + domain: mood + CATASTROPHIZING: + description: Pain catastrophizing thoughts and behaviors + annotations: + instrument: PCS + domain: cognition + scale_range: 0-52 + SOMATIZATION: + description: Somatic symptom expression + annotations: + instrument: SCL-90 + domain: somatic + PERCEIVED_STRESS: + description: Subjective experience of stress + annotations: + instrument: PSS + domain: stress + COPING_STRATEGIES: + description: Pain coping mechanisms and strategies + annotations: + instrument: CSQ + domain: behavioral + SOCIAL_SUPPORT: + description: Perceived social support systems + annotations: + domain: social + SLEEP_QUALITY: + description: Sleep disturbance and quality + meaning: HP:0002360 + annotations: + instrument: PSQI + domain: sleep + QuantitativeSensoryTestingModalityEnum: + description: Stimulus modalities used in quantitative sensory testing + permissible_values: + HEAT: + description: Thermal heat stimuli + meaning: OBI:0002044 + annotations: + stimulus_type: thermal + equipment: thermode + measures: heat pain threshold, tolerance + COLD: + description: Thermal cold stimuli + meaning: OBI:0002045 + annotations: + stimulus_type: thermal + equipment: thermode + measures: cold pain threshold, tolerance + PRESSURE: + description: Mechanical pressure stimuli + meaning: OBI:0002046 + annotations: + stimulus_type: mechanical + equipment: algometer + measures: pressure pain threshold + ELECTRICAL: + description: Electrical stimuli + annotations: + stimulus_type: electrical + equipment: electrical stimulator + measures: electrical pain threshold + VIBRATION: + description: Vibratory stimuli + annotations: + stimulus_type: mechanical + equipment: vibrometer + measures: vibration detection threshold + TOUCH: + description: Light touch stimuli + annotations: + stimulus_type: mechanical + equipment: von Frey filaments + measures: tactile detection threshold + PINPRICK: + description: Sharp mechanical stimuli + annotations: + stimulus_type: mechanical + equipment: pinprick stimulator + measures: mechanical pain threshold + CHEMICAL: + description: Chemical stimuli (e.g., capsaicin) + annotations: + stimulus_type: chemical + equipment: topical application + measures: chemical pain sensitivity + StartleReflexResponseEnum: + description: Categories of startle reflex responses in autonomic testing + permissible_values: + NORMAL: + description: Normal startle response + meaning: HP:0031466 + annotations: + magnitude: within normal range + latency: normal + EXAGGERATED: + description: Exaggerated startle response + meaning: HP:0000752 + annotations: + magnitude: increased amplitude + clinical_significance: possible hypervigilance + DIMINISHED: + description: Diminished startle response + annotations: + magnitude: decreased amplitude + clinical_significance: possible habituation + ABSENT: + description: No startle response detected + annotations: + magnitude: no response + clinical_significance: possible dysfunction + DELAYED: + description: Delayed startle response + annotations: + latency: increased response time + clinical_significance: possible processing delay + PainFrequencyEnum: + description: Frequency patterns of pain episodes + permissible_values: + CONSTANT: + description: Continuous, unremitting pain + annotations: + pattern: no pain-free periods + temporal: 24/7 + DAILY: + description: Pain occurring every day + annotations: + pattern: daily episodes + temporal: once or more per day + SEVERAL_TIMES_WEEKLY: + description: Pain occurring multiple times per week + annotations: + pattern: 3-6 times per week + temporal: frequent episodes + WEEKLY: + description: Pain occurring approximately once per week + annotations: + pattern: weekly episodes + temporal: once per week + MONTHLY: + description: Pain occurring approximately once per month + annotations: + pattern: monthly episodes + temporal: once per month + OCCASIONAL: + description: Infrequent, sporadic pain episodes + annotations: + pattern: irregular episodes + temporal: unpredictable + RARE: + description: Very infrequent pain episodes + annotations: + pattern: rare episodes + temporal: few times per year + PainOnsetPatternEnum: + description: Patterns of pain onset and development + permissible_values: + SUDDEN: + description: Abrupt, immediate onset + annotations: + onset_time: seconds to minutes + characteristics: acute onset + GRADUAL: + description: Slow, progressive onset + annotations: + onset_time: hours to days + characteristics: insidious onset + INSIDIOUS: + description: Very gradual, barely noticeable onset + annotations: + onset_time: weeks to months + characteristics: imperceptible onset + TRIGGERED: + description: Onset following specific trigger or event + annotations: + onset_pattern: event-related + characteristics: identifiable precipitant + SPONTANEOUS: + description: Onset without apparent cause + annotations: + onset_pattern: idiopathic + characteristics: no identifiable trigger + PROGRESSIVE: + description: Gradually worsening over time + annotations: + course: deteriorating + characteristics: increasing severity + FLUCTUATING: + description: Variable intensity over time + annotations: + course: variable + characteristics: waxing and waning + SEASONAL: + description: Onset related to seasonal patterns + annotations: + pattern: seasonal variation + characteristics: climate or weather related \ No newline at end of file diff --git a/src/valuesets/schema/valuesets.yaml b/src/valuesets/schema/valuesets.yaml index 7f920d6..f6aa31f 100644 --- a/src/valuesets/schema/valuesets.yaml +++ b/src/valuesets/schema/valuesets.yaml @@ -83,6 +83,7 @@ imports: - medical/clinical - medical/neuroimaging - medical/family_history +- medical/pain - clinical/nih_demographics - clinical/phenopackets - bioprocessing/scale_up