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Trying to fix basic functionality again.

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This commit is contained in:
Gabe Richman
2025-03-23 11:53:47 -07:00
parent ebda48190a
commit 2141e81f42
406 changed files with 173963 additions and 69 deletions
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8
src/main/resources/disease/custom_disease_list.json Normal file
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[
{
"disease_name": "Hypertension",
"id": "X99",
"ICD-10_name": "Hypertension",
"snomed": "123456789"
}
]

1129
src/main/resources/disease/disease_list.csv Normal file
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src/main/resources/disease/disease_list.json Normal file
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[
{
"disease_name": "Multiple Sclerosis",
"id": "G35",
"ICD-10_name": "Multiple sclerosis",
"snomed": "24700007"
},
{
"disease_name": "Parkinson's Disease",
"id": "G20",
"ICD-10_name": "Parkinson's disease",
"snomed": "49049000"
},
{
"disease_name": "Migraine",
"id": "G43",
"ICD-10_name": "Migraine",
"snomed": "37796009"
},
{
"disease_name": "Epilepsy",
"id": "G40",
"ICD-10_name": "Epilepsy",
"snomed": "84757009"
},
{
"disease_name": "Alzheimer's Disease",
"id": "G30",
"ICD-10_name": "Alzheimer's disease",
"snomed": "26929004"
}
]

32
src/main/resources/disease_list.json Normal file
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[
{
"disease_name": "Hypertension",
"id": "I10",
"ICD-10_name": "Essential (primary) hypertension",
"snomed": "38341003"
},
{
"disease_name": "Migraine",
"id": "G43",
"ICD-10_name": "Migraine",
"snomed": "37796009"
},
{
"disease_name": "Osteoarthritis",
"id": "M19",
"ICD-10_name": "Other and unspecified osteoarthritis",
"snomed": "396275006"
},
{
"disease_name": "Gastroesophageal Reflux Disease",
"id": "K21",
"ICD-10_name": "Gastro-esophageal reflux disease",
"snomed": "235595009"
},
{
"disease_name": "Urinary Tract Infection",
"id": "N39.0",
"ICD-10_name": "Urinary tract infection, site not specified",
"snomed": "68566005"
}
]

6
src/main/resources/disease_modules_progress.md Normal file
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# Disease Module Progress
## Completed Modules
## Planned Modules

403
src/main/resources/modules/acne_vulgaris.json Normal file
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{
"name": "Acne Vulgaris",
"remarks": [
"This module models the diagnosis and treatment of Acne Vulgaris (ICD-10 code: 20002_1548).",
"Acne vulgaris is a chronic inflammatory skin condition that primarily affects adolescents and young adults.",
"It is characterized by comedones (blackheads and whiteheads), papules, pustules, nodules, and cysts.",
"Category: Skin and Subcutaneous Tissue"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Age_Guard"
},
"Age_Guard": {
"type": "Guard",
"allow": {
"age_range": {
"low": 10,
"high": 30
}
},
"direct_transition": "Acne_Onset"
},
"Acne_Onset": {
"type": "Delay",
"range": {
"low": 0,
"high": 60,
"unit": "months"
},
"direct_transition": "Acne_Severity_Determination"
},
"Acne_Severity_Determination": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.5,
"transition": "Mild_Acne"
},
{
"distribution": 0.3,
"transition": "Moderate_Acne"
},
{
"distribution": 0.2,
"transition": "Severe_Acne"
}
]
},
"Mild_Acne": {
"type": "ConditionOnset",
"target_encounter": "Acne_Diagnosis_Encounter",
"codes": [
{
"system": "ICD-10-CM",
"code": "20002_1548",
"display": "Acne vulgaris"
}
],
"assign_to_attribute": "acne",
"direct_transition": "Acne_Diagnosis_Encounter"
},
"Moderate_Acne": {
"type": "ConditionOnset",
"target_encounter": "Acne_Diagnosis_Encounter",
"codes": [
{
"system": "ICD-10-CM",
"code": "20002_1548",
"display": "Acne vulgaris"
}
],
"assign_to_attribute": "acne",
"direct_transition": "Acne_Diagnosis_Encounter"
},
"Severe_Acne": {
"type": "ConditionOnset",
"target_encounter": "Acne_Diagnosis_Encounter",
"codes": [
{
"system": "ICD-10-CM",
"code": "20002_1548",
"display": "Acne vulgaris"
}
],
"assign_to_attribute": "acne",
"direct_transition": "Acne_Diagnosis_Encounter"
},
"Acne_Diagnosis_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "acne",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem"
}
],
"direct_transition": "Acne_Diagnosis"
},
"Acne_Diagnosis": {
"type": "Procedure",
"target_encounter": "Acne_Diagnosis_Encounter",
"reason": "acne",
"codes": [
{
"system": "SNOMED-CT",
"code": "76058001",
"display": "Assessment of skin condition"
}
],
"conditional_transition": [
{
"condition": {
"condition_type": "PriorState",
"name": "Mild_Acne"
},
"transition": "Prescribe_Mild_Treatment"
},
{
"condition": {
"condition_type": "PriorState",
"name": "Moderate_Acne"
},
"transition": "Prescribe_Moderate_Treatment"
},
{
"condition": {
"condition_type": "PriorState",
"name": "Severe_Acne"
},
"transition": "Prescribe_Severe_Treatment"
}
]
},
"Prescribe_Mild_Treatment": {
"type": "MedicationOrder",
"target_encounter": "Acne_Diagnosis_Encounter",
"reason": "acne",
"codes": [
{
"system": "RxNorm",
"code": "1043400",
"display": "Benzoyl Peroxide 5% Topical Gel"
}
],
"direct_transition": "Lifestyle_Education"
},
"Prescribe_Moderate_Treatment": {
"type": "MedicationOrder",
"target_encounter": "Acne_Diagnosis_Encounter",
"reason": "acne",
"codes": [
{
"system": "RxNorm",
"code": "1043400",
"display": "Benzoyl Peroxide 5% Topical Gel"
}
],
"direct_transition": "Prescribe_Topical_Antibiotic"
},
"Prescribe_Topical_Antibiotic": {
"type": "MedicationOrder",
"target_encounter": "Acne_Diagnosis_Encounter",
"reason": "acne",
"codes": [
{
"system": "RxNorm",
"code": "1153378",
"display": "Clindamycin 1% Topical Solution"
}
],
"direct_transition": "Lifestyle_Education"
},
"Prescribe_Severe_Treatment": {
"type": "MedicationOrder",
"target_encounter": "Acne_Diagnosis_Encounter",
"reason": "acne",
"codes": [
{
"system": "RxNorm",
"code": "197698",
"display": "Isotretinoin 20 MG Oral Capsule"
}
],
"direct_transition": "Lifestyle_Education"
},
"Lifestyle_Education": {
"type": "Procedure",
"target_encounter": "Acne_Diagnosis_Encounter",
"reason": "acne",
"codes": [
{
"system": "SNOMED-CT",
"code": "409063005",
"display": "Counseling"
}
],
"direct_transition": "End_Diagnosis_Encounter"
},
"End_Diagnosis_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Treatment_Period"
},
"Treatment_Period": {
"type": "Delay",
"range": {
"low": 4,
"high": 12,
"unit": "weeks"
},
"direct_transition": "Follow_Up_Encounter"
},
"Follow_Up_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "acne",
"codes": [
{
"system": "SNOMED-CT",
"code": "390906007",
"display": "Follow-up encounter"
}
],
"direct_transition": "Assess_Treatment_Response"
},
"Assess_Treatment_Response": {
"type": "Procedure",
"target_encounter": "Follow_Up_Encounter",
"reason": "acne",
"codes": [
{
"system": "SNOMED-CT",
"code": "76058001",
"display": "Assessment of skin condition"
}
],
"distributed_transition": [
{
"distribution": 0.7,
"transition": "Treatment_Successful"
},
{
"distribution": 0.3,
"transition": "Treatment_Adjustment_Needed"
}
]
},
"Treatment_Successful": {
"type": "Simple",
"direct_transition": "End_Follow_Up_Encounter"
},
"Treatment_Adjustment_Needed": {
"type": "Simple",
"conditional_transition": [
{
"condition": {
"condition_type": "PriorState",
"name": "Mild_Acne"
},
"transition": "Escalate_To_Moderate_Treatment"
},
{
"condition": {
"condition_type": "PriorState",
"name": "Moderate_Acne"
},
"transition": "Escalate_To_Severe_Treatment"
},
{
"condition": {
"condition_type": "PriorState",
"name": "Severe_Acne"
},
"transition": "Adjust_Severe_Treatment"
}
]
},
"Escalate_To_Moderate_Treatment": {
"type": "MedicationOrder",
"target_encounter": "Follow_Up_Encounter",
"reason": "acne",
"codes": [
{
"system": "RxNorm",
"code": "1153378",
"display": "Clindamycin 1% Topical Solution"
}
],
"direct_transition": "End_Follow_Up_Encounter"
},
"Escalate_To_Severe_Treatment": {
"type": "MedicationOrder",
"target_encounter": "Follow_Up_Encounter",
"reason": "acne",
"codes": [
{
"system": "RxNorm",
"code": "197698",
"display": "Isotretinoin 20 MG Oral Capsule"
}
],
"direct_transition": "End_Follow_Up_Encounter"
},
"Adjust_Severe_Treatment": {
"type": "MedicationOrder",
"target_encounter": "Follow_Up_Encounter",
"reason": "acne",
"codes": [
{
"system": "RxNorm",
"code": "197699",
"display": "Isotretinoin 40 MG Oral Capsule"
}
],
"direct_transition": "End_Follow_Up_Encounter"
},
"End_Follow_Up_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Check_For_Complications"
},
"Check_For_Complications": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.05,
"transition": "Develop_Scarring"
},
{
"distribution": 0.95,
"transition": "Continued_Treatment"
}
]
},
"Develop_Scarring": {
"type": "ConditionOnset",
"target_encounter": "Complication_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "429127001",
"display": "Acne scar"
}
],
"direct_transition": "Complication_Encounter"
},
"Complication_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem"
}
],
"direct_transition": "Treat_Scarring"
},
"Treat_Scarring": {
"type": "Procedure",
"target_encounter": "Complication_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "277358003",
"display": "Topical treatment"
}
],
"direct_transition": "End_Complication_Encounter"
},
"End_Complication_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Continued_Treatment"
},
"Continued_Treatment": {
"type": "Delay",
"range": {
"low": 3,
"high": 6,
"unit": "months"
},
"distributed_transition": [
{
"distribution": 0.7,
"transition": "Acne_Resolves"
},
{
"distribution": 0.3,
"transition": "Follow_Up_Encounter"
}
]
},
"Acne_Resolves": {
"type": "ConditionEnd",
"referenced_by_attribute": "acne",
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
}
}

397
src/main/resources/modules/acute_bronchitis.json Normal file
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{
"name": "Acute Bronchitis",
"remarks": [
"This module represents acute bronchitis, a common respiratory infection.",
"Acute bronchitis is usually caused by viruses, less commonly by bacteria.",
"Sources: https://www.cdc.gov/antibiotic-use/bronchitis.html",
"https://www.ncbi.nlm.nih.gov/books/NBK448067/",
"https://www.aafp.org/pubs/afp/issues/2016/1001/p560.html"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Potential_Onset"
},
"Potential_Onset": {
"type": "Delay",
"range": {
"low": 0,
"high": 80,
"unit": "years"
},
"direct_transition": "Bronchitis_Incidence"
},
"Bronchitis_Incidence": {
"type": "Simple",
"remarks": [
"Acute bronchitis affects approximately 5% of adults annually.",
"Risk is higher in winter months and in those with underlying conditions."
],
"distributed_transition": [
{
"distribution": 0.05,
"transition": "Bronchitis_Onset"
},
{
"distribution": 0.95,
"transition": "No_Bronchitis"
}
]
},
"No_Bronchitis": {
"type": "Delay",
"exact": {
"quantity": 1,
"unit": "years"
},
"direct_transition": "Bronchitis_Incidence"
},
"Bronchitis_Onset": {
"type": "ConditionOnset",
"target_encounter": "Bronchitis_Encounter",
"assign_to_attribute": "bronchitis_condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "10509002",
"display": "Acute bronchitis (disorder)"
},
{
"system": "ICD-10-CM",
"code": "J20.9",
"display": "Acute bronchitis, unspecified"
}
],
"direct_transition": "Bronchitis_Symptom_Cough"
},
"Bronchitis_Symptom_Cough": {
"type": "Symptom",
"symptom": "Cough",
"range": {
"low": 60,
"high": 95
},
"direct_transition": "Bronchitis_Symptom_Sputum"
},
"Bronchitis_Symptom_Sputum": {
"type": "Symptom",
"symptom": "Sputum production",
"range": {
"low": 45,
"high": 85
},
"direct_transition": "Bronchitis_Symptom_Fatigue"
},
"Bronchitis_Symptom_Fatigue": {
"type": "Symptom",
"symptom": "Fatigue",
"range": {
"low": 30,
"high": 70
},
"direct_transition": "Bronchitis_Symptom_Fever"
},
"Bronchitis_Symptom_Fever": {
"type": "Symptom",
"symptom": "Fever",
"range": {
"low": 0,
"high": 40
},
"direct_transition": "Bronchitis_Symptom_Chest_Discomfort"
},
"Bronchitis_Symptom_Chest_Discomfort": {
"type": "Symptom",
"symptom": "Chest discomfort",
"range": {
"low": 20,
"high": 60
},
"direct_transition": "Bronchitis_Symptom_Shortness_Of_Breath"
},
"Bronchitis_Symptom_Shortness_Of_Breath": {
"type": "Symptom",
"symptom": "Shortness of breath",
"range": {
"low": 10,
"high": 50
},
"direct_transition": "Bronchitis_Symptom_Wheezing"
},
"Bronchitis_Symptom_Wheezing": {
"type": "Symptom",
"symptom": "Wheezing",
"range": {
"low": 5,
"high": 40
},
"direct_transition": "Delay_Until_Doctor"
},
"Delay_Until_Doctor": {
"type": "Delay",
"range": {
"low": 2,
"high": 7,
"unit": "days"
},
"direct_transition": "Bronchitis_Encounter"
},
"Bronchitis_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "bronchitis_condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "185345009",
"display": "Encounter for symptom (procedure)"
}
],
"direct_transition": "Bronchitis_Diagnosis"
},
"Bronchitis_Diagnosis": {
"type": "Procedure",
"target_encounter": "Bronchitis_Encounter",
"reason": "bronchitis_condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "162673000",
"display": "General examination of patient (procedure)"
}
],
"direct_transition": "Bronchitis_Treatment_Decision"
},
"Bronchitis_Treatment_Decision": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.3,
"transition": "Prescribe_Antibiotics",
"remarks": "Despite guidelines recommending against routine antibiotic use, many patients still receive them"
},
{
"distribution": 0.7,
"transition": "Symptomatic_Treatment"
}
]
},
"Prescribe_Antibiotics": {
"type": "MedicationOrder",
"target_encounter": "Bronchitis_Encounter",
"reason": "bronchitis_condition",
"codes": [
{
"system": "RxNorm",
"code": "1658139",
"display": "Azithromycin 250 MG Oral Tablet"
}
],
"direct_transition": "Symptomatic_Treatment"
},
"Symptomatic_Treatment": {
"type": "MedicationOrder",
"target_encounter": "Bronchitis_Encounter",
"reason": "bronchitis_condition",
"codes": [
{
"system": "RxNorm",
"code": "313782",
"display": "Acetaminophen 325 MG Oral Tablet"
}
],
"direct_transition": "Bronchitis_CarePlan"
},
"Bronchitis_CarePlan": {
"type": "CarePlanStart",
"target_encounter": "Bronchitis_Encounter",
"assign_to_attribute": "bronchitis_careplan",
"reason": "bronchitis_condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "408906008",
"display": "Respiratory therapy (regime/therapy)"
}
],
"activities": [
{
"system": "SNOMED-CT",
"code": "409002008",
"display": "Respiratory therapy (regime/therapy)"
},
{
"system": "SNOMED-CT",
"code": "56251003",
"display": "Supportive care (regime/therapy)"
},
{
"system": "SNOMED-CT",
"code": "11816003",
"display": "Increased fluid intake (regime/therapy)"
}
],
"direct_transition": "End_Encounter"
},
"End_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Recovery_Period"
},
"Recovery_Period": {
"type": "Delay",
"range": {
"low": 10,
"high": 21,
"unit": "days"
},
"direct_transition": "Bronchitis_Resolves"
},
"Bronchitis_Resolves": {
"type": "ConditionEnd",
"referenced_by_attribute": "bronchitis_condition",
"direct_transition": "End_Bronchitis_Symptoms"
},
"End_Bronchitis_Symptoms": {
"type": "Symptom",
"symptom": "Cough",
"exact": {
"quantity": 0
},
"direct_transition": "End_Sputum"
},
"End_Sputum": {
"type": "Symptom",
"symptom": "Sputum production",
"exact": {
"quantity": 0
},
"direct_transition": "End_Fatigue"
},
"End_Fatigue": {
"type": "Symptom",
"symptom": "Fatigue",
"exact": {
"quantity": 0
},
"direct_transition": "End_Fever"
},
"End_Fever": {
"type": "Symptom",
"symptom": "Fever",
"exact": {
"quantity": 0
},
"direct_transition": "End_Chest_Discomfort"
},
"End_Chest_Discomfort": {
"type": "Symptom",
"symptom": "Chest discomfort",
"exact": {
"quantity": 0
},
"direct_transition": "End_Shortness_Of_Breath"
},
"End_Shortness_Of_Breath": {
"type": "Symptom",
"symptom": "Shortness of breath",
"exact": {
"quantity": 0
},
"direct_transition": "End_Wheezing"
},
"End_Wheezing": {
"type": "Symptom",
"symptom": "Wheezing",
"exact": {
"quantity": 0
},
"direct_transition": "End_Medications"
},
"End_Medications": {
"type": "Simple",
"conditional_transition": [
{
"condition": {
"condition_type": "Active Medication",
"codes": [
{
"system": "RxNorm",
"code": "1658139",
"display": "Azithromycin 250 MG Oral Tablet"
}
]
},
"transition": "End_Antibiotics"
},
{
"transition": "End_Pain_Medication"
}
]
},
"End_Antibiotics": {
"type": "MedicationEnd",
"medication_order": {
"codes": [
{
"system": "RxNorm",
"code": "1658139",
"display": "Azithromycin 250 MG Oral Tablet"
}
]
},
"direct_transition": "End_Pain_Medication"
},
"End_Pain_Medication": {
"type": "MedicationEnd",
"medication_order": {
"codes": [
{
"system": "RxNorm",
"code": "313782",
"display": "Acetaminophen 325 MG Oral Tablet"
}
]
},
"direct_transition": "End_CarePlan"
},
"End_CarePlan": {
"type": "CarePlanEnd",
"referenced_by_attribute": "bronchitis_careplan",
"direct_transition": "Potential_Followup"
},
"Potential_Followup": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.1,
"transition": "Followup_Encounter",
"remarks": "Only a small percentage of patients need followup for acute bronchitis"
},
{
"distribution": 0.9,
"transition": "Potential_Onset"
}
]
},
"Followup_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"codes": [
{
"system": "SNOMED-CT",
"code": "390906007",
"display": "Follow-up encounter (procedure)"
}
],
"direct_transition": "End_Followup"
},
"End_Followup": {
"type": "EncounterEnd",
"direct_transition": "Potential_Onset"
},
"Terminal": {
"type": "Terminal"
}
},
"gmf_version": 2
}

879
src/main/resources/modules/acute_myeloid_leukemia.json Normal file
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{
"name": "Acute Myeloid Leukemia for PCOR Research",
"states": {
"Initial": {
"type": "Initial",
"complex_transition": [
{
"condition": {
"condition_type": "Gender",
"gender": "F"
},
"distributions": [
{
"transition": "Cancerous",
"distribution": 0.002
},
{
"transition": "Terminal",
"distribution": 0.998
}
]
},
{
"condition": {
"condition_type": "Gender",
"gender": "M"
},
"distributions": [
{
"transition": "Cancerous",
"distribution": 0.003
},
{
"transition": "Terminal",
"distribution": 0.997
}
]
}
]
},
"Terminal": {
"type": "Terminal"
},
"Levofloxacin": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 199885,
"display": "levofloxacin 500 MG Oral Tablet"
}
],
"chronic": false,
"assign_to_attribute": "levofloxacin",
"administration": true,
"reason": "Acute_Myeloid_Leukemia_AML",
"prescription": {
"dosage": {
"amount": 1,
"frequency": 1,
"period": 1,
"unit": "days"
},
"duration": {
"quantity": 1,
"unit": "days"
}
},
"direct_transition": "Absolute_Neutrophil_Count_ANC"
},
"No_Levofloxacin_Prophylaxis": {
"type": "Simple",
"direct_transition": "Absolute_Neutrophil_Count_ANC2"
},
"Absolute_Neutrophil_Count_ANC": {
"type": "Observation",
"category": "laboratory",
"unit": "10*3/uL",
"codes": [
{
"system": "LOINC",
"code": "751-8",
"display": "Neutrophils [#/volume] in Blood by Automated count"
}
],
"range": {
"low": 250,
"high": 500
},
"direct_transition": "Check_Fever"
},
"Febrile_Neutropenia": {
"type": "ConditionOnset",
"assign_to_attribute": "",
"target_encounter": "Chemotherapy_Inpatient_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "409089005",
"display": "Febrile neutropenia (disorder)"
}
],
"direct_transition": "Check_Bacteremia"
},
"Non-Febrile_Neutropenia": {
"type": "ConditionOnset",
"assign_to_attribute": "",
"target_encounter": "Chemotherapy_Inpatient_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "47318007",
"display": "Drug-induced neutropenia (disorder)"
}
],
"direct_transition": "Transfer_to_Stepdown"
},
"Bacteremia": {
"type": "ConditionOnset",
"assign_to_attribute": "bacteremia",
"target_encounter": "Chemotherapy_Inpatient_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "5758002",
"display": "Bacteremia (finding)"
}
],
"distributed_transition": [
{
"transition": "Transfer_to_ICU",
"distribution": 0.112
},
{
"transition": "Transfer_to_Stepdown",
"distribution": 0.8620000000000001
},
{
"transition": "Death_Event",
"distribution": 0.026
}
]
},
"Check_Bacteremia": {
"type": "Delay",
"distribution": {
"kind": "GAUSSIAN",
"parameters": {
"mean": 90,
"standardDeviation": 30
}
},
"unit": "minutes",
"complex_transition": [
{
"condition": {
"condition_type": "Active Medication",
"codes": [
{
"system": "RxNorm",
"code": 199885,
"display": "levofloxacin 500 MG Oral Tablet"
}
]
},
"distributions": [
{
"transition": "Bacteremia",
"distribution": 0.137
},
{
"transition": "No_Bacteremia",
"distribution": 0.863
}
]
},
{
"condition": {
"condition_type": "Attribute",
"attribute": "levofloxacin",
"operator": "is nil"
},
"distributions": [
{
"transition": "Bacteremia",
"distribution": 0.33
},
{
"transition": "No_Bacteremia",
"distribution": 0.6699999999999999
}
]
}
]
},
"No_Bacteremia": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Transfer_to_ICU",
"distribution": 0.041
},
{
"transition": "Death_Event",
"distribution": 0.015
},
{
"transition": "Transfer_to_Stepdown",
"distribution": 0.944
}
]
},
"Death": {
"type": "Death",
"direct_transition": "End_Encounter2",
"remarks": [
""
],
"codes": [
{
"system": "SNOMED-CT",
"code": "91861009",
"display": "Acute myeloid leukemia (disorder)"
}
]
},
"End_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Terminal",
"discharge_disposition": {
"system": "NUBC",
"code": 1,
"display": "Discharge to Home"
}
},
"Absolute_Neutrophil_Count_ANC2": {
"type": "Observation",
"category": "laboratory",
"unit": "10*3/uL",
"codes": [
{
"system": "LOINC",
"code": "751-8",
"display": "Neutrophils [#/volume] in Blood by Automated count"
}
],
"direct_transition": "Check_Fever2",
"range": {
"low": 250,
"high": 500
}
},
"Normal_Body_Temp": {
"type": "Observation",
"category": "vital-signs",
"unit": "[degF]",
"codes": [
{
"system": "LOINC",
"code": "8310-5",
"display": "Body Temperature"
}
],
"direct_transition": "Non-Febrile_Neutropenia",
"range": {
"low": 96,
"high": 99
}
},
"Fever": {
"type": "Observation",
"category": "vital-signs",
"unit": "[degF]",
"codes": [
{
"system": "LOINC",
"code": "8310-5",
"display": "Body Temperature"
}
],
"range": {
"low": 100.4,
"high": 103
},
"direct_transition": "Febrile_Neutropenia"
},
"Check_Fever": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Fever",
"distribution": 0.656
},
{
"transition": "Normal_Body_Temp",
"distribution": 0.344
}
]
},
"Check_Fever2": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Fever",
"distribution": 0.795
},
{
"transition": "Normal_Body_Temp",
"distribution": 0.20500000000000007
}
]
},
"Chemotherapy": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "367336001",
"display": "Chemotherapy (procedure)"
}
],
"duration": {
"low": 60,
"high": 120,
"unit": "minutes"
},
"reason": "Acute_Myeloid_Leukemia_AML",
"direct_transition": "Determine_Levofloxacin_Prophylaxis"
},
"Transfer_to_ICU": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "305351004",
"display": "Admission to intensive care unit (procedure)"
}
],
"duration": {
"low": 30,
"high": 120,
"unit": "minutes"
},
"complex_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "5758002",
"display": "Bacteremia (finding)"
}
]
},
"distributions": [
{
"transition": "Death_Event",
"distribution": 0.167
},
{
"transition": "Transfer_to_Stepdown",
"distribution": 0.833
}
]
},
{
"distributions": [
{
"transition": "Death_Event",
"distribution": 0.061
},
{
"transition": "Transfer_to_Stepdown",
"distribution": 0.9390000000000001
}
]
}
],
"reason": "Febrile_Neutropenia"
},
"Chemotherapy_Inpatient_Encounter": {
"type": "Encounter",
"encounter_class": "inpatient",
"reason": "Acute_Myeloid_Leukemia_AML",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem (procedure)"
}
],
"direct_transition": "Wait for Treatment"
},
"Death_Event": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "16983000",
"display": "Death in hospital (event)"
}
],
"duration": {
"low": 30,
"high": 60,
"unit": "minutes"
},
"direct_transition": "Death",
"reason": "Acute_Myeloid_Leukemia_AML"
},
"Determine_Levofloxacin_Prophylaxis": {
"type": "Delay",
"distribution": {
"kind": "GAUSSIAN",
"parameters": {
"mean": 90,
"standardDeviation": 30
}
},
"unit": "minutes",
"lookup_table_transition": [
{
"transition": "Levofloxacin",
"default_probability": 0.2638,
"lookup_table_name": "AML.csv"
},
{
"transition": "No_Levofloxacin_Prophylaxis",
"default_probability": 0.7362,
"lookup_table_name": "AML.csv"
}
]
},
"End_Encounter2": {
"type": "EncounterEnd",
"direct_transition": "Terminal",
"discharge_disposition": {
"system": "NUBC",
"code": 41,
"display": "Expired in medical facility"
}
},
"Transfer_to_Stepdown": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "449214001",
"display": "Transfer to stepdown unit (procedure)"
}
],
"duration": {
"low": 60,
"high": 120,
"unit": "minutes"
},
"direct_transition": "Wait for Discharge",
"reason": "Acute_Myeloid_Leukemia_AML"
},
"Delay_1": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 1
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_2": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 2
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_3": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 3
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_4": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 4
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_5": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 5
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_6": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 6
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_7": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 7
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_8": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 8
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_9": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 9
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_10": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 10
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_11": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 11
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_12": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 12
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_13": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 13
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_14": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 14
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_15": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 15
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_16": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 16
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_17": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 17
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_18": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 18
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_19": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 19
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_20": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 20
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_21": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 21
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Delay_0": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 0
}
},
"unit": "years",
"direct_transition": "Acute_Myeloid_Leukemia_AML"
},
"Acute_Myeloid_Leukemia_AML": {
"type": "ConditionOnset",
"assign_to_attribute": "",
"codes": [
{
"system": "SNOMED-CT",
"code": "91861009",
"display": "Acute myeloid leukemia (disorder)"
}
],
"direct_transition": "Chemotherapy_Inpatient_Encounter"
},
"End_Levofloxacin": {
"type": "MedicationEnd",
"direct_transition": "End_AML",
"medication_order": "Levofloxacin",
"codes": [
{
"system": "RxNorm",
"code": 199885,
"display": "levofloxacin 500MG Oral tablet"
}
]
},
"End_Non-Febrile_Neutropenia": {
"type": "ConditionEnd",
"direct_transition": "End_Febrile_Neutropenia",
"condition_onset": "Non-Febrile_Neutropenia"
},
"End_Febrile_Neutropenia": {
"type": "ConditionEnd",
"direct_transition": "End_Bacteremia",
"condition_onset": "Febrile_Neutropenia"
},
"End_Bacteremia": {
"type": "ConditionEnd",
"direct_transition": "End_Encounter",
"condition_onset": "Bacteremia"
},
"End_AML": {
"type": "ConditionEnd",
"direct_transition": "End_Non-Febrile_Neutropenia",
"condition_onset": "Acute_Myeloid_Leukemia_AML"
},
"Cancerous": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Delay_1",
"distribution": 0.098
},
{
"transition": "Delay_2",
"distribution": 0.1264
},
{
"transition": "Delay_3",
"distribution": 0.1094
},
{
"transition": "Delay_4",
"distribution": 0.0645
},
{
"transition": "Delay_5",
"distribution": 0.0533
},
{
"transition": "Delay_6",
"distribution": 0.0345
},
{
"transition": "Delay_7",
"distribution": 0.0362
},
{
"transition": "Delay_8",
"distribution": 0.0318
},
{
"transition": "Delay_9",
"distribution": 0.0354
},
{
"transition": "Delay_10",
"distribution": 0.0346
},
{
"transition": "Delay_11",
"distribution": 0.0289
},
{
"transition": "Delay_12",
"distribution": 0.0312
},
{
"transition": "Delay_13",
"distribution": 0.033
},
{
"transition": "Delay_14",
"distribution": 0.03
},
{
"transition": "Delay_15",
"distribution": 0.0343
},
{
"transition": "Delay_16",
"distribution": 0.0289
},
{
"transition": "Delay_17",
"distribution": 0.0323
},
{
"transition": "Delay_18",
"distribution": 0.0323
},
{
"transition": "Delay_19",
"distribution": 0.0346
},
{
"transition": "Delay_20",
"distribution": 0.0315
},
{
"transition": "Delay_21",
"distribution": 0.0173
},
{
"transition": "Delay_0",
"distribution": 0.04159999999999997
}
]
},
"Wait for Treatment": {
"type": "Delay",
"distribution": {
"kind": "GAUSSIAN",
"parameters": {
"mean": 180,
"standardDeviation": 60
}
},
"unit": "minutes",
"direct_transition": "Chemotherapy"
},
"Wait for Discharge": {
"type": "Delay",
"distribution": {
"kind": "GAUSSIAN",
"parameters": {
"mean": 180,
"standardDeviation": 60
}
},
"unit": "minutes",
"direct_transition": "End_Levofloxacin"
}
},
"remarks": [
"Module Title: Acute Myeloid Leukemia for PCOR Research",
"Version Number: 1.0",
"Date Created: 8/12/2021",
"Module Steward: ONC",
"Module Developer: Clinovations Government + Health",
"Description: This module models Levofloxacin prophylaxis in patients age <=21 years of age. It is based on a microsimulation study to effectively test the utility of Synthea data for PCOR hypothesis testing. This module was designed with a microsimulation-based hypothesis from a study by McCormick et al., which provides an evaluation of the cost effectiveness of levofloxacin use in children with acute myeloid leukemia (AML). The McCormick study includes a decision-analysis model designed to evaluate the cost-effectiveness of levofloxacin prophylaxis compared to no prophylaxis in patients less than or equal to 21 years of age with AML during a single chemotherapy inpatient visit. The study reports outcomes, including the cost of bacterial infection, cost per ICU admission, and cost per death avoided. In order to replicate the costs within this study, costs within appropriate Synthea cost lookup files were updated. In addition, one city in the default demographics file within Synthea was updated with gender, race, and ethnicity parameters from the McCormick study in order to generate similar population characteristics. This module is not intended to include all possible clinical issues related to the patient with acute myeloid leukemia (AML) or represent a clinical care guideline of any kind.",
"",
"Reference: McCormick M, Friehling E, Kalpatthi R, Siripong N, Smith K. Cost‐effectiveness of levofloxacin prophylaxis against bacterial infection in pediatric patients with acute myeloid leukemia. Pediatric Blood & Cancer. 2020 Oct;67(10):e28469",
"",
"Update January 2023 -- inserted delays and changed population who get AML from everyone to 0.2% of the females and 0.3% of males, according to the American Cancer Society, Cancer Facts & Figures, 2022. https://www.cancer.org/content/dam/cancer-org/research/cancer-facts-and-statistics/annual-cancer-facts-and-figures/2022/2022-cancer-facts-and-figures.pdf",
""
],
"gmf_version": 2
}

493
src/main/resources/modules/acute_myocardial_infarction.json Normal file
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{
"name": "Acute Myocardial Infarction",
"remarks": [
"Acute myocardial infarction (AMI) is commonly known as a heart attack.",
"It occurs when blood flow to a part of the heart is blocked, causing damage to the heart muscle.",
"Risk factors include age, smoking, hypertension, diabetes, obesity, and family history.",
"This module models the onset, diagnosis, treatment, and potential complications of AMI.",
"Information sources:",
"https://www.heart.org/en/health-topics/heart-attack",
"https://www.ncbi.nlm.nih.gov/books/NBK537076/",
"https://www.ahajournals.org/doi/10.1161/CIR.0000000000000617"
],
"states": {
"Initial": {
"type": "Initial",
"remarks": [
"======================================================================",
" INCIDENCE ",
"======================================================================",
"AMI incidence increases with age and is higher in males than females.",
"Approximately 805,000 Americans have a heart attack each year.",
"About 605,000 are first heart attacks and 200,000 are recurrent attacks."
],
"direct_transition": "Age_Guard"
},
"Age_Guard": {
"type": "Guard",
"allow": {
"condition_type": "Age",
"operator": ">=",
"quantity": 35,
"unit": "years"
},
"direct_transition": "AMI_Risk_Assessment"
},
"AMI_Risk_Assessment": {
"type": "Simple",
"complex_transition": [
{
"condition": {
"condition_type": "Gender",
"gender": "M"
},
"distributions": [
{
"distribution": 0.08,
"transition": "AMI_Onset"
},
{
"distribution": 0.92,
"transition": "Terminal"
}
]
},
{
"condition": {
"condition_type": "Gender",
"gender": "F"
},
"distributions": [
{
"distribution": 0.05,
"transition": "AMI_Onset"
},
{
"distribution": 0.95,
"transition": "Terminal"
}
]
}
]
},
"AMI_Onset": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.7,
"transition": "STEMI_Onset"
},
{
"distribution": 0.3,
"transition": "NSTEMI_Onset"
}
]
},
"STEMI_Onset": {
"type": "ConditionOnset",
"target_encounter": "Emergency_Department_Visit",
"assign_to_attribute": "ami",
"codes": [
{
"system": "SNOMED-CT",
"code": "401303003",
"display": "Acute ST segment elevation myocardial infarction (disorder)"
},
{
"system": "ICD-10-CM",
"code": "I21.3",
"display": "ST elevation (STEMI) myocardial infarction of unspecified site"
}
],
"direct_transition": "AMI_Symptoms"
},
"NSTEMI_Onset": {
"type": "ConditionOnset",
"target_encounter": "Emergency_Department_Visit",
"assign_to_attribute": "ami",
"codes": [
{
"system": "SNOMED-CT",
"code": "401314000",
"display": "Acute non-ST segment elevation myocardial infarction (disorder)"
},
{
"system": "ICD-10-CM",
"code": "I21.4",
"display": "Non-ST elevation (NSTEMI) myocardial infarction"
}
],
"direct_transition": "AMI_Symptoms"
},
"AMI_Symptoms": {
"type": "Symptom",
"symptom": "Chest Pain",
"range": {
"low": 80,
"high": 100
},
"direct_transition": "Shortness_of_Breath"
},
"Shortness_of_Breath": {
"type": "Symptom",
"symptom": "Shortness of Breath",
"range": {
"low": 60,
"high": 90
},
"direct_transition": "Nausea"
},
"Nausea": {
"type": "Symptom",
"symptom": "Nausea",
"range": {
"low": 30,
"high": 70
},
"direct_transition": "Diaphoresis"
},
"Diaphoresis": {
"type": "Symptom",
"symptom": "Diaphoresis",
"range": {
"low": 40,
"high": 80
},
"direct_transition": "Arm_Pain"
},
"Arm_Pain": {
"type": "Symptom",
"symptom": "Arm Pain",
"range": {
"low": 30,
"high": 70
},
"direct_transition": "Jaw_Pain"
},
"Jaw_Pain": {
"type": "Symptom",
"symptom": "Jaw Pain",
"range": {
"low": 20,
"high": 60
},
"direct_transition": "Emergency_Department_Visit"
},
"Emergency_Department_Visit": {
"type": "Encounter",
"encounter_class": "emergency",
"reason": "ami",
"codes": [
{
"system": "SNOMED-CT",
"code": "50849002",
"display": "Emergency room admission (procedure)"
}
],
"direct_transition": "Vital_Signs"
},
"Vital_Signs": {
"type": "Procedure",
"reason": "ami",
"codes": [
{
"system": "SNOMED-CT",
"code": "5880005",
"display": "Physical examination procedure (procedure)"
}
],
"direct_transition": "Blood_Pressure"
},
"Blood_Pressure": {
"type": "Observation",
"category": "vital-signs",
"unit": "mm[Hg]",
"codes": [
{
"system": "LOINC",
"code": "8480-6",
"display": "Systolic blood pressure"
}
],
"range": {
"low": 90,
"high": 160
},
"direct_transition": "Heart_Rate"
},
"Heart_Rate": {
"type": "Observation",
"category": "vital-signs",
"unit": "/min",
"codes": [
{
"system": "LOINC",
"code": "8867-4",
"display": "Heart rate"
}
],
"range": {
"low": 80,
"high": 120
},
"direct_transition": "ECG"
},
"ECG": {
"type": "Procedure",
"reason": "ami",
"codes": [
{
"system": "SNOMED-CT",
"code": "29303009",
"display": "Electrocardiographic procedure (procedure)"
}
],
"direct_transition": "Cardiac_Enzymes"
},
"Cardiac_Enzymes": {
"type": "Procedure",
"reason": "ami",
"codes": [
{
"system": "SNOMED-CT",
"code": "313791000",
"display": "Laboratory test (procedure)"
}
],
"direct_transition": "Troponin_Test"
},
"Troponin_Test": {
"type": "Observation",
"category": "laboratory",
"unit": "ng/mL",
"codes": [
{
"system": "LOINC",
"code": "10839-9",
"display": "Troponin I [Mass/volume] in Serum or Plasma"
}
],
"range": {
"low": 0.4,
"high": 10.0
},
"direct_transition": "CK_MB_Test"
},
"CK_MB_Test": {
"type": "Observation",
"category": "laboratory",
"unit": "ng/mL",
"codes": [
{
"system": "LOINC",
"code": "13969-1",
"display": "Creatine kinase.MB [Mass/volume] in Serum or Plasma"
}
],
"range": {
"low": 10.0,
"high": 30.0
},
"direct_transition": "Initial_Treatment"
},
"Initial_Treatment": {
"type": "Simple",
"direct_transition": "Aspirin"
},
"Aspirin": {
"type": "MedicationOrder",
"reason": "ami",
"codes": [
{
"system": "RxNorm",
"code": "1191",
"display": "Aspirin 325 MG Oral Tablet"
}
],
"direct_transition": "Oxygen_Therapy"
},
"Oxygen_Therapy": {
"type": "Procedure",
"reason": "ami",
"codes": [
{
"system": "SNOMED-CT",
"code": "57485005",
"display": "Oxygen therapy (procedure)"
}
],
"direct_transition": "Morphine"
},
"Morphine": {
"type": "MedicationOrder",
"reason": "ami",
"codes": [
{
"system": "RxNorm",
"code": "863671",
"display": "Morphine Sulfate 2 MG/ML Injectable Solution"
}
],
"direct_transition": "Nitroglycerin"
},
"Nitroglycerin": {
"type": "MedicationOrder",
"reason": "ami",
"codes": [
{
"system": "RxNorm",
"code": "705129",
"display": "Nitroglycerin 0.4 MG Sublingual Tablet"
}
],
"direct_transition": "Treatment_Decision"
},
"Treatment_Decision": {
"type": "Simple",
"conditional_transition": [
{
"condition": {
"condition_type": "Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "401303003",
"display": "Acute ST segment elevation myocardial infarction (disorder)"
}
]
},
"transition": "STEMI_Treatment_Decision"
},
{
"transition": "NSTEMI_Treatment"
}
]
},
"STEMI_Treatment_Decision": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.7,
"transition": "Primary_PCI"
},
{
"distribution": 0.3,
"transition": "Thrombolytic_Therapy"
}
]
},
"Primary_PCI": {
"type": "Procedure",
"reason": "ami",
"codes": [
{
"system": "SNOMED-CT",
"code": "415070008",
"display": "Percutaneous coronary intervention (procedure)"
}
],
"duration": {
"low": 60,
"high": 120,
"unit": "minutes"
},
"direct_transition": "Stent_Placement"
},
"Stent_Placement": {
"type": "Procedure",
"reason": "ami",
"codes": [
{
"system": "SNOMED-CT",
"code": "36969009",
"display": "Placement of stent in coronary artery (procedure)"
}
],
"direct_transition": "Post_PCI_Care"
},
"Post_PCI_Care": {
"type": "Procedure",
"reason": "ami",
"codes": [
{
"system": "SNOMED-CT",
"code": "305351004",
"display": "Admission to intensive care unit (procedure)"
}
],
"direct_transition": "Dual_Antiplatelet_Therapy"
},
"Dual_Antiplatelet_Therapy": {
"type": "MedicationOrder",
"reason": "ami",
"codes": [
{
"system": "RxNorm",
"code": "1116632",
"display": "Clopidogrel 75 MG Oral Tablet"
}
],
"direct_transition": "Beta_Blocker"
},
"Thrombolytic_Therapy": {
"type": "Procedure",
"reason": "ami",
"codes": [
{
"system": "SNOMED-CT",
"code": "75540009",
"display": "Thrombolytic therapy (procedure)"
}
],
"direct_transition": "Alteplase"
},
"Alteplase": {
"type": "MedicationOrder",
"reason": "ami",
"codes": [
{
"system": "RxNorm",
"code": "308056",
"display": "Alteplase 50 MG Injection"
}
],
"direct_transition": "Post_Thrombolytic_Care"
},
"Post_Thrombolytic_Care": {
"type": "Procedure",
"reason": "ami",
"codes": [
{
"system": "SNOMED-CT",
"code": "305351004",
"display": "Admission to intensive care unit (procedure)"
}
],
"direct_transition": "Dual_Antiplatelet_Therapy"
},
"NSTEMI_Treatment": {
"type": "Procedure",
"reason": "ami",
"codes": [
{
"system": "SNOMED-CT",
"code": "305351004",
"display": "Admission to intensive care unit (procedure)"
}
],
"direct_transition": "Anticoagulation"
},
"Anticoagulation": {
"type": "MedicationOrder",
"reason": "ami",
"codes": [
{
"system": "RxNorm",
"code": "1361493",
"display": "Heparin Sodium 5000 UNT/ML Injectable Solution"
}
],
"direct_transition": "Dual_Antiplatelet_Therapy"
}
}
}

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{
"name": "Acute pharyngitis",
"remarks": [
"Acute pharyngitis is an inflammation of the pharynx (throat) that typically causes a sore throat and pain with swallowing. It is most commonly caused by viral infections, though bacterial infections (particularly group A Streptococcus) account for 5-15% of cases in adults and 20-30% in children. Acute pharyngitis is highly contagious and spreads through respiratory droplets or direct contact with infected individuals. Most cases resolve within 7-10 days, with or without treatment.",
"Category: Respiratory System",
"Risk factors: - Age: Most common in children aged 5-15 years - Season: More prevalent in winter and early spring - Exposure: Close contact with infected individuals - Environment: Crowded settings (schools, daycare centers, military barracks) - Smoking or exposure to secondhand smoke - Air pollution or irritants - Allergies - Weakened immune system - Chronic fatigue"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Age_Guard"
},
"Age_Guard": {
"type": "Guard",
"allow": {
"condition_type": "Age",
"operator": ">=",
"quantity": 18,
"unit": "years"
},
"direct_transition": "Delay_Until_Onset"
},
"Delay_Until_Onset": {
"type": "Delay",
"range": {
"low": 0,
"high": 20,
"unit": "years"
},
"direct_transition": "Onset"
},
"Onset": {
"type": "ConditionOnset",
"target_encounter": "Diagnosis_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "64109004",
"display": "Acute pharyngitis"
}
],
"direct_transition": "Diagnosis_Encounter"
},
"Diagnosis_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem"
}
],
"direct_transition": "End_Diagnosis_Encounter"
},
"End_Diagnosis_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Symptom_0"
},
"Symptom_0": {
"type": "ConditionOnset",
"target_encounter": "Diagnosis_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "418107008",
"display": "Sore throat"
}
],
"direct_transition": "Symptom_1"
},
"Symptom_1": {
"type": "ConditionOnset",
"target_encounter": "Diagnosis_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "418107008",
"display": "Pain when swallowing"
}
],
"direct_transition": "Symptom_2"
},
"Symptom_2": {
"type": "ConditionOnset",
"target_encounter": "Diagnosis_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "418107008",
"display": "Fever (typically higher in bacterial pharyngitis)"
}
],
"direct_transition": "DiagnosticTest_0"
},
"DiagnosticTest_0": {
"type": "Procedure",
"target_encounter": "Diagnosis_Encounter",
"reason": "Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "386053000",
"display": "Physical examination of throat"
}
],
"direct_transition": "DiagnosticTest_1"
},
"DiagnosticTest_1": {
"type": "Procedure",
"target_encounter": "Diagnosis_Encounter",
"reason": "Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "386053000",
"display": "Rapid strep test (rapid antigen detection test)"
}
],
"direct_transition": "Prescribe_0"
},
"Prescribe_0": {
"type": "MedicationOrder",
"target_encounter": "Diagnosis_Encounter",
"reason": "Onset",
"codes": [
{
"system": "RxNorm",
"code": "308047",
"display": "Analgesics/antipyretics: acetaminophen"
}
],
"direct_transition": "Prescribe_1"
},
"Prescribe_1": {
"type": "MedicationOrder",
"target_encounter": "Diagnosis_Encounter",
"reason": "Onset",
"codes": [
{
"system": "RxNorm",
"code": "308047",
"display": "ibuprofen"
}
],
"direct_transition": "Prescribe_2"
},
"Prescribe_2": {
"type": "MedicationOrder",
"target_encounter": "Diagnosis_Encounter",
"reason": "Onset",
"codes": [
{
"system": "RxNorm",
"code": "308047",
"display": "Antibiotics"
}
],
"direct_transition": "Follow_Up_Encounter"
},
"Follow_Up_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "390906007",
"display": "Follow-up encounter"
}
],
"direct_transition": "End_Follow_Up_Encounter"
},
"End_Follow_Up_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
}
}

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# Acute Pharyngitis Disease Module Information
## 1. DESCRIPTION
Acute pharyngitis is an inflammation of the pharynx (throat) that typically causes a sore throat and pain with swallowing. It is most commonly caused by viral infections, though bacterial infections (particularly group A Streptococcus) account for 5-15% of cases in adults and 20-30% in children. Acute pharyngitis is highly contagious and spreads through respiratory droplets or direct contact with infected individuals. Most cases resolve within 7-10 days, with or without treatment.
## 2. RISK_FACTORS
- Age: Most common in children aged 5-15 years
- Season: More prevalent in winter and early spring
- Exposure: Close contact with infected individuals
- Environment: Crowded settings (schools, daycare centers, military barracks)
- Smoking or exposure to secondhand smoke
- Air pollution or irritants
- Allergies
- Weakened immune system
- Chronic fatigue
## 3. SYMPTOMS
- Sore throat
- Pain when swallowing
- Fever (typically higher in bacterial pharyngitis)
- Headache
- Fatigue
- Swollen, tender lymph nodes in neck
- Red, inflamed throat and tonsils
- White or yellow patches on tonsils (in streptococcal pharyngitis)
- Hoarseness
- Cough (more common in viral pharyngitis)
- Runny nose (more common in viral pharyngitis)
- Body aches
- Loss of appetite
## 4. DIAGNOSTIC_TESTS
- Physical examination of throat
- Rapid strep test (rapid antigen detection test)
- Throat culture
- Complete blood count (CBC)
- Monospot test (if mononucleosis is suspected)
- Respiratory viral panel (for viral causes)
- C-reactive protein or erythrocyte sedimentation rate (to assess inflammation)
## 5. TREATMENTS
- Medications:
- Analgesics/antipyretics: acetaminophen, ibuprofen (for pain and fever relief)
- Antibiotics (for bacterial pharyngitis only):
- Penicillin V
- Amoxicillin
- Cephalexin (for penicillin-allergic patients)
- Azithromycin (for penicillin-allergic patients)
- Clindamycin (for penicillin-allergic patients)
- Throat lozenges or sprays containing local anesthetics (benzocaine, phenol)
- Corticosteroids (in severe cases): prednisone
- Other interventions:
- Rest
- Increased fluid intake
- Warm salt water gargles
- Humidified air
- Soft, cool foods and avoiding irritating foods
- Honey for symptom relief (not for children under 1 year)
## 6. COMPLICATIONS
- Peritonsillar abscess (quinsy)
- Retropharyngeal abscess
- Sinusitis
- Otitis media (middle ear infection)
- Rheumatic fever (rare complication of untreated strep throat)
- Post-streptococcal glomerulonephritis
- Scarlet fever (with certain strains of strep)
- Dehydration (due to painful swallowing)
- Airway obstruction (in severe cases with significant swelling)
## 7. PROGRESSION
- Initial phase: Begins with throat irritation, progressing to pain within hours to days, often accompanied by fever and malaise
- Peak symptoms: Usually occur 2-3 days after onset, with throat pain, difficulty swallowing, and systemic symptoms
- Resolution: Viral pharyngitis typically resolves within 7-10 days without specific treatment; bacterial pharyngitis improves within 24-48 hours of starting antibiotics
- Outcomes: Most cases resolve completely without sequelae; recurrence is possible with new exposures; some patients may develop chronic or recurrent pharyngitis
## 8. FOLLOW_UP
- Return visit if symptoms worsen or don't improve within expected timeframe
- Complete full course of antibiotics if prescribed (typically 10 days for penicillin)
- Follow-up throat culture may be needed in high-risk patients or recurrent cases
- No routine follow-up needed for uncomplicated cases that resolve
- Evaluation of household contacts may be considered in cases of streptococcal pharyngitis
- Tonsillectomy may be considered for patients with recurrent streptococcal pharyngitis (typically >7 episodes in one year or >5 episodes per year for two consecutive years)

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{
"name": "Acute sinusitis",
"remarks": [
"Acute sinusitis is an inflammation of the paranasal sinuses lasting less than 4 weeks, typically caused by viral or bacterial infections. It often develops after an upper respiratory infection when mucus becomes trapped in the sinuses, creating an environment for pathogens to grow. Symptoms include facial pain, nasal congestion, and purulent nasal discharge. Most cases resolve spontaneously, but some require medical intervention.",
"Category: Respiratory System",
"Risk factors: - Age: All ages affected, but more common in adults 18-45 years - Gender: Slightly more common in women - Anatomical factors: Nasal polyps, deviated septum, nasal bone spurs - Environmental: Allergies, cigarette smoke exposure, air pollution - Medical conditions: Recent upper respiratory infections, dental infections, immunodeficiency - Seasonal: More common during cold and flu season (fall and winter)"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Age_Guard"
},
"Age_Guard": {
"type": "Guard",
"allow": {
"condition_type": "Age",
"operator": ">=",
"quantity": 18,
"unit": "years"
},
"direct_transition": "Delay_Until_Onset"
},
"Delay_Until_Onset": {
"type": "Delay",
"range": {
"low": 0,
"high": 20,
"unit": "years"
},
"direct_transition": "Onset"
},
"Onset": {
"type": "ConditionOnset",
"target_encounter": "Diagnosis_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "64109004",
"display": "Acute sinusitis"
}
],
"direct_transition": "Diagnosis_Encounter"
},
"Diagnosis_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem"
}
],
"direct_transition": "End_Diagnosis_Encounter"
},
"End_Diagnosis_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Symptom_0"
},
"Symptom_0": {
"type": "ConditionOnset",
"target_encounter": "Diagnosis_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "418107008",
"display": "Facial pain/pressure (particularly over affected sinuses)"
}
],
"direct_transition": "Symptom_1"
},
"Symptom_1": {
"type": "ConditionOnset",
"target_encounter": "Diagnosis_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "418107008",
"display": "Nasal congestion"
}
],
"direct_transition": "Symptom_2"
},
"Symptom_2": {
"type": "ConditionOnset",
"target_encounter": "Diagnosis_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "418107008",
"display": "Purulent nasal discharge"
}
],
"direct_transition": "DiagnosticTest_0"
},
"DiagnosticTest_0": {
"type": "Procedure",
"target_encounter": "Diagnosis_Encounter",
"reason": "Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "386053000",
"display": "Physical examination (including nasal endoscopy)"
}
],
"direct_transition": "DiagnosticTest_1"
},
"DiagnosticTest_1": {
"type": "Procedure",
"target_encounter": "Diagnosis_Encounter",
"reason": "Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "386053000",
"display": "Nasal swab culture (in persistent cases)"
}
],
"direct_transition": "Prescribe_0"
},
"Prescribe_0": {
"type": "MedicationOrder",
"target_encounter": "Diagnosis_Encounter",
"reason": "Onset",
"codes": [
{
"system": "RxNorm",
"code": "308047",
"display": "Analgesics: acetaminophen"
}
],
"direct_transition": "Prescribe_1"
},
"Prescribe_1": {
"type": "MedicationOrder",
"target_encounter": "Diagnosis_Encounter",
"reason": "Onset",
"codes": [
{
"system": "RxNorm",
"code": "308047",
"display": "ibuprofen"
}
],
"direct_transition": "Prescribe_2"
},
"Prescribe_2": {
"type": "MedicationOrder",
"target_encounter": "Diagnosis_Encounter",
"reason": "Onset",
"codes": [
{
"system": "RxNorm",
"code": "308047",
"display": "Intranasal corticosteroids: fluticasone"
}
],
"direct_transition": "Follow_Up_Encounter"
},
"Follow_Up_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "390906007",
"display": "Follow-up encounter"
}
],
"direct_transition": "End_Follow_Up_Encounter"
},
"End_Follow_Up_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
}
}

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# Acute Sinusitis Disease Module Information
## 1. DESCRIPTION
Acute sinusitis is an inflammation of the paranasal sinuses lasting less than 4 weeks, typically caused by viral or bacterial infections. It often develops after an upper respiratory infection when mucus becomes trapped in the sinuses, creating an environment for pathogens to grow. Symptoms include facial pain, nasal congestion, and purulent nasal discharge. Most cases resolve spontaneously, but some require medical intervention.
## 2. RISK_FACTORS
- Age: All ages affected, but more common in adults 18-45 years
- Gender: Slightly more common in women
- Anatomical factors: Nasal polyps, deviated septum, nasal bone spurs
- Environmental: Allergies, cigarette smoke exposure, air pollution
- Medical conditions: Recent upper respiratory infections, dental infections, immunodeficiency
- Seasonal: More common during cold and flu season (fall and winter)
## 3. SYMPTOMS
- Facial pain/pressure (particularly over affected sinuses)
- Nasal congestion
- Purulent nasal discharge
- Decreased sense of smell
- Fever (more common in bacterial sinusitis)
- Headache
- Fatigue
- Cough (often worse at night)
- Ear pressure
- Halitosis (bad breath)
## 4. DIAGNOSTIC_TESTS
- Physical examination (including nasal endoscopy)
- Nasal swab culture (in persistent cases)
- Imaging studies (for complicated cases):
- CT scan of sinuses
- X-ray of sinuses
- Allergy testing (if allergic sinusitis suspected)
- Transillumination of sinuses
## 5. TREATMENTS
- Medications:
- Analgesics: acetaminophen, ibuprofen (for pain relief)
- Intranasal corticosteroids: fluticasone, mometasone (reduce inflammation)
- Antibiotics: amoxicillin, amoxicillin-clavulanate, doxycycline (for bacterial sinusitis)
- Decongestants: pseudoephedrine (short-term relief of congestion)
- Antihistamines: loratadine, cetirizine (if allergic component)
- Saline nasal sprays (moisturize nasal passages)
- Procedures:
- Nasal irrigation with saline solution
- Sinus drainage (in severe cases)
- Other interventions:
- Increased fluid intake
- Warm compresses to face
- Humidification of air
- Elevation of head while sleeping
## 6. COMPLICATIONS
- Chronic sinusitis (lasting >12 weeks)
- Orbital cellulitis (infection of eye socket)
- Osteomyelitis (bone infection)
- Meningitis
- Brain abscess
- Cavernous sinus thrombosis
- Mucocele formation
- Spread of infection to nearby structures
## 7. PROGRESSION
- Starts: Usually begins after a viral upper respiratory infection (common cold), with initial symptoms of nasal congestion and discharge
- Development: If drainage is blocked, bacteria may grow in the sinuses, leading to bacterial sinusitis with worsening pain, pressure, and purulent discharge
- Outcomes:
- Most viral cases (>70%) resolve spontaneously within 7-10 days
- Bacterial cases typically improve with antibiotics within 10-14 days
- Some cases may progress to chronic sinusitis
- Rare cases develop serious complications requiring urgent intervention
## 8. FOLLOW_UP
- Return visit if symptoms worsen or fail to improve after 7-10 days
- Follow-up visit after completing antibiotic course for bacterial sinusitis
- Referral to otolaryngologist (ENT) if:
- Symptoms persist despite treatment
- Recurrent episodes (>3-4 per year)
- Anatomical abnormalities suspected
- Complications develop
- Allergy evaluation if allergic triggers suspected

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{
"name": "All anxiety disorders",
"remarks": [
"This module models the prevalence and progression of anxiety disorders based on epidemiological data",
"Anxiety disorders are the most common mental disorders in the US, affecting approximately 19.1% of adults annually",
"Women are more likely than men to experience anxiety disorders (23.4% vs 14.3%)",
"Sources: https://www.nimh.nih.gov/health/statistics/any-anxiety-disorder and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5573566/"
],
"states": {
"Initial": {
"type": "Initial",
"conditional_transition": [
{
"transition": "Female",
"condition": {
"condition_type": "Gender",
"gender": "F"
}
},
{
"transition": "Male",
"condition": {
"condition_type": "Gender",
"gender": "M"
}
},
{
"transition": "Terminal"
}
]
},
"Terminal": {
"type": "Terminal"
},
"Female": {
"type": "Simple",
"remarks": [
"Women have higher prevalence of anxiety disorders at 23.4%",
"Source: https://www.nimh.nih.gov/health/statistics/any-anxiety-disorder"
],
"distributed_transition": [
{
"transition": "Female_Anxiety_Onset",
"distribution": 0.234
},
{
"transition": "Terminal",
"distribution": 0.766
}
]
},
"Male": {
"type": "Simple",
"remarks": [
"Men have lower prevalence of anxiety disorders at 14.3%",
"Source: https://www.nimh.nih.gov/health/statistics/any-anxiety-disorder"
],
"distributed_transition": [
{
"transition": "Male_Anxiety_Onset",
"distribution": 0.143
},
{
"transition": "Terminal",
"distribution": 0.857
}
]
},
"Female_Anxiety_Onset": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Childhood_Onset",
"distribution": 0.31
},
{
"transition": "Adolescent_Onset",
"distribution": 0.47
},
{
"transition": "Adult_Onset",
"distribution": 0.22
}
],
"remarks": [
"Age of onset distribution based on epidemiological studies",
"Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3018839/"
]
},
"Male_Anxiety_Onset": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Childhood_Onset",
"distribution": 0.38
},
{
"transition": "Adolescent_Onset",
"distribution": 0.43
},
{
"transition": "Adult_Onset",
"distribution": 0.19
}
],
"remarks": [
"Age of onset distribution based on epidemiological studies",
"Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3018839/"
]
},
"Childhood_Onset": {
"type": "Delay",
"range": {
"low": 5,
"high": 11,
"unit": "years"
},
"direct_transition": "Anxiety_Disorder_Onset"
},
"Adolescent_Onset": {
"type": "Delay",
"range": {
"low": 12,
"high": 19,
"unit": "years"
},
"direct_transition": "Anxiety_Disorder_Onset"
},
"Adult_Onset": {
"type": "Delay",
"range": {
"low": 20,
"high": 50,
"unit": "years"
},
"direct_transition": "Anxiety_Disorder_Onset"
},
"Anxiety_Disorder_Onset": {
"type": "ConditionOnset",
"target_encounter": "Anxiety_Diagnosis_Encounter",
"codes": [
{
"system": "ICD-10-CM",
"code": "F41.9",
"display": "Anxiety disorder, unspecified"
},
{
"system": "SNOMED-CT",
"code": "197480006",
"display": "Anxiety disorder"
}
],
"direct_transition": "Symptom_Worry"
},
"Symptom_Worry": {
"type": "Symptom",
"symptom": "Excessive worry",
"range": {
"low": 50,
"high": 100
},
"direct_transition": "Symptom_Restlessness"
},
"Symptom_Restlessness": {
"type": "Symptom",
"symptom": "Restlessness",
"range": {
"low": 40,
"high": 90
},
"direct_transition": "Symptom_Fatigue"
},
"Symptom_Fatigue": {
"type": "Symptom",
"symptom": "Fatigue",
"range": {
"low": 30,
"high": 80
},
"direct_transition": "Symptom_Concentration"
},
"Symptom_Concentration": {
"type": "Symptom",
"symptom": "Difficulty concentrating",
"range": {
"low": 30,
"high": 70
},
"direct_transition": "Symptom_Irritability"
},
"Symptom_Irritability": {
"type": "Symptom",
"symptom": "Irritability",
"range": {
"low": 40,
"high": 90
},
"direct_transition": "Symptom_Tension"
},
"Symptom_Tension": {
"type": "Symptom",
"symptom": "Muscle tension",
"range": {
"low": 30,
"high": 80
},
"direct_transition": "Symptom_Sleep"
},
"Symptom_Sleep": {
"type": "Symptom",
"symptom": "Sleep disturbance",
"range": {
"low": 40,
"high": 90
},
"direct_transition": "Delay_Until_Diagnosis"
},
"Delay_Until_Diagnosis": {
"type": "Delay",
"range": {
"low": 3,
"high": 24,
"unit": "months"
},
"direct_transition": "Anxiety_Diagnosis_Encounter"
},
"Anxiety_Diagnosis_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem"
}
],
"direct_transition": "Anxiety_Diagnosis"
},
"Anxiety_Diagnosis": {
"type": "ConditionOnset",
"assign_to_attribute": "anxiety_disorder",
"codes": [
{
"system": "ICD-10-CM",
"code": "F5_ALLANXIOUS",
"display": "All anxiety disorders"
},
{
"system": "SNOMED-CT",
"code": "197480006",
"display": "Anxiety disorder"
}
],
"direct_transition": "Anxiety_CarePlan"
},
"Anxiety_CarePlan": {
"type": "CarePlanStart",
"codes": [
{
"system": "SNOMED-CT",
"code": "304561007",
"display": "Anxiety management plan"
}
],
"activities": [
{
"system": "SNOMED-CT",
"code": "183401009",
"display": "Stress management"
},
{
"system": "SNOMED-CT",
"code": "304481008",
"display": "Psychotherapy"
}
],
"direct_transition": "Treatment_Decision"
},
"Treatment_Decision": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Medication_SSRI",
"distribution": 0.5
},
{
"transition": "Medication_SNRI",
"distribution": 0.2
},
{
"transition": "Medication_Benzodiazepine",
"distribution": 0.15
},
{
"transition": "Psychotherapy_Only",
"distribution": 0.15
}
]
},
"Medication_SSRI": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": "312940",
"display": "Sertraline 50 MG Oral Tablet"
}
],
"direct_transition": "Anxiety_Followup"
},
"Medication_SNRI": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": "849727",
"display": "Venlafaxine 75 MG Oral Tablet"
}
],
"direct_transition": "Anxiety_Followup"
},
"Medication_Benzodiazepine": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": "197319",
"display": "Lorazepam 0.5 MG Oral Tablet"
}
],
"direct_transition": "Anxiety_Followup"
},
"Psychotherapy_Only": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "304891004",
"display": "Cognitive behavioral therapy"
}
],
"direct_transition": "Anxiety_Followup"
},
"Anxiety_Followup": {
"type": "Encounter",
"encounter_class": "ambulatory",
"codes": [
{
"system": "SNOMED-CT",
"code": "390906007",
"display": "Follow-up encounter"
}
],
"direct_transition": "Anxiety_Progression"
},
"Anxiety_Progression": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Anxiety_Remission",
"distribution": 0.4
},
{
"transition": "Anxiety_Chronic",
"distribution": 0.6
}
],
"remarks": [
"About 40% of anxiety patients achieve remission within 1 year of treatment",
"Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5573566/"
]
},
"Anxiety_Remission": {
"type": "ConditionEnd",
"referenced_by_attribute": "anxiety_disorder",
"direct_transition": "End_Anxiety_CarePlan"
},
"Anxiety_Chronic": {
"type": "Delay",
"range": {
"low": 2,
"high": 10,
"unit": "years"
},
"direct_transition": "Anxiety_Recurrence_Chance"
},
"Anxiety_Recurrence_Chance": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Anxiety_Remission",
"distribution": 0.3
},
{
"transition": "Anxiety_Chronic",
"distribution": 0.7
}
],
"remarks": [
"Chronic anxiety often follows a relapsing-remitting course",
"Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5573566/"
]
},
"End_Anxiety_CarePlan": {
"type": "CarePlanEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "304561007",
"display": "Anxiety management plan"
}
],
"direct_transition": "Terminal"
}
},
"gmf_version": 2
}

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src/main/resources/modules/allergic_rhinitis.json Normal file
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{
"name": "Allergic Rhinitis",
"remarks": [
"Better known as 'hay fever' or 'seasonal allergies'.",
"Statistics are from the American College of Allergy, Asthma, & Immunology (ACAAI):",
"http://acaai.org/news/facts-statistics/allergies",
"or the Allergy and Asthma Foundation of America (AAFA):",
"http://www.aafa.org/page/allergy-facts.aspx"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Delay_For_Atopy"
},
"Delay_For_Atopy": {
"type": "Delay",
"remarks": [
"The Atopy module must be processed before any of the allergy modules so ",
"atopy can appropriately influence allergies. Delaying the smallest possible ",
"time step to ensure this happens."
],
"exact": {
"quantity": 1,
"unit": "weeks"
},
"conditional_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "atopic",
"operator": "is not nil"
},
"transition": "Atopic"
},
{
"transition": "Not_Atopic"
}
]
},
"Atopic": {
"type": "Simple",
"remarks": [
"85% of all atopic patients develop allergic rhinitis. See the Atopy model for more info."
],
"distributed_transition": [
{
"distribution": 0.85,
"transition": "Delay_Until_Early_Mid_Childhood"
},
{
"distribution": 0.15,
"transition": "Terminal"
}
]
},
"Not_Atopic": {
"type": "Simple",
"remarks": [
"Estimated 50 million Americans affected by nasal allergies (ACAAI). 50M / 318.9M => 15.7%.",
"It makes more sense to wait until early-mid childhood (2-6 years old) for these ",
"symptoms to appear and to be diagnosed by a doctor."
],
"distributed_transition": [
{
"distribution": 0.029,
"transition": "Delay_Until_Early_Mid_Childhood"
},
{
"distribution": 0.971,
"transition": "Terminal"
}
]
},
"Delay_Until_Early_Mid_Childhood": {
"type": "Delay",
"range": {
"low": 2,
"high": 6,
"unit": "years"
},
"direct_transition": "Has_Allergic_Rhinitis"
},
"Has_Allergic_Rhinitis": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.2,
"transition": "Has_Seasonal_Allergic_Rhinitis",
"remarks": [
"Seasonal allergies occur only at a specific time of year. They can be more actue but ",
"are easily treated. 20% of Americans have just seasonal allergies.",
"source: http://www.neilmed.com/neilmedblog/2014/08/seasonal-and-perennial-allergic-rhinitis/"
]
},
{
"distribution": 0.4,
"transition": "Has_Perennial_Allergic_Rhinitis",
"remarks": [
"Perennial allergies are not influenced by the seasons. They are typically tied to other ",
"allergens like pet dander, mold, and dust mites."
]
},
{
"distribution": 0.4,
"transition": "Has_Perennial_And_Seasonal_Allergic_Rhinitis",
"remarks": [
"Perennial allergies flare up in the spring with additional allergies, like grass and ",
"tree pollens."
]
}
]
},
"Has_Seasonal_Allergic_Rhinitis": {
"type": "ConditionOnset",
"assign_to_attribute": "allergic_rhinitis",
"target_encounter": "Allergic_Rhinitis_Diagnosis",
"codes": [
{
"system": "SNOMED-CT",
"code": "367498001",
"display": "Seasonal allergic rhinitis (disorder)"
}
],
"direct_transition": "Allergic_Rhinitis_Symptom1"
},
"Has_Perennial_Allergic_Rhinitis": {
"type": "ConditionOnset",
"assign_to_attribute": "allergic_rhinitis",
"target_encounter": "Allergic_Rhinitis_Diagnosis",
"codes": [
{
"system": "SNOMED-CT",
"code": "446096008",
"display": "Perennial allergic rhinitis (disorder)"
}
],
"direct_transition": "Allergic_Rhinitis_Symptom1"
},
"Has_Perennial_And_Seasonal_Allergic_Rhinitis": {
"type": "ConditionOnset",
"assign_to_attribute": "allergic_rhinitis",
"target_encounter": "Allergic_Rhinitis_Diagnosis",
"codes": [
{
"system": "SNOMED-CT",
"code": "232353008",
"display": "Perennial allergic rhinitis with seasonal variation (disorder)"
}
],
"direct_transition": "Allergic_Rhinitis_Symptom1"
},
"Allergic_Rhinitis_Diagnosis": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "allergic_rhinitis",
"telemedicine_possibility": "possible",
"codes": [
{
"system": "SNOMED-CT",
"code": "185345009",
"display": "Encounter for symptom (procedure)"
}
],
"direct_transition": "Prescribe_OTC_Antihistamine"
},
"Allergic_Rhinitis_Symptom1": {
"type": "Symptom",
"symptom": "Nasal Congestion",
"range": {
"low": 0,
"high": 25
},
"direct_transition": "Allergic_Rhinitis_Symptom2"
},
"Allergic_Rhinitis_Symptom2": {
"type": "Symptom",
"symptom": "Nasal Discharge",
"range": {
"low": 0,
"high": 25
},
"direct_transition": "Allergic_Rhinitis_Symptom3"
},
"Allergic_Rhinitis_Symptom3": {
"type": "Symptom",
"symptom": "Itching",
"range": {
"low": 0,
"high": 25
},
"direct_transition": "Allergic_Rhinitis_Symptom4"
},
"Allergic_Rhinitis_Symptom4": {
"type": "Symptom",
"symptom": "Sneezing Fits",
"range": {
"low": 0,
"high": 25
},
"direct_transition": "Allergic_Rhinitis_Symptom5"
},
"Allergic_Rhinitis_Symptom5": {
"type": "Symptom",
"symptom": "Ear Pressure",
"range": {
"low": 0,
"high": 25
},
"direct_transition": "Symptom_Period"
},
"Symptom_Period": {
"type": "Delay",
"range": {
"low": 2,
"high": 3,
"unit": "weeks"
},
"direct_transition": "Allergic_Rhinitis_Diagnosis"
},
"Prescribe_OTC_Antihistamine": {
"type": "CallSubmodule",
"remarks": [
"This submodule will only prescribe an antihistamine if one is ",
"not already prescribed."
],
"submodule": "medications/otc_antihistamine",
"direct_transition": "Advise_To_Visit_Allergist"
},
"Advise_To_Visit_Allergist": {
"type": "SetAttribute",
"attribute": "visit_allergist",
"value": true,
"direct_transition": "End_Allergic_Rhinitis_Diagnosis"
},
"End_Allergic_Rhinitis_Diagnosis": {
"type": "EncounterEnd",
"direct_transition": "Living_With_Allergic_Rhinitis"
},
"Living_With_Allergic_Rhinitis": {
"type": "Guard",
"allow": {
"condition_type": "Age",
"operator": ">",
"quantity": 18,
"unit": "years"
},
"direct_transition": "Outgrow_Allergic_Rhinitis?"
},
"Outgrow_Allergic_Rhinitis?": {
"type": "Guard",
"remarks": [
"It's very uncommon for a person to 'outgrow' allergic rhinitis, ",
"but symptoms can lessen or disappear as a child ages or if they ",
"are given immunotherapy (85%)."
],
"allow": {
"condition_type": "Not",
"condition": {
"condition_type": "Or",
"conditions": [
{
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "419263009",
"display": "Allergy to tree pollen (finding)"
}
]
},
{
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "418689008",
"display": "Allergy to grass pollen (finding)"
}
]
},
{
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "717234006",
"display": "Allergy to animal protein (finding)"
}
]
},
{
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "232350006",
"display": "Allergy to dust mite protein (finding)"
}
]
},
{
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "419474003",
"display": "Allergy to mold (finding)"
}
]
}
]
}
},
"direct_transition": "Allergic_Rhinitis_Subsides"
},
"Allergic_Rhinitis_Subsides": {
"type": "ConditionEnd",
"referenced_by_attribute": "allergic_rhinitis",
"direct_transition": "Allergic_Rhinitis_Symptom1_Ends"
},
"Allergic_Rhinitis_Symptom1_Ends": {
"type": "Symptom",
"symptom": "Nasal Congestion",
"exact": {
"quantity": 0
},
"direct_transition": "Allergic_Rhinitis_Symptom2_Ends"
},
"Allergic_Rhinitis_Symptom2_Ends": {
"type": "Symptom",
"symptom": "Nasal Discharge",
"exact": {
"quantity": 0
},
"direct_transition": "Allergic_Rhinitis_Symptom3_Ends"
},
"Allergic_Rhinitis_Symptom3_Ends": {
"type": "Symptom",
"symptom": "Itching",
"exact": {
"quantity": 0
},
"direct_transition": "Allergic_Rhinitis_Symptom4_Ends"
},
"Allergic_Rhinitis_Symptom4_Ends": {
"type": "Symptom",
"symptom": "Sneezing Fits",
"exact": {
"quantity": 0
},
"direct_transition": "Allergic_Rhinitis_Symptom5_Ends"
},
"Allergic_Rhinitis_Symptom5_Ends": {
"type": "Symptom",
"symptom": "Ear Pressure",
"exact": {
"quantity": 0
},
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

274
src/main/resources/modules/allergies.json Normal file
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{
"name": "Allergies and Treatment",
"remarks": [
"This module onsets allergies and manages the treatment of allergies and ",
"allergic diseases. After the initial series of AllergyOnset states, the ",
"module waits for an allergic condition (as a result of a person's allergies)",
"to prompt treatment.",
"Primary reference for allergy statistics: ",
"https://web.archive.org/web/20100407195412/http://www.niaid.nih.gov/topics/foodAllergy/understanding/Pages/quickFacts.aspx"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Delay_For_Atopy"
},
"Delay_For_Atopy": {
"type": "Delay",
"remarks": [
"The Atopy module must be processed before any of the allergy modules so ",
"atopy can appropriately influence allergies. Delaying the smallest possible ",
"time step to ensure this happens."
],
"exact": {
"quantity": 1,
"unit": "weeks"
},
"direct_transition": "Food_Allergy_Incidence_Submodule"
},
"Food_Allergy_Incidence_Submodule": {
"type": "CallSubmodule",
"remarks": [
"This submodule onsets the various food allergies that ",
"a person can get, with different incidences for atopic and non-atopic ",
"patients."
],
"submodule": "allergies/food_allergy_incidence",
"direct_transition": "Drug_Allergy_Incidence_Submodule"
},
"Drug_Allergy_Incidence_Submodule": {
"type": "CallSubmodule",
"remarks": [
"This submodule onsets the various drug allergies that a person can get."
],
"submodule": "allergies/drug_allergy_incidence",
"direct_transition": "Environmental_Allergy_Incidence_Submodule"
},
"Environmental_Allergy_Incidence_Submodule": {
"type": "CallSubmodule",
"remarks": [
"This submodule onsets the various environmental allergies that ",
"a person can get, with different incidences for atopic and non-atopic ",
"patients."
],
"submodule": "allergies/environmental_allergy_incidence",
"direct_transition": "Allergist_Guard"
},
"Allergist_Guard": {
"type": "Guard",
"remarks": [
"======================================================================",
" ALLERGY TREATMENT/CARE ",
"======================================================================",
"Now that the patient is suspected to have an allergy, we refer them to ",
"an allergist for specialized treatment.",
"The following can prompt a visit to the allergist: ",
"- Asthma attack ",
"- Moderate to severe eczema ",
"- Any allergic reaction to food ",
"- Moderate to severe allergic rhinitis symptoms ",
"The asthma, eczema, and allergic rhinitis submodules set the 'visit_allergist' ",
"attribute to trigger the visit. At the first visit to an allergist an ",
"allergy panel is always performed."
],
"allow": {
"condition_type": "Attribute",
"attribute": "visit_allergist",
"operator": "is not nil"
},
"direct_transition": "Allergy_Unspecified"
},
"Delay_For_Allergist_Initial_Visit": {
"type": "Delay",
"remarks": [
"Other modules are not expected to make this delay after making a ",
"'visit_allergist' recommendation."
],
"range": {
"low": 1,
"high": 7,
"unit": "days"
},
"direct_transition": "Allergist_Initial_Visit"
},
"Allergist_Initial_Visit": {
"type": "Encounter",
"remarks": [
"This is the big one! Whatever allergies a patient has will be formally ",
"diagnosed at this encounter."
],
"encounter_class": "ambulatory",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem (procedure)"
}
],
"conditional_transition": [
{
"condition": {
"condition_type": "Date",
"operator": ">",
"year": 1974
},
"transition": "Administer_Allergy_Test"
},
{
"transition": "General_Allergy_CarePlan"
}
],
"reason": "Allergy_Unspecified"
},
"Administer_Allergy_Test": {
"type": "Procedure",
"duration": {
"low": 20,
"high": 40,
"unit": "minutes"
},
"codes": [
{
"system": "SNOMED-CT",
"code": "395142003",
"display": "Allergy screening test (procedure)"
}
],
"direct_transition": "Allergy_Panel"
},
"Allergy_Panel": {
"type": "CallSubmodule",
"submodule": "allergies/allergy_panel",
"direct_transition": "Prescribe_OTC_Antihistamine"
},
"Prescribe_OTC_Antihistamine": {
"type": "CallSubmodule",
"remarks": [
"This submodule will only prescribe an antihistamine if one is ",
"not already prescribed."
],
"submodule": "medications/otc_antihistamine",
"direct_transition": "General_Allergy_CarePlan"
},
"General_Allergy_CarePlan": {
"type": "CarePlanStart",
"remarks": [
"Allergy maintenance is all about self care."
],
"codes": [
{
"system": "SNOMED-CT",
"code": "384758001",
"display": "Self-care interventions (procedure)"
}
],
"activities": [
{
"system": "SNOMED-CT",
"code": "58332002",
"display": "Allergy education (procedure)"
}
],
"conditional_transition": [
{
"condition": {
"condition_type": "Date",
"operator": ">=",
"year": 1987
},
"transition": "Prescribe_Epipen"
},
{
"transition": "End_Allergist_Initial_Visit"
}
]
},
"Prescribe_Epipen": {
"type": "MedicationOrder",
"remarks": [
"FDA approved in 1987. It's highly likely that this prescription ",
"will never end - it will just be periodically renewed during the ",
"patient's lifetime."
],
"codes": [
{
"system": "RxNorm",
"code": "1870230",
"display": "NDA020800 0.3 ML Epinephrine 1 MG/ML Auto-Injector"
}
],
"prescription": {
"as_needed": true
},
"direct_transition": "End_Allergist_Initial_Visit"
},
"End_Allergist_Initial_Visit": {
"type": "EncounterEnd",
"direct_transition": "Living_With_Allergies"
},
"Living_With_Allergies": {
"type": "Guard",
"remarks": [
"======================================================================",
" LIVING WITH ALLERGIES ",
"======================================================================",
"Whatever allergies the patients have, they will continue to passively ",
"live with them until an allergic condition or a severe reaction ",
"prompts a visit to their PCP and a referral to an allergist. Allergies ",
"aren't officially diagnosed until after an allergy test is performed.",
"For patient's 12 or older we can consider immunotherapy. This will ",
"not work for everyone but it's worth discussing. Immunotherapy is not ",
"an option before 1990."
],
"allow": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Age",
"operator": ">",
"quantity": 12,
"unit": "years"
},
{
"condition_type": "Date",
"operator": ">=",
"year": 1990
},
{
"condition_type": "Attribute",
"attribute": "immunotherapy_status",
"operator": "is nil"
}
]
},
"direct_transition": "Immunotherapy_Submodule"
},
"Immunotherapy_Submodule": {
"type": "CallSubmodule",
"remarks": [
"This submodule may or may not give the patient immunotherapy. If ",
"immunotherapy is given a series of 60 treatments will be provided ",
"over the course of 3-5 years."
],
"submodule": "allergies/immunotherapy",
"direct_transition": "Living_With_Allergies"
},
"Allergy_Unspecified": {
"allergy_type": "allergy",
"category": "environment",
"type": "AllergyOnset",
"target_encounter": "Allergist_Initial_Visit",
"codes": [
{
"system": "SNOMED-CT",
"code": 419199007,
"display": "Allergy to substance (finding)"
}
],
"reactions": [],
"direct_transition": "Delay_For_Allergist_Initial_Visit",
"assign_to_attribute": "allergy_unspecified"
}
},
"gmf_version": 1
}

928
src/main/resources/modules/allergies/allergy_panel.json Normal file
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@@ -0,0 +1,928 @@
{
"name": "Allergy Panel",
"remarks": [
"This submodule explicity references states in the 'Allergies and Treatment' module. ",
"In the future an Active Condition test should be favored instead of PriorState once ",
"there's a distinction between an 'Active' and 'Diagnosed' condition.",
"Most of these tests measure the amount of IgE Ab antibody in serum. ",
"http://www.mayomedicallaboratories.com/interpretive-guide/?alpha=S&unit_code=82716",
"IgE Ab < 0.35 kU/L == Negative Result ",
"IgE Ab > 0.70 kU/L == Positive ",
"IgE Ab > 17.5 kU/L == Strongly Positive ",
"The following allergens are tested here, and expected to be onset in allergies.json: ",
"Peanut, Treenut, Fish, Shellfish, Wheat, Egg, Dairy, Tree Pollen, Grass Pollen, ",
"Pet Dander, Dust Mite, Mold, Bee, Latex"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Peanut_Test"
},
"Peanut_Test": {
"type": "Simple",
"remarks": [
"======================================================================",
" PEANUT ALLERGY TEST ",
"======================================================================"
],
"conditional_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "91935009",
"display": "Allergy to peanut (finding)"
}
]
},
"transition": "Peanut_Test_Positive"
},
{
"transition": "Peanut_Test_Negative"
}
]
},
"Peanut_Test_Positive": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6206-7",
"display": "Peanut IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0.7,
"high": 100
},
"direct_transition": "Nut_Test"
},
"Peanut_Test_Negative": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6206-7",
"display": "Peanut IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0,
"high": 0.35
},
"direct_transition": "Nut_Test"
},
"Nut_Test": {
"type": "Simple",
"remarks": [
"======================================================================",
" NUT ALLERGY TEST ",
"======================================================================"
],
"conditional_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "91934008",
"display": "Allergy to nut (finding)"
}
]
},
"transition": "Nut_Test_Positive"
},
{
"transition": "Nut_Test_Negative"
}
]
},
"Nut_Test_Positive": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6273-7",
"display": "Walnut IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0.7,
"high": 100
},
"direct_transition": "Fish_Test"
},
"Nut_Test_Negative": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6273-7",
"display": "Walnut IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0,
"high": 0.35
},
"direct_transition": "Fish_Test"
},
"Fish_Test": {
"type": "Simple",
"remarks": [
"======================================================================",
" FISH ALLERGY TEST ",
"======================================================================"
],
"conditional_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "417532002",
"display": "Allergy to fish (finding)"
}
]
},
"transition": "Fish_Test_Positive"
},
{
"transition": "Fish_Test_Negative"
}
]
},
"Fish_Test_Positive": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6082-2",
"display": "Codfish IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0.7,
"high": 100
},
"direct_transition": "Shellfish_Test"
},
"Fish_Test_Negative": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6082-2",
"display": "Codfish IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0,
"high": 0.35
},
"direct_transition": "Shellfish_Test"
},
"Shellfish_Test": {
"type": "Simple",
"remarks": [
"======================================================================",
" SHELLFISH ALLERGY TEST ",
"======================================================================",
"There were LOINC codes available for shrimp, scallops, and clam. ",
"I chose to include only the shrimp test at this time."
],
"conditional_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "300913006",
"display": "Allergy to shellfish (finding)"
}
]
},
"transition": "Shellfish_Test_Positive"
},
{
"transition": "Shellfish_Test_Negative"
}
]
},
"Shellfish_Test_Positive": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6246-3",
"display": "Shrimp IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0.7,
"high": 100
},
"direct_transition": "Wheat_Test"
},
"Shellfish_Test_Negative": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6246-3",
"display": "Shrimp IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0,
"high": 0.35
},
"direct_transition": "Wheat_Test"
},
"Wheat_Test": {
"type": "Simple",
"remarks": [
"======================================================================",
" WHEAT ALLERGY TEST ",
"======================================================================"
],
"conditional_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "420174000",
"display": "Allergy to wheat (finding)"
}
]
},
"transition": "Wheat_Test_Positive"
},
{
"transition": "Wheat_Test_Negative"
}
]
},
"Wheat_Test_Positive": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6276-0",
"display": "Wheat IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0.7,
"high": 100
},
"direct_transition": "Egg_Test"
},
"Wheat_Test_Negative": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6276-0",
"display": "Wheat IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0,
"high": 0.35
},
"direct_transition": "Egg_Test"
},
"Egg_Test": {
"type": "Simple",
"remarks": [
"======================================================================",
" EGG ALLERGY TEST ",
"======================================================================"
],
"conditional_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "213020009",
"display": "Allergy to egg protein (finding)"
}
]
},
"transition": "Egg_Test_Positive"
},
{
"transition": "Egg_Test_Negative"
}
]
},
"Egg_Test_Positive": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6106-9",
"display": "Egg white IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0.7,
"high": 100
},
"direct_transition": "Soy_Test"
},
"Egg_Test_Negative": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6106-9",
"display": "Egg white IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0,
"high": 0.35
},
"direct_transition": "Soy_Test"
},
"Soy_Test": {
"type": "Simple",
"remarks": [
"======================================================================",
" SOY ALLERGY TEST ",
"======================================================================"
],
"conditional_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "782594005",
"display": "Allergy to soy protein (finding)"
}
]
},
"transition": "Soy_Test_Positive"
},
{
"transition": "Soy_Test_Negative"
}
]
},
"Soy_Test_Positive": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6248-9",
"display": "Soybean IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0.7,
"high": 100
},
"direct_transition": "Milk_Test"
},
"Soy_Test_Negative": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6248-9",
"display": "Soybean IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0,
"high": 0.35
},
"direct_transition": "Milk_Test"
},
"Milk_Test": {
"type": "Simple",
"remarks": [
"======================================================================",
" DAIRY ALLERGY TEST ",
"======================================================================"
],
"conditional_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "414285001",
"display": "Allergy to food (finding)"
}
]
},
"transition": "Milk_Test_Positive"
},
{
"transition": "Milk_Test_Negative"
}
]
},
"Milk_Test_Positive": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "7258-7",
"display": "Cow milk IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0.7,
"high": 100
},
"direct_transition": "Tree_Test"
},
"Milk_Test_Negative": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "7258-7",
"display": "Cow milk IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0,
"high": 0.35
},
"direct_transition": "Tree_Test"
},
"Tree_Test": {
"type": "Simple",
"remarks": [
"======================================================================",
" TREE ALLERGY TEST ",
"======================================================================"
],
"conditional_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "419263009",
"display": "Allergy to tree pollen (finding)"
}
]
},
"transition": "Tree_Test_Positive"
},
{
"transition": "Tree_Test_Negative"
}
]
},
"Tree_Test_Positive": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6189-5",
"display": "White oak IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0.7,
"high": 100
},
"direct_transition": "Grass_Test"
},
"Tree_Test_Negative": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6189-5",
"display": "White oak IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0,
"high": 0.35
},
"direct_transition": "Grass_Test"
},
"Grass_Test": {
"type": "Simple",
"remarks": [
"======================================================================",
" GRASS ALLERGY TEST ",
"======================================================================"
],
"conditional_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "418689008",
"display": "Allergy to grass pollen (finding)"
}
]
},
"transition": "Grass_Test_Positive"
},
{
"transition": "Grass_Test_Negative"
}
]
},
"Grass_Test_Positive": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6085-5",
"display": "Common Ragweed IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0.7,
"high": 100
},
"direct_transition": "Dander_Test"
},
"Grass_Test_Negative": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6085-5",
"display": "Common Ragweed IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0,
"high": 0.35
},
"direct_transition": "Dander_Test"
},
"Dander_Test": {
"type": "Simple",
"remarks": [
"======================================================================",
" PET DANDER ALLERGY TEST ",
"======================================================================"
],
"conditional_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "717234006",
"display": "Allergy to animal protein (finding)"
}
]
},
"transition": "Dander_Test_Positive"
},
{
"transition": "Dander_Test_Negative"
}
]
},
"Dander_Test_Positive": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6833-8",
"display": "Cat dander IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0.7,
"high": 100
},
"direct_transition": "Mite_Test"
},
"Dander_Test_Negative": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6833-8",
"display": "Cat dander IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0,
"high": 0.35
},
"direct_transition": "Mite_Test"
},
"Mite_Test": {
"type": "Simple",
"remarks": [
"======================================================================",
" MITE ALLERGY TEST ",
"======================================================================"
],
"conditional_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "232350006",
"display": "Allergy to dust mite protein (finding)"
}
]
},
"transition": "Mite_Test_Positive"
},
{
"transition": "Mite_Test_Negative"
}
]
},
"Mite_Test_Positive": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6095-4",
"display": "American house dust mite IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0.7,
"high": 100
},
"direct_transition": "Mold_Test"
},
"Mite_Test_Negative": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6095-4",
"display": "American house dust mite IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0,
"high": 0.35
},
"direct_transition": "Mold_Test"
},
"Mold_Test": {
"type": "Simple",
"remarks": [
"======================================================================",
" MOLD ALLERGY TEST ",
"======================================================================"
],
"conditional_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "419474003",
"display": "Allergy to mold (finding)"
}
]
},
"transition": "Mold_Test_Positive"
},
{
"transition": "Mold_Test_Negative"
}
]
},
"Mold_Test_Positive": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6075-6",
"display": "Cladosporium herbarum IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0.7,
"high": 100
},
"direct_transition": "Bee_Test"
},
"Mold_Test_Negative": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6075-6",
"display": "Cladosporium herbarum IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0,
"high": 0.35
},
"direct_transition": "Bee_Test"
},
"Bee_Test": {
"type": "Simple",
"remarks": [
"======================================================================",
" BEE ALLERGY TEST ",
"======================================================================"
],
"conditional_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "424213003",
"display": "Allergy to bee venom (finding)"
}
]
},
"transition": "Bee_Test_Positive"
},
{
"transition": "Bee_Test_Negative"
}
]
},
"Bee_Test_Positive": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6844-5",
"display": "Honey bee IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0.7,
"high": 100
},
"direct_transition": "Latex_Test"
},
"Bee_Test_Negative": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6844-5",
"display": "Honey bee IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0,
"high": 0.35
},
"direct_transition": "Latex_Test"
},
"Latex_Test": {
"type": "Simple",
"remarks": [
"======================================================================",
" LATEX ALLERGY TEST ",
"======================================================================"
],
"conditional_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "1003755004",
"display": "Allergy to Hevea brasiliensis latex protein (finding)"
}
]
},
"transition": "Latex_Test_Positive"
},
{
"transition": "Latex_Test_Negative"
}
]
},
"Latex_Test_Positive": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6158-0",
"display": "Latex IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0.7,
"high": 100
},
"direct_transition": "Allergy_Test_Terminal"
},
"Latex_Test_Negative": {
"type": "Observation",
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6158-0",
"display": "Latex IgE Ab [Units/volume] in Serum"
}
],
"unit": "kU/L",
"range": {
"low": 0,
"high": 0.35
},
"direct_transition": "Allergy_Test_Terminal"
},
"Allergy_Test_Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

812
src/main/resources/modules/allergies/drug_allergy_incidence.json Normal file
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@@ -0,0 +1,812 @@
{
"name": "Drug_Allergies",
"remarks": [
"This submodule onsets various drug allergies and is intended to be called by the main allergies module."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Penicillin_Allergy"
},
"Terminal": {
"type": "Terminal"
},
"Penicillin_Allergy": {
"type": "Simple",
"remarks": [
"Actual penicillin allergies happen in about 1% of individuals.",
"About 10% of people have a penicillin allergy listed in the medical record.",
"This will set an attribute indicating a real allergy on 1% of people, but ensure that 10% have allergies in their record.",
"https://www.cdc.gov/antibiotic-use/community/pdfs/penicillin-factsheet.pdf"
],
"distributed_transition": [
{
"transition": "True_Penicillin_Allergy",
"distribution": 0.01
},
{
"transition": "Penicillin_Allergy_Onset",
"distribution": 0.09
},
{
"transition": "Aspirin_Allergy_Intolerance",
"distribution": 0.9
}
]
},
"True_Penicillin_Allergy": {
"type": "SetAttribute",
"attribute": "Penicillin_Allergy",
"direct_transition": "Penicillin_Allergy_Onset",
"value": true
},
"Penicillin_Allergy_Onset": {
"type": "AllergyOnset",
"allergy_type": "allergy",
"category": "medication",
"target_encounter": "Allergist_Initial_Visit",
"codes": [
{
"system": "RxNorm",
"code": 7984,
"display": "Penicillin V"
}
],
"reactions": [
{
"reaction": {
"system": "SNOMED-CT",
"code": "49727002",
"display": "Cough (finding)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.05
},
{
"level": "none",
"value": 0.95
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "402387002",
"display": "Allergic angioedema (disorder)"
},
"possible_severities": [
{
"level": "mild",
"value": 0.11
},
{
"level": "none",
"value": 0.89
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "404640003",
"display": "Dizziness (finding)"
},
"possible_severities": [
{
"level": "mild",
"value": 0.01
},
{
"level": "none",
"value": 0.99
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "267036007",
"display": "Dyspnea (finding)"
},
"possible_severities": [
{
"level": "mild",
"value": 0.06
},
{
"level": "none",
"value": 0.94
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "247472004",
"display": "Wheal (finding)"
},
"possible_severities": [
{
"level": "mild",
"value": 0.52
},
{
"level": "none",
"value": 0.48
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "39579001",
"display": "Anaphylaxis (disorder)"
},
"possible_severities": [
{
"level": "severe",
"value": 0.03
},
{
"level": "none",
"value": 0.97
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "271807003",
"display": "Eruption of skin (disorder)"
},
"possible_severities": [
{
"level": "mild",
"value": 0.34
},
{
"level": "none",
"value": 0.6599999999999999
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "878820003",
"display": "Rhinoconjunctivitis (disorder)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.04
},
{
"level": "none",
"value": 0.96
}
]
}
],
"direct_transition": "Aspirin_Allergy_Intolerance"
},
"Aspirin_Allergy_Intolerance": {
"type": "Simple",
"remarks": [
"About 1% of individuals have an allergy to aspirin",
"About 20% of individuals have an intolerance",
""
],
"distributed_transition": [
{
"transition": "Aspirin_Allergy_Onset",
"distribution": 0.2
},
{
"transition": "NSAID_Allergy",
"distribution": 0.8
}
]
},
"Aspirin_Allergy_Onset": {
"type": "AllergyOnset",
"allergy_type": "allergy",
"category": "medication",
"target_encounter": "Allergist_Initial_Visit",
"codes": [
{
"system": "RxNorm",
"code": 1191,
"display": "Aspirin"
}
],
"reactions": [
{
"reaction": {
"system": "SNOMED-CT",
"code": "247472004",
"display": "Wheal (finding)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.19
},
{
"level": "none",
"value": 0.81
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "402387002",
"display": "Allergic angioedema (disorder)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.05
},
{
"level": "none",
"value": 0.95
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "39579001",
"display": "Anaphylaxis (disorder)"
},
"possible_severities": [
{
"level": "severe",
"value": 0.028
},
{
"level": "none",
"value": 0.972
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "21522001",
"display": "Abdominal pain (finding)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.32
},
{
"level": "none",
"value": 0.68
}
]
}
],
"direct_transition": "NSAID_Allergy"
},
"NSAID_Allergy": {
"type": "Simple",
"remarks": [
"1.6% of people have a Non-steroidal anti-inflammatory drugs (NSAIDs), ibuprofen allergy.",
"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6004000/"
],
"distributed_transition": [
{
"transition": "Onset_Ibuprofen_Allergy",
"distribution": 0.016
},
{
"transition": "Sulfa_Drug_Allergy",
"distribution": 0.984
}
]
},
"Sulfa_Drug_Allergy": {
"type": "Simple",
"remarks": [
"Allergy to sulfa drugs occurs in 3% - 8% of the population. We will give it to 5% of individuals.",
"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6789825/",
""
],
"distributed_transition": [
{
"transition": "Onset_Sulfa_Drug_Allergy",
"distribution": 0.05
},
{
"transition": "Cephalosporin_Allergy",
"distribution": 0.95
}
]
},
"Onset_Ibuprofen_Allergy": {
"type": "AllergyOnset",
"allergy_type": "allergy",
"category": "medication",
"target_encounter": "Allergist_Initial_Visit",
"codes": [
{
"system": "RxNorm",
"code": "5640",
"display": "Ibuprofen"
}
],
"reactions": [
{
"reaction": {
"system": "SNOMED-CT",
"code": "418290006",
"display": "Itching (finding)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.4
},
{
"level": "none",
"value": 0.6
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "247472004",
"display": "Wheal (finding)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.29
},
{
"level": "none",
"value": 0.71
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "271811009",
"display": "Face goes red (finding)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.15
},
{
"level": "none",
"value": 0.85
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "878820003",
"display": "Rhinoconjunctivitis (disorder)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.3
},
{
"level": "none",
"value": 0.7
}
]
}
],
"direct_transition": "Sulfa_Drug_Allergy"
},
"Onset_Sulfa_Drug_Allergy": {
"type": "AllergyOnset",
"allergy_type": "allergy",
"category": "medication",
"target_encounter": "Allergist_Initial_Visit",
"codes": [
{
"system": "RxNorm",
"code": "10831",
"display": "Sulfamethoxazole / Trimethoprim"
}
],
"reactions": [
{
"reaction": {
"system": "SNOMED-CT",
"code": "402387002",
"display": "Allergic angioedema (disorder)"
},
"possible_severities": [
{
"level": "mild",
"value": 0.126
},
{
"level": "none",
"value": 0.874
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "247472004",
"display": "Wheal (finding)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.46
},
{
"level": "none",
"value": 0.54
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "39579001",
"display": "Anaphylaxis (disorder)"
},
"possible_severities": [
{
"level": "severe",
"value": 0.01
},
{
"level": "none",
"value": 0.99
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "271807003",
"display": "Eruption of skin (disorder)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.63
},
{
"level": "none",
"value": 0.37
}
]
}
],
"direct_transition": "Cephalosporin_Allergy"
},
"Cephalosporin_Allergy": {
"type": "Simple",
"remarks": [
"1% to 3% of individuals are allergic to cphalosporins. This module sets it fo 2% of people."
],
"distributed_transition": [
{
"transition": "Onset_Cephalosporin_Allergy",
"distribution": 0.02
},
{
"transition": "ACE_Inhibitor_Intolerance",
"distribution": 0.98
}
]
},
"Onset_Cephalosporin_Allergy": {
"type": "AllergyOnset",
"allergy_type": "allergy",
"category": "medication",
"target_encounter": "Allergist_Initial_Visit",
"codes": [
{
"system": "RxNorm",
"code": "25037",
"display": "cefdinir"
},
{
"system": "RxNorm",
"code": "25033",
"display": "Cefixime"
},
{
"system": "RxNorm",
"code": "20489",
"display": "cefpodoxime"
},
{
"system": "RxNorm",
"code": "2191",
"display": "Ceftazidime"
},
{
"system": "RxNorm",
"code": "2193",
"display": "Ceftriaxone"
},
{
"system": "RxNorm",
"code": "2180",
"display": "Cefazolin"
},
{
"system": "RxNorm",
"code": "2231",
"display": "Cephalexin"
},
{
"system": "RxNorm",
"code": "2176",
"display": "Cefaclor"
},
{
"system": "RxNorm",
"code": "20481",
"display": "cefepime"
},
{
"system": "RxNorm",
"code": "2189",
"display": "Cefoxitin"
},
{
"system": "RxNorm",
"code": "2194",
"display": "Cefuroxime"
}
],
"reactions": [
{
"reaction": {
"system": "SNOMED-CT",
"code": "402387002",
"display": "Allergic angioedema (disorder)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.08
},
{
"level": "none",
"value": 0.92
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "247472004",
"display": "Wheal (finding)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.08
},
{
"level": "none",
"value": 0.92
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "39579001",
"display": "Anaphylaxis (disorder)"
},
"possible_severities": [
{
"level": "severe",
"value": 0.2
},
{
"level": "none",
"value": 0.8
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "271807003",
"display": "Eruption of skin (disorder)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.2
},
{
"level": "none",
"value": 0.8
}
]
}
],
"direct_transition": "ACE_Inhibitor_Intolerance"
},
"ACE_Inhibitor_Intolerance": {
"type": "Simple",
"remarks": [
"11.48% of individuals have an intolerance to ACE inhibitors.",
"https://www.sciencedirect.com/science/article/pii/S0735109718304315?viewFullText=true"
],
"distributed_transition": [
{
"transition": "Onset_ACE_Inhibitor_Intolerance",
"distribution": 0.1148
},
{
"transition": "Terminal",
"distribution": 0.8852
}
]
},
"Onset_ACE_Inhibitor_Intolerance": {
"type": "AllergyOnset",
"allergy_type": "intolerance",
"category": "medication",
"target_encounter": "Allergist_Initial_Visit",
"codes": [
{
"system": "RxNorm",
"code": "29046",
"display": "Lisinopril"
},
{
"system": "RxNorm",
"code": "1998",
"display": "Captopril"
},
{
"system": "RxNorm",
"code": "3827",
"display": "Enalapril"
},
{
"system": "RxNorm",
"code": "18867",
"display": "benazepril"
},
{
"system": "RxNorm",
"code": "35208",
"display": "quinapril"
},
{
"system": "RxNorm",
"code": "35296",
"display": "Ramipril"
}
],
"reactions": [
{
"reaction": {
"system": "SNOMED-CT",
"code": "49727002",
"display": "Cough (finding)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.2
},
{
"level": "none",
"value": 0.8
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "402387002",
"display": "Allergic angioedema (disorder)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.007
},
{
"level": "none",
"value": 0.993
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "404640003",
"display": "Dizziness (finding)"
},
"possible_severities": [
{
"level": "mild",
"value": 0.002
},
{
"level": "none",
"value": 0.998
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "236428007",
"display": "Acute kidney injury due to nephrotoxicity (disorder)"
},
"possible_severities": [
{
"level": "severe",
"value": 0.008
},
{
"level": "none",
"value": 0.992
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "267036007",
"display": "Dyspnea (finding)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.06
},
{
"level": "none",
"value": 0.94
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "237849008",
"display": "Drug-induced hyperkalemia (disorder)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.04
},
{
"level": "none",
"value": 0.96
}
]
}
],
"direct_transition": "Terminal"
}
},
"gmf_version": 2
}

717
src/main/resources/modules/allergies/environmental_allergy_incidence.json Normal file
View File

@@ -0,0 +1,717 @@
{
"name": "Environmental Allergy Incidence",
"remarks": [
"This submodule onsets various allergies and is intended to be called ",
"by the main allergies module."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Chance_of_Tree_Pollen_Allergy"
},
"Chance_of_Tree_Pollen_Allergy": {
"type": "Simple",
"remarks": [
"======================================================================",
" TREE POLLEN ALLERGY ",
"======================================================================",
"At present, up to 20% of children are diagnosed with a tree pollen allergy. ",
"Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4098757/",
"In this model most of those children are also atopic, aligning with the ",
"prevalence of allergic rhinitis."
],
"complex_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "atopic",
"operator": "is not nil"
},
"distributions": [
{
"distribution": 0.85,
"transition": "Tree_Pollen_Allergy"
},
{
"distribution": 0.15,
"transition": "Chance_of_Grass_Pollen_Allergy"
}
]
},
{
"distributions": [
{
"distribution": 0.03,
"transition": "Tree_Pollen_Allergy"
},
{
"distribution": 0.97,
"transition": "Chance_of_Grass_Pollen_Allergy"
}
]
}
]
},
"Tree_Pollen_Allergy": {
"type": "AllergyOnset",
"allergy_type": "allergy",
"category": "environment",
"target_encounter": "Allergist_Initial_Visit",
"codes": [
{
"system": "SNOMED-CT",
"code": "782576004",
"display": "Tree pollen (substance)"
}
],
"direct_transition": "Chance_of_Grass_Pollen_Allergy"
},
"Chance_of_Grass_Pollen_Allergy": {
"type": "Simple",
"remarks": [
"======================================================================",
" GRASS POLLEN ALLERGY ",
"======================================================================",
"At present, up to 20% of children are diagnosed with a grass pollen allergy. ",
"Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4098757/",
"In this model most of those children are also atopic, aligning with the ",
"prevalence of allergic rhinitis."
],
"complex_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "atopic",
"operator": "is not nil"
},
"distributions": [
{
"distribution": 0.85,
"transition": "Grass_Pollen_Allergy"
},
{
"distribution": 0.15,
"transition": "Chance_of_Pet_Dander_Allergy"
}
]
},
{
"distributions": [
{
"distribution": 0.03,
"transition": "Grass_Pollen_Allergy"
},
{
"distribution": 0.97,
"transition": "Chance_of_Pet_Dander_Allergy"
}
]
}
]
},
"Grass_Pollen_Allergy": {
"type": "AllergyOnset",
"allergy_type": "allergy",
"category": "environment",
"target_encounter": "Allergist_Initial_Visit",
"codes": [
{
"system": "SNOMED-CT",
"code": "256277009",
"display": "Grass pollen (substance)"
}
],
"direct_transition": "Chance_of_Pet_Dander_Allergy"
},
"Chance_of_Pet_Dander_Allergy": {
"type": "Simple",
"remarks": [
"======================================================================",
" PET DANDER ALLERGY ",
"======================================================================",
"At present, up to 30% of people are diagnosed with a pet dander allergy. ",
"Source: http://allergicliving.com/2010/07/02/pet-allergies-a-gander-at-dander/",
"In this model most of these people are also atopic, aligning with the ",
"prevalence of allergic rhinitis and asthma."
],
"complex_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "atopic",
"operator": "is not nil"
},
"distributions": [
{
"distribution": 1,
"transition": "Pet_Dander_Allergy"
}
]
},
{
"distributions": [
{
"distribution": 0.1,
"transition": "Pet_Dander_Allergy"
},
{
"distribution": 0.9,
"transition": "Chance_of_Dust_Mite_Allergy"
}
]
}
]
},
"Pet_Dander_Allergy": {
"type": "AllergyOnset",
"allergy_type": "allergy",
"category": "environment",
"target_encounter": "Allergist_Initial_Visit",
"codes": [
{
"system": "SNOMED-CT",
"code": "264287008",
"display": "Animal dander (substance)"
}
],
"reactions": [
{
"reaction": {
"system": "SNOMED-CT",
"code": "49727002",
"display": "Cough (finding)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.23
},
{
"level": "none",
"value": 0.77
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "267036007",
"display": "Dyspnea (finding)"
},
"possible_severities": [
{
"level": "mild",
"value": 0.2
},
{
"level": "none",
"value": 0.8
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "247472004",
"display": "Wheal (finding)"
},
"possible_severities": [
{
"level": "mild",
"value": 0.36
},
{
"level": "none",
"value": 0.64
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "271807003",
"display": "Eruption of skin (disorder)"
},
"possible_severities": [
{
"level": "mild",
"value": 0.53
},
{
"level": "none",
"value": 0.47
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "878820003",
"display": "Rhinoconjunctivitis (disorder)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.8
},
{
"level": "none",
"value": 0.19999999999999996
}
]
}
],
"direct_transition": "Chance_of_Dust_Mite_Allergy"
},
"Chance_of_Dust_Mite_Allergy": {
"type": "Simple",
"remarks": [
"======================================================================",
" DUST MITE ALLERGY ",
"======================================================================",
"About 85% of all atopic patients have mite allergies. ",
"Source: https://www.ncbi.nlm.nih.gov/pubmed/12190652"
],
"complex_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "atopic",
"operator": "is not nil"
},
"distributions": [
{
"distribution": 0.85,
"transition": "Dust_Mite_Allergy"
},
{
"distribution": 0.15,
"transition": "Chance_of_Mold_Allergy"
}
]
},
{
"distributions": [
{
"distribution": 0.02,
"transition": "Dust_Mite_Allergy"
},
{
"distribution": 0.98,
"transition": "Chance_of_Mold_Allergy"
}
]
}
]
},
"Dust_Mite_Allergy": {
"type": "AllergyOnset",
"allergy_type": "allergy",
"category": "environment",
"target_encounter": "Allergist_Initial_Visit",
"codes": [
{
"system": "SNOMED-CT",
"code": "260147004",
"display": "House dust mite (organism)"
}
],
"direct_transition": "Chance_of_Mold_Allergy"
},
"Chance_of_Mold_Allergy": {
"type": "Simple",
"remarks": [
"======================================================================",
" MOLD ALLERGY ",
"======================================================================",
"Sensitization to mold is very common, but symptoms are usually mild.",
"Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240910/"
],
"complex_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "atopic",
"operator": "is not nil"
},
"distributions": [
{
"distribution": 1,
"transition": "Mold_Allergy"
}
]
},
{
"distributions": [
{
"distribution": 0.15,
"transition": "Mold_Allergy"
},
{
"distribution": 0.85,
"transition": "Chance_of_Bee_Allergy"
}
]
}
]
},
"Mold_Allergy": {
"type": "AllergyOnset",
"allergy_type": "allergy",
"category": "environment",
"remarks": [
"Back to the American English spelling of mold."
],
"target_encounter": "Allergist_Initial_Visit",
"codes": [
{
"system": "SNOMED-CT",
"code": "84489001",
"display": "Mold (organism)"
}
],
"reactions": [
{
"reaction": {
"system": "SNOMED-CT",
"code": "21626009",
"display": "Cutaneous hypersensitivity (disorder)"
},
"possible_severities": [
{
"level": "mild",
"value": 0.292
},
{
"level": "none",
"value": 0.7
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "76067001",
"display": "Sneezing (finding)"
},
"possible_severities": [
{
"level": "mild",
"value": 0.139
},
{
"level": "none",
"value": 0.86
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "267101005",
"display": "Nasal discharge present (situation)"
},
"possible_severities": [
{
"level": "mild",
"value": 0.183
},
{
"level": "none",
"value": 0.81
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "56018004",
"display": "Wheezing (finding)"
},
"possible_severities": [
{
"level": "mild",
"value": 0.075
},
{
"level": "none",
"value": 0.92
}
]
}
],
"direct_transition": "Chance_of_Bee_Allergy"
},
"Chance_of_Bee_Allergy": {
"type": "Simple",
"remarks": [
"======================================================================",
" BEE STING ALLERGY ",
"======================================================================",
"Estimates range from 1-7%. Source: ",
"http://www.worldallergy.org/professional/allergic_diseases_center/insect_allergy/"
],
"complex_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "atopic",
"operator": "is not nil"
},
"distributions": [
{
"distribution": 0.33,
"transition": "Bee_Allergy"
},
{
"distribution": 0.67,
"transition": "Chance_of_Latex_Allergy"
}
]
},
{
"distributions": [
{
"distribution": 0.01,
"transition": "Bee_Allergy"
},
{
"distribution": 0.99,
"transition": "Chance_of_Latex_Allergy"
}
]
}
]
},
"Bee_Allergy": {
"type": "AllergyOnset",
"allergy_type": "allergy",
"category": "environment",
"target_encounter": "Allergist_Initial_Visit",
"codes": [
{
"system": "SNOMED-CT",
"code": "288328004",
"display": "Bee venom (substance)"
}
],
"reactions": [
{
"reaction": {
"system": "SNOMED-CT",
"code": "39579001",
"display": "Anaphylaxis (disorder)"
},
"possible_severities": [
{
"level": "severe",
"value": 0.03
},
{
"level": "none",
"value": 0.96
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "271807003",
"display": "Eruption of skin (disorder)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.264
},
{
"level": "none",
"value": 0.73
}
]
}
],
"direct_transition": "Chance_of_Latex_Allergy"
},
"Chance_of_Latex_Allergy": {
"type": "Simple",
"remarks": [
"======================================================================",
" LATEX ALLERGY ",
"======================================================================",
"Estimates range from 4-9%. Prevalence is especially high in healthcare ",
"workers and those who had frequent surgeries during childhood.",
"https://www.ncbi.nlm.nih.gov/pubmed/27010091"
],
"complex_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "atopic",
"operator": "is not nil"
},
"distributions": [
{
"distribution": 0.33,
"transition": "Latex_Allergy"
},
{
"distribution": 0.67,
"transition": "Environmental_Allergy_Incidence_Terminal"
}
]
},
{
"distributions": [
{
"distribution": 0.02,
"transition": "Latex_Allergy"
},
{
"distribution": 0.98,
"transition": "Environmental_Allergy_Incidence_Terminal"
}
]
}
]
},
"Latex_Allergy": {
"type": "AllergyOnset",
"allergy_type": "allergy",
"category": "environment",
"target_encounter": "Allergist_Initial_Visit",
"codes": [
{
"system": "SNOMED-CT",
"code": "111088007",
"display": "Latex (substance)"
}
],
"reactions": [
{
"reaction": {
"system": "SNOMED-CT",
"code": "402387002",
"display": "Allergic angioedema (disorder)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.17
},
{
"level": "none",
"value": 0.83
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "267036007",
"display": "Dyspnea (finding)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.1
},
{
"level": "none",
"value": 0.9
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "247472004",
"display": "Wheal (finding)"
},
"possible_severities": [
{
"level": "mild",
"value": 0.8
},
{
"level": "none",
"value": 0.19999999999999996
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "39579001",
"display": "Anaphylaxis (disorder)"
},
"possible_severities": [
{
"level": "severe",
"value": 0.13
},
{
"level": "none",
"value": 0.87
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "271807003",
"display": "Eruption of skin (disorder)"
},
"possible_severities": [
{
"level": "mild",
"value": 0.06
},
{
"level": "none",
"value": 0.94
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "878820003",
"display": "Rhinoconjunctivitis (disorder)"
},
"possible_severities": [
{
"level": "mild",
"value": 0.16
},
{
"level": "none",
"value": 0.84
}
]
},
{
"reaction": {
"system": "SNOMED-CT",
"code": "418290006",
"display": "Itching (finding)"
},
"possible_severities": [
{
"level": "moderate",
"value": 0.11
},
{
"level": "none",
"value": 0.89
}
]
}
],
"direct_transition": "Environmental_Allergy_Incidence_Terminal"
},
"Environmental_Allergy_Incidence_Terminal": {
"type": "Terminal"
}
}
}

1357
src/main/resources/modules/allergies/food_allergy_incidence.json Normal file
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267
src/main/resources/modules/allergies/immunotherapy.json Normal file
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{
"name": "Allergy Immunotherapy",
"remarks": [
"This submodule is called by 'allergies.json'. This models a series of ",
"immunotherapy treatments designed to lessen the severity of allergy ",
"symptoms, or even eliminate the sensitivity altogether. ",
"Immunotherapy is most effective against outdoor allergens (trees, grass), ",
"and common indoor allergens (mold, mites, pet dander). Immunotherapy is ",
"minimally effective against food allergens."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Immunotherapy_Consultation"
},
"Immunotherapy_Consultation": {
"type": "Encounter",
"remarks": [
"======================================================================",
" IMMUNOTHERAPY ",
"======================================================================",
"Allergen immunotherapy for hay fever has been common practice since the ",
"1930's. It was first proven by scientists in the UK in 1911. It has since ",
"been expanded to include additional environmental and food allergens."
],
"encounter_class": "ambulatory",
"codes": [
{
"system": "SNOMED-CT",
"code": "170837001",
"display": "Allergic disorder initial assessment (regime/therapy)"
}
],
"distributed_transition": [
{
"distribution": 0.75,
"transition": "Immunotherapy_Given"
},
{
"distribution": 0.25,
"transition": "Immunotherapy_Not_Given",
"remarks": [
"The distribution here is somewhat arbitrary. I could not find reasonable stats for",
"what percentage of people are given immunotherapy but it's not everyone.",
"I went with a 75/25 split. Reasons to not give immunotherapy include fear of needles,",
"pre-existing immune conditions (like AIDS), and prohibitive cost."
]
}
],
"reason": "allergy_unspecified"
},
"Immunotherapy_Given": {
"type": "SetAttribute",
"attribute": "immunotherapy_status",
"value": "given",
"direct_transition": "Immunotherapy_CarePlan"
},
"Immunotherapy_Not_Given": {
"type": "SetAttribute",
"attribute": "immunotherapy_status",
"value": "not-given",
"direct_transition": "End_Consultation"
},
"Immunotherapy_CarePlan": {
"type": "CarePlanStart",
"codes": [
{
"system": "SNOMED-CT",
"code": "170836005",
"display": "Allergic disorder monitoring (regime/therapy)"
}
],
"activities": [
{
"system": "SNOMED-CT",
"code": "182678001",
"display": "Allergen immunotherapy (regime/therapy)"
}
],
"direct_transition": "Benchmark_Allergy_Test"
},
"Benchmark_Allergy_Test": {
"type": "Procedure",
"duration": {
"low": 20,
"high": 40,
"unit": "minutes"
},
"codes": [
{
"system": "SNOMED-CT",
"code": "395142003",
"display": "Allergy screening test (procedure)"
}
],
"direct_transition": "Benchmark_Allergy_Panel"
},
"Benchmark_Allergy_Panel": {
"type": "CallSubmodule",
"submodule": "allergies/allergy_panel",
"direct_transition": "End_Consultation"
},
"End_Consultation": {
"type": "EncounterEnd",
"conditional_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "immunotherapy_status",
"operator": "==",
"value": "not-given"
},
"transition": "Terminal"
},
{
"transition": "Initialize_Immunotherapy_Counter"
}
]
},
"Initialize_Immunotherapy_Counter": {
"type": "SetAttribute",
"attribute": "immunotherapy_counter",
"value": 0,
"direct_transition": "Undergoing_Immunotherapy_Treatment"
},
"Undergoing_Immunotherapy_Treatment": {
"type": "Delay",
"remarks": [
"Patients get immunotherapy treatments for an average of 5 years.",
"Given monthly appointments we count a total of 60 appointments before ",
"ending the immunotherapy."
],
"range": {
"low": 3,
"high": 4,
"unit": "weeks"
},
"conditional_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "immunotherapy_counter",
"operator": "<",
"value": 60
},
"transition": "Immunotherapy_Treatment"
},
{
"transition": "Immunotherapy_Treatment_Complete"
}
]
},
"Immunotherapy_Treatment": {
"type": "Encounter",
"encounter_class": "ambulatory",
"codes": [
{
"system": "SNOMED-CT",
"code": "371883000",
"display": "Outpatient procedure (procedure)"
}
],
"direct_transition": "Immunotherapy_Procedure",
"reason": "allergy_unspecified"
},
"Immunotherapy_Procedure": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "180256009",
"display": "Subcutaneous immunotherapy (procedure)"
}
],
"duration": {
"low": 15,
"high": 60,
"unit": "minutes"
},
"direct_transition": "End_Treatment_Session"
},
"End_Treatment_Session": {
"type": "EncounterEnd",
"direct_transition": "Count_A_Treatment"
},
"Count_A_Treatment": {
"type": "Counter",
"action": "increment",
"attribute": "immunotherapy_counter",
"direct_transition": "Undergoing_Immunotherapy_Treatment"
},
"Immunotherapy_Treatment_Complete": {
"type": "Simple",
"direct_transition": "Immunotherapy_Followup"
},
"Immunotherapy_Followup": {
"type": "Encounter",
"encounter_class": "ambulatory",
"codes": [
{
"system": "SNOMED-CT",
"code": "170838006",
"display": "Allergic disorder follow-up assessment (regime/therapy)"
}
],
"direct_transition": "Immunotherapy_CarePlan_Ends",
"reason": "allergy_unspecified"
},
"Immunotherapy_CarePlan_Ends": {
"type": "CarePlanEnd",
"careplan": "Immunotherapy_CarePlan",
"direct_transition": "Immunotherapy_Success_Rate"
},
"Immunotherapy_Success_Rate": {
"type": "Simple",
"remarks": [
"My research has shown up to 85% of people respond positively to ",
"immunotherapy treatment. This allows patients to 'outgrow' their ",
"environmental allergies."
],
"distributed_transition": [
{
"distribution": 0.8,
"transition": "Outgrown_Environmental_Allergies"
},
{
"distribution": 0.2,
"transition": "Followup_Test"
}
]
},
"Outgrown_Environmental_Allergies": {
"type": "CallSubmodule",
"submodule": "allergies/outgrow_env_allergies",
"direct_transition": "Followup_Test"
},
"Followup_Test": {
"type": "Procedure",
"duration": {
"low": 20,
"high": 40,
"unit": "minutes"
},
"codes": [
{
"system": "SNOMED-CT",
"code": "395142003",
"display": "Allergy screening test (procedure)"
}
],
"direct_transition": "Followup_Allergy_Panel"
},
"Followup_Allergy_Panel": {
"type": "CallSubmodule",
"submodule": "allergies/allergy_panel",
"direct_transition": "Followup_End"
},
"Followup_End": {
"type": "EncounterEnd",
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

273
src/main/resources/modules/allergies/outgrow_env_allergies.json Normal file
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{
"name": "Outgrow Environmental Allergies",
"remarks": [
"When children reach adolescence or early adulthood, especially if they've ",
"undergone immunotherapy, the potential to outgrow environmental allergies ",
"is pretty high. Using the same general 'outgrow' percentage of 75%."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Tree_Allergy"
},
"Tree_Allergy": {
"type": "Simple",
"remarks": [
"======================================================================",
" OUTGROW TREE ALLERGY ",
"======================================================================"
],
"complex_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "419263009",
"display": "Allergy to tree pollen (finding)"
}
]
},
"distributions": [
{
"distribution": 0.75,
"transition": "Outgrow_Tree_Allergy"
},
{
"distribution": 0.25,
"transition": "Grass_Allergy"
}
]
},
{
"distributions": [
{
"distribution": 1,
"transition": "Grass_Allergy"
}
]
}
]
},
"Outgrow_Tree_Allergy": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "419263009",
"display": "Allergy to tree pollen (finding)"
}
],
"direct_transition": "Grass_Allergy"
},
"Grass_Allergy": {
"type": "Simple",
"remarks": [
"======================================================================",
" OUTGROW GRASS ALLERGY ",
"======================================================================"
],
"complex_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "418689008",
"display": "Allergy to grass pollen (finding)"
}
]
},
"distributions": [
{
"distribution": 0.75,
"transition": "Outgrow_Grass_Allergy"
},
{
"distribution": 0.25,
"transition": "Mold_Allergy"
}
]
},
{
"distributions": [
{
"distribution": 1,
"transition": "Mold_Allergy"
}
]
}
]
},
"Outgrow_Grass_Allergy": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "418689008",
"display": "Allergy to grass pollen (finding)"
}
],
"direct_transition": "Mold_Allergy"
},
"Mold_Allergy": {
"type": "Simple",
"remarks": [
"======================================================================",
" OUTGROW MOLD ALLERGY ",
"======================================================================"
],
"complex_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "419474003",
"display": "Allergy to mold (finding)"
}
]
},
"distributions": [
{
"distribution": 0.75,
"transition": "Outgrow_Mold_Allergy"
},
{
"distribution": 0.25,
"transition": "Pet_Dander_Allergy"
}
]
},
{
"distributions": [
{
"distribution": 1,
"transition": "Pet_Dander_Allergy"
}
]
}
]
},
"Outgrow_Mold_Allergy": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "419474003",
"display": "Allergy to mold (finding)"
}
],
"direct_transition": "Pet_Dander_Allergy"
},
"Pet_Dander_Allergy": {
"type": "Simple",
"remarks": [
"======================================================================",
" OUTGROW PET DANDER ALLERGY ",
"======================================================================"
],
"complex_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "717234006",
"display": "Allergy to animal protein (finding)"
}
]
},
"distributions": [
{
"distribution": 0.75,
"transition": "Outgrow_Pet_Dander_Allergy"
},
{
"distribution": 0.25,
"transition": "Mite_Allergy"
}
]
},
{
"distributions": [
{
"distribution": 1,
"transition": "Mite_Allergy"
}
]
}
]
},
"Outgrow_Pet_Dander_Allergy": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "717234006",
"display": "Allergy to animal protein (finding)"
}
],
"direct_transition": "Mite_Allergy"
},
"Mite_Allergy": {
"type": "Simple",
"remarks": [
"======================================================================",
" OUTGROW DUST MITE ALLERGY ",
"======================================================================"
],
"complex_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "232350006",
"display": "Allergy to dust mite protein (finding)"
}
]
},
"distributions": [
{
"distribution": 0.75,
"transition": "Outgrow_Mite_Allergy"
},
{
"distribution": 0.25,
"transition": "Terminal"
}
]
},
{
"distributions": [
{
"distribution": 1,
"transition": "Terminal"
}
]
}
]
},
"Outgrow_Mite_Allergy": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "232350006",
"display": "Allergy to dust mite protein (finding)"
}
],
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

341
src/main/resources/modules/allergies/outgrow_food_allergies.json Normal file
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{
"name": "Outgrow Food Allergies",
"remarks": [
"75% of children with food allergies outgrow their sensitivity to ",
"milk, soy, eggs, and wheat. However, allergies to peanuts, tree ",
"nuts, fish, and shellfish are rarely outgrown."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Wheat_Allergy"
},
"Wheat_Allergy": {
"type": "Simple",
"remarks": [
"======================================================================",
" OUTGROW WHEAT ALLERGY ",
"======================================================================"
],
"complex_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "420174000",
"display": "Allergy to wheat (finding)"
}
]
},
"distributions": [
{
"distribution": 0.75,
"transition": "Outgrow_Wheat_Allergy"
},
{
"distribution": 0.25,
"transition": "Dairy_Allergy"
}
]
},
{
"distributions": [
{
"distribution": 1,
"transition": "Dairy_Allergy"
}
]
}
]
},
"Outgrow_Wheat_Allergy": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "420174000",
"display": "Allergy to wheat (finding)"
}
],
"direct_transition": "Dairy_Allergy"
},
"Dairy_Allergy": {
"type": "Simple",
"remarks": [
"======================================================================",
" OUTGROW DAIRY ALLERGY ",
"======================================================================"
],
"complex_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "414285001",
"display": "Allergy to food (finding)"
}
]
},
"distributions": [
{
"distribution": 0.75,
"transition": "Outgrow_Dairy_Allergy"
},
{
"distribution": 0.25,
"transition": "Eggs_Allergy"
}
]
},
{
"distributions": [
{
"distribution": 1,
"transition": "Eggs_Allergy"
}
]
}
]
},
"Outgrow_Dairy_Allergy": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "414285001",
"display": "Allergy to food (finding)"
}
],
"direct_transition": "Eggs_Allergy"
},
"Eggs_Allergy": {
"type": "Simple",
"remarks": [
"======================================================================",
" OUTGROW EGGS ALLERGY ",
"======================================================================"
],
"complex_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "213020009",
"display": "Allergy to egg protein (finding)"
}
]
},
"distributions": [
{
"distribution": 0.75,
"transition": "Outgrow_Eggs_Allergy"
},
{
"distribution": 0.25,
"transition": "Soy_Allergy"
}
]
},
{
"distributions": [
{
"distribution": 1,
"transition": "Soy_Allergy"
}
]
}
]
},
"Outgrow_Eggs_Allergy": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "213020009",
"display": "Allergy to egg protein (finding)"
}
],
"direct_transition": "Soy_Allergy"
},
"Soy_Allergy": {
"type": "Simple",
"remarks": [
"======================================================================",
" OUTGROW SOY ALLERGY ",
"======================================================================"
],
"complex_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "782594005",
"display": "Allergy to soy protein (finding)"
}
]
},
"distributions": [
{
"distribution": 0.75,
"transition": "Outgrow_Soy_Allergy"
},
{
"distribution": 0.25,
"transition": "Latex_Allergy"
}
]
},
{
"distributions": [
{
"distribution": 1,
"transition": "Latex_Allergy"
}
]
}
]
},
"Outgrow_Soy_Allergy": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "782594005",
"display": "Allergy to soy protein (finding)"
}
],
"direct_transition": "Latex_Allergy"
},
"Latex_Allergy": {
"type": "Simple",
"remarks": [
"======================================================================",
" OUTGROW LATEX ALLERGY ",
"======================================================================"
],
"complex_transition": [
{
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "1003755004",
"display": "Allergy to Hevea brasiliensis latex protein (finding)"
}
]
},
"distributions": [
{
"distribution": 0.75,
"transition": "Outgrow_Latex_Allergy"
},
{
"distribution": 0.25,
"transition": "Check_For_Other_Food_Allergies"
}
]
},
{
"distributions": [
{
"distribution": 1,
"transition": "Check_For_Other_Food_Allergies"
}
]
}
]
},
"Outgrow_Latex_Allergy": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "1003755004",
"display": "Allergy to Hevea brasiliensis latex protein (finding)"
}
],
"direct_transition": "Check_For_Other_Food_Allergies"
},
"Check_For_Other_Food_Allergies": {
"type": "Simple",
"conditional_transition": [
{
"condition": {
"condition_type": "Or",
"conditions": [
{
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "91935009",
"display": "Allergy to peanut (finding)"
}
]
},
{
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "91934008",
"display": "Allergy to nut (finding)"
}
]
},
{
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "417532002",
"display": "Allergy to fish (finding)"
}
]
},
{
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "300913006",
"display": "Allergy to shellfish (finding)"
}
]
}
]
},
"transition": "Still_Has_Some_Food_Allergies"
},
{
"transition": "No_Food_Allergies_Here"
}
]
},
"Still_Has_Some_Food_Allergies": {
"type": "SetAttribute",
"attribute": "outgrew_food_allergies",
"value": "false",
"direct_transition": "Terminal"
},
"No_Food_Allergies_Here": {
"type": "SetAttribute",
"attribute": "outgrew_food_allergies",
"value": "true",
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

97
src/main/resources/modules/allergies/severe_allergic_reaction.json Normal file
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{
"name": "Severe Allergic Reaction",
"remarks": [
"A severe allergic reaction is characterized by: ",
"1. A visit to the ED ",
"2. Recording of 'Acute allergic reaction' ",
"3. A dose of adrenaline (epinephrine) to stop the reaction ",
"4. An observation period of 2-6 hours ",
"5. A short prescription for oral steroids, usually prednisone "
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Acute_Allergic_Reaction"
},
"ED_Visit_For_Allergic_Reaction": {
"type": "Encounter",
"encounter_class": "emergency",
"codes": [
{
"system": "SNOMED-CT",
"code": "50849002",
"display": "Emergency room admission (procedure)"
}
],
"direct_transition": "Administer_Epinephrine",
"reason": "Acute_Allergic_Reaction"
},
"Acute_Allergic_Reaction": {
"type": "ConditionOnset",
"target_encounter": "ED_Visit_For_Allergic_Reaction",
"codes": [
{
"system": "SNOMED-CT",
"code": "241929008",
"display": "Acute allergic reaction (disorder)"
}
],
"direct_transition": "ED_Visit_For_Allergic_Reaction"
},
"Administer_Epinephrine": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "313191000",
"display": "Injection of epinephrine (procedure)"
}
],
"direct_transition": "Observation_Period"
},
"Observation_Period": {
"type": "Delay",
"range": {
"low": 2,
"high": 6,
"unit": "hours"
},
"direct_transition": "Mild_Steroid"
},
"Mild_Steroid": {
"type": "MedicationOrder",
"remarks": [
"Typically a mild steroid is given to reduce the chance of the ",
"reaction returning after the adrenaline wears off. Usually this is ",
"just one dose, administered at the hospital."
],
"codes": [
{
"system": "RxNorm",
"code": "312617",
"display": "predniSONE 5 MG Oral Tablet"
}
],
"administration": true,
"direct_transition": "End_Mild_Steroid"
},
"End_Mild_Steroid": {
"type": "MedicationEnd",
"medication_order": "Mild_Steroid",
"direct_transition": "End_Acute_Reaction"
},
"End_Acute_Reaction": {
"type": "ConditionEnd",
"condition_onset": "Acute_Allergic_Reaction",
"direct_transition": "Discharge"
},
"Discharge": {
"type": "EncounterEnd",
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

1157
src/main/resources/modules/anemia/anemia_sub.json Normal file
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391
src/main/resources/modules/anemia___unknown_etiology.json Normal file
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{
"name": "Anemia - Unknown Etiology",
"remarks": [
"A blank module"
],
"states": {
"Initial": {
"type": "Initial",
"conditional_transition": [
{
"transition": "White_Males",
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Gender",
"gender": "M"
},
{
"condition_type": "Race",
"race": "White"
}
]
}
},
{
"transition": "White_Females",
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Gender",
"gender": "F"
},
{
"condition_type": "Race",
"race": "White"
}
]
}
},
{
"transition": "Black_Males",
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Gender",
"gender": "M"
},
{
"condition_type": "Race",
"race": "Black"
}
]
}
},
{
"transition": "Black_Females",
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Gender",
"gender": "F"
},
{
"condition_type": "Race",
"race": "Black"
}
]
}
},
{
"transition": "Hispanic_Males",
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Gender",
"gender": "M"
},
{
"condition_type": "Race",
"race": "Hispanic"
}
]
}
},
{
"transition": "Hispanic_Females",
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Gender",
"gender": "F"
},
{
"condition_type": "Race",
"race": "Hispanic"
}
]
}
}
]
},
"White_Males": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.0031,
"transition": "Delay_0_14"
},
{
"distribution": 0.0031,
"transition": "Delay_15-49"
},
{
"distribution": 0.0215,
"transition": "Delay_50_79"
},
{
"distribution": 0.0209,
"transition": "Delay_80_85"
},
{
"transition": "Terminal",
"distribution": 0.9514
}
]
},
"White_Females": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Delay_0_14",
"distribution": 0.0033
},
{
"distribution": 0.025,
"transition": "Delay_15-49"
},
{
"distribution": 0.0216,
"transition": "Delay_50_79"
},
{
"transition": "Delay_80_85",
"distribution": 0.0142
},
{
"transition": "Terminal",
"distribution": 0.9359
}
]
},
"Black_Males": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.0218,
"transition": "Delay_0_14"
},
{
"distribution": 0.0198,
"transition": "Delay_15-49"
},
{
"transition": "Delay_50_79",
"distribution": 0.0422
},
{
"distribution": 0.0056,
"transition": "Delay_80_85"
},
{
"transition": "Terminal",
"distribution": 0.9106
}
]
},
"Black_Females": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Delay_0_14",
"distribution": 0.0351
},
{
"transition": "Delay_15-49",
"distribution": 0.1309
},
{
"distribution": 0.0586,
"transition": "Delay_50_79"
},
{
"distribution": 0.0093,
"transition": "Delay_80_85"
},
{
"transition": "Terminal",
"distribution": 0.7661
}
]
},
"Hispanic_Males": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.007,
"transition": "Delay_0_14"
},
{
"distribution": 0.003,
"transition": "Delay_15-49"
},
{
"distribution": 0.0124,
"transition": "Delay_50_79"
},
{
"distribution": 0.0024,
"transition": "Delay_80_85"
},
{
"transition": "Terminal",
"distribution": 0.9752
}
]
},
"Hispanic_Females": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.0116,
"transition": "Delay_0_14"
},
{
"distribution": 0.0552,
"transition": "Delay_15-49"
},
{
"distribution": 0.0217,
"transition": "Delay_50_79"
},
{
"distribution": 0.004,
"transition": "Delay_80_85"
},
{
"transition": "Terminal",
"distribution": 0.9075
}
]
},
"Terminal": {
"type": "Terminal"
},
"Fatigue": {
"type": "Symptom",
"symptom": "Fatigue",
"cause": "",
"direct_transition": "Check_Anemia_Exist",
"exact": {
"quantity": 1
}
},
"SOB": {
"type": "Symptom",
"symptom": "Shortness of breath",
"cause": "",
"exact": {
"quantity": 1
},
"direct_transition": "Next_Symptom_2"
},
"Anemia_Submodule": {
"type": "CallSubmodule",
"submodule": "anemia/anemia_sub",
"direct_transition": "Anemia_End"
},
"Delay_0_14": {
"type": "Delay",
"direct_transition": "Anemia_Risk_Group",
"range": {
"low": 0,
"high": 14,
"unit": "years"
}
},
"Delay_15-49": {
"type": "Delay",
"direct_transition": "Anemia_Risk_Group",
"range": {
"low": 15,
"high": 49,
"unit": "years"
}
},
"Delay_50_79": {
"type": "Delay",
"direct_transition": "Anemia_Risk_Group",
"range": {
"low": 50,
"high": 79,
"unit": "years"
}
},
"Delay_80_85": {
"type": "Delay",
"direct_transition": "Anemia_Risk_Group",
"range": {
"low": 80,
"high": 85,
"unit": "years"
}
},
"Tachycardia": {
"type": "Symptom",
"symptom": "Tachycardia",
"cause": "",
"exact": {
"quantity": 1
},
"direct_transition": "Next_Symptom_1"
},
"Anemia_Risk_Group": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Tachycardia",
"distribution": 0.15
},
{
"transition": "Next_Symptom_1",
"distribution": 0.85
}
]
},
"Next_Symptom_1": {
"type": "Simple",
"distributed_transition": [
{
"transition": "SOB",
"distribution": 0.1
},
{
"transition": "Next_Symptom_2",
"distribution": 0.9
}
]
},
"Next_Symptom_2": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Fatigue",
"distribution": 0.15
},
{
"transition": "Check_Anemia_Exist",
"distribution": 0.85
}
]
},
"Check_Anemia_Exist": {
"type": "Simple",
"conditional_transition": [
{
"transition": "Anemia_Submodule",
"condition": {
"condition_type": "Attribute",
"attribute": "anemia",
"operator": "is nil"
}
},
{
"transition": "Terminal"
}
]
},
"Anemia_End": {
"type": "ConditionEnd",
"direct_transition": "Terminal",
"referenced_by_attribute": "anemia"
}
},
"gmf_version": 1
}

598
src/main/resources/modules/angina_pectoris.json Normal file
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{
"name": "Angina Pectoris",
"remarks": [
"Angina pectoris is a type of chest pain caused by reduced blood flow to the heart muscle.",
"It is a common symptom of coronary artery disease and often described as a feeling of",
"pressure, heaviness, tightness or pain in the chest.",
"Angina can be stable (predictable pain during exertion) or unstable (occurs at rest or worsening pattern).",
"Information on prevalence, risk factors and treatment obtained from:",
"https://www.ncbi.nlm.nih.gov/books/NBK430728/",
"https://www.ahajournals.org/doi/full/10.1161/CIR.0000000000000743"
],
"states": {
"Initial": {
"type": "Initial",
"remarks": [
"======================================================================",
" INCIDENCE ",
"======================================================================",
"Angina affects approximately 3.4% of the US population. The incidence increases with age",
"and is slightly higher in men than women until older ages, when rates equalize.",
"Annual incidence is approximately 0.1-0.2% with higher rates in older populations."
],
"complex_transition": [
{
"condition": {
"condition_type": "Gender",
"gender": "M"
},
"distributions": [
{
"distribution": 0.002,
"transition": "Delay_Until_Angina"
},
{
"distribution": 0.998,
"transition": "Terminal"
}
]
},
{
"condition": {
"condition_type": "Gender",
"gender": "F"
},
"distributions": [
{
"distribution": 0.0015,
"transition": "Delay_Until_Angina"
},
{
"distribution": 0.9985,
"transition": "Terminal"
}
]
}
]
},
"Delay_Until_Angina": {
"type": "Delay",
"range": {
"low": 40,
"high": 85,
"unit": "years"
},
"direct_transition": "Angina_Onset"
},
"Angina_Onset": {
"type": "ConditionOnset",
"target_encounter": "Angina_Diagnosis",
"codes": [
{
"system": "SNOMED-CT",
"code": "194828000",
"display": "Angina pectoris (disorder)"
},
{
"system": "ICD-10-CM",
"code": "I20.9",
"display": "Angina pectoris, unspecified"
}
],
"direct_transition": "Angina_Type_Decision"
},
"Angina_Type_Decision": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.8,
"transition": "Stable_Angina"
},
{
"distribution": 0.2,
"transition": "Unstable_Angina"
}
]
},
"Stable_Angina": {
"type": "ConditionOnset",
"assign_to_attribute": "angina_type",
"codes": [
{
"system": "SNOMED-CT",
"code": "29562005",
"display": "Stable angina (disorder)"
},
{
"system": "ICD-10-CM",
"code": "I20.8",
"display": "Other forms of angina pectoris"
}
],
"direct_transition": "Angina_Symptom_Chest_Pain"
},
"Unstable_Angina": {
"type": "ConditionOnset",
"assign_to_attribute": "angina_type",
"codes": [
{
"system": "SNOMED-CT",
"code": "4557003",
"display": "Preinfarction syndrome (disorder)"
},
{
"system": "ICD-10-CM",
"code": "I20.0",
"display": "Unstable angina"
}
],
"direct_transition": "Angina_Symptom_Chest_Pain"
},
"Angina_Symptom_Chest_Pain": {
"type": "Symptom",
"symptom": "Chest Pain",
"range": {
"low": 40,
"high": 90
},
"direct_transition": "Angina_Symptom_Shortness_of_Breath"
},
"Angina_Symptom_Shortness_of_Breath": {
"type": "Symptom",
"symptom": "Shortness of Breath",
"range": {
"low": 30,
"high": 70
},
"direct_transition": "Angina_Symptom_Fatigue"
},
"Angina_Symptom_Fatigue": {
"type": "Symptom",
"symptom": "Fatigue",
"range": {
"low": 20,
"high": 60
},
"direct_transition": "Angina_Symptom_Nausea"
},
"Angina_Symptom_Nausea": {
"type": "Symptom",
"symptom": "Nausea",
"range": {
"low": 0,
"high": 40
},
"direct_transition": "Angina_Symptom_Sweating"
},
"Angina_Symptom_Sweating": {
"type": "Symptom",
"symptom": "Sweating",
"range": {
"low": 10,
"high": 50
},
"direct_transition": "Angina_Diagnosis"
},
"Angina_Diagnosis": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Angina_Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "185345009",
"display": "Encounter for symptom"
}
],
"conditional_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "angina_type",
"operator": "==",
"value": "Unstable_Angina"
},
"transition": "Emergency_Encounter"
},
{
"transition": "Angina_ECG"
}
]
},
"Emergency_Encounter": {
"type": "Encounter",
"encounter_class": "emergency",
"reason": "angina_type",
"codes": [
{
"system": "SNOMED-CT",
"code": "50849002",
"display": "Emergency room admission (procedure)"
}
],
"direct_transition": "Angina_ECG"
},
"Angina_ECG": {
"type": "Procedure",
"reason": "Angina_Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "29303009",
"display": "Electrocardiographic procedure (procedure)"
}
],
"duration": {
"low": 10,
"high": 15,
"unit": "minutes"
},
"direct_transition": "Angina_Lab_Test"
},
"Angina_Lab_Test": {
"type": "Procedure",
"reason": "Angina_Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "275907003",
"display": "Cardiac enzyme measurement (procedure)"
}
],
"duration": {
"low": 5,
"high": 10,
"unit": "minutes"
},
"direct_transition": "Angina_Stress_Test_Decision"
},
"Angina_Stress_Test_Decision": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.7,
"transition": "Angina_Stress_Test"
},
{
"distribution": 0.3,
"transition": "Angina_Treatment_Decision"
}
]
},
"Angina_Stress_Test": {
"type": "Procedure",
"reason": "Angina_Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "13647002",
"display": "Coronary stress test using bicycle ergometer (procedure)"
}
],
"duration": {
"low": 30,
"high": 60,
"unit": "minutes"
},
"direct_transition": "Angina_Treatment_Decision"
},
"Angina_Treatment_Decision": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.85,
"transition": "Angina_Medical_Management"
},
{
"distribution": 0.15,
"transition": "Angina_Advanced_Treatment"
}
]
},
"Angina_Medical_Management": {
"type": "CarePlanStart",
"assign_to_attribute": "angina_careplan",
"reason": "Angina_Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "395144009",
"display": "Cardiac patient monitoring (regime/therapy)"
}
],
"activities": [
{
"system": "SNOMED-CT",
"code": "229065009",
"display": "Exercise therapy (regime/therapy)"
},
{
"system": "SNOMED-CT",
"code": "226234005",
"display": "Healthy diet (finding)"
},
{
"system": "SNOMED-CT",
"code": "225323000",
"display": "Smoking cessation education (procedure)"
}
],
"direct_transition": "Angina_Medication"
},
"Angina_Medication": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.5,
"transition": "Angina_Nitrates"
},
{
"distribution": 0.3,
"transition": "Angina_Beta_Blockers"
},
{
"distribution": 0.2,
"transition": "Angina_Calcium_Channel_Blockers"
}
]
},
"Angina_Nitrates": {
"type": "MedicationOrder",
"assign_to_attribute": "angina_medication",
"reason": "Angina_Onset",
"codes": [
{
"system": "RxNorm",
"code": "564666",
"display": "Nitroglycerin 0.4 MG/ACTUAT Mucosal Spray"
}
],
"direct_transition": "Angina_Aspirin"
},
"Angina_Beta_Blockers": {
"type": "MedicationOrder",
"assign_to_attribute": "angina_medication",
"reason": "Angina_Onset",
"codes": [
{
"system": "RxNorm",
"code": "197361",
"display": "Atenolol 50 MG Oral Tablet"
}
],
"direct_transition": "Angina_Aspirin"
},
"Angina_Calcium_Channel_Blockers": {
"type": "MedicationOrder",
"assign_to_attribute": "angina_medication",
"reason": "Angina_Onset",
"codes": [
{
"system": "RxNorm",
"code": "835605",
"display": "Amlodipine 5 MG Oral Tablet"
}
],
"direct_transition": "Angina_Aspirin"
},
"Angina_Aspirin": {
"type": "MedicationOrder",
"assign_to_attribute": "angina_aspirin",
"reason": "Angina_Onset",
"codes": [
{
"system": "RxNorm",
"code": "313782",
"display": "Aspirin 81 MG Oral Tablet"
}
],
"direct_transition": "Angina_Statin"
},
"Angina_Statin": {
"type": "MedicationOrder",
"assign_to_attribute": "angina_statin",
"reason": "Angina_Onset",
"codes": [
{
"system": "RxNorm",
"code": "617311",
"display": "Atorvastatin 10 MG Oral Tablet"
}
],
"direct_transition": "End_Diagnosis_Encounter"
},
"Angina_Advanced_Treatment": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.6,
"transition": "Angina_Cardiac_Catheterization"
},
{
"distribution": 0.4,
"transition": "Angina_Coronary_Bypass_Assessment"
}
]
},
"Angina_Cardiac_Catheterization": {
"type": "Procedure",
"reason": "Angina_Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "80146002",
"display": "Cardiac catheterization (procedure)"
}
],
"duration": {
"low": 1,
"high": 2,
"unit": "hours"
},
"distributed_transition": [
{
"distribution": 0.7,
"transition": "Angina_PCI"
},
{
"distribution": 0.3,
"transition": "Angina_Medical_Management"
}
]
},
"Angina_PCI": {
"type": "Procedure",
"reason": "Angina_Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "415070008",
"display": "Percutaneous coronary intervention (procedure)"
}
],
"duration": {
"low": 1,
"high": 3,
"unit": "hours"
},
"direct_transition": "Angina_Medical_Management"
},
"Angina_Coronary_Bypass_Assessment": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.6,
"transition": "Angina_CABG"
},
{
"distribution": 0.4,
"transition": "Angina_Medical_Management"
}
]
},
"Angina_CABG": {
"type": "Procedure",
"reason": "Angina_Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "232717009",
"display": "Coronary artery bypass grafting (procedure)"
}
],
"duration": {
"low": 3,
"high": 5,
"unit": "hours"
},
"direct_transition": "Angina_Medical_Management"
},
"End_Diagnosis_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Followup_Encounter_Delay"
},
"Followup_Encounter_Delay": {
"type": "Delay",
"range": {
"low": 1,
"high": 3,
"unit": "months"
},
"direct_transition": "Angina_Followup"
},
"Angina_Followup": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Angina_Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "390906007",
"display": "Follow-up encounter (procedure)"
}
],
"distributed_transition": [
{
"distribution": 0.85,
"transition": "Continue_Angina_Management"
},
{
"distribution": 0.1,
"transition": "Worsen_To_Unstable_Angina"
},
{
"distribution": 0.05,
"transition": "Progress_To_MI"
}
]
},
"Continue_Angina_Management": {
"type": "EncounterEnd",
"direct_transition": "Ongoing_Angina_Care"
},
"Ongoing_Angina_Care": {
"type": "Delay",
"range": {
"low": 4,
"high": 8,
"unit": "months"
},
"direct_transition": "Angina_Followup"
},
"Worsen_To_Unstable_Angina": {
"type": "ConditionEnd",
"condition_onset": "angina_type",
"direct_transition": "Unstable_Angina_Transition"
},
"Unstable_Angina_Transition": {
"type": "Simple",
"conditional_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "angina_type",
"operator": "==",
"value": "Stable_Angina"
},
"transition": "Unstable_Angina"
},
{
"transition": "End_Followup_Encounter"
}
]
},
"Progress_To_MI": {
"type": "ConditionEnd",
"condition_onset": "Angina_Onset",
"direct_transition": "End_Angina_Medications"
},
"End_Angina_Medications": {
"type": "MedicationEnd",
"referenced_by_attribute": "angina_medication",
"direct_transition": "End_Angina_Aspirin"
},
"End_Angina_Aspirin": {
"type": "MedicationEnd",
"referenced_by_attribute": "angina_aspirin",
"direct_transition": "End_Angina_Statin"
},
"End_Angina_Statin": {
"type": "MedicationEnd",
"referenced_by_attribute": "angina_statin",
"direct_transition": "End_Angina_CarePlan"
},
"End_Angina_CarePlan": {
"type": "CarePlanEnd",
"referenced_by_attribute": "angina_careplan",
"direct_transition": "End_Followup_Encounter"
},
"End_Followup_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
},
"gmf_version": 2
}

479
src/main/resources/modules/anxiety_disorders.json Normal file
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{
"name": "Anxiety Disorders",
"gmf_version": 2,
"remarks": [
"Anxiety disorders are the most common mental health disorders in the US, affecting approximately 19.1% of adults annually.",
"Women are more likely to be diagnosed with anxiety disorders than men (lifetime prevalence: 30.5% vs 19.2%).",
"References: https://www.nimh.nih.gov/health/statistics/any-anxiety-disorder",
"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3135672/",
"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4610617/"
],
"states": {
"Initial": {
"type": "Initial",
"conditional_transition": [
{
"condition": {
"condition_type": "Gender",
"gender": "F"
},
"transition": "Female"
},
{
"condition": {
"condition_type": "Gender",
"gender": "M"
},
"transition": "Male"
},
{
"transition": "Terminal"
}
]
},
"Female": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.305,
"transition": "Age_Onset_Determination"
},
{
"distribution": 0.695,
"transition": "Terminal"
}
],
"remarks": [
"Lifetime prevalence of anxiety disorders in women is approximately 30.5%",
"Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4610617/"
]
},
"Male": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.192,
"transition": "Age_Onset_Determination"
},
{
"distribution": 0.808,
"transition": "Terminal"
}
],
"remarks": [
"Lifetime prevalence of anxiety disorders in men is approximately 19.2%",
"Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4610617/"
]
},
"Age_Onset_Determination": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.25,
"transition": "Childhood_Onset"
},
{
"distribution": 0.45,
"transition": "Young_Adult_Onset"
},
{
"distribution": 0.2,
"transition": "Adult_Onset"
},
{
"distribution": 0.1,
"transition": "Late_Adult_Onset"
}
],
"remarks": [
"Anxiety disorders often begin in childhood, adolescence, or early adulthood",
"Median age of onset is 11 years",
"Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3135672/"
]
},
"Childhood_Onset": {
"type": "Delay",
"range": {
"low": 5,
"high": 17,
"unit": "years"
},
"direct_transition": "Anxiety_Symptoms_Begin"
},
"Young_Adult_Onset": {
"type": "Delay",
"range": {
"low": 18,
"high": 30,
"unit": "years"
},
"direct_transition": "Anxiety_Symptoms_Begin"
},
"Adult_Onset": {
"type": "Delay",
"range": {
"low": 31,
"high": 50,
"unit": "years"
},
"direct_transition": "Anxiety_Symptoms_Begin"
},
"Late_Adult_Onset": {
"type": "Delay",
"range": {
"low": 51,
"high": 75,
"unit": "years"
},
"direct_transition": "Anxiety_Symptoms_Begin"
},
"Anxiety_Symptoms_Begin": {
"type": "Symptom",
"symptom": "Excessive Worry",
"range": {
"low": 50,
"high": 100
},
"direct_transition": "Anxiety_Symptom_Restlessness"
},
"Anxiety_Symptom_Restlessness": {
"type": "Symptom",
"symptom": "Restlessness",
"range": {
"low": 40,
"high": 90
},
"direct_transition": "Anxiety_Symptom_Fatigue"
},
"Anxiety_Symptom_Fatigue": {
"type": "Symptom",
"symptom": "Fatigue",
"range": {
"low": 30,
"high": 80
},
"direct_transition": "Anxiety_Symptom_Concentration"
},
"Anxiety_Symptom_Concentration": {
"type": "Symptom",
"symptom": "Difficulty Concentrating",
"range": {
"low": 30,
"high": 80
},
"direct_transition": "Anxiety_Symptom_Irritability"
},
"Anxiety_Symptom_Irritability": {
"type": "Symptom",
"symptom": "Irritability",
"range": {
"low": 40,
"high": 90
},
"direct_transition": "Anxiety_Symptom_Muscle_Tension"
},
"Anxiety_Symptom_Muscle_Tension": {
"type": "Symptom",
"symptom": "Muscle Tension",
"range": {
"low": 30,
"high": 80
},
"direct_transition": "Anxiety_Symptom_Sleep_Problems"
},
"Anxiety_Symptom_Sleep_Problems": {
"type": "Symptom",
"symptom": "Sleep Problems",
"range": {
"low": 40,
"high": 90
},
"direct_transition": "Symptom_Period"
},
"Symptom_Period": {
"type": "Delay",
"range": {
"low": 2,
"high": 8,
"unit": "weeks"
},
"direct_transition": "Seek_Care_Decision"
},
"Seek_Care_Decision": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.6,
"transition": "Anxiety_Disorder_Diagnosis"
},
{
"distribution": 0.4,
"transition": "Untreated_Anxiety"
}
],
"remarks": [
"Only about 60% of people with anxiety disorders seek treatment",
"Source: https://www.nimh.nih.gov/health/statistics/any-anxiety-disorder"
]
},
"Untreated_Anxiety": {
"type": "Delay",
"range": {
"low": 1,
"high": 10,
"unit": "years"
},
"distributed_transition": [
{
"distribution": 0.3,
"transition": "Anxiety_Disorder_Diagnosis"
},
{
"distribution": 0.7,
"transition": "Living_With_Untreated_Anxiety"
}
],
"remarks": [
"Some patients may eventually seek care after prolonged symptoms"
]
},
"Living_With_Untreated_Anxiety": {
"type": "Simple",
"direct_transition": "Terminal"
},
"Anxiety_Disorder_Diagnosis": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Excessive Worry",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem (procedure)"
}
],
"direct_transition": "Anxiety_Disorder_Onset"
},
"Anxiety_Disorder_Onset": {
"type": "ConditionOnset",
"target_encounter": "Anxiety_Disorder_Diagnosis",
"assign_to_attribute": "anxiety_disorder",
"codes": [
{
"system": "SNOMED-CT",
"code": "197480006",
"display": "Anxiety disorder (disorder)"
},
{
"system": "ICD-10-CM",
"code": "F41.9",
"display": "Anxiety disorder, unspecified"
}
],
"direct_transition": "Anxiety_Screening"
},
"Anxiety_Screening": {
"type": "Procedure",
"target_encounter": "Anxiety_Disorder_Diagnosis",
"reason": "anxiety_disorder",
"codes": [
{
"system": "LOINC",
"code": "70274-6",
"display": "Generalized anxiety disorder 7 item (GAD-7) total score [Reported]"
}
],
"direct_transition": "Treatment_Decision"
},
"Treatment_Decision": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.5,
"transition": "Medication_Treatment"
},
{
"distribution": 0.3,
"transition": "Therapy_Treatment"
},
{
"distribution": 0.2,
"transition": "Combined_Treatment"
}
],
"remarks": [
"Treatment approaches vary based on severity, patient preference, and provider recommendation"
]
},
"Medication_Treatment": {
"type": "MedicationOrder",
"target_encounter": "Anxiety_Disorder_Diagnosis",
"reason": "anxiety_disorder",
"codes": [
{
"system": "RxNorm",
"code": "866924",
"display": "Sertraline 50 MG Oral Tablet"
}
],
"direct_transition": "Follow_Up_Encounter"
},
"Therapy_Treatment": {
"type": "Procedure",
"target_encounter": "Anxiety_Disorder_Diagnosis",
"reason": "anxiety_disorder",
"codes": [
{
"system": "SNOMED-CT",
"code": "304891004",
"display": "Cognitive behavioral therapy (procedure)"
}
],
"direct_transition": "Follow_Up_Encounter"
},
"Combined_Treatment": {
"type": "MedicationOrder",
"target_encounter": "Anxiety_Disorder_Diagnosis",
"reason": "anxiety_disorder",
"codes": [
{
"system": "RxNorm",
"code": "866924",
"display": "Sertraline 50 MG Oral Tablet"
}
],
"direct_transition": "Add_Therapy"
},
"Add_Therapy": {
"type": "Procedure",
"target_encounter": "Anxiety_Disorder_Diagnosis",
"reason": "anxiety_disorder",
"codes": [
{
"system": "SNOMED-CT",
"code": "304891004",
"display": "Cognitive behavioral therapy (procedure)"
}
],
"direct_transition": "Follow_Up_Encounter"
},
"Follow_Up_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "anxiety_disorder",
"codes": [
{
"system": "SNOMED-CT",
"code": "390906007",
"display": "Follow-up encounter (procedure)"
}
],
"direct_transition": "End_Initial_Encounter"
},
"End_Initial_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Anxiety_Symptom_Improvement"
},
"Anxiety_Symptom_Improvement": {
"type": "Delay",
"range": {
"low": 4,
"high": 12,
"unit": "weeks"
},
"direct_transition": "Reduce_Excessive_Worry"
},
"Reduce_Excessive_Worry": {
"type": "Symptom",
"symptom": "Excessive Worry",
"range": {
"low": 10,
"high": 50
},
"direct_transition": "Reduce_Restlessness"
},
"Reduce_Restlessness": {
"type": "Symptom",
"symptom": "Restlessness",
"range": {
"low": 10,
"high": 40
},
"direct_transition": "Reduce_Fatigue"
},
"Reduce_Fatigue": {
"type": "Symptom",
"symptom": "Fatigue",
"range": {
"low": 10,
"high": 40
},
"direct_transition": "Reduce_Concentration_Issues"
},
"Reduce_Concentration_Issues": {
"type": "Symptom",
"symptom": "Difficulty Concentrating",
"range": {
"low": 10,
"high": 40
},
"direct_transition": "Reduce_Irritability"
},
"Reduce_Irritability": {
"type": "Symptom",
"symptom": "Irritability",
"range": {
"low": 10,
"high": 40
},
"direct_transition": "Reduce_Muscle_Tension"
},
"Reduce_Muscle_Tension": {
"type": "Symptom",
"symptom": "Muscle Tension",
"range": {
"low": 10,
"high": 40
},
"direct_transition": "Reduce_Sleep_Problems"
},
"Reduce_Sleep_Problems": {
"type": "Symptom",
"symptom": "Sleep Problems",
"range": {
"low": 10,
"high": 40
},
"direct_transition": "Ongoing_Care"
},
"Ongoing_Care": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.7,
"transition": "Maintenance_Phase"
},
{
"distribution": 0.2,
"transition": "Relapse"
},
{
"distribution": 0.1,
"transition": "Remission"
}
],
"remarks": [
"Most patients require ongoing treatment, some experience relapse, and a small percentage achieve full remission"
]
},
"Maintenance_Phase": {
"type": "Delay",
"range": {
"low": 6,
"high": 24,
"unit": "months"
},
"direct_transition": "Maintenance_Encounter"
}
}
}

402
src/main/resources/modules/appendicitis.json Normal file
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{
"name": "Appendicitis",
"states": {
"Initial": {
"type": "Initial",
"conditional_transition": [
{
"condition": {
"condition_type": "Gender",
"gender": "M"
},
"transition": "Male"
},
{
"condition": {
"condition_type": "Gender",
"gender": "F"
},
"transition": "Female"
},
{
"transition": "Terminal"
}
]
},
"Male": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.086,
"transition": "Pre_appendicitis"
},
{
"distribution": 0.914,
"transition": "Terminal"
}
],
"remarks": [
"Men have an approx lifetime risk of appendicitis of 8.6%. Ref: http://www.ncbi.nlm.nih.gov/pubmed/2239906"
]
},
"Female": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.067,
"transition": "Pre_appendicitis"
},
{
"distribution": 0.933,
"transition": "Terminal"
}
],
"remarks": [
"Women have an approx lifetime risk of appendicitis of 6.7%. Ref: http://www.ncbi.nlm.nih.gov/pubmed/2239906"
]
},
"Pre_appendicitis": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.263,
"transition": "Ages_1_17"
},
{
"distribution": 0.423,
"transition": "Ages_18_44"
},
{
"distribution": 0.221,
"transition": "Ages_45_64"
},
{
"distribution": 0.093,
"transition": "Ages_65_Plus"
}
],
"remarks": [
"Age distribution of appendicitis from https://www.ncbi.nlm.nih.gov/books/NBK169006/ , Table 1"
]
},
"Ages_1_17": {
"type": "Delay",
"range": {
"low": 1,
"high": 17,
"unit": "years"
},
"direct_transition": "Appendicitis_Symptom1"
},
"Ages_18_44": {
"type": "Delay",
"range": {
"low": 18,
"high": 44,
"unit": "years"
},
"direct_transition": "Appendicitis_Symptom1"
},
"Ages_45_64": {
"type": "Delay",
"range": {
"low": 45,
"high": 64,
"unit": "years"
},
"direct_transition": "Appendicitis_Symptom1"
},
"Ages_65_Plus": {
"type": "Delay",
"range": {
"low": 65,
"high": 99,
"unit": "years"
},
"direct_transition": "Appendicitis_Symptom1"
},
"Appendicitis_Symptom1": {
"type": "Symptom",
"symptom": "Abdominal Pain",
"range": {
"low": 50,
"high": 150
},
"direct_transition": "Appendicitis_Symptom2"
},
"Appendicitis_Symptom2": {
"type": "Symptom",
"symptom": "Fever",
"range": {
"low": 50,
"high": 100
},
"direct_transition": "Appendicitis_Symptom3"
},
"Appendicitis_Symptom3": {
"type": "Symptom",
"symptom": "Loss of Appetite",
"range": {
"low": 50,
"high": 100
},
"direct_transition": "Appendicitis_Symptom4"
},
"Appendicitis_Symptom4": {
"type": "Symptom",
"symptom": "Nausea/Vomiting",
"range": {
"low": 0,
"high": 50
},
"direct_transition": "Appendicitis_Symptom5"
},
"Appendicitis_Symptom5": {
"type": "Symptom",
"symptom": "Diarrhea",
"range": {
"low": 0,
"high": 50
},
"direct_transition": "Appendicitis_Symptom6"
},
"Appendicitis_Symptom6": {
"type": "Symptom",
"symptom": "Bloating/Gas",
"range": {
"low": 0,
"high": 50
},
"direct_transition": "Appendicitis_Symptom7"
},
"Appendicitis_Symptom7": {
"type": "Symptom",
"symptom": "Constipation",
"range": {
"low": 0,
"high": 50
},
"direct_transition": "Symptom_Period"
},
"Symptom_Period": {
"type": "Delay",
"range": {
"low": 1,
"high": 3,
"unit": "days"
},
"direct_transition": "Appendicitis"
},
"Appendicitis": {
"type": "ConditionOnset",
"target_encounter": "Appendicitis_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "74400008",
"display": "Appendicitis (disorder)"
}
],
"distributed_transition": [
{
"distribution": 0.7,
"transition": "Appendicitis_Encounter"
},
{
"distribution": 0.3,
"transition": "Rupture"
}
],
"remarks": [
"The rate of perforation varies from 16% to 40%, with a higher frequency occurring in younger age groups (40-57%)",
"and in patients older than 50 years (55-70%), in whom misdiagnosis and delayed diagnosis are common.",
"(ref: http://emedicine.medscape.com/article/773895-overview#a7 )",
"From table 1 here: https://www.ncbi.nlm.nih.gov/books/NBK169006/ it's about 30%",
"For simplicity here I just round to 30% for all age groups."
]
},
"Rupture": {
"type": "ConditionOnset",
"target_encounter": "Appendicitis_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "47693006",
"display": "Rupture of appendix (disorder)"
}
],
"direct_transition": "Appendicitis_Encounter"
},
"Appendicitis_Encounter": {
"type": "Encounter",
"encounter_class": "emergency",
"reason": "Appendicitis",
"remarks": [
"Currently the GMF does not include Vital Signs, if we decide to add that then there are some lab tests we could add at this Encounter."
],
"codes": [
{
"system": "SNOMED-CT",
"code": "50849002",
"display": "Emergency room admission (procedure)"
}
],
"direct_transition": "History_of_Appendectomy"
},
"History_of_Appendectomy": {
"type": "ConditionOnset",
"target_encounter": "Appendectomy_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "428251008",
"display": "History of appendectomy (situation)"
}
],
"direct_transition": "Transfer_To_Inpatient"
},
"Appendectomy_Encounter": {
"type": "Encounter",
"encounter_class": "inpatient",
"reason": "Appendicitis",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem (procedure)"
}
],
"direct_transition": "Appendectomy"
},
"Appendectomy": {
"type": "Procedure",
"reason": "Appendicitis",
"codes": [
{
"system": "SNOMED-CT",
"code": "80146002",
"display": "Excision of appendix (procedure)"
}
],
"duration": {
"low": 40,
"high": 70,
"unit": "minutes"
},
"remarks": [
"Avg operative time is ~55 minutes",
"https://www.ncbi.nlm.nih.gov/pubmed/17658102"
],
"direct_transition": "End_Appendicitis"
},
"Appendicitis_Symptom1_Ends": {
"type": "Symptom",
"symptom": "Abdominal Pain",
"exact": {
"quantity": 0
},
"direct_transition": "Appendicitis_Symptom2_Ends"
},
"Appendicitis_Symptom2_Ends": {
"type": "Symptom",
"symptom": "Fever",
"exact": {
"quantity": 0
},
"direct_transition": "Appendicitis_Symptom3_Ends"
},
"Appendicitis_Symptom3_Ends": {
"type": "Symptom",
"symptom": "Loss of Appetite",
"exact": {
"quantity": 0
},
"direct_transition": "Appendicitis_Symptom4_Ends"
},
"Appendicitis_Symptom4_Ends": {
"type": "Symptom",
"symptom": "Nausea/Vomiting",
"exact": {
"quantity": 0
},
"direct_transition": "Appendicitis_Symptom5_Ends"
},
"Appendicitis_Symptom5_Ends": {
"type": "Symptom",
"symptom": "Diarrhea",
"exact": {
"quantity": 0
},
"direct_transition": "Appendicitis_Symptom6_Ends"
},
"Appendicitis_Symptom6_Ends": {
"type": "Symptom",
"symptom": "Bloating/Gas",
"exact": {
"quantity": 0
},
"direct_transition": "Appendicitis_Symptom7_Ends"
},
"Appendicitis_Symptom7_Ends": {
"type": "Symptom",
"symptom": "Constipation",
"exact": {
"quantity": 0
},
"direct_transition": "Recovery"
},
"Recovery": {
"type": "Delay",
"range": {
"low": 1,
"high": 5,
"unit": "days"
},
"remarks": [
"Traditionally, patients are hospitalized for 24 hours after laparoscopic appendectomy. ",
"A retrospective review of 119 patients [...] ",
"Forty-two patients were dismissed on the day of surgery and 77 were admitted for 1 to 5 days postoperatively.",
"https://www.ncbi.nlm.nih.gov/pubmed/22369831"
],
"direct_transition": "End_Appendectomy_Encounter"
},
"End_Appendectomy_Encounter": {
"type": "EncounterEnd",
"discharge_disposition": {
"system": "NUBC",
"code": "01",
"display": "Discharged to home care or self care (routine discharge)"
},
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
},
"Transfer_To_Inpatient": {
"type": "EncounterEnd",
"direct_transition": "Appendectomy_Encounter"
},
"End_Appendicitis": {
"type": "ConditionEnd",
"condition_onset": "Appendicitis",
"conditional_transition": [
{
"transition": "End_Rupture",
"condition": {
"condition_type": "PriorState",
"name": "Rupture"
}
},
{
"transition": "Appendicitis_Symptom1_Ends"
}
]
},
"End_Rupture": {
"type": "ConditionEnd",
"direct_transition": "Appendicitis_Symptom1_Ends",
"condition_onset": "Rupture"
}
},
"gmf_version": 1
}

593
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{
"name": "Asthma",
"remarks": [
"This module is mostly based on statistics from the AAAAI and CDC. See:",
"http://www.aaaai.org/about-aaaai/newsroom/asthma-statistics",
"http://www.cdc.gov/nchs/fastats/asthma.htm",
"http://www.cdc.gov/nchs/products/databriefs/db94.htm"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Delay_For_Atopy"
},
"Delay_For_Atopy": {
"type": "Delay",
"remarks": [
"The Atopy module must be processed before any of the allergy modules so ",
"atopy can appropriately influence allergies. Delaying the smallest possible ",
"time step to ensure this happens."
],
"exact": {
"quantity": 1,
"unit": "weeks"
},
"conditional_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "atopic",
"operator": "is not nil"
},
"transition": "Atopic"
},
{
"transition": "Not_Atopic"
}
]
},
"Atopic": {
"type": "Simple",
"remarks": [
"45% of all atopic patients develop asthma. See the Atopy model for more info."
],
"distributed_transition": [
{
"distribution": 0.45,
"transition": "Asthma_Incidence"
},
{
"distribution": 0.55,
"transition": "Terminal"
}
]
},
"Not_Atopic": {
"type": "Simple",
"remarks": [
"There is a possibility that non-atopic patients develop asthma. However, ",
"this asthma is likely more environmental and more likely to develop in ",
"adulthood. Overall, 8-9% of the population gets asthma. In this model 6.8% ",
"of those patients are atopic. The remaining 1.2-2% are not."
],
"distributed_transition": [
{
"distribution": 0.023,
"transition": "Asthma_Incidence"
},
{
"distribution": 0.977,
"transition": "Terminal"
}
]
},
"Asthma_Incidence": {
"type": "Simple",
"remarks": [
"8.6% of children have asthma, 7.4% of adults. To model childhood-only, lifetime, and adult-onset",
"asthma I try to distribute the patients in a reasonable (but slightly arbitrary) manner:",
" ,-> 1.6% childhood-only ",
" birth --> 7.0% lifetime = 8.6% childhood asthma",
" `-> 0.4% adult-onset = 7.4% adult asthma ",
"Collectively this sums to 9% of people getting asthma in their lifetime, which is consistent with",
"my extrapolation based on the AAAAI's estimates: (1/14 had asthma in 2001, 1/12 in 2009, so I extrapolate",
"1/11 for 2016)."
],
"distributed_transition": [
{
"distribution": 0.95,
"transition": "Delay_For_Childhood_Asthma"
},
{
"distribution": 0.05,
"transition": "Delay_Until_Adulthood"
}
]
},
"Delay_For_Childhood_Asthma": {
"type": "Delay",
"remarks": [
"Typically asthma symptoms don't appear until the child is at least 3."
],
"range": {
"low": 2,
"high": 5,
"unit": "years"
},
"direct_transition": "Childhood_Asthma_Begins"
},
"Delay_Until_Adulthood": {
"type": "Delay",
"range": {
"low": 18,
"high": 40,
"unit": "years"
},
"direct_transition": "Adult_Asthma_Begins"
},
"Childhood_Asthma_Begins": {
"type": "ConditionOnset",
"target_encounter": "Asthma_Diagnosis",
"assign_to_attribute": "asthma_condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "233678006",
"display": "Childhood asthma (disorder)"
}
],
"direct_transition": "Set_Childhood_Asthma"
},
"Set_Childhood_Asthma": {
"type": "SetAttribute",
"attribute": "asthma_type",
"value": "childhood",
"direct_transition": "Asthma_Diagnosis"
},
"Adult_Asthma_Begins": {
"type": "ConditionOnset",
"target_encounter": "Asthma_Diagnosis",
"assign_to_attribute": "asthma_condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "195967001",
"display": "Asthma (disorder)"
}
],
"direct_transition": "Set_Adult_Asthma"
},
"Set_Adult_Asthma": {
"type": "SetAttribute",
"attribute": "asthma_type",
"value": "lifelong",
"direct_transition": "Asthma_Diagnosis"
},
"Asthma_Diagnosis": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "asthma_condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "185345009",
"display": "Encounter for symptom (procedure)"
}
],
"direct_transition": "Asthma_Symptom1"
},
"Asthma_Symptom1": {
"type": "Symptom",
"symptom": "Wheezing",
"range": {
"low": 25,
"high": 75
},
"direct_transition": "Asthma_Symptom2"
},
"Asthma_Symptom2": {
"type": "Symptom",
"symptom": "Shortness of Breath",
"range": {
"low": 25,
"high": 75
},
"direct_transition": "Asthma_Symptom3"
},
"Asthma_Symptom3": {
"type": "Symptom",
"symptom": "Chest Pressure",
"range": {
"low": 0,
"high": 50
},
"direct_transition": "Asthma_Symptom4"
},
"Asthma_Symptom4": {
"type": "Symptom",
"symptom": "Cough",
"range": {
"low": 0,
"high": 25
},
"direct_transition": "Asthma_Symptom5"
},
"Asthma_Symptom5": {
"type": "Symptom",
"symptom": "Nasal Congestion",
"range": {
"low": 0,
"high": 25
},
"direct_transition": "Asthma_Symptom6"
},
"Asthma_Symptom6": {
"type": "Symptom",
"symptom": "Mucus Secretion",
"range": {
"low": 0,
"high": 25
},
"direct_transition": "Asthma_Screening"
},
"Asthma_Screening": {
"type": "Procedure",
"reason": "asthma_condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "171231001",
"display": "Asthma screening (procedure)"
}
],
"direct_transition": "Prescribe_Maintenance_Inhaler"
},
"Prescribe_Maintenance_Inhaler": {
"type": "CallSubmodule",
"submodule": "medications/maintenance_inhaler",
"direct_transition": "Prescribe_Emergency_Inhaler"
},
"Prescribe_Emergency_Inhaler": {
"type": "CallSubmodule",
"submodule": "medications/emergency_inhaler",
"direct_transition": "Asthma_CarePlan_Selector"
},
"Asthma_CarePlan_Selector": {
"type": "Simple",
"conditional_transition": [
{
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Age",
"operator": ">=",
"quantity": 18,
"unit": "years"
},
{
"condition_type": "Attribute",
"attribute": "smoker",
"operator": "==",
"value": true
}
]
},
"transition": "Smoker_CarePlan"
},
{
"transition": "Nonsmoker_CarePlan"
}
]
},
"Smoker_CarePlan": {
"type": "CarePlanStart",
"assign_to_attribute": "asthma_careplan",
"reason": "asthma_condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "699728000",
"display": "Asthma self management (regime/therapy)"
}
],
"activities": [
{
"system": "SNOMED-CT",
"code": "710081004",
"display": "Smoking cessation therapy (regime/therapy)"
},
{
"system": "SNOMED-CT",
"code": "710818004",
"display": "Inhaled steroid therapy (procedure)"
},
{
"system": "SNOMED-CT",
"code": "708409001",
"display": "Home nebulizer therapy (procedure)"
}
],
"direct_transition": "End_Diagnosis_Encounter"
},
"Nonsmoker_CarePlan": {
"type": "CarePlanStart",
"assign_to_attribute": "asthma_careplan",
"reason": "asthma_condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "699728000",
"display": "Asthma self management (regime/therapy)"
}
],
"activities": [
{
"system": "SNOMED-CT",
"code": "710818004",
"display": "Inhaled steroid therapy (procedure)"
},
{
"system": "SNOMED-CT",
"code": "708409001",
"display": "Home nebulizer therapy (procedure)"
},
{
"system": "SNOMED-CT",
"code": "229298005",
"display": "Breathing control (regime/therapy)"
}
],
"direct_transition": "End_Diagnosis_Encounter"
},
"End_Diagnosis_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Maintaining_Asthma"
},
"Maintaining_Asthma": {
"type": "Delay",
"exact": {
"quantity": 6,
"unit": "months"
},
"conditional_transition": [
{
"condition": {
"remarks": [
"Childhood-only asthma ends"
],
"condition_type": "And",
"conditions": [
{
"condition_type": "Age",
"operator": ">",
"quantity": 18,
"unit": "years"
},
{
"condition_type": "Attribute",
"attribute": "asthma_type",
"operator": "==",
"value": "childhood"
}
]
},
"transition": "Childhood_Asthma_May_Subside"
},
{
"transition": "Potential_Asthma_Attack"
}
]
},
"Childhood_Asthma_May_Subside": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.83,
"transition": "Childhood_Asthma_Becomes_Lifelong_Asthma"
},
{
"distribution": 0.17,
"transition": "Next_Wellness_Encounter"
}
],
"remarks": [
"After a validation study, 248 children were identified as having asthma; these children were reassessed annually until age 19 years when 205 (83%) remained.",
"\"Remission and persistence of asthma followed from 7 to 19 years of age.\" Andersson M, Hedman L, Bjerg A, Forsberg B, Lundbäck B, Rönmark E. Pediatrics. 2013 Aug;132(2):e435-42. doi: 10.1542/peds.2013-0741.",
"https://www.ncbi.nlm.nih.gov/pubmed/23897917"
]
},
"Childhood_Asthma_Becomes_Lifelong_Asthma": {
"type": "ConditionEnd",
"referenced_by_attribute": "asthma_condition",
"direct_transition": "Lifelong_Asthma"
},
"Lifelong_Asthma": {
"type": "SetAttribute",
"attribute": "asthma_type",
"value": "lifelong",
"direct_transition": "Next_Adult_Welness_Encounter"
},
"Next_Adult_Welness_Encounter": {
"type": "Encounter",
"wellness": true,
"direct_transition": "Lifelong_Asthma_Begins",
"reason": "asthma_condition"
},
"Lifelong_Asthma_Begins": {
"type": "ConditionOnset",
"target_encounter": "Next_Adult_Welness_Encounter",
"assign_to_attribute": "asthma_condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "195967001",
"display": "Asthma (disorder)"
}
],
"direct_transition": "End_Wellness_1"
},
"Potential_Asthma_Attack": {
"type": "Simple",
"remarks": [
"Once every 6 months we simulate whether or not the patient has an asthma attack",
"53% have an attack each year (57% children, 51% adults), source: AAAAI.",
"This means a 26.5% rate of attack per 6 month period."
],
"distributed_transition": [
{
"distribution": 0.735,
"transition": "Maintaining_Asthma",
"remarks": [
"No asthma attack occured"
]
},
{
"distribution": 0.265,
"transition": "Asthma_Attack"
}
]
},
"Asthma_Attack": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.1885,
"transition": "Asthma_ED_Visit",
"remarks": [
"The CDC documented 10 ED visits per 100 people with asthma each year.",
"http://www.cdc.gov/nchs/products/databriefs/db94.htm",
"Assuming hospitalization always comes from an attack, for those that have attacks each 6-month period (26.5%)",
"5/26.5 people (per 100) --> 18.85% rate of hospitalization from attack."
]
},
{
"distribution": 0.8115,
"transition": "Asthma_Attack_Followup",
"remarks": [
"If the attack did not result in an ED visit the patient still visited his/her physician for a followup"
]
}
]
},
"Asthma_ED_Visit": {
"type": "Encounter",
"encounter_class": "emergency",
"reason": "asthma_condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "183478001",
"display": "Emergency hospital admission for asthma (procedure)"
}
],
"direct_transition": "End_Asthma_ED_Visit"
},
"End_Asthma_ED_Visit": {
"type": "EncounterEnd",
"direct_transition": "Delay_For_Followup"
},
"Delay_For_Followup": {
"type": "Delay",
"range": {
"low": 1,
"high": 3,
"unit": "days"
},
"direct_transition": "Asthma_Attack_Followup"
},
"Asthma_Attack_Followup": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "asthma_condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "394701000",
"display": "Asthma follow-up (regime/therapy)"
}
],
"direct_transition": "Followup_End"
},
"Followup_End": {
"type": "EncounterEnd",
"direct_transition": "Maintaining_Asthma"
},
"Next_Wellness_Encounter": {
"type": "Encounter",
"wellness": true,
"direct_transition": "Maintenance_Medication_End",
"reason": "asthma_condition"
},
"Maintenance_Medication_End": {
"type": "MedicationEnd",
"referenced_by_attribute": "maintenance_inhaler",
"direct_transition": "Emergency_Medication_End"
},
"Emergency_Medication_End": {
"type": "MedicationEnd",
"referenced_by_attribute": "emergency_inhaler",
"direct_transition": "Childhood_Asthma_Subsides"
},
"Childhood_Asthma_Subsides": {
"type": "ConditionEnd",
"referenced_by_attribute": "asthma_condition",
"direct_transition": "Asthma_Symptom1_Ends"
},
"Asthma_Symptom1_Ends": {
"type": "Symptom",
"symptom": "Wheezing",
"exact": {
"quantity": 0
},
"direct_transition": "Asthma_Symptom2_Ends"
},
"Asthma_Symptom2_Ends": {
"type": "Symptom",
"symptom": "Shortness of Breath",
"exact": {
"quantity": 0
},
"direct_transition": "Asthma_Symptom3_Ends"
},
"Asthma_Symptom3_Ends": {
"type": "Symptom",
"symptom": "Chest Pressure",
"exact": {
"quantity": 0
},
"direct_transition": "Asthma_Symptom4_Ends"
},
"Asthma_Symptom4_Ends": {
"type": "Symptom",
"symptom": "Cough",
"exact": {
"quantity": 0
},
"direct_transition": "Asthma_Symptom5_Ends"
},
"Asthma_Symptom5_Ends": {
"type": "Symptom",
"symptom": "Nasal Congestion",
"exact": {
"quantity": 0
},
"direct_transition": "Asthma_Symptom6_Ends"
},
"Asthma_Symptom6_Ends": {
"type": "Symptom",
"symptom": "Mucus Secretion",
"exact": {
"quantity": 0
},
"direct_transition": "End_Asthma_CarePlan"
},
"End_Asthma_CarePlan": {
"type": "CarePlanEnd",
"referenced_by_attribute": "asthma_careplan",
"direct_transition": "End_Wellness_2"
},
"Terminal": {
"type": "Terminal"
},
"End_Wellness_1": {
"type": "EncounterEnd",
"direct_transition": "Maintaining_Asthma"
},
"End_Wellness_2": {
"type": "EncounterEnd",
"direct_transition": "Terminal"
}
},
"gmf_version": 1
}

196
src/main/resources/modules/atopy.json Normal file
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{
"name": "Atopy",
"remarks": [
"'Atopy' specifically refers to the genetic tendency to develop allergic diseases.",
"https://www.aaaai.org/conditions-and-treatments/conditions-dictionary/atopy",
"Atopy is the most significant factor in the 'atopic triad' of: ",
"1. Atopic Dermatitis (Eczema) ",
"2. Asthma ",
"3. Environmental and Food Allergies ",
"4. Allergic Rhinitis (Hay Fever) ",
"Okay... so maybe the atopic triad could be a 'quartet'.",
"Up to 20% of children display signs of atopy, 50% by age 1 and 95% by age 5.",
"75% of children with atopic symptoms outgrow them by adolescence or early ",
"adulthood. However, 25% show symptoms for life. It is of course possible to be ",
"non-atopic and still develop allergies and asthma.",
"The prevalence of atopy and allergies has increased substantially in the 20th ",
"century, especially after the 1960's, typically at a rate of 0.15 - 0.3% per ",
"year. To model this historical increase in allergy prevalence atopy is the driving ",
"factor. In this model the incidence of atopy increases at 1.875% per decade, or about ",
"0.19% per year since 1940.",
"Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4629767/",
"There is a complex relationship between allergies, asthma, and eczema.",
"In a word, those with atopy have a significantly increased risk of severe ",
"and moderate allergies.",
"The final model: ",
" Total ,--> 85% Allergic Rhinitis (12.8% overall)",
" Population ---> 15% ATOPIC ---> 55% Atopic Dermatitis (8.25% overall)",
" |`--> 45% Asthma (6.75% overall)",
" `---> 25% Food & Environmental Allergies (3.75% overall)",
"Above, 15% of all people are atopic by 2010."
],
"states": {
"Initial": {
"type": "Initial",
"complex_transition": [
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 1940
},
"distributions": [
{
"distribution": 1,
"transition": "Terminal"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 1950
},
"distributions": [
{
"distribution": 0.01875,
"transition": "Is_Atopic"
},
{
"distribution": 0.98125,
"transition": "Terminal"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 1960
},
"distributions": [
{
"distribution": 0.0375,
"transition": "Is_Atopic"
},
{
"distribution": 0.9625,
"transition": "Terminal"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 1970
},
"distributions": [
{
"distribution": 0.05625,
"transition": "Is_Atopic"
},
{
"distribution": 0.94375,
"transition": "Terminal"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 1980
},
"distributions": [
{
"distribution": 0.075,
"transition": "Is_Atopic"
},
{
"distribution": 0.925,
"transition": "Terminal"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 1990
},
"distributions": [
{
"distribution": 0.09375,
"transition": "Is_Atopic"
},
{
"distribution": 0.90625,
"transition": "Terminal"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 2000
},
"distributions": [
{
"distribution": 0.1125,
"transition": "Is_Atopic"
},
{
"distribution": 0.8875,
"transition": "Terminal"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 2010
},
"distributions": [
{
"distribution": 0.13125,
"transition": "Is_Atopic"
},
{
"distribution": 0.86875,
"transition": "Terminal"
}
]
},
{
"remarks": [
"After 2010, the overall prevalence of atopy settles at 15%."
],
"distributions": [
{
"distribution": 0.15,
"transition": "Is_Atopic"
},
{
"distribution": 0.85,
"transition": "Terminal"
}
]
}
]
},
"Is_Atopic": {
"type": "SetAttribute",
"attribute": "atopic",
"value": true,
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

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src/main/resources/modules/atrial_fibrillation.json Normal file
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{
"name": "Atrial Fibrillation",
"specialty": "CARDIOVASCULAR DISEASE (CARDIOLOGY)",
"remarks": [
"This module is not intended to model clinical workflow, it is intended to funnel eligible patients into heart surgery."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Chance_of_AFib"
},
"Terminal": {
"type": "Terminal"
},
"Chance_of_AFib": {
"type": "Delay",
"exact": {
"quantity": 1,
"unit": "months"
},
"distributed_transition": [
{
"transition": "Diagnosis",
"distribution": {
"attribute": "atrial_fibrillation_risk",
"default": 0
}
},
{
"transition": "Chance_of_AFib",
"distribution": 1
}
]
},
"Diagnosis": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "49436004",
"display": "Atrial fibrillation (disorder)"
}
],
"direct_transition": "Next Wellness Visit",
"target_encounter": "Next Wellness Visit",
"assign_to_attribute": "atrial_fibrillation"
},
"Next Wellness Visit": {
"type": "Encounter",
"reason": "Diagnosis",
"telemedicine_possibility": "none",
"wellness": true,
"conditional_transition": [
{
"transition": "Verapamil",
"condition": {
"condition_type": "Date",
"operator": ">=",
"year": 1981
}
},
{
"transition": "Warfarin",
"condition": {
"condition_type": "Date",
"operator": ">=",
"year": 1954
}
},
{
"transition": "Procedure Check"
}
]
},
"Warfarin": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 855332,
"display": "Warfarin Sodium 5 MG Oral Tablet"
}
],
"direct_transition": "Digoxin",
"reason": "Diagnosis",
"chronic": true
},
"Verapamil": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 897685,
"display": "verapamil hydrochloride 80 MG Oral Tablet"
}
],
"direct_transition": "Warfarin",
"reason": "Diagnosis",
"chronic": true
},
"Digoxin": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 197604,
"display": "Digoxin 0.125 MG Oral Tablet"
}
],
"reason": "Diagnosis",
"chronic": true,
"direct_transition": "Procedure Check"
},
"Procedure Check": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Catheter Ablation",
"distribution": 0.2
},
{
"transition": "Electrical Cardioversion",
"distribution": 0.8
}
]
},
"Catheter Ablation": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "18286008",
"display": "Catheter ablation of tissue of heart (procedure)"
}
],
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 60,
"low": 30
}
},
"unit": "minutes",
"reason": "Diagnosis",
"distributed_transition": [
{
"transition": "Pacemaker",
"distribution": 0.1
},
{
"transition": "End Encounter",
"distribution": 0.9
}
]
},
"Electrical Cardioversion": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "180325003",
"display": "Direct current cardioversion (procedure)"
}
],
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 60,
"low": 30
}
},
"unit": "minutes",
"direct_transition": "End Encounter",
"reason": "Diagnosis"
},
"End Encounter": {
"type": "EncounterEnd",
"direct_transition": "Terminal"
},
"Pacemaker": {
"type": "Device",
"code": {
"system": "SNOMED-CT",
"code": "706004007",
"display": "Implantable cardiac pacemaker (physical object)"
},
"direct_transition": "End Encounter"
}
},
"gmf_version": 2
}

463
src/main/resources/modules/attention_deficit_disorder.json Normal file
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{
"name": "Attention Deficit Disorder",
"remarks": [
"The CDC estimates that 11% of children are diagnosed with ADHD. Althought ADHD ",
"is possible in adults we only model this in children. ",
"Source: http://www.cdc.gov/ncbddd/adhd/data.html"
],
"states": {
"Initial": {
"type": "Initial",
"remarks": [
"The CDC found that 13.2% of boys and 5.6% of girls were diagnosed with ADHD."
],
"complex_transition": [
{
"condition": {
"condition_type": "Gender",
"gender": "M"
},
"distributions": [
{
"distribution": 0.132,
"transition": "Delay_Until_ADHD"
},
{
"distribution": 0.868,
"transition": "Terminal"
}
]
},
{
"condition": {
"condition_type": "Gender",
"gender": "F"
},
"distributions": [
{
"distribution": 0.056,
"transition": "Delay_Until_ADHD"
},
{
"distribution": 0.944,
"transition": "Terminal"
}
]
}
]
},
"Delay_Until_ADHD": {
"type": "Delay",
"range": {
"low": 7,
"high": 15,
"unit": "years"
},
"direct_transition": "ADHD"
},
"ADHD": {
"type": "ConditionOnset",
"target_encounter": "ADHD_Diagnosis",
"codes": [
{
"system": "SNOMED-CT",
"code": "192127007",
"display": "Child attention deficit disorder (disorder)"
}
],
"direct_transition": "ADHD_Diagnosis"
},
"ADHD_Diagnosis": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "ADHD",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem (procedure)"
}
],
"direct_transition": "ADD_Symptom1"
},
"ADD_Symptom1": {
"type": "Symptom",
"symptom": "Poor Eye Contact",
"range": {
"low": 0,
"high": 30
},
"direct_transition": "ADD_Symptom2"
},
"ADD_Symptom2": {
"type": "Symptom",
"symptom": "Delayed Verbal/Language Skills",
"range": {
"low": 0,
"high": 30
},
"direct_transition": "ADD_Symptom3"
},
"ADD_Symptom3": {
"type": "Symptom",
"symptom": "Hyperactive Behavior",
"range": {
"low": 0,
"high": 15
},
"direct_transition": "ADD_Symptom4"
},
"ADD_Symptom4": {
"type": "Symptom",
"symptom": "Inability to Focus/Concentrate",
"range": {
"low": 0,
"high": 15
},
"direct_transition": "ADD_Symptom5"
},
"ADD_Symptom5": {
"type": "Symptom",
"symptom": "Poor Socialization",
"range": {
"low": 0,
"high": 15
},
"direct_transition": "ADHD_CarePlan"
},
"ADHD_CarePlan": {
"type": "CarePlanStart",
"reason": "ADHD",
"codes": [
{
"system": "SNOMED-CT",
"code": "386522008",
"display": "Overactivity/inattention behavior management (regime/therapy)"
}
],
"activities": [
{
"system": "SNOMED-CT",
"code": "409063005",
"display": "Counseling (procedure)"
},
{
"system": "SNOMED-CT",
"code": "405783006",
"display": "Psychological assessment (procedure)"
}
],
"remarks": [
"The CDC found that as many as 17.5% of children were not receiving any form of treatment ",
"for their ADHD. Setting this at a round 15%."
],
"distributed_transition": [
{
"distribution": 0.15,
"transition": "End_Diagnosis_Encounter_without_BT",
"remarks": [
"This will just wait until adulthood before ending the ADHD and terminating the module."
]
},
{
"distribution": 0.35,
"transition": "End_Diagnosis_Encounter_with_BT",
"remarks": [
"Additionally 50% of those treated with medication will also receive behavioral ",
"therapy, for about 55% in total."
]
},
{
"distribution": 0.5,
"transition": "ADHD_Medication_Selection"
}
]
},
"Behavior_Therapy": {
"type": "Delay",
"remarks": [
"Behavior therapy is favored over medication. We give behavior therapy for ",
"awhile, until the patient reaches adulthood or the condition subsides."
],
"range": {
"low": 4,
"high": 6,
"unit": "weeks"
},
"direct_transition": "Behavior_Treatment_Encounter"
},
"Behavior_Treatment_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "ADHD",
"telemedicine_possibility": "possible",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem (procedure)"
}
],
"direct_transition": "Behavior_Treatment_Procedure"
},
"Behavior_Treatment_Procedure": {
"type": "Procedure",
"reason": "ADHD",
"codes": [
{
"system": "SNOMED-CT",
"code": "228557008",
"display": "Cognitive and behavioral therapy (regime/therapy)"
}
],
"duration": {
"low": 1,
"high": 1,
"unit": "hours"
},
"direct_transition": "End_Behavior_Treatment_Encounter"
},
"End_Behavior_Treatment_Encounter": {
"type": "EncounterEnd",
"complex_transition": [
{
"condition": {
"condition_type": "Age",
"operator": "<",
"quantity": 18,
"unit": "years"
},
"distributions": [
{
"distribution": 0.05,
"transition": "ADHD_Ends",
"remarks": [
"We give the ADHD a chance to subside (meaning the behavioral treatment ",
"has worked) during childhood. ADHD will eventually subside anyway once ",
"the patient reaches adulthood. "
]
},
{
"distribution": 0.95,
"transition": "Behavior_Therapy"
}
]
},
{
"distributions": [
{
"distribution": 1,
"transition": "ADHD_Ends"
}
]
}
]
},
"ADHD_Medication_Selection": {
"type": "Simple",
"remarks": [
"Ritalin was introduced in 1955. Strattera wasn't approved by the FDA for ",
"treating ADHD until 2006."
],
"complex_transition": [
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 1955
},
"distributions": [
{
"distribution": 0.4,
"transition": "End_Diagnosis_Encounter_with_BT",
"remarks": [
"If no medication is available we defer additional patients to behavioral therapy. ",
"The rest get no form of treatment at all."
]
},
{
"distribution": 0.6,
"transition": "End_Diagnosis_Encounter_without_BT"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 2006
},
"distributions": [
{
"distribution": 0.6,
"transition": "Ritalin",
"remarks": [
"Even with Ritalin available not all patients are ideal candidates. ADHD medication ",
"was also prescribed at much lower rates historically. Deferring some of the remaining ",
"patients to behavioral therapy, the rest to no form of treatment."
]
},
{
"distribution": 0.15,
"transition": "End_Diagnosis_Encounter_with_BT"
},
{
"distribution": 0.25,
"transition": "End_Diagnosis_Encounter_without_BT"
}
]
},
{
"remarks": [
"With both Ritalin and Strattera available, and ADHD medication prescribed at the higher ",
"rates of the 2000's all patients that reach this state are now directed to some form of ",
"medication."
],
"distributions": [
{
"distribution": 0.5,
"transition": "Ritalin"
},
{
"distribution": 0.5,
"transition": "Strattera"
}
]
}
]
},
"Ritalin": {
"type": "MedicationOrder",
"assign_to_attribute": "adhd_medication",
"reason": "ADHD",
"codes": [
{
"system": "RxNorm",
"code": "1091392",
"display": "Methylphenidate Hydrochloride 20 MG Oral Tablet"
}
],
"distributed_transition": [
{
"distribution": 0.5,
"transition": "End_Diagnosis_Encounter_with_BT"
},
{
"distribution": 0.5,
"transition": "End_Diagnosis_Encounter_without_BT"
}
]
},
"Strattera": {
"type": "MedicationOrder",
"assign_to_attribute": "adhd_medication",
"reason": "ADHD",
"codes": [
{
"system": "RxNorm",
"code": "608139",
"display": "atomoxetine 100 MG Oral Capsule"
}
],
"distributed_transition": [
{
"distribution": 0.5,
"transition": "End_Diagnosis_Encounter_with_BT"
},
{
"distribution": 0.5,
"transition": "End_Diagnosis_Encounter_without_BT"
}
]
},
"End_Diagnosis_Encounter_without_BT": {
"type": "EncounterEnd",
"direct_transition": "Age_Guard"
},
"End_Diagnosis_Encounter_with_BT": {
"type": "EncounterEnd",
"direct_transition": "Behavior_Therapy"
},
"Age_Guard": {
"type": "Guard",
"allow": {
"condition_type": "Age",
"operator": ">=",
"quantity": 18,
"unit": "years"
},
"direct_transition": "ADHD_Ends"
},
"ADHD_Ends": {
"type": "ConditionEnd",
"condition_onset": "ADHD",
"direct_transition": "ADD_Symptom1_Ends"
},
"ADD_Symptom1_Ends": {
"type": "Symptom",
"symptom": "Poor Eye Contact",
"exact": {
"quantity": 0
},
"direct_transition": "ADD_Symptom2_Ends"
},
"ADD_Symptom2_Ends": {
"type": "Symptom",
"symptom": "Delayed Verbal/Language Skills",
"exact": {
"quantity": 0
},
"direct_transition": "ADD_Symptom3_Ends"
},
"ADD_Symptom3_Ends": {
"type": "Symptom",
"symptom": "Hyperactive Behavior",
"exact": {
"quantity": 0
},
"direct_transition": "ADD_Symptom4_Ends"
},
"ADD_Symptom4_Ends": {
"type": "Symptom",
"symptom": "Inability to Focus/Concentrate",
"exact": {
"quantity": 0
},
"direct_transition": "ADD_Symptom5_Ends"
},
"ADD_Symptom5_Ends": {
"type": "Symptom",
"symptom": "Poor Socialization",
"exact": {
"quantity": 0
},
"direct_transition": "ADHD_CarePlan_Ends"
},
"ADHD_CarePlan_Ends": {
"type": "CarePlanEnd",
"careplan": "ADHD_CarePlan",
"conditional_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "adhd_medication",
"operator": "is not nil"
},
"transition": "End_ADHD_Medication"
},
{
"transition": "Terminal"
}
]
},
"End_ADHD_Medication": {
"type": "MedicationEnd",
"referenced_by_attribute": "adhd_medication",
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

484
src/main/resources/modules/autism_asperger_s_or_autistic_spectrum_disorder.json Normal file
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{
"name": "Autism Spectrum Disorder",
"remarks": [
"This module models the diagnosis and management of Autism Spectrum Disorder (ASD),",
"including what was previously known as Asperger's Syndrome before DSM-5 unified the diagnosis.",
"ASD is typically diagnosed in early childhood but can be diagnosed later.",
"The module includes screening, diagnosis, interventions, and ongoing management.",
"ICD-10 code: 20544_14",
"Category: Mental and Behavioral Disorders"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Age_Guard"
},
"Age_Guard": {
"type": "Guard",
"allow": {
"age_years": {
"operator": "<",
"quantity": 3
}
},
"direct_transition": "Potential_ASD_Risk"
},
"Potential_ASD_Risk": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.02,
"transition": "ASD_Prevalence_Gender_Split"
},
{
"distribution": 0.98,
"transition": "Terminal"
}
]
},
"ASD_Prevalence_Gender_Split": {
"type": "Simple",
"remarks": [
"ASD is approximately 4 times more common in males than females"
],
"conditional_transition": [
{
"condition": {
"condition_type": "Gender",
"gender": "M"
},
"transition": "Initial_Developmental_Concerns"
},
{
"condition": {
"condition_type": "Gender",
"gender": "F"
},
"transition": "Female_Prevalence_Check"
}
]
},
"Female_Prevalence_Check": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.25,
"transition": "Initial_Developmental_Concerns"
},
{
"distribution": 0.75,
"transition": "Terminal"
}
]
},
"Initial_Developmental_Concerns": {
"type": "Delay",
"range": {
"low": 12,
"high": 24,
"unit": "months"
},
"direct_transition": "Initial_Pediatric_Visit"
},
"Initial_Pediatric_Visit": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Developmental concerns",
"codes": [
{
"system": "SNOMED-CT",
"code": "170258001",
"display": "Screening for developmental delay"
}
],
"direct_transition": "M_CHAT_Screening"
},
"M_CHAT_Screening": {
"type": "Procedure",
"target_encounter": "Initial_Pediatric_Visit",
"reason": "Developmental screening",
"codes": [
{
"system": "SNOMED-CT",
"code": "710081004",
"display": "Autism screening using Modified Checklist for Autism in Toddlers"
}
],
"direct_transition": "Refer_To_Specialist"
},
"Refer_To_Specialist": {
"type": "Simple",
"direct_transition": "Specialist_Evaluation"
},
"Specialist_Evaluation": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Autism spectrum disorder evaluation",
"codes": [
{
"system": "SNOMED-CT",
"code": "390906007",
"display": "Child and Adolescent Psychiatry"
}
],
"direct_transition": "Comprehensive_Assessment"
},
"Comprehensive_Assessment": {
"type": "Procedure",
"target_encounter": "Specialist_Evaluation",
"reason": "Autism spectrum disorder evaluation",
"codes": [
{
"system": "SNOMED-CT",
"code": "385991005",
"display": "Developmental assessment"
}
],
"direct_transition": "ADOS_Assessment"
},
"ADOS_Assessment": {
"type": "Procedure",
"target_encounter": "Specialist_Evaluation",
"reason": "Autism spectrum disorder evaluation",
"codes": [
{
"system": "SNOMED-CT",
"code": "699690005",
"display": "Autism Diagnostic Observation Schedule"
}
],
"direct_transition": "ASD_Diagnosis"
},
"ASD_Diagnosis": {
"type": "ConditionOnset",
"target_encounter": "Specialist_Evaluation",
"assign_to_attribute": "asd_diagnosis",
"codes": [
{
"system": "ICD-10-CM",
"code": "F84.0",
"display": "Autistic disorder"
},
{
"system": "SNOMED-CT",
"code": "20544_14",
"display": "Autism spectrum disorder"
}
],
"direct_transition": "ASD_CarePlan"
},
"ASD_CarePlan": {
"type": "CarePlanStart",
"target_encounter": "Specialist_Evaluation",
"assign_to_attribute": "asd_care_plan",
"reason": "asd_diagnosis",
"codes": [
{
"system": "SNOMED-CT",
"code": "225337009",
"display": "Autism care plan"
}
],
"activities": [
{
"system": "SNOMED-CT",
"code": "10298004",
"display": "Speech therapy"
},
{
"system": "SNOMED-CT",
"code": "311401005",
"display": "Occupational therapy"
},
{
"system": "SNOMED-CT",
"code": "310092004",
"display": "Behavioral therapy"
}
],
"direct_transition": "Determine_Severity"
},
"Determine_Severity": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.3,
"transition": "Mild_ASD"
},
{
"distribution": 0.4,
"transition": "Moderate_ASD"
},
{
"distribution": 0.3,
"transition": "Severe_ASD"
}
]
},
"Mild_ASD": {
"type": "SetAttribute",
"attribute": "asd_severity",
"value": "mild",
"direct_transition": "Consider_Comorbidities"
},
"Moderate_ASD": {
"type": "SetAttribute",
"attribute": "asd_severity",
"value": "moderate",
"direct_transition": "Consider_Comorbidities"
},
"Severe_ASD": {
"type": "SetAttribute",
"attribute": "asd_severity",
"value": "severe",
"direct_transition": "Consider_Comorbidities"
},
"Consider_Comorbidities": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.3,
"transition": "ADHD_Comorbidity"
},
{
"distribution": 0.2,
"transition": "Anxiety_Comorbidity"
},
{
"distribution": 0.1,
"transition": "Epilepsy_Comorbidity"
},
{
"distribution": 0.4,
"transition": "End_Initial_Diagnosis"
}
]
},
"ADHD_Comorbidity": {
"type": "ConditionOnset",
"target_encounter": "Specialist_Evaluation",
"codes": [
{
"system": "ICD-10-CM",
"code": "F90.0",
"display": "Attention-deficit hyperactivity disorder, predominantly inattentive type"
}
],
"direct_transition": "End_Initial_Diagnosis"
},
"Anxiety_Comorbidity": {
"type": "ConditionOnset",
"target_encounter": "Specialist_Evaluation",
"codes": [
{
"system": "ICD-10-CM",
"code": "F41.9",
"display": "Anxiety disorder, unspecified"
}
],
"direct_transition": "End_Initial_Diagnosis"
},
"Epilepsy_Comorbidity": {
"type": "ConditionOnset",
"target_encounter": "Specialist_Evaluation",
"codes": [
{
"system": "ICD-10-CM",
"code": "G40.909",
"display": "Epilepsy, unspecified, not intractable, without status epilepticus"
}
],
"direct_transition": "End_Initial_Diagnosis"
},
"End_Initial_Diagnosis": {
"type": "Simple",
"direct_transition": "Consider_Medication"
},
"Consider_Medication": {
"type": "Simple",
"conditional_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "asd_severity",
"operator": "==",
"value": "severe"
},
"transition": "Medication_Decision"
},
{
"condition": {
"condition_type": "Attribute",
"attribute": "asd_severity",
"operator": "==",
"value": "moderate"
},
"transition": "Medication_Decision"
},
{
"transition": "Ongoing_Therapy"
}
]
},
"Medication_Decision": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.4,
"transition": "Prescribe_Risperidone"
},
{
"distribution": 0.3,
"transition": "Prescribe_Aripiprazole"
},
{
"distribution": 0.3,
"transition": "Ongoing_Therapy"
}
]
},
"Prescribe_Risperidone": {
"type": "MedicationOrder",
"reason": "asd_diagnosis",
"codes": [
{
"system": "RxNorm",
"code": "85071",
"display": "Risperidone"
}
],
"prescription": {
"dosage": {
"amount": 1,
"frequency": 1,
"period": 1,
"unit": "days"
},
"duration": {
"quantity": 1,
"unit": "years"
},
"refills": 4
},
"direct_transition": "Ongoing_Therapy"
},
"Prescribe_Aripiprazole": {
"type": "MedicationOrder",
"reason": "asd_diagnosis",
"codes": [
{
"system": "RxNorm",
"code": "349484",
"display": "Aripiprazole"
}
],
"prescription": {
"dosage": {
"amount": 5,
"frequency": 1,
"period": 1,
"unit": "days"
},
"duration": {
"quantity": 1,
"unit": "years"
},
"refills": 4
},
"direct_transition": "Ongoing_Therapy"
},
"Ongoing_Therapy": {
"type": "Delay",
"range": {
"low": 3,
"high": 6,
"unit": "months"
},
"direct_transition": "ABA_Therapy"
},
"ABA_Therapy": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "412779008",
"display": "Applied behavior analysis"
}
],
"reason": "asd_diagnosis",
"duration": {
"low": 1,
"high": 2,
"unit": "hours"
},
"direct_transition": "Speech_Therapy"
},
"Speech_Therapy": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "10298004",
"display": "Speech therapy"
}
],
"reason": "asd_diagnosis",
"duration": {
"low": 30,
"high": 60,
"unit": "minutes"
},
"direct_transition": "Occupational_Therapy"
},
"Occupational_Therapy": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "311401005",
"display": "Occupational therapy"
}
],
"reason": "asd_diagnosis",
"duration": {
"low": 30,
"high": 60,
"unit": "minutes"
},
"direct_transition": "Follow_Up_Encounter"
},
"Follow_Up_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "asd_diagnosis",
"codes": [
{
"system": "SNOMED-CT",
"code": "390906007",
"display": "Child and Adolescent Psychiatry"
}
],
"direct_transition": "Progress_Assessment"
},
"Progress_Assessment": {
"type": "Procedure",
"target_encounter": "Follow_Up_Encounter",
"reason": "asd_diagnosis",
"codes": [
{
"system": "SNOMED-CT",
"code": "385991005",
"display": "Developmental assessment"
}
],
"direct_transition": "Ongoing_Care_Loop"
},
"Ongoing_Care_Loop": {
"type": "Simple",
"direct_transition": "Ongoing_Therapy"
},
"Terminal": {
"type": "Terminal"
}
}
}

482
src/main/resources/modules/bacterial_pneumonia.json.fixed.raw Normal file
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{
"name": "Bacterial Pneumonia",
"remarks": [
"This module simulates the onset, progression, diagnosis, treatment, and management of bacterial pneumonia.",
"Bacterial pneumonia is an infection of the lungs caused by various bacteria, most commonly Streptococcus pneumoniae.",
"Risk factors include age (very young and elderly), smoking, COPD, immunocompromised status, and other chronic conditions.",
"The module includes appropriate diagnostic tests, treatment options, and potential complications."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Age_Guard"
},
"Age_Guard": {
"type": "Guard",
"allow": {
"condition_type": "Age",
"operator": ">=",
"quantity": 1,
"unit": "years"
},
"direct_transition": "Risk_Assessment"
},
"Risk_Assessment": {
"type": "Delay",
"exact": {
"quantity": 1,
"unit": "days"
},
"distributed_transition": [
{
"distribution": 0.4,
"transition": "High_Risk_Group"
},
{
"distribution": 0.6,
"transition": "Normal_Risk_Group"
}
]
},
"High_Risk_Group": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.3,
"transition": "Pneumonia_Onset"
},
{
"distribution": 0.7,
"transition": "Terminal"
}
]
},
"Normal_Risk_Group": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.05,
"transition": "Pneumonia_Onset"
},
{
"distribution": 0.95,
"transition": "Terminal"
}
]
},
"Pneumonia_Onset": {
"type": "ConditionOnset",
"target_encounter": "Pneumonia_Encounter",
"assign_to_attribute": "pneumonia",
"codes": [
{
"system": "SNOMED-CT",
"code": "53084003",
"display": "Bacterial pneumonia"
}
],
"direct_transition": "Pneumonia_Symptoms"
},
"Pneumonia_Symptoms": {
"type": "Symptom",
"symptom": "Cough",
"cause": "pneumonia",
"range": {
"low": 50,
"high": 100
},
"direct_transition": "Pneumonia_Symptom_Fever"
},
"Pneumonia_Symptom_Fever": {
"type": "Symptom",
"symptom": "Fever",
"cause": "pneumonia",
"range": {
"low": 60,
"high": 100
},
"direct_transition": "Pneumonia_Symptom_Dyspnea"
},
"Pneumonia_Symptom_Dyspnea": {
"type": "Symptom",
"symptom": "Shortness of Breath",
"cause": "pneumonia",
"range": {
"low": 40,
"high": 90
},
"direct_transition": "Pneumonia_Symptom_ChestPain"
},
"Pneumonia_Symptom_ChestPain": {
"type": "Symptom",
"symptom": "Chest Pain",
"cause": "pneumonia",
"range": {
"low": 30,
"high": 70
},
"direct_transition": "Delay_Before_Encounter"
},
"Delay_Before_Encounter": {
"type": "Delay",
"range": {
"low": 1,
"high": 3,
"unit": "days"
},
"direct_transition": "Pneumonia_Encounter"
},
"Pneumonia_Encounter": {
"type": "Encounter",
"encounter_class": "emergency",
"reason": "pneumonia",
"codes": [
{
"system": "SNOMED-CT",
"code": "185345009",
"display": "Encounter for symptom"
}
],
"direct_transition": "Pneumonia_Diagnosis"
},
"Pneumonia_Diagnosis": {
"type": "DiagnosticReport",
"codes": [
{
"system": "LOINC",
"code": "24360-0",
"display": "Bacterial identification"
}
],
"direct_transition": "Chest_Xray"
},
"Chest_Xray": {
"type": "Procedure",
"target_encounter": "Pneumonia_Encounter",
"reason": "pneumonia",
"codes": [
{
"system": "SNOMED-CT",
"code": "399208008",
"display": "Chest X-ray"
}
],
"direct_transition": "CBC_Test"
},
"CBC_Test": {
"type": "Procedure",
"target_encounter": "Pneumonia_Encounter",
"reason": "pneumonia",
"codes": [
{
"system": "LOINC",
"code": "58410-2",
"display": "Complete blood count (CBC) panel - Blood by Automated count"
}
],
"direct_transition": "Sputum_Culture"
},
"Sputum_Culture": {
"type": "Procedure",
"target_encounter": "Pneumonia_Encounter",
"reason": "pneumonia",
"codes": [
{
"system": "SNOMED-CT",
"code": "269957009",
"display": "Sputum culture"
}
],
"direct_transition": "Severity_Assessment"
},
"Severity_Assessment": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.7,
"transition": "Mild_Pneumonia"
},
{
"distribution": 0.2,
"transition": "Moderate_Pneumonia"
},
{
"distribution": 0.1,
"transition": "Severe_Pneumonia"
}
]
},
"Mild_Pneumonia": {
"type": "SetAttribute",
"attribute": "pneumonia_severity",
"value": "mild",
"direct_transition": "Prescribe_Antibiotics_Mild"
},
"Moderate_Pneumonia": {
"type": "SetAttribute",
"attribute": "pneumonia_severity",
"value": "moderate",
"direct_transition": "Prescribe_Antibiotics_Moderate"
},
"Severe_Pneumonia": {
"type": "SetAttribute",
"attribute": "pneumonia_severity",
"value": "severe",
"direct_transition": "Hospital_Admission"
},
"Prescribe_Antibiotics_Mild": {
"type": "MedicationOrder",
"target_encounter": "Pneumonia_Encounter",
"reason": "pneumonia",
"codes": [
{
"system": "RxNorm",
"code": "1658084",
"display": "Amoxicillin 500 MG Oral Tablet"
}
],
"direct_transition": "Pneumonia_Followup_Encounter"
},
"Prescribe_Antibiotics_Moderate": {
"type": "MedicationOrder",
"target_encounter": "Pneumonia_Encounter",
"reason": "pneumonia",
"codes": [
{
"system": "RxNorm",
"code": "1373737",
"display": "Azithromycin 250 MG Oral Tablet"
}
],
"direct_transition": "Pneumonia_Followup_Encounter"
},
"Hospital_Admission": {
"type": "Encounter",
"encounter_class": "inpatient",
"reason": "pneumonia",
"codes": [
{
"system": "SNOMED-CT",
"code": "183495009",
"display": "Hospital admission"
}
],
"direct_transition": "IV_Antibiotics"
},
"IV_Antibiotics": {
"type": "MedicationOrder",
"target_encounter": "Hospital_Admission",
"reason": "pneumonia",
"codes": [
{
"system": "RxNorm",
"code": "1665051",
"display": "Ceftriaxone 1000 MG Injection"
}
],
"direct_transition": "Oxygen_Therapy"
},
"Oxygen_Therapy": {
"type": "Procedure",
"target_encounter": "Hospital_Admission",
"reason": "pneumonia",
"codes": [
{
"system": "SNOMED-CT",
"code": "57485005",
"display": "Oxygen therapy"
}
],
"direct_transition": "Check_For_Complications"
},
"Check_For_Complications": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.15,
"transition": "Develop_Complications"
},
{
"distribution": 0.85,
"transition": "Hospital_Stay"
}
]
},
"Develop_Complications": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.4,
"transition": "Pleural_Effusion"
},
{
"distribution": 0.3,
"transition": "Respiratory_Failure"
},
{
"distribution": 0.3,
"transition": "Sepsis"
}
]
},
"Pleural_Effusion": {
"type": "ConditionOnset",
"target_encounter": "Hospital_Admission",
"codes": [
{
"system": "SNOMED-CT",
"code": "60046008",
"display": "Pleural effusion"
}
],
"direct_transition": "Thoracentesis"
},
"Thoracentesis": {
"type": "Procedure",
"target_encounter": "Hospital_Admission",
"codes": [
{
"system": "SNOMED-CT",
"code": "91602002",
"display": "Thoracentesis"
}
],
"direct_transition": "Extended_Hospital_Stay"
},
"Respiratory_Failure": {
"type": "ConditionOnset",
"target_encounter": "Hospital_Admission",
"codes": [
{
"system": "SNOMED-CT",
"code": "409622000",
"display": "Respiratory failure"
}
],
"direct_transition": "Mechanical_Ventilation"
},
"Mechanical_Ventilation": {
"type": "Procedure",
"target_encounter": "Hospital_Admission",
"codes": [
{
"system": "SNOMED-CT",
"code": "40617009",
"display": "Mechanical ventilation"
}
],
"direct_transition": "ICU_Stay"
},
"Sepsis": {
"type": "ConditionOnset",
"target_encounter": "Hospital_Admission",
"codes": [
{
"system": "SNOMED-CT",
"code": "91302008",
"display": "Sepsis"
}
],
"direct_transition": "Vasopressors"
},
"Vasopressors": {
"type": "MedicationOrder",
"target_encounter": "Hospital_Admission",
"codes": [
{
"system": "RxNorm",
"code": "1732136",
"display": "Norepinephrine 1 MG/ML Injectable Solution"
}
],
"direct_transition": "ICU_Stay"
},
"ICU_Stay": {
"type": "Delay",
"range": {
"low": 3,
"high": 10,
"unit": "days"
},
"direct_transition": "ICU_Outcome"
},
"ICU_Outcome": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.7,
"transition": "Extended_Hospital_Stay"
},
{
"distribution": 0.3,
"transition": "Death"
}
]
},
"Hospital_Stay": {
"type": "Delay",
"range": {
"low": 3,
"high": 7,
"unit": "days"
},
"direct_transition": "Hospital_Discharge"
},
"Extended_Hospital_Stay": {
"type": "Delay",
"range": {
"low": 7,
"high": 14,
"unit": "days"
},
"direct_transition": "Hospital_Discharge"
},
"Hospital_Discharge": {
"type": "EncounterEnd",
"direct_transition": "Pneumonia_Followup_Encounter"
},
"Pneumonia_Followup_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "pneumonia",
"codes": [
{
"system": "SNOMED-CT",
"code": "390906007",
"display": "Follow-up encounter"
}
],
"direct_transition": "Followup_Chest_Xray"
},
"Followup_Chest_Xray": {
"type": "Procedure",
"target_encounter": "Pneumonia_Followup_Encounter",
"reason": "pneumonia",
"codes": [
{
"system": "SNOMED-CT",
"code": "399208008",
"display": "Chest X-ray"
}
],
"direct_transition": "Recovery_Assessment"
},
"Recovery_Assessment": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.9,
"transition": "Pneumonia_Resolves"
},
{
"distribution": 0.1,
"transition": "Pneumonia_Persists"
}
]
},
"Pneumonia_Resolves": {
"type": "ConditionEnd",
"referenced_by_attribute": "pneumonia",
"direct_transition": "End_Followup_Encounter"
},
"Pneumonia_Pers

482
src/main/resources/modules/bacterial_pneumonia.json.raw Normal file
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@@ -0,0 +1,482 @@
{
"name": "Bacterial Pneumonia",
"remarks": [
"This module simulates the onset, progression, diagnosis, treatment, and management of bacterial pneumonia.",
"Bacterial pneumonia is an infection of the lungs caused by various bacteria, most commonly Streptococcus pneumoniae.",
"Risk factors include age (very young and elderly), smoking, COPD, immunocompromised status, and other chronic conditions.",
"The module includes appropriate diagnostic tests, treatment options, and potential complications."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Age_Guard"
},
"Age_Guard": {
"type": "Guard",
"allow": {
"condition_type": "Age",
"operator": ">=",
"quantity": 1,
"unit": "years"
},
"direct_transition": "Risk_Assessment"
},
"Risk_Assessment": {
"type": "Delay",
"exact": {
"quantity": 1,
"unit": "days"
},
"distributed_transition": [
{
"distribution": 0.4,
"transition": "High_Risk_Group"
},
{
"distribution": 0.6,
"transition": "Normal_Risk_Group"
}
]
},
"High_Risk_Group": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.3,
"transition": "Pneumonia_Onset"
},
{
"distribution": 0.7,
"transition": "Terminal"
}
]
},
"Normal_Risk_Group": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.05,
"transition": "Pneumonia_Onset"
},
{
"distribution": 0.95,
"transition": "Terminal"
}
]
},
"Pneumonia_Onset": {
"type": "ConditionOnset",
"target_encounter": "Pneumonia_Encounter",
"assign_to_attribute": "pneumonia",
"codes": [
{
"system": "SNOMED-CT",
"code": "53084003",
"display": "Bacterial pneumonia"
}
],
"direct_transition": "Pneumonia_Symptoms"
},
"Pneumonia_Symptoms": {
"type": "Symptom",
"symptom": "Cough",
"cause": "pneumonia",
"range": {
"low": 50,
"high": 100
},
"direct_transition": "Pneumonia_Symptom_Fever"
},
"Pneumonia_Symptom_Fever": {
"type": "Symptom",
"symptom": "Fever",
"cause": "pneumonia",
"range": {
"low": 60,
"high": 100
},
"direct_transition": "Pneumonia_Symptom_Dyspnea"
},
"Pneumonia_Symptom_Dyspnea": {
"type": "Symptom",
"symptom": "Shortness of Breath",
"cause": "pneumonia",
"range": {
"low": 40,
"high": 90
},
"direct_transition": "Pneumonia_Symptom_ChestPain"
},
"Pneumonia_Symptom_ChestPain": {
"type": "Symptom",
"symptom": "Chest Pain",
"cause": "pneumonia",
"range": {
"low": 30,
"high": 70
},
"direct_transition": "Delay_Before_Encounter"
},
"Delay_Before_Encounter": {
"type": "Delay",
"range": {
"low": 1,
"high": 3,
"unit": "days"
},
"direct_transition": "Pneumonia_Encounter"
},
"Pneumonia_Encounter": {
"type": "Encounter",
"encounter_class": "emergency",
"reason": "pneumonia",
"codes": [
{
"system": "SNOMED-CT",
"code": "185345009",
"display": "Encounter for symptom"
}
],
"direct_transition": "Pneumonia_Diagnosis"
},
"Pneumonia_Diagnosis": {
"type": "DiagnosticReport",
"codes": [
{
"system": "LOINC",
"code": "24360-0",
"display": "Bacterial identification"
}
],
"direct_transition": "Chest_Xray"
},
"Chest_Xray": {
"type": "Procedure",
"target_encounter": "Pneumonia_Encounter",
"reason": "pneumonia",
"codes": [
{
"system": "SNOMED-CT",
"code": "399208008",
"display": "Chest X-ray"
}
],
"direct_transition": "CBC_Test"
},
"CBC_Test": {
"type": "Procedure",
"target_encounter": "Pneumonia_Encounter",
"reason": "pneumonia",
"codes": [
{
"system": "LOINC",
"code": "58410-2",
"display": "Complete blood count (CBC) panel - Blood by Automated count"
}
],
"direct_transition": "Sputum_Culture"
},
"Sputum_Culture": {
"type": "Procedure",
"target_encounter": "Pneumonia_Encounter",
"reason": "pneumonia",
"codes": [
{
"system": "SNOMED-CT",
"code": "269957009",
"display": "Sputum culture"
}
],
"direct_transition": "Severity_Assessment"
},
"Severity_Assessment": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.7,
"transition": "Mild_Pneumonia"
},
{
"distribution": 0.2,
"transition": "Moderate_Pneumonia"
},
{
"distribution": 0.1,
"transition": "Severe_Pneumonia"
}
]
},
"Mild_Pneumonia": {
"type": "SetAttribute",
"attribute": "pneumonia_severity",
"value": "mild",
"direct_transition": "Prescribe_Antibiotics_Mild"
},
"Moderate_Pneumonia": {
"type": "SetAttribute",
"attribute": "pneumonia_severity",
"value": "moderate",
"direct_transition": "Prescribe_Antibiotics_Moderate"
},
"Severe_Pneumonia": {
"type": "SetAttribute",
"attribute": "pneumonia_severity",
"value": "severe",
"direct_transition": "Hospital_Admission"
},
"Prescribe_Antibiotics_Mild": {
"type": "MedicationOrder",
"target_encounter": "Pneumonia_Encounter",
"reason": "pneumonia",
"codes": [
{
"system": "RxNorm",
"code": "1658084",
"display": "Amoxicillin 500 MG Oral Tablet"
}
],
"direct_transition": "Pneumonia_Followup_Encounter"
},
"Prescribe_Antibiotics_Moderate": {
"type": "MedicationOrder",
"target_encounter": "Pneumonia_Encounter",
"reason": "pneumonia",
"codes": [
{
"system": "RxNorm",
"code": "1373737",
"display": "Azithromycin 250 MG Oral Tablet"
}
],
"direct_transition": "Pneumonia_Followup_Encounter"
},
"Hospital_Admission": {
"type": "Encounter",
"encounter_class": "inpatient",
"reason": "pneumonia",
"codes": [
{
"system": "SNOMED-CT",
"code": "183495009",
"display": "Hospital admission"
}
],
"direct_transition": "IV_Antibiotics"
},
"IV_Antibiotics": {
"type": "MedicationOrder",
"target_encounter": "Hospital_Admission",
"reason": "pneumonia",
"codes": [
{
"system": "RxNorm",
"code": "1665051",
"display": "Ceftriaxone 1000 MG Injection"
}
],
"direct_transition": "Oxygen_Therapy"
},
"Oxygen_Therapy": {
"type": "Procedure",
"target_encounter": "Hospital_Admission",
"reason": "pneumonia",
"codes": [
{
"system": "SNOMED-CT",
"code": "57485005",
"display": "Oxygen therapy"
}
],
"direct_transition": "Check_For_Complications"
},
"Check_For_Complications": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.15,
"transition": "Develop_Complications"
},
{
"distribution": 0.85,
"transition": "Hospital_Stay"
}
]
},
"Develop_Complications": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.4,
"transition": "Pleural_Effusion"
},
{
"distribution": 0.3,
"transition": "Respiratory_Failure"
},
{
"distribution": 0.3,
"transition": "Sepsis"
}
]
},
"Pleural_Effusion": {
"type": "ConditionOnset",
"target_encounter": "Hospital_Admission",
"codes": [
{
"system": "SNOMED-CT",
"code": "60046008",
"display": "Pleural effusion"
}
],
"direct_transition": "Thoracentesis"
},
"Thoracentesis": {
"type": "Procedure",
"target_encounter": "Hospital_Admission",
"codes": [
{
"system": "SNOMED-CT",
"code": "91602002",
"display": "Thoracentesis"
}
],
"direct_transition": "Extended_Hospital_Stay"
},
"Respiratory_Failure": {
"type": "ConditionOnset",
"target_encounter": "Hospital_Admission",
"codes": [
{
"system": "SNOMED-CT",
"code": "409622000",
"display": "Respiratory failure"
}
],
"direct_transition": "Mechanical_Ventilation"
},
"Mechanical_Ventilation": {
"type": "Procedure",
"target_encounter": "Hospital_Admission",
"codes": [
{
"system": "SNOMED-CT",
"code": "40617009",
"display": "Mechanical ventilation"
}
],
"direct_transition": "ICU_Stay"
},
"Sepsis": {
"type": "ConditionOnset",
"target_encounter": "Hospital_Admission",
"codes": [
{
"system": "SNOMED-CT",
"code": "91302008",
"display": "Sepsis"
}
],
"direct_transition": "Vasopressors"
},
"Vasopressors": {
"type": "MedicationOrder",
"target_encounter": "Hospital_Admission",
"codes": [
{
"system": "RxNorm",
"code": "1732136",
"display": "Norepinephrine 1 MG/ML Injectable Solution"
}
],
"direct_transition": "ICU_Stay"
},
"ICU_Stay": {
"type": "Delay",
"range": {
"low": 3,
"high": 10,
"unit": "days"
},
"direct_transition": "ICU_Outcome"
},
"ICU_Outcome": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.7,
"transition": "Extended_Hospital_Stay"
},
{
"distribution": 0.3,
"transition": "Death"
}
]
},
"Hospital_Stay": {
"type": "Delay",
"range": {
"low": 3,
"high": 7,
"unit": "days"
},
"direct_transition": "Hospital_Discharge"
},
"Extended_Hospital_Stay": {
"type": "Delay",
"range": {
"low": 7,
"high": 14,
"unit": "days"
},
"direct_transition": "Hospital_Discharge"
},
"Hospital_Discharge": {
"type": "EncounterEnd",
"direct_transition": "Pneumonia_Followup_Encounter"
},
"Pneumonia_Followup_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "pneumonia",
"codes": [
{
"system": "SNOMED-CT",
"code": "390906007",
"display": "Follow-up encounter"
}
],
"direct_transition": "Followup_Chest_Xray"
},
"Followup_Chest_Xray": {
"type": "Procedure",
"target_encounter": "Pneumonia_Followup_Encounter",
"reason": "pneumonia",
"codes": [
{
"system": "SNOMED-CT",
"code": "399208008",
"display": "Chest X-ray"
}
],
"direct_transition": "Recovery_Assessment"
},
"Recovery_Assessment": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.9,
"transition": "Pneumonia_Resolves"
},
{
"distribution": 0.1,
"transition": "Pneumonia_Persists"
}
]
},
"Pneumonia_Resolves": {
"type": "ConditionEnd",
"referenced_by_attribute": "pneumonia",
"direct_transition": "End_Followup_Encounter"
},
"Pneumonia_Pers

807
src/main/resources/modules/bone_marrow_transplant.json Normal file
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@@ -0,0 +1,807 @@
{
"name": "Bone Marrow Transplant",
"remarks": [
"Bone marrow transplants are sometimes used to treat patients with cancer or other immune deficiencies.",
"",
"Recipients may spend a few weeks in the hospital or nearby, undergoing frequent blood tests and appointments to monitor response to the transplant.",
"",
"Post transplant complications are not modeled.",
"",
"In a study of 2017 data, 60% of transplants were autologous, and 40% were allogeneic. This can be further refined based on the root cause -- i.e., why the patient is receiving a bone marrow transplant, but that is not modeled here.",
"",
"The use of peripheral-blood stem cells has increased and now accounts for 75% of stem-cell transplants from unrelated adult donors.",
"",
"References",
"- https://www.mayoclinic.org/tests-procedures/bone-marrow-transplant/about/pac-20384854",
"- https://www.ncbi.nlm.nih.gov/books/NBK536951",
"- https://doi.org/10.1038/s41409-019-0465-9",
"- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3816375/",
"- https://bloodstemcell.hrsa.gov/data/donation-and-transplantation-statistics",
""
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Guard Until Bone Marrow Transplant"
},
"Donor Check": {
"type": "Simple",
"distributed_transition": [
{
"transition": "from own body (autologous transplant)",
"distribution": 0.6
},
{
"transition": "from a donor (allogeneic marrow)",
"distribution": 0.1
},
{
"transition": "from a donor (allogeneic stem cells)",
"distribution": 0.3
}
]
},
"from own body (autologous transplant)": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "58776007",
"display": "Autologous bone marrow transplant (procedure)"
}
],
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 120,
"low": 60
}
},
"unit": "minutes",
"direct_transition": "History of autologous bone marrow transplant"
},
"History of allotransplantation of bone marrow": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "152621000119105",
"display": "History of allotransplantation of bone marrow (situation)"
}
],
"direct_transition": "End Wait",
"assign_to_attribute": "history_of_bone_marrow_transplant"
},
"History of autologous bone marrow transplant": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "108631000119101",
"display": "History of autologous bone marrow transplant (situation)"
}
],
"assign_to_attribute": "history_of_bone_marrow_transplant",
"direct_transition": "End Wait"
},
"Set Recovery LOS": {
"type": "SetAttribute",
"attribute": "bone_marrow_transplant_los",
"direct_transition": "Recovery",
"distribution": {
"kind": "EXPONENTIAL",
"round": false,
"parameters": {
"mean": 14
}
}
},
"Recovery": {
"type": "Counter",
"attribute": "bone_marrow_transplant_los",
"action": "decrement",
"direct_transition": "Postoperative care"
},
"Continue": {
"type": "Delay",
"distribution": {
"kind": "EXACT",
"parameters": {
"value": 1
}
},
"unit": "days",
"conditional_transition": [
{
"transition": "Recovery",
"condition": {
"condition_type": "Attribute",
"attribute": "bone_marrow_transplant_los",
"operator": ">",
"value": 0
}
},
{
"transition": "End Transplant Encounter"
}
]
},
"Record_CBC_Panel": {
"type": "DiagnosticReport",
"number_of_observations": 4,
"codes": [
{
"system": "LOINC",
"code": "58410-2",
"display": "CBC panel - Blood by Automated count"
}
],
"observations": [
{
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6690-2",
"display": "Leukocytes [#/volume] in Blood by Automated count"
}
],
"unit": "10*3/uL",
"range": {
"low": 3.5,
"high": 10.5
}
},
{
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "789-8",
"display": "Erythrocytes [#/volume] in Blood by Automated count"
}
],
"unit": "10*6/uL",
"range": {
"low": 3.9,
"high": 5.5
}
},
{
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "718-7",
"display": "Hemoglobin [Mass/volume] in Blood"
}
],
"unit": "g/dL",
"range": {
"low": 12,
"high": 17.5
}
},
{
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "4544-3",
"display": "Hematocrit [Volume Fraction] of Blood by Automated count"
}
],
"unit": "%",
"range": {
"low": 35,
"high": 50
}
},
{
"category": "laboratory",
"unit": "fL",
"codes": [
{
"system": "LOINC",
"code": "787-2",
"display": "MCV [Entitic volume] by Automated count"
}
],
"range": {
"low": 80,
"high": 95
}
},
{
"category": "laboratory",
"unit": "pg",
"codes": [
{
"system": "LOINC",
"code": "785-6",
"display": "MCH [Entitic mass] by Automated count"
}
],
"range": {
"low": 27,
"high": 33
}
},
{
"category": "laboratory",
"unit": "g/dL",
"codes": [
{
"system": "LOINC",
"code": "786-4",
"display": "MCHC [Mass/volume] by Automated count"
}
],
"range": {
"low": 33,
"high": 36
}
},
{
"category": "laboratory",
"unit": "fL",
"codes": [
{
"system": "LOINC",
"code": "21000-5",
"display": "Erythrocyte distribution width [Entitic volume] by Automated count"
}
],
"range": {
"low": 39,
"high": 46
}
},
{
"category": "laboratory",
"unit": "10*3/uL",
"codes": [
{
"system": "LOINC",
"code": "777-3",
"display": "Platelets [#/volume] in Blood by Automated count"
}
],
"range": {
"low": 150,
"high": 450
}
},
{
"category": "laboratory",
"unit": "fL",
"codes": [
{
"system": "LOINC",
"code": "32207-3",
"display": "Platelet distribution width [Entitic volume] in Blood by Automated count"
}
],
"range": {
"low": 150,
"high": 520
}
},
{
"category": "laboratory",
"unit": "fL",
"codes": [
{
"system": "LOINC",
"code": "32623-1",
"display": "Platelet mean volume [Entitic volume] in Blood by Automated count"
}
],
"range": {
"low": 9.4,
"high": 12.3
}
}
],
"direct_transition": "Hematologic disorder medication review"
},
"Hematologic disorder medication review": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "473220001",
"display": "Hematologic disorder medication review (procedure)"
}
],
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 15,
"low": 10
}
},
"unit": "minutes",
"reason": "history_of_bone_marrow_transplant",
"direct_transition": "Continue"
},
"Postoperative care": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "133899007",
"display": "Postoperative care (regime/therapy)"
}
],
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 60,
"low": 30
}
},
"unit": "minutes",
"direct_transition": "Record_CBC_Panel",
"reason": "history_of_bone_marrow_transplant"
},
"Wait_for_Consultation": {
"type": "Delay",
"distribution": {
"kind": "GAUSSIAN",
"parameters": {
"mean": 3,
"standardDeviation": 1
}
},
"unit": "months",
"direct_transition": "Consultation"
},
"Consultation": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Awaiting transplantation of bone marrow",
"telemedicine_possibility": "none",
"codes": [
{
"system": "SNOMED-CT",
"code": "386395000",
"display": "Preoperative coordination (regime/therapy)"
}
],
"direct_transition": "Record_CBC_Preop"
},
"Hematologic_disorder_medication_review": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "473220001",
"display": "Hematologic disorder medication review (procedure)"
}
],
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 30,
"low": 20
}
},
"unit": "minutes",
"reason": "Awaiting transplantation of bone marrow",
"direct_transition": "Treatment failure risk education"
},
"Awaiting transplantation of bone marrow": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "698303004",
"display": "Awaiting transplantation of bone marrow (situation)"
}
],
"direct_transition": "Wait_for_Consultation",
"target_encounter": "Consultation",
"assign_to_attribute": "bone_marrow_dental_reason"
},
"Treatment failure risk education": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "304532001",
"display": "Treatment failure risk education (procedure)"
}
],
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 15,
"low": 10
}
},
"unit": "minutes",
"direct_transition": "Treatment side effects education",
"reason": "Awaiting transplantation of bone marrow"
},
"Treatment side effects education": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "304531008",
"display": "Treatment side effects education (procedure)"
}
],
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 15,
"low": 10
}
},
"unit": "minutes",
"reason": "Awaiting transplantation of bone marrow",
"direct_transition": "Pre-operative chemotherapy"
},
"Referral": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "306316000",
"display": "Referral to transplant surgeon (procedure)"
}
],
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 15,
"low": 10
}
},
"unit": "minutes",
"reason": "Awaiting transplantation of bone marrow",
"direct_transition": "End Consultation"
},
"End Consultation": {
"type": "EncounterEnd",
"direct_transition": "Initiate_Dental_Cleaning"
},
"Transplant Encounter": {
"type": "Encounter",
"encounter_class": "inpatient",
"reason": "Awaiting transplantation of bone marrow",
"telemedicine_possibility": "none",
"codes": [
{
"system": "SNOMED-CT",
"code": "305432006",
"display": "Admission to surgical transplant department (procedure)"
}
],
"direct_transition": "Donor Check"
},
"End Wait": {
"type": "ConditionEnd",
"direct_transition": "Set Recovery LOS",
"condition_onset": "Awaiting transplantation of bone marrow"
},
"Initiate_Dental_Cleaning": {
"type": "SetAttribute",
"attribute": "dental_referral",
"value_attribute": "bone_marrow_dental_reason",
"direct_transition": "Wait_for_Cleaning"
},
"Wait_for_Cleaning": {
"type": "Delay",
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 7,
"low": 1
}
},
"unit": "days",
"direct_transition": "Check_Cleaning_Status"
},
"Check_Cleaning_Status": {
"type": "Simple",
"conditional_transition": [
{
"transition": "Wait_for_Cleaning",
"condition": {
"condition_type": "Attribute",
"attribute": "dental_referral",
"operator": "is not nil"
}
},
{
"transition": "Wait_for_Transplant"
}
]
},
"End Transplant Encounter": {
"type": "EncounterEnd",
"direct_transition": "End Bone Marrow"
},
"Guard Until Bone Marrow Transplant": {
"type": "Guard",
"allow": {
"condition_type": "Attribute",
"attribute": "bone_marrow",
"operator": "is not nil"
},
"direct_transition": "Awaiting transplantation of bone marrow"
},
"End Bone Marrow": {
"type": "SetAttribute",
"attribute": "bone_marrow",
"value": null,
"direct_transition": "Guard Until Bone Marrow Transplant"
},
"Wait_for_Transplant": {
"type": "Delay",
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 21,
"low": 3
}
},
"unit": "days",
"direct_transition": "Transplant Encounter"
},
"Pre-operative chemotherapy": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "394894008",
"display": "Pre-operative chemotherapy (procedure)"
}
],
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 120,
"low": 60
}
},
"unit": "minutes",
"direct_transition": "Referral",
"reason": "Awaiting transplantation of bone marrow"
},
"History of peripheral stem cell transplant": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "153351000119102",
"display": "History of peripheral stem cell transplant (situation)"
}
],
"direct_transition": "End Wait",
"assign_to_attribute": "history_of_bone_marrow_transplant"
},
"from a donor (allogeneic stem cells)": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "234336002",
"display": "Hemopoietic stem cell transplant (procedure)"
}
],
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 120,
"low": 60
}
},
"unit": "minutes",
"direct_transition": "History of peripheral stem cell transplant",
"reason": "Awaiting transplantation of bone marrow"
},
"from a donor (allogeneic marrow)": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "58390007",
"display": "Allogeneic bone marrow transplantation (procedure)"
}
],
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 120,
"low": 60
}
},
"unit": "minutes",
"direct_transition": "History of allotransplantation of bone marrow"
},
"Record_CBC_Preop": {
"type": "DiagnosticReport",
"number_of_observations": 4,
"codes": [
{
"system": "LOINC",
"code": "58410-2",
"display": "CBC panel - Blood by Automated count"
}
],
"observations": [
{
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "6690-2",
"display": "Leukocytes [#/volume] in Blood by Automated count"
}
],
"unit": "10*3/uL",
"range": {
"low": 0.5,
"high": 5
}
},
{
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "789-8",
"display": "Erythrocytes [#/volume] in Blood by Automated count"
}
],
"unit": "10*6/uL",
"range": {
"low": 3.9,
"high": 5.5
}
},
{
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "718-7",
"display": "Hemoglobin [Mass/volume] in Blood"
}
],
"unit": "g/dL",
"range": {
"low": 6,
"high": 15
}
},
{
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "4544-3",
"display": "Hematocrit [Volume Fraction] of Blood by Automated count"
}
],
"unit": "%",
"range": {
"low": 25,
"high": 35
}
},
{
"category": "laboratory",
"unit": "fL",
"codes": [
{
"system": "LOINC",
"code": "787-2",
"display": "MCV [Entitic volume] by Automated count"
}
],
"range": {
"low": 80,
"high": 95
}
},
{
"category": "laboratory",
"unit": "pg",
"codes": [
{
"system": "LOINC",
"code": "785-6",
"display": "MCH [Entitic mass] by Automated count"
}
],
"range": {
"low": 27,
"high": 33
}
},
{
"category": "laboratory",
"unit": "g/dL",
"codes": [
{
"system": "LOINC",
"code": "786-4",
"display": "MCHC [Mass/volume] by Automated count"
}
],
"range": {
"low": 33,
"high": 36
}
},
{
"category": "laboratory",
"unit": "fL",
"codes": [
{
"system": "LOINC",
"code": "21000-5",
"display": "Erythrocyte distribution width [Entitic volume] by Automated count"
}
],
"range": {
"low": 39,
"high": 46
}
},
{
"category": "laboratory",
"unit": "10*3/uL",
"codes": [
{
"system": "LOINC",
"code": "777-3",
"display": "Platelets [#/volume] in Blood by Automated count"
}
],
"range": {
"low": 150,
"high": 450
}
},
{
"category": "laboratory",
"unit": "fL",
"codes": [
{
"system": "LOINC",
"code": "32207-3",
"display": "Platelet distribution width [Entitic volume] in Blood by Automated count"
}
],
"range": {
"low": 150,
"high": 520
}
},
{
"category": "laboratory",
"unit": "fL",
"codes": [
{
"system": "LOINC",
"code": "32623-1",
"display": "Platelet mean volume [Entitic volume] in Blood by Automated count"
}
],
"range": {
"low": 9.4,
"high": 12.3
}
}
],
"direct_transition": "Hematologic_disorder_medication_review"
}
},
"gmf_version": 2
}

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src/main/resources/modules/breast_cancer.json Normal file
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src/main/resources/modules/breast_cancer/chemotherapy_breast.json Normal file
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{
"name": "chemotherapy_breast",
"remarks": [
"This module consists of the different chemo drugs and goes through the adjuvant chemo cycle after surgery. "
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Set chemo counter"
},
"Cyclophosphamide": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 1734919,
"display": "Cyclophosphamide 1000 MG Injection"
}
],
"direct_transition": "Adjuvant Chemotherapy Procedure",
"assign_to_attribute": "chemoMed",
"reason": "breast_cancer_condition",
"administration": true
},
"Anthracyclines": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Doxorubicin",
"distribution": 0.5
},
{
"transition": "Epirubicin",
"distribution": 0.5
}
]
},
"Carboplatin": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 597195,
"display": "Carboplatin 10 MG/ML Injectable Solution"
}
],
"direct_transition": "Adjuvant Chemotherapy Procedure",
"assign_to_attribute": "chemoMed",
"reason": "breast_cancer_condition",
"administration": true
},
"Taxanes": {
"type": "Simple",
"direct_transition": "Paclitaxel"
},
"5-fluorouracil": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 1791701,
"display": "10 ML Fluorouracil 50 MG/ML Injection"
}
],
"direct_transition": "Adjuvant Chemotherapy Procedure",
"assign_to_attribute": "chemoMed",
"reason": "breast_cancer_condition",
"administration": true
},
"Doxorubicin": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 1790099,
"display": "10 ML Doxorubicin Hydrochloride 2 MG/ML Injection"
}
],
"direct_transition": "Adjuvant Chemotherapy Procedure",
"remarks": [
"- Doxorubicin (Adriamycin)",
"- Epriubicin (Ellence) ",
"https://www.cancer.org/cancer/breast-cancer/treatment/chemotherapy-for-breast-cancer.html"
],
"assign_to_attribute": "chemoMed",
"reason": "breast_cancer_condition",
"administration": true
},
"Epirubicin": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 1732186,
"display": "100 ML Epirubicin Hydrochloride 2 MG/ML Injection"
}
],
"direct_transition": "Adjuvant Chemotherapy Procedure",
"assign_to_attribute": "chemoMed",
"reason": "breast_cancer_condition",
"administration": true
},
"Paclitaxel": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 583214,
"display": "Paclitaxel 100 MG Injection"
}
],
"direct_transition": "Adjuvant Chemotherapy Procedure",
"assign_to_attribute": "chemoMed",
"reason": "breast_cancer_condition",
"administration": true
},
"Adjuvant Chemotherapy Procedure": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "367336001",
"display": "Chemotherapy (procedure)"
}
],
"duration": {
"low": 0,
"high": 2,
"unit": "hours"
},
"direct_transition": "End Current Adjuvant Chemo Medication"
},
"Terminal": {
"type": "Terminal"
},
"End Current Chemo Treatment": {
"type": "EncounterEnd",
"conditional_transition": [
{
"transition": "Increment Chemo Counter",
"condition": {
"condition_type": "Attribute",
"attribute": "breast_cancer_chemoCount",
"operator": "<",
"value": 7
}
},
{
"transition": "Terminal"
}
]
},
"Increment Chemo Counter": {
"type": "Counter",
"attribute": "breast_cancer_chemoCount",
"action": "increment",
"direct_transition": "Delay Until Next Cycle (3 Weeks)"
},
"Start New Cycle": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Breast Cancer",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem (procedure)"
}
],
"direct_transition": "Choose Chemo Drug"
},
"Set chemo counter": {
"type": "SetAttribute",
"attribute": "breast_cancer_chemoCount",
"value": 0,
"remarks": [
"https://www.cancer.org/cancer/breast-cancer/treatment/chemotherapy-for-breast-cancer.html",
"",
"Which chemotherapy drugs are used for breast cancer?",
"In most cases (especially as adjuvant or neoadjuvant treatment), chemo is most effective when combinations of drugs are used. Today, doctors use many different combinations, and it's not clear that any single combination is clearly the best.",
"",
"The most common drugs used for adjuvant and neoadjuvant chemo include:",
"Anthracyclines, such as doxorubicin (Adriamycin) and epirubicin (Ellence)",
"Taxanes, such as paclitaxel (Taxol) and docetaxel (Taxotere)",
"5-fluorouracil (5-FU)",
"Cyclophosphamide (Cytoxan)",
"Carboplatin (Paraplatin)",
"Most often, combinations of 2 or 3 of these drugs are used."
],
"direct_transition": "Choose Chemo Drug"
},
"Delay Until Next Cycle (3 Weeks)": {
"type": "Delay",
"direct_transition": "Start New Cycle",
"range": {
"low": 19,
"high": 23,
"unit": "days"
}
},
"Choose Chemo Drug": {
"type": "Simple",
"remarks": [
"https://www.cancer.org/cancer/breast-cancer/treatment/chemotherapy-for-breast-cancer.html",
"",
"Which chemotherapy drugs are used for breast cancer?",
"In most cases (especially as adjuvant or neoadjuvant treatment), chemo is most effective when combinations of drugs are used. Today, doctors use many different combinations, and it's not clear that any single combination is clearly the best.",
"",
"The most common drugs used for adjuvant and neoadjuvant chemo include:",
"Anthracyclines, such as doxorubicin (Adriamycin) and epirubicin (Ellence)",
"Taxanes, such as paclitaxel (Taxol) and docetaxel (Taxotere)",
"5-fluorouracil (5-FU)",
"Cyclophosphamide (Cytoxan)",
"Carboplatin (Paraplatin)",
"Most often, combinations of 2 or 3 of these drugs are used."
],
"complex_transition": [
{
"condition": {
"condition_type": "PriorState",
"name": "Cyclophosphamide"
},
"distributions": [
{
"transition": "Cyclophosphamide",
"distribution": 1
}
]
},
{
"condition": {
"condition_type": "PriorState",
"name": "Doxorubicin"
},
"distributions": [
{
"transition": "Doxorubicin",
"distribution": 1
}
]
},
{
"condition": {
"condition_type": "PriorState",
"name": "Epirubicin"
},
"distributions": [
{
"transition": "Epirubicin",
"distribution": 1
}
]
},
{
"distributions": [
{
"transition": "Carboplatin",
"distribution": 1
}
],
"condition": {
"condition_type": "PriorState",
"name": "Carboplatin"
}
},
{
"condition": {
"condition_type": "PriorState",
"name": "Paclitaxel"
},
"distributions": [
{
"transition": "Paclitaxel",
"distribution": 1
}
]
},
{
"condition": {
"condition_type": "PriorState",
"name": "5-fluorouracil"
},
"distributions": [
{
"transition": "5-fluorouracil",
"distribution": 1
}
]
},
{
"distributions": [
{
"transition": "Cyclophosphamide",
"distribution": 0.3
},
{
"transition": "Anthracyclines",
"distribution": 0.3
},
{
"transition": "Carboplatin",
"distribution": 0.05
},
{
"transition": "Taxanes",
"distribution": 0.3
},
{
"transition": "5-fluorouracil",
"distribution": 0.05
}
]
}
]
},
"End Current Adjuvant Chemo Medication": {
"type": "MedicationEnd",
"direct_transition": "End Current Chemo Treatment",
"referenced_by_attribute": "chemoMed"
}
},
"gmf_version": 1
}

431
src/main/resources/modules/breast_cancer/hormone_diagnosis.json Normal file
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{
"name": "Hormone_Diagnosis",
"remarks": [
"This module checks for HER2 and then assigns either HER2 positive/negative. This follows suit for ER and PR. Finally, it accounts for the Triple negative factor at the end. "
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Human_Epidermal_Growth_Factor_Receptor_2__HER2__Detection___Fluorescence_in_situ_Hybridization__FISH_"
},
"Terminal": {
"type": "Terminal"
},
"Human_Epidermal_Growth_Factor_Receptor_2__HER2__Detection___Fluorescence_in_situ_Hybridization__FISH_": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "434363004",
"display": "Human epidermal growth factor receptor 2 gene detection by fluorescence in situ hybridization (procedure)"
}
],
"duration": {
"low": 1,
"high": 2,
"unit": "days"
},
"remarks": [
"Fluorescence in situ hybridization (FISH), which detects the number of HER2 genes in the cancer cells:",
"https://ww5.komen.org/BreastCancer/TumorCharacteristics.html",
"",
"FISH results are usually available from the lab within a few days:",
"https://www.verywellhealth.com/fish-test-2252457"
],
"direct_transition": "Human_Epidermal_Growth_Factor_Receptor_2_HER2_Detection_Immunochemistry",
"reason": "breast_cancer_condition"
},
"HER2_negative": {
"type": "Observation",
"category": "laboratory",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "85319-2",
"display": "HER2 [Presence] in Breast cancer specimen by Immune stain"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": "260385009",
"display": "Negative (qualifier value)"
},
"direct_transition": "HER2 ratio less than 1point8"
},
"HER2_positive": {
"type": "Observation",
"category": "laboratory",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "85319-2",
"display": "HER2 [Presence] in Breast cancer specimen by Immune stain"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": "10828004",
"display": "Positive (qualifier value)"
},
"direct_transition": "HER2_ratio_greater_than_2point2"
},
"Tumor_Biopsy_to_Test_Estrogen_Receptor_Status": {
"type": "Simple",
"distributed_transition": [
{
"transition": "ER_negative",
"distribution": 0.2
},
{
"transition": "ER_positive",
"distribution": 0.8
}
],
"remarks": [
"About 80% of all breast cancers are “ER-positive.” That means the cancer cells grow in response to the hormone estrogen.:",
"https://www.webmd.com/breast-cancer/breast-cancer-types-er-positive-her2-positive#1"
]
},
"ER_negative": {
"type": "Observation",
"category": "laboratory",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "85337-4",
"display": "Estrogen receptor Ag [Presence] in Breast cancer specimen by Immune stain"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": "260385009",
"display": "Negative (qualifier value)"
},
"direct_transition": "ER-"
},
"ER_positive": {
"type": "Observation",
"category": "laboratory",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "85337-4",
"display": "Estrogen receptor Ag [Presence] in Breast cancer specimen by Immune stain"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": "10828004",
"display": "Positive (qualifier value)"
},
"direct_transition": "ER+"
},
"Tumor_Biopsy_to_Test_Progesterone_Receptor_Status": {
"type": "Simple",
"distributed_transition": [
{
"transition": "PR_negative",
"distribution": 0.35
},
{
"transition": "PR_positive",
"distribution": 0.65
}
],
"remarks": [
"About 80% of all breast cancers are “ER-positive.” That means the cancer cells grow in response to the hormone estrogen. About 65% of these are also “PR-positive.” They grow in response to another hormone, progesterone.:",
"https://www.webmd.com/breast-cancer/breast-cancer-types-er-positive-her2-positive#1"
]
},
"PR_negative": {
"type": "Observation",
"category": "laboratory",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "85339-0",
"display": "Progesterone receptor Ag [Presence] in Breast cancer specimen by Immune stain"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": "260385009",
"display": "Negative (qualifier value)"
},
"direct_transition": "PR-"
},
"PR_positive": {
"type": "Observation",
"category": "laboratory",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "85339-0",
"display": "Progesterone receptor Ag [Presence] in Breast cancer specimen by Immune stain"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": "10828004",
"display": "Positive (qualifier value)"
},
"direct_transition": "PR+"
},
"Overall_Receptor_Analysis": {
"type": "Simple",
"remarks": [
"If all hormones are negative transition to triple negative"
],
"conditional_transition": [
{
"transition": "Hormone Receptor Negative",
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "breast_cancer_ER",
"operator": "==",
"value": "ER-negative"
},
{
"condition_type": "Attribute",
"attribute": "breast_cancer_PR",
"operator": "==",
"value": "PR-negative"
}
]
}
},
{
"transition": "Hormone Receptor Positive",
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "breast_cancer_ER",
"operator": "==",
"value": "ER-positive"
},
{
"condition_type": "Attribute",
"attribute": "breast_cancer_PR",
"operator": "==",
"value": "PR-positive"
}
]
}
},
{
"transition": "Terminal"
}
]
},
"HER2-": {
"type": "SetAttribute",
"attribute": "breast_cancer_HER2",
"direct_transition": "Tumor_Biopsy_to_Test_Estrogen_Receptor_Status",
"value": "HER2-negative"
},
"HER2+": {
"type": "SetAttribute",
"attribute": "breast_cancer_HER2",
"value": "HER2-positive",
"direct_transition": "Tumor_Biopsy_to_Test_Estrogen_Receptor_Status"
},
"ER-": {
"type": "SetAttribute",
"attribute": "breast_cancer_ER",
"direct_transition": "Tumor_Biopsy_to_Test_Progesterone_Receptor_Status",
"value": "ER-negative"
},
"ER+": {
"type": "SetAttribute",
"attribute": "breast_cancer_ER",
"direct_transition": "Tumor_Biopsy_to_Test_Progesterone_Receptor_Status",
"value": "ER-positive"
},
"PR-": {
"type": "SetAttribute",
"attribute": "breast_cancer_PR",
"direct_transition": "Overall_Receptor_Analysis",
"value": "PR-negative"
},
"PR+": {
"type": "SetAttribute",
"attribute": "breast_cancer_PR",
"direct_transition": "Overall_Receptor_Analysis",
"value": "PR-positive"
},
"Triple_Negative": {
"type": "Observation",
"category": "laboratory",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "21924-6",
"display": "Tumor marker Cancer"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": "260385009",
"display": "Negative (qualifier value)"
},
"direct_transition": "Triple_Negative_Patient",
"remarks": [
"In women with triple-negative breast cancer, the malignant cells do not contain receptors for estrogen, progesterone or HER2. Breast cancer that is ER-, PR- and HER2-negative cannot be treated with hormone therapy or medications that work by blocking HER2, such as trastuzumab."
]
},
"Hormone Receptor Positive": {
"type": "Observation",
"category": "laboratory",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "10480-2",
"display": "Estrogen+Progesterone receptor Ag [Presence] in Tissue by Immune stain"
}
],
"direct_transition": "Terminal",
"value_code": {
"system": "SNOMED-CT",
"code": "10828004",
"display": "Positive (qualifier value)"
},
"remarks": [
"Hormone receptor-positive (estrogen receptor-positive (ER-positive)/progesterone receptor-positive (PR-positive)) tumors express (have a lot of) hormone receptors.:",
"https://ww5.komen.org/BreastCancer/TumorCharacteristics.html"
]
},
"Hormone Receptor Negative": {
"type": "Observation",
"category": "laboratory",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "10480-2",
"display": "Estrogen+Progesterone receptor Ag [Presence] in Tissue by Immune stain"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": "260385009",
"display": "Negative (qualifier value)"
},
"conditional_transition": [
{
"transition": "Triple_Negative",
"condition": {
"condition_type": "Attribute",
"attribute": "breast_cancer_HER2",
"operator": "==",
"value": "HER2-negative"
}
},
{
"transition": "Terminal"
}
],
"remarks": [
"Hormone receptor-negative (estrogen receptor-negative (ER-negative)/progesterone receptor-negative (PR- negative)) tumors do not express (have few or no) hormone receptors.:",
"https://ww5.komen.org/BreastCancer/TumorCharacteristics.html"
]
},
"Human_Epidermal_Growth_Factor_Receptor_2_HER2_Detection_Immunochemistry": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "433114000",
"display": "Human epidermal growth factor receptor 2 gene detection by immunohistochemistry (procedure)"
}
],
"duration": {
"low": 2,
"high": 4,
"unit": "hours"
},
"remarks": [
"Immunohistochemistry (IHC), which detects the number of HER2 protein receptors in the cancer cells:",
"https://ww5.komen.org/BreastCancer/TumorCharacteristics.html",
"",
"In about 20% of breast cancers, the cells make too much of a protein known as HER2. These cancers tend to be aggressive and fast-growing:",
"https://www.webmd.com/breast-cancer/breast-cancer-types-er-positive-her2-positive#1",
"",
"All antibody-antigen interactions investigated in this study, both the primary antibody binding to its target and the secondary antibody binding to the primary, require several hours to reach equilibrium at the concentrations used:",
"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3878317/"
],
"distributed_transition": [
{
"transition": "HER2_negative",
"distribution": 0.8
},
{
"transition": "HER2_positive",
"distribution": 0.2
}
],
"reason": "breast_cancer_condition"
},
"Triple_Negative_Patient": {
"type": "SetAttribute",
"attribute": "breast_cancer_triple_negative",
"direct_transition": "Terminal",
"value": true
},
"HER2 ratio less than 1point8": {
"type": "Observation",
"category": "laboratory",
"unit": "ratio",
"codes": [
{
"system": "LOINC",
"code": "85318-4",
"display": "HER2 [Presence] in Breast cancer specimen by FISH"
}
],
"direct_transition": "HER2-",
"remarks": [
"Title of the article: HER2 Evaluation and Its Impact on Breast Cancer Treatment Decisions",
"",
"https://wwwncbinlmnihgov/pmc/articles/PMC3225235/"
],
"exact": {
"quantity": "less than 1.8"
}
},
"HER2_ratio_greater_than_2point2": {
"type": "Observation",
"category": "laboratory",
"unit": "ratio",
"codes": [
{
"system": "LOINC",
"code": "85318-4",
"display": "HER2 [Presence] in Breast cancer specimen by FISH"
}
],
"direct_transition": "HER2+",
"remarks": [
"Title of the article: HER2 Evaluation and Its Impact on Breast Cancer Treatment Decisions",
"",
"https://wwwncbinlmnihgov/pmc/articles/PMC3225235/"
],
"exact": {
"quantity": "greater than 2.2"
}
}
},
"gmf_version": 1
}

544
src/main/resources/modules/breast_cancer/hormonetherapy_breast.json Normal file
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{
"name": "hormonetherapy_breast",
"remarks": [
"This module has ER/PR and HER2 treatments depending on whether each receptor is positive or negative. There is also treatment for if ER/PR are both positive. "
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "ER-encounter"
},
"Fulvestrant": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 727762,
"display": "5 ML fulvestrant 50 MG/ML Prefilled Syringe"
}
],
"direct_transition": "ER_medication_end",
"assign_to_attribute": "ER_medication",
"remarks": [
"https://www.cancer.org/cancer/breast-cancer/treatment/hormone-therapy-for-breast-cancer.html",
"",
"Fulvestrant (Faslodex)",
"Fulvestrant is a drug that blocks and damages estrogen receptors.This drug is not a SERM – it acts like an anti-estrogen throughout the body. It is also known as a selective estrogen receptor degrader (SERD).",
"",
"Fulvestrant is used to treat metastatic breast cancer, most often after other hormone drugs (like tamoxifen and often an aromatase inhibitor) have stopped working.",
"",
"It is given by injections into the buttocks. For the first month, the shots are given 2 weeks apart. After that, they are given once a month. Common short-term side effects can include:",
"",
"Hot flashes and/or night sweats",
"Headache",
"Mild nausea",
"Bone pain",
"Injection site pain",
"Because fulvestrant blocks estrogen, in theory it could cause weakened bones (osteoporosis) if taken for a long time. Fulvestrant is currently approved only for use in post-menopausal women. It is sometimes used “off-label” in pre-menopausal women, often combined with a luteinizing-hormone releasing hormone (LHRH) agonist to turn off the ovaries (see the section on Ovarian Ablation below)."
],
"reason": "breast_cancer_condition",
"administration": true
},
"Aromatase Inhibitors (AI)": {
"type": "SetAttribute",
"attribute": "breast_cancer_aromatase_inhibitors",
"distributed_transition": [
{
"transition": "Letrozole",
"distribution": 0.33
},
{
"transition": "Anastrozole",
"distribution": 0.33
},
{
"transition": "Exemestane",
"distribution": 0.34
}
],
"value": true,
"remarks": [
"https://www.cancer.org/cancer/breast-cancer/treatment/hormone-therapy-for-breast-cancer.html",
"",
"Aromatase inhibitors (AIs)",
"Aromatase inhibitors (AIs) are drugs that stop estrogen production. Before menopause, most estrogen is made by the ovaries. But for women whose ovaries aren’t working, either due to menopause or certain treatments, a small amount of estrogen is still made in the fat tissue by an enzyme (called aromatase). AIs work by blocking aromatase from making estrogen.",
"",
"These drugs are useful in women who are past menopause, although they can also be used in premenopausal women in combination with ovarian suppression (see below).",
"",
"There are 3 AIs that seem to work about equally well in treating breast cancer:",
"",
"Letrozole (Femara)",
"Anastrozole (Arimidex)",
"Exemestane (Aromasin)",
"These drugs are pills taken daily.",
"",
"Use in adjuvant therapy: After surgery, taking an AI, either alone or after tamoxifen, has been shown to work better than taking just tamoxifen for 5 years to reduce the risk of the cancer coming back .",
"",
"Schedules that are known to be helpful include:",
"",
"Tamoxifen for 2 to 3 years, followed by an AI to complete 5 years of treatment",
"An AI for 2 to 3 years followed by Tamoxifen to complete 5 years of treatment",
"Tamoxifen for 5 years, followed by an AI for 5 years",
"An AI for 5 years",
"Tamoxifen for 5 to 10 years (if you are unable to take an AI)",
"For most post-menopausal women whose cancers are hormone receptor-positive, most doctors recommend taking an AI at some point during adjuvant therapy. Right now, standard treatment is to take these drugs for about 5 years, or to alternate with tamoxifen for a total of at least 5 years, or to take in sequence with tamoxifen for at least 3 years. Studies are now being done to see if taking an AI for more than 5 years would be more helpful. Tamoxifen is an option for some women who cannot take an AI. Taking tamoxifen for 10 years is considered more effective than taking it for 5 years, but you and your doctor will decide the best schedule of treatment for you.",
"",
"If you have early-stage breast cancer and had not gone through menopause when you were first diagnosed, your doctor might recommend taking tamoxifen first, and then taking an AI later if you go through menopause during treatment. Another option is taking a drug called a luteinizing hormone-releasing hormone (LHRH) analog, which turns off the ovaries, along with an AI. An AI should not be taken alone for breast cancer treatment in pre-menopausal women because it is unsafe and can increase hormone levels.",
"",
"Use in cancer that comes back or has spread: AIs can also be used to treat more advanced hormone-positive breast cancers, especially in post-menopausal women. They are often continued for as long as they are helpful.",
"",
"Possible side effects: The AIs tend to have fewer serious side effects than tamoxifen. They don't cause uterine cancers and very rarely cause blood clots. They can, however, cause muscle pain and joint stiffness and/or pain. The joint pain may be similar to a feeling of having arthritis in many different joints at one time. Switching to a different AI may improve this side effect, but it has led some women to stop treatment. If this happens, most doctors recommend using tamoxifen to complete 5 to 10 years of hormone treatment.",
"",
"Because AIs drastically lower the estrogen level in women after menopause, they can also cause bone thinning, sometimes leading to osteoporosis and even fractures. If you are taking an AI, your bone density may be tested and you may also be given drugs, such as bisphosphonates or denosumab (Xgeva, Prolia), to strengthen your bones.",
"",
""
]
},
"Letrozole": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 200064,
"display": "letrozole 2.5 MG Oral Tablet"
}
],
"direct_transition": "ER_medication_end",
"assign_to_attribute": "ER_medication",
"prescription": {
"dosage": {
"amount": 1,
"frequency": 1,
"period": 1,
"unit": "days"
},
"duration": {
"quantity": 7,
"unit": "years"
}
},
"reason": "breast_cancer_condition",
"administration": true
},
"Anastrozole": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 199224,
"display": "anastrozole 1 MG Oral Tablet"
}
],
"direct_transition": "ER_medication_end",
"assign_to_attribute": "ER_medication",
"prescription": {
"dosage": {
"amount": 1,
"frequency": 1,
"period": 1,
"unit": "days"
},
"duration": {
"quantity": 7,
"unit": "years"
}
},
"reason": "breast_cancer_condition",
"administration": true
},
"Exemestane": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 310261,
"display": "exemestane 25 MG Oral Tablet"
}
],
"direct_transition": "ER_medication_end",
"assign_to_attribute": "ER_medication",
"prescription": {
"dosage": {
"amount": 1,
"frequency": 1,
"period": 1,
"unit": "days"
},
"duration": {
"quantity": 7,
"unit": "years"
}
},
"reason": "breast_cancer_condition",
"administration": true
},
"ER-Treatments": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Estrogen Blocking Receptors",
"distribution": 0.6
},
{
"transition": "Fulvestrant",
"distribution": 0.1
},
{
"transition": "Aromatase Inhibitors (AI)",
"distribution": 0.3
}
],
"remarks": [
"https://www.breastcancer.org/research-news/5-more-years-of-ais-no-better-than-2-more",
""
]
},
"HER2-Treatment": {
"type": "Simple",
"remarks": [
"https://www.cancer.org/cancer/breast-cancer/treatment/targeted-therapy-for-breast-cancer.html",
"",
"For about 1 in 5 women with breast cancer, the cancer cells have too much of a growth-promoting protein known as HER2/neu (or just HER2) on their surface. These cancers, known as HER2-positive breast cancers, tend to grow and spread more aggressively. A number of drugs have been developed that target this protein:",
"",
"Trastuzumab (Herceptin): This is a monoclonal antibody, which is a man-made version of a very specific immune system protein. It is often given along with chemo, but it might also be used alone (especially if chemo alone has already been tried). Trastuzumab can be used to treat both early- and late-stage breast cancer. When started before or after surgery to treat early breast cancer, this drug is usually given for a total of 6 months to a year. For advanced breast cancer, treatment is often given for as long as the drug is helpful. This drug is given into a vein (IV) and is infused over 30-90 minutes. Another type of trastuzumab called trastuzumab and hyaluronidase-oysk injection (Herceptin Hylecta) is also available. It is given as a subcutaneous (under the skin) shot that takes about 2 to 5 minutes to inject.",
"Pertuzumab (Perjeta): This monoclonal antibody can be given with trastuzumab and chemo, either before surgery to treat early-stage breast cancer, or to treat advanced breast cancer. This drug is given into a vein (IV).",
"Ado-trastuzumab emtansine (Kadcyla, also known as TDM-1): This is a monoclonal antibody attached to a chemotherapy drug. It is used by itself to treat advanced breast cancer in women who have already been treated with trastuzumab and chemo. This drug is also given in a vein (IV).",
"Lapatinib (Tykerb): This is a kinase inhibitor. It is a pill taken daily. Lapatinib is used to treat advanced breast cancer, and might be used along with certain chemotherapy drugs, trastuzumab, or hormone therapy drugs.",
"Neratinib (Nerlynx): This is another kinase inhibitor. It is a pill that is taken daily. Neratinib is used to treat early-stage breast cancer after a woman has completed one year of trastuzumab and is usually given for one year. Some clinical trials show that it may also be effective in advanced breast cancer, as well.",
"Side effects of targeted therapy for HER2-positive breast cancer",
"The side effects of these drugs are often mild, but some can be serious. Discuss what you can expect with your doctor.",
"",
"Some women develop heart damage during or after treatment with trastuzumab, pertuzumab, or ado-trastuzumab emtansine. This can lead to congestive heart failure. For most (but not all) women, this effect lasts a short time and gets better when the drug is stopped. The risk of heart problems is higher when these drugs are given with certain chemo drugs that also can cause heart damage, such as doxorubicin (Adriamycin) and epirubicin (Ellence). Because these drugs can cause heart damage, doctors often check your heart function (with an echocardiogram or a MUGA scan) before treatment, and again while you are taking the drug. Let your doctor know if you develop symptoms such as shortness of breath, leg swelling, and severe fatigue.",
"",
"Lapatinib and neratinib can cause severe diarrhea, so it’s very important to let your health care team know about any changes in bowel habits as soon as they happen. Lapatinib can also cause hand-foot syndrome, in which the hands and feet become sore and red, and may blister and peel. Pertuzumab can also cause diarrhea. ",
"",
"If you are pregnant, you should not take these drugs. They can harm and even cause death to the fetus. If you could become pregnant, talk to your doctor about using effective birth control while taking these drugs.",
"",
"Targeted therapy for hormone receptor-positive breast cancer",
"About 2 of 3 breast cancers are hormone receptor-positive (ER-positive or PR-positive). For women with these cancers, treatment with hormone therapy is often helpful. Certain targeted therapy drugs can make hormone therapy even more effective, although these targeted drugs might also add to the side effects."
],
"complex_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "breast_cancer_HER2",
"operator": "==",
"value": "HER2-positive"
},
"distributions": [
{
"transition": "Trastuzumab_her2",
"distribution": 0.9
},
{
"transition": "Ado_trastuzumab_emtansine",
"distribution": 0.03
},
{
"transition": "Lapatinib",
"distribution": 0.03
},
{
"transition": "Neratinib",
"distribution": 0.04
}
]
},
{
"distributions": [
{
"distribution": 1,
"transition": "Hormone_Receptor_Positive_Treatments"
}
]
}
]
},
"Ado_trastuzumab_emtansine": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 1658084,
"display": "ado-trastuzumab emtansine 100 MG Injection"
}
],
"direct_transition": "HER2_medication_end",
"assign_to_attribute": "HER2_medication",
"reason": "breast_cancer_condition",
"administration": true
},
"Lapatinib": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 672149,
"display": "lapatinib 250 MG Oral Tablet"
}
],
"direct_transition": "HER2_medication_end",
"assign_to_attribute": "HER2_medication",
"reason": "breast_cancer_condition",
"administration": true
},
"Neratinib": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 1940648,
"display": "neratinib 40 MG Oral Tablet"
}
],
"direct_transition": "HER2_medication_end",
"assign_to_attribute": "HER2_medication",
"reason": "breast_cancer_condition",
"administration": true
},
"Trastuzumab_her2": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 2119714,
"display": "5 ML hyaluronidase-oysk 2000 UNT/ML / trastuzumab 120 MG/ML Injection"
}
],
"direct_transition": "HER2_medication_end",
"assign_to_attribute": "HER2_medication",
"reason": "breast_cancer_condition",
"administration": true
},
"CDK4/6 Inhibitors": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Abemaciclib",
"distribution": 0.33
},
{
"transition": "Palbociclib",
"distribution": 0.33
},
{
"transition": "Ribociclib",
"distribution": 0.34
}
],
"remarks": [
"https://www.cancer.org/cancer/breast-cancer/treatment/targeted-therapy-for-breast-cancer.html",
"",
"CDK4/6 inhibitors",
"Palbociclib (Ibrance), ribociclib (Kisqali), and abemaciclib (Verzenio) are drugs that block proteins in the cell called cyclin-dependent kinases (CDKs), particularly CDK4 and CDK6. Blocking these proteins in hormone receptor-positive breast cancer cells helps stop the cells from dividing. This can slow cancer growth.",
"",
"These drugs are approved for women with advanced hormone receptor-positive, HER2-negative breast cancer and are taken as pills, typically once or twice a day.",
"",
"There are different ways to use these drugs.",
"",
"Any of the three drugs can be given along with an aromatase inhibitor (such as letrozole) or fulvestrant to women who have gone through menopause.",
"Palbociclib or abemaciclib can be given with fulvestrant to women who are still having regular periods (premenopausal) or are almost in menopause (perimenopausal). These women, however, must also be on medicines, such as luteinizing hormone-releasing hormone (LHRH) analogs, that stop the ovaries from making estrogen.",
"Ribociclib can be given with an aromatase inhibitor to women who have not gone through menopause. Again, these women must also be on medicines that suppress the ovaries, such as a luteinizing hormone-releasing hormone (LHRH) analogs. ",
"Abemaciclib can also be used by itself in women who have previously been treated with hormone therapy and chemotherapy.",
"",
"Side effects of these drugs tend to be mild. The most common side effects are low blood cell counts and fatigue. Nausea and vomiting, mouth sores, hair loss, diarrhea, and headache are less common side effects. Very low white blood cell counts can increase the risk of serious infection.",
"",
""
]
},
"Abemaciclib": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 1946840,
"display": "Verzenio 100 MG Oral Tablet"
}
],
"direct_transition": "ER_PR_medication_end",
"assign_to_attribute": "ER_PR_medication",
"reason": "breast_cancer_condition",
"administration": true
},
"Palbociclib": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 1601380,
"display": "palbociclib 100 MG Oral Capsule"
}
],
"direct_transition": "ER_PR_medication_end",
"assign_to_attribute": "ER_PR_medication",
"reason": "breast_cancer_condition",
"administration": true
},
"Ribociclib": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 1873983,
"display": "ribociclib 200 MG Oral Tablet"
}
],
"direct_transition": "ER_PR_medication_end",
"assign_to_attribute": "ER_PR_medication",
"reason": "breast_cancer_condition",
"administration": true
},
"ER-encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "breast_cancer_condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem (procedure)"
}
],
"conditional_transition": [
{
"transition": "ER-Treatments",
"condition": {
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "breast_cancer_PR",
"operator": "==",
"value": "PR-positive"
},
{
"condition_type": "Attribute",
"attribute": "breast_cancer_ER",
"operator": "==",
"value": "ER-positive"
}
]
}
},
{
"transition": "Upper Stage Treatment"
}
]
},
"Upper Stage Treatment": {
"type": "Simple",
"direct_transition": "HER2-Treatment"
},
"Terminal": {
"type": "Terminal"
},
"end_encounter": {
"type": "EncounterEnd",
"direct_transition": "Terminal"
},
"Hormone_Receptor_Positive_Treatments": {
"type": "Simple",
"conditional_transition": [
{
"transition": "CDK4/6 Inhibitors",
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "breast_cancer_ER",
"operator": "==",
"value": "ER-positive"
},
{
"condition_type": "Attribute",
"attribute": "breast_cancer_PR",
"operator": "==",
"value": "PR-positive"
}
]
}
},
{
"transition": "end_encounter"
}
]
},
"Tamoxifen": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 198240,
"display": "Tamoxifen 10 MG Oral Tablet"
}
],
"direct_transition": "ER_medication_end",
"assign_to_attribute": "ER_medication",
"prescription": {
"dosage": {
"amount": 1,
"frequency": 1,
"period": 1,
"unit": "days"
},
"duration": {
"quantity": 10,
"unit": "years"
}
},
"reason": "breast_cancer_condition",
"administration": true
},
"Estrogen Blocking Receptors": {
"type": "SetAttribute",
"attribute": "breast_cancer_tamoxifen",
"direct_transition": "Tamoxifen",
"value": true,
"remarks": [
"https://www.cancer.org/cancer/breast-cancer/treatment/hormone-therapy-for-breast-cancer.html",
"",
"Tamoxifen",
"This drug blocks estrogen receptors on breast cancer cells. It stops estrogen from connecting to the cancer cells and telling them to grow and divide. While tamoxifen acts like an anti-estrogen in breast cells, it acts like an estrogen in other tissues, like the uterus and the bones. Because of this, it is called a selective estrogen receptor modulator (SERM).",
"",
"Tamoxifen can be used in several ways:",
"",
"For women with hormone receptor-positive breast cancer treated with surgery, tamoxifen can help lower the chances of the cancer coming back and raise the chances of living longer. It can also lower the risk of getting a new cancer in the other breast. Tamoxifen can be started either after surgery (adjuvant therapy) or before surgery (neoadjuvant therapy) and is usually taken for 5 to 10 years. For early- stage breast cancer, this drug is mainly used for women who have not yet gone through menopause. (If you have gone through menopause, aromatase inhibitors are usually used instead.)",
"For women who have been treated for ductal carcinoma in situ (DCIS) that is hormone receptor-positive, taking tamoxifen for 5 years lowers the chance of the DCIS coming back. It also lowers the chance of getting an invasive breast cancer.",
"For women with hormone-positive breast cancer that has spread to other parts of the body, tamoxifen can often help slow or stop the growth of the cancer, and might even shrink some tumors.",
"In women at high risk of breast cancer, tamoxifen can be used to help lower the risk of developing breast cancer.",
"Toremifene (Fareston) is another SERM that works in a similar way, but it is used less often and is only approved to treat metastatic breast cancer. It is not likely to work if tamoxifen has already been used and has stopped working. These drugs are taken by mouth as a pill. The most common side effects of tamoxifen and toremifene are:",
"",
"Hot flashes",
"Vaginal dryness or discharge",
"Mood swings",
"Some women with cancer spread to the bones may have a tumor flare with pain and swelling in the muscles and bones. This usually decreases quickly, but in some rare cases a woman may also develop a high calcium level in the blood that is hard to control. If this happens, the treatment may need to be stopped for a time.",
"",
"Rare, but more serious side effects are also possible:",
"",
"If a woman has gone through menopause, these drugs can increase her risk of developing uterine cancer . Tell your doctor right away about any unusual vaginal bleeding (a common symptom of both of these cancers). Most uterine bleeding is not from cancer, but this symptom always needs prompt attention.",
"Blood clots are another uncommon, but serious side effect. They usually form in the legs (called deep vein thrombosis or DVT), but sometimes a piece of clot may break off and end up blocking an artery in the lungs (pulmonary embolism or PE). Call your doctor or nurse right away if you develop pain, redness, or swelling in your lower leg (calf), shortness of breath, or chest pain, because these can be symptoms of a DVT or PE.",
"Rarely, tamoxifen has been associated with strokes in post-menopausal women, so tell your doctor if you have severe headaches, confusion, or trouble speaking or moving.",
"Depending on a woman's menopausal status, tamoxifen can have different effects on the bones. In pre-menopausal women, tamoxifen can cause some bone thinning, but in post-menopausal women it is often good to strengthen bone. The benefits of taking these drugs outweigh the risks for almost all women with hormone receptor-positive breast cancer.",
"",
""
]
},
"ER_medication_end": {
"type": "MedicationEnd",
"direct_transition": "Upper Stage Treatment",
"referenced_by_attribute": "ER_medication"
},
"HER2_medication_end": {
"type": "MedicationEnd",
"direct_transition": "Hormone_Receptor_Positive_Treatments",
"referenced_by_attribute": "HER2_medication"
},
"ER_PR_medication_end": {
"type": "MedicationEnd",
"referenced_by_attribute": "ER_PR_medication",
"direct_transition": "end_encounter"
}
},
"gmf_version": 1
}

1129
src/main/resources/modules/breast_cancer/surgery_therapy_breast.json Normal file
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src/main/resources/modules/breast_cancer/tnm_diagnosis.json Normal file
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{
"name": "TNM_Diagnosis",
"remarks": [
"This module goes through and diagnoses which T, N, and M stage a person would encounter through the screening. "
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "M Marker"
},
"Terminal": {
"type": "Terminal"
},
"M Marker": {
"type": "Simple",
"distributed_transition": [
{
"transition": "No Evidence of Distant Metastasis ",
"distribution": 0.94
},
{
"transition": "Distant Metastases Detected",
"distribution": 0.06
}
],
"remarks": [
"About 6% of women have metastatic cancer when they are first diagnosed with breast cancer:",
"https://www.cancer.net/cancer-types/breast-cancer/statistics"
]
},
"N Marker": {
"type": "Simple",
"complex_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "breast_cancer_Location",
"operator": "==",
"value": "local"
},
"transition": "No Regional Lymph Node Metastasis"
},
{
"distributions": [
{
"distribution": 0.34,
"transition": "Micrometastasis in 1 - 3 Lymph Nodes"
},
{
"distribution": 0.33,
"transition": "Macrometastases in 4 - 9 Lymph Nodes"
},
{
"distribution": 0.33,
"transition": "Macrometastases in 10+ Lymph Nodes"
}
],
"condition": {
"condition_type": "Attribute",
"attribute": "breast_cancer_M",
"operator": "==",
"value": "M1"
}
},
{
"distributions": [
{
"transition": "Micrometastasis in 1 - 3 Lymph Nodes",
"distribution": 0.6
},
{
"transition": "Macrometastases in 4 - 9 Lymph Nodes",
"distribution": 0.3
},
{
"transition": "Macrometastases in 10+ Lymph Nodes",
"distribution": 0.10000000000000009
}
],
"condition": {
"condition_type": "Attribute",
"attribute": "breast_cancer_Location",
"operator": "==",
"value": "regional"
}
}
],
"remarks": [
"Lymph node status shows whether or not the lymph nodes in the underarm area (axillary lymph nodes) contain cancer:",
"Lymph node-negative means the axillary lymph nodes do not contain cancer.",
"Lymph node-positive means the axillary lymph nodes contain cancer.",
"Prognosis is better when cancer has not spread to the lymph nodes (lymph node-negative) [13].",
"The more lymph nodes that contain cancer, the poorer prognosis tends to be [13].",
"The number of positive nodes guides treatment and helps predict prognosis (chances for survival).",
"See Figure 4.4 for an illustration of the breast and lymph nodes.",
"https://ww5.komen.org/BreastCancer/LymphNodeStatusandStaging.html"
]
},
"T4": {
"type": "SetAttribute",
"attribute": "breast_cancer_T",
"direct_transition": "T4_Diagnosed",
"value": "T4",
"remarks": [
"AJCC Cancer Staging Manual; 8th Edition"
]
},
"N1": {
"type": "SetAttribute",
"attribute": "breast_cancer_N",
"direct_transition": "N1_Diagnosed",
"value": "N1"
},
"N2": {
"type": "SetAttribute",
"attribute": "breast_cancer_N",
"direct_transition": "N2_Diagnosed",
"value": "N2"
},
"N3": {
"type": "SetAttribute",
"attribute": "breast_cancer_N",
"direct_transition": "N3_Diagnosed",
"value": "N3"
},
"Distant Breast Cancer": {
"type": "SetAttribute",
"attribute": "breast_cancer_Location",
"direct_transition": "Tumor Size Any",
"value": "distant"
},
"Regional Breast Cancer": {
"type": "SetAttribute",
"attribute": "breast_cancer_Location",
"distributed_transition": [
{
"transition": "Tumor Size Less than 2 cm",
"distribution": 0.3011
},
{
"transition": "Tumor Size 2 -5 cm",
"distribution": 0.5053
},
{
"transition": "Tumor Size Greater Than 5 cm",
"distribution": 0.1398
},
{
"transition": "No Evidence of Primary Tumor in Breast",
"distribution": 0.0538
}
],
"remarks": [
"Adjusted Tumor Data for Regional Breast Cancer:",
"https://onlinelibrary.wiley.com/doi/full/10.1002/cncr.21285"
],
"value": "regional"
},
"Local Breast Cancer": {
"type": "SetAttribute",
"attribute": "breast_cancer_Location",
"distributed_transition": [
{
"transition": "Tumor Size Less than 2 cm",
"distribution": 0.7052
},
{
"transition": "Tumor Size 2 -5 cm",
"distribution": 0.2632
},
{
"transition": "Tumor Size Greater Than 5 cm",
"distribution": 0.0316
}
],
"remarks": [
"Adjusted Tumor Data for Local Breast Cancer:",
"https://onlinelibrary.wiley.com/doi/full/10.1002/cncr.21285"
],
"value": "local"
},
"M1_Diagnosed": {
"type": "Observation",
"category": "imaging",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "21907-1",
"display": "Distant metastases.clinical [Class] Cancer"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": 55440008,
"display": "M1 category (finding)"
},
"direct_transition": "Distant Breast Cancer"
},
"M0_Diagnosed": {
"type": "Observation",
"category": "imaging",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "21907-1",
"display": "Distant metastases.clinical [Class] Cancer"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": 30893008,
"display": "M0 category (finding)"
},
"distributed_transition": [
{
"transition": "Local Breast Cancer",
"distribution": 0.62
},
{
"transition": "Regional Breast Cancer",
"distribution": 0.38
}
],
"remarks": [
"If the cancer is located only in the breast, the 5-year survival rate of women with breast cancer is 99%. Sixty-two percent (62%) of cases are diagnosed at this stage:",
"https://www.cancer.net/cancer-types/breast-cancer/statistics"
]
},
"T0_Diagnosed": {
"type": "Observation",
"category": "imaging",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "21905-5",
"display": "Primary tumor.clinical [Class] Cancer"
}
],
"direct_transition": "N Marker",
"value_code": {
"system": "SNOMED-CT",
"code": 58790005,
"display": "T0 category (finding)"
}
},
"T1_Diagnosed": {
"type": "Observation",
"category": "imaging",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "21905-5",
"display": "Primary tumor.clinical [Class] Cancer"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": 23351008,
"display": "T1 category (finding)"
},
"direct_transition": "N Marker"
},
"T2_Diagnosed": {
"type": "Observation",
"category": "imaging",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "21905-5",
"display": "Primary tumor.clinical [Class] Cancer"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": 67673008,
"display": "T2 category (finding)"
},
"direct_transition": "N Marker"
},
"T3_Diagnosed": {
"type": "Observation",
"category": "imaging",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "21905-5",
"display": "Primary tumor.clinical [Class] Cancer"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": 14410001,
"display": "T3 category (finding)"
},
"direct_transition": "N Marker",
"remarks": [
"https://www.cancer.net/cancer-types/breast-cancer/statistics"
]
},
"T4_Diagnosed": {
"type": "Observation",
"category": "imaging",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "21905-5",
"display": "Primary tumor.clinical [Class] Cancer"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": 65565005,
"display": "T4 category (finding)"
},
"direct_transition": "N Marker"
},
"N1_Diagnosed": {
"type": "Observation",
"category": "imaging",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "21906-3",
"display": "Regional lymph nodes.clinical [Class] Cancer"
}
],
"direct_transition": "Terminal",
"value_code": {
"system": "SNOMED-CT",
"code": 53623008,
"display": "N1 category (finding)"
}
},
"N0_Diagnosed": {
"type": "Observation",
"category": "imaging",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "21906-3",
"display": "Regional lymph nodes.clinical [Class] Cancer"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": 62455006,
"display": "N0 category (finding)"
},
"direct_transition": "Terminal"
},
"N2_Diagnosed": {
"type": "Observation",
"category": "imaging",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "21906-3",
"display": "Regional lymph nodes.clinical [Class] Cancer"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": 46059003,
"display": "N2 category (finding)"
},
"direct_transition": "Terminal"
},
"N3_Diagnosed": {
"type": "Observation",
"category": "imaging",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "21906-3",
"display": "Regional lymph nodes.clinical [Class] Cancer"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": 5856006,
"display": "N3 category (finding)"
},
"direct_transition": "Terminal"
},
"T1": {
"type": "SetAttribute",
"attribute": "breast_cancer_T",
"value": "T1",
"direct_transition": "T1_Diagnosed",
"remarks": [
"AJCC Cancer Staging Manual; 8th Edition"
]
},
"No Evidence of Primary Tumor in Breast": {
"type": "Simple",
"direct_transition": "T0",
"remarks": [
"AJCC Cancer Staging Manual; 8th Edition"
]
},
"T0": {
"type": "SetAttribute",
"attribute": "breast_cancer_T",
"value": "T0",
"direct_transition": "T0_Diagnosed"
},
"Tumor Size 2 -5 cm": {
"type": "Observation",
"category": "imaging",
"unit": "cm",
"codes": [
{
"system": "LOINC",
"code": "33728-7",
"display": "Size.maximum dimension in Tumor"
}
],
"direct_transition": "T2",
"remarks": [
"AJCC Cancer Staging Manual; 8th Edition"
],
"range": {
"low": 2,
"high": 5
}
},
"T2": {
"type": "SetAttribute",
"attribute": "breast_cancer_T",
"value": "T2",
"direct_transition": "T2_Diagnosed",
"remarks": [
"AJCC Cancer Staging Manual; 8th Edition"
]
},
"Tumor Size Greater Than 5 cm": {
"type": "Observation",
"category": "imaging",
"unit": "cm",
"codes": [
{
"system": "LOINC",
"code": "33728-7",
"display": "Size.maximum dimension in Tumor"
}
],
"direct_transition": "T3",
"remarks": [
"AJCC Cancer Staging Manual; 8th Edition"
],
"range": {
"low": 5,
"high": 6
}
},
"Tumor Size Less than 2 cm": {
"type": "Observation",
"category": "imaging",
"unit": "cm",
"codes": [
{
"system": "LOINC",
"code": "33728-7",
"display": "Size.maximum dimension in Tumor"
}
],
"direct_transition": "T1",
"range": {
"low": 0,
"high": 2
},
"remarks": [
"AJCC Cancer Staging Manual; 8th Edition"
]
},
"T3": {
"type": "SetAttribute",
"attribute": "breast_cancer_T",
"value": "T3",
"direct_transition": "T3_Diagnosed",
"remarks": [
"AJCC Cancer Staging Manual; 8th Edition"
]
},
"Tumor Size Any": {
"type": "Observation",
"category": "imaging",
"unit": "cm",
"codes": [
{
"system": "LOINC",
"code": "33728-7",
"display": "Size.maximum dimension in Tumor"
}
],
"remarks": [
"AJCC Cancer Staging Manual; 8th Edition"
],
"range": {
"low": 0,
"high": 6
},
"direct_transition": "T4"
},
"No Evidence of Distant Metastasis ": {
"type": "Observation",
"category": "imaging",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "44667-4",
"display": "Site of distant metastasis in Breast tumor"
}
],
"direct_transition": "M0",
"remarks": [
"https://www.cancer.net/cancer-types/breast-cancer/statistics",
"AJCC Cancer Staging Manual; 8th Edition"
],
"value_code": {
"system": "SNOMED-CT",
"code": "260413007",
"display": "None (qualifier value)"
}
},
"M0": {
"type": "SetAttribute",
"attribute": "breast_cancer_M",
"value": "M0",
"remarks": [
"AJCC Cancer Staging Manual; 8th Edition",
"Cancer has either spread beyond the breast and nearby lymph nodes to other areas of the body (M1) or it has not (MO):",
"https://ww5.komen.org/BreastCancer/MetastasesandStaging.html"
],
"direct_transition": "M0_Diagnosed"
},
"Distant Metastases Detected": {
"type": "Simple",
"direct_transition": "M1",
"remarks": [
"AJCC Cancer Staging Manual; 8th Edition"
]
},
"M1": {
"type": "SetAttribute",
"attribute": "breast_cancer_M",
"value": "M1",
"direct_transition": "M1_Diagnosed",
"remarks": [
"AJCC Cancer Staging Manual; 8th Edition"
]
},
"No Regional Lymph Node Metastasis": {
"type": "Observation",
"category": "imaging",
"unit": "{#}",
"codes": [
{
"system": "LOINC",
"code": "85352-3",
"display": "Lymph nodes with isolated tumor cells [#] in Cancer specimen by Light microscopy"
}
],
"exact": {
"quantity": 0
},
"direct_transition": "N0",
"remarks": [
"AJCC Cancer Staging Manual; 8th Edition",
"https://ww5.komen.org/BreastCancer/LymphNodeStatusandStaging.html"
]
},
"N0": {
"type": "SetAttribute",
"attribute": "breast_cancer_N",
"value": "N0",
"direct_transition": "N0_Diagnosed"
},
"Micrometastasis in 1 - 3 Lymph Nodes": {
"type": "Observation",
"category": "imaging",
"unit": "{#}",
"codes": [
{
"system": "LOINC",
"code": "85344-0",
"display": "Lymph nodes with micrometastases [#] in Cancer specimen by Light microscopy"
}
],
"direct_transition": "N1",
"range": {
"low": 1,
"high": 3
},
"remarks": [
"AJCC Cancer Staging Manual; 8th Edition",
"https://ww5.komen.org/BreastCancer/LymphNodeStatusandStaging.html"
]
},
"Macrometastases in 4 - 9 Lymph Nodes": {
"type": "Observation",
"category": "imaging",
"unit": "{#}",
"codes": [
{
"system": "LOINC",
"code": "85343-2",
"display": "Lymph nodes with macrometastases [#] in Cancer specimen by Light microscopy"
}
],
"direct_transition": "N2",
"range": {
"low": 4,
"high": 9
},
"remarks": [
"AJCC Cancer Staging Manual; 8th Edition",
"https://ww5.komen.org/BreastCancer/LymphNodeStatusandStaging.html"
]
},
"Macrometastases in 10+ Lymph Nodes": {
"type": "Observation",
"category": "imaging",
"unit": "{#}",
"codes": [
{
"system": "LOINC",
"code": "85343-2",
"display": "Lymph nodes with macrometastases [#] in Cancer specimen by Light microscopy"
}
],
"direct_transition": "N3",
"range": {
"low": 10,
"high": 30
},
"remarks": [
"AJCC Cancer Staging Manual; 8th Edition",
"https://ww5.komen.org/BreastCancer/LymphNodeStatusandStaging.html",
"https://www.medicalnewstoday.com/articles/319713.php"
]
}
},
"gmf_version": 1
}

541
src/main/resources/modules/bronchitis.json Normal file
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{
"name": "Bronchitis",
"remarks": [
"For now this covers only acute bronchitis. Chronic bronchitis is one of the conditions included in chronic obstructive pulmonary disease (COPD).",
"Acute bronchitis is the fifth most common reason why adults see their GP; 5% of the adult population seeks medical advice for bronchitis each year.",
"Most of the data here comes from the following sources: ",
"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2278319/",
"http://www.aafp.org/afp/1998/0315/p1270.html"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Potential_Infection"
},
"Potential_Infection": {
"type": "Delay",
"exact": {
"quantity": 1,
"unit": "months"
},
"complex_transition": [
{
"condition": {
"condition_type": "Age",
"operator": "<",
"quantity": 18,
"unit": "years"
},
"distributions": [
{
"distribution": 0.005,
"transition": "Bronchitis_Infection",
"remarks": [
"6% of children get bronchitis each year.",
"6% / year == ~ .5% per month?"
]
},
{
"distribution": 0.995,
"transition": "Potential_Infection"
}
]
},
{
"distributions": [
{
"distribution": 0.00416,
"transition": "Bronchitis_Infection",
"remarks": [
"5% of the adult population seeks medical advice for bronchitis each year.",
"5% / year == ~ .42% per month?"
]
},
{
"distribution": 0.99584,
"transition": "Potential_Infection"
}
]
}
]
},
"Bronchitis_Infection": {
"type": "ConditionOnset",
"target_encounter": "Doctor_Visit",
"codes": [
{
"system": "SNOMED-CT",
"code": "10509002",
"display": "Acute bronchitis (disorder)"
}
],
"direct_transition": "Bronchitis_Symptom1"
},
"Bronchitis_Symptom1": {
"type": "Symptom",
"symptom": "Cough",
"range": {
"low": 25,
"high": 75
},
"direct_transition": "Bronchitis_Symptom2"
},
"Bronchitis_Symptom2": {
"type": "Symptom",
"symptom": "Mucus",
"range": {
"low": 25,
"high": 50
},
"direct_transition": "Bronchitis_Symptom3"
},
"Bronchitis_Symptom3": {
"type": "Symptom",
"symptom": "Shortness of Breath",
"range": {
"low": 25,
"high": 75
},
"direct_transition": "Bronchitis_Symptom4"
},
"Bronchitis_Symptom4": {
"type": "Symptom",
"symptom": "Sore Throat",
"range": {
"low": 25,
"high": 50
},
"direct_transition": "Bronchitis_Symptom5"
},
"Bronchitis_Symptom5": {
"type": "Symptom",
"symptom": "Fatigue",
"range": {
"low": 25,
"high": 75
},
"direct_transition": "Bronchitis_Symptom6"
},
"Bronchitis_Symptom6": {
"type": "Symptom",
"symptom": "Fever",
"range": {
"low": 25,
"high": 50
},
"direct_transition": "Bronchitis_Symptom7"
},
"Bronchitis_Symptom7": {
"type": "Symptom",
"symptom": "Body Aches",
"range": {
"low": 0,
"high": 25
},
"direct_transition": "Bronchitis_Symptom8"
},
"Bronchitis_Symptom8": {
"type": "Symptom",
"symptom": "Nasal Congestion",
"range": {
"low": 25,
"high": 50
},
"direct_transition": "Bronchitis_Symptom9"
},
"Bronchitis_Symptom9": {
"type": "Symptom",
"symptom": "Nausea/Vomiting",
"range": {
"low": 0,
"high": 25
},
"direct_transition": "Bronchitis_Symptom10"
},
"Bronchitis_Symptom10": {
"type": "Symptom",
"symptom": "Diarrhea",
"range": {
"low": 0,
"high": 25
},
"direct_transition": "Symptoms_Dont_improve"
},
"Symptoms_Dont_improve": {
"type": "Delay",
"range": {
"low": 1,
"high": 3,
"unit": "days"
},
"direct_transition": "Doctor_Visit"
},
"Doctor_Visit": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Bronchitis_Infection",
"remarks": [
"There are no reliable diagnostic signs or laboratory tests, so the diagnosis of acute bronchitis is essentially a clinical one. ",
"The most important condition to rule out is acute pneumonia. "
],
"codes": [
{
"system": "SNOMED-CT",
"code": "185345009",
"display": "Encounter for symptom (procedure)"
}
],
"distributed_transition": [
{
"distribution": 0.05,
"transition": "Chest_Xray"
},
{
"distribution": 0.2,
"transition": "Sputum_Test"
},
{
"distribution": 0.5,
"transition": "Lung_Function_Test"
},
{
"distribution": 0.2,
"transition": "Bronchitis_CarePlan_Selector"
}
]
},
"Chest_Xray": {
"type": "Procedure",
"reason": "Bronchitis_Infection",
"codes": [
{
"system": "SNOMED-CT",
"code": "399208008",
"display": "Plain X-ray of chest (procedure)"
}
],
"duration": {
"low": 10,
"high": 25,
"unit": "minutes"
},
"direct_transition": "Bronchitis_CarePlan_Selector"
},
"Sputum_Test": {
"type": "Procedure",
"reason": "Bronchitis_Infection",
"codes": [
{
"system": "SNOMED-CT",
"code": "269911007",
"display": "Sputum examination (procedure)"
}
],
"duration": {
"low": 3,
"high": 15,
"unit": "minutes"
},
"direct_transition": "Bronchitis_CarePlan_Selector"
},
"Lung_Function_Test": {
"type": "Procedure",
"reason": "Bronchitis_Infection",
"codes": [
{
"system": "SNOMED-CT",
"code": "23426006",
"display": "Measurement of respiratory function (procedure)"
}
],
"duration": {
"low": 10,
"high": 25,
"unit": "minutes"
},
"direct_transition": "Bronchitis_CarePlan_Selector"
},
"Bronchitis_CarePlan_Selector": {
"type": "Simple",
"conditional_transition": [
{
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Age",
"operator": ">=",
"quantity": 18,
"unit": "years"
},
{
"condition_type": "Attribute",
"attribute": "smoker",
"operator": "==",
"value": true
}
]
},
"transition": "Smoker_CarePlan"
},
{
"transition": "Nonsmoker_CarePlan"
}
]
},
"Smoker_CarePlan": {
"type": "CarePlanStart",
"assign_to_attribute": "bronchitis_careplan",
"reason": "Bronchitis_Infection",
"codes": [
{
"system": "SNOMED-CT",
"code": "53950000",
"display": "Respiratory therapy (procedure)"
}
],
"activities": [
{
"system": "SNOMED-CT",
"code": "710081004",
"display": "Smoking cessation therapy (regime/therapy)"
},
{
"system": "SNOMED-CT",
"code": "304510005",
"display": "Recommendation to avoid exercise (procedure)"
},
{
"system": "SNOMED-CT",
"code": "371605008",
"display": "Deep breathing and coughing exercises (regime/therapy)"
}
],
"direct_transition": "OTC_Medicine"
},
"Nonsmoker_CarePlan": {
"type": "CarePlanStart",
"assign_to_attribute": "bronchitis_careplan",
"reason": "Bronchitis_Infection",
"codes": [
{
"system": "SNOMED-CT",
"code": "53950000",
"display": "Respiratory therapy (procedure)"
}
],
"activities": [
{
"system": "SNOMED-CT",
"code": "304510005",
"display": "Recommendation to avoid exercise (procedure)"
},
{
"system": "SNOMED-CT",
"code": "371605008",
"display": "Deep breathing and coughing exercises (regime/therapy)"
}
],
"direct_transition": "OTC_Medicine"
},
"OTC_Medicine": {
"type": "Simple",
"remarks": [
"Up to 95% of bronchitis cases are viral so antibiotics are rarely prescribed",
"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2278319/"
],
"complex_transition": [
{
"condition": {
"condition_type": "Symptom",
"symptom": "Mucus",
"operator": "<",
"value": 30
},
"distributions": [
{
"distribution": 0.8,
"transition": "Cough_suppressant"
},
{
"distribution": 0.2,
"transition": "Acetaminophen"
}
],
"remarks": [
"cough suppressants shouldn't be given if the cough brings up mucus"
]
},
{
"distributions": [
{
"distribution": 0.1,
"transition": "Cough_suppressant"
},
{
"distribution": 0.9,
"transition": "Acetaminophen"
}
]
}
]
},
"Cough_suppressant": {
"type": "MedicationOrder",
"assign_to_attribute": "OTC_Bronchitis_Med",
"reason": "Bronchitis_Infection",
"codes": [
{
"system": "RxNorm",
"code": "1043400",
"display": "Acetaminophen 21.7 MG/ML / Dextromethorphan Hydrobromide 1 MG/ML / doxylamine succinate 0.417 MG/ML Oral Solution"
}
],
"direct_transition": "End_Doctor_Visit"
},
"Acetaminophen": {
"type": "MedicationOrder",
"assign_to_attribute": "OTC_Bronchitis_Med",
"reason": "Bronchitis_Infection",
"codes": [
{
"system": "RxNorm",
"code": "313782",
"display": "Acetaminophen 325 MG Oral Tablet"
}
],
"direct_transition": "End_Doctor_Visit"
},
"End_Doctor_Visit": {
"type": "EncounterEnd",
"direct_transition": "Wait_for_condition_to_resolve"
},
"Wait_for_condition_to_resolve": {
"type": "Delay",
"range": {
"low": 1,
"high": 3,
"unit": "weeks"
},
"direct_transition": "Bronchitis_Subsides"
},
"Bronchitis_Subsides": {
"type": "ConditionEnd",
"condition_onset": "Bronchitis_Infection",
"direct_transition": "Bronchitis_Symptom1_Subsides"
},
"Bronchitis_Symptom1_Subsides": {
"type": "Symptom",
"symptom": "Cough",
"exact": {
"quantity": 0
},
"direct_transition": "Bronchitis_Symptom2_Subsides"
},
"Bronchitis_Symptom2_Subsides": {
"type": "Symptom",
"symptom": "Mucus",
"exact": {
"quantity": 0
},
"direct_transition": "Bronchitis_Symptom4_Subsides"
},
"Bronchitis_Symptom4_Subsides": {
"type": "Symptom",
"symptom": "Sore Throat",
"exact": {
"quantity": 0
},
"direct_transition": "Bronchitis_Symptom5_Subsides"
},
"Bronchitis_Symptom5_Subsides": {
"type": "Symptom",
"symptom": "Fatigue",
"exact": {
"quantity": 0
},
"direct_transition": "Bronchitis_Symptom6_Subsides"
},
"Bronchitis_Symptom6_Subsides": {
"type": "Symptom",
"symptom": "Fever",
"exact": {
"quantity": 0
},
"direct_transition": "Bronchitis_Symptom7_Subsides"
},
"Bronchitis_Symptom7_Subsides": {
"type": "Symptom",
"symptom": "Body Aches",
"exact": {
"quantity": 0
},
"direct_transition": "Bronchitis_Symptom8_Subsides"
},
"Bronchitis_Symptom8_Subsides": {
"type": "Symptom",
"symptom": "Nasal Congestion",
"exact": {
"quantity": 0
},
"direct_transition": "Bronchitis_Symptom9_Subsides"
},
"Bronchitis_Symptom9_Subsides": {
"type": "Symptom",
"symptom": "Nausea/Vomiting",
"exact": {
"quantity": 0
},
"direct_transition": "Bronchitis_Symptom10_Subsides"
},
"Bronchitis_Symptom10_Subsides": {
"type": "Symptom",
"symptom": "Diarrhea",
"exact": {
"quantity": 0
},
"direct_transition": "Bronchitis_Symptom3_Subsides"
},
"Bronchitis_Symptom3_Subsides": {
"type": "Symptom",
"symptom": "Shortness of Breath",
"exact": {
"quantity": 0
},
"conditional_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "OTC_Bronchitis_Med",
"operator": "is not nil"
},
"transition": "End_OTC_Medication"
},
{
"transition": "Next_Well_Visit"
}
]
},
"End_OTC_Medication": {
"type": "MedicationEnd",
"referenced_by_attribute": "OTC_Bronchitis_Med",
"direct_transition": "Next_Well_Visit"
},
"Next_Well_Visit": {
"type": "Encounter",
"wellness": true,
"direct_transition": "End_Bronchitis_CarePlan",
"reason": "Bronchitis_Infection"
},
"End_Bronchitis_CarePlan": {
"type": "CarePlanEnd",
"referenced_by_attribute": "bronchitis_careplan",
"direct_transition": "End_Wellness_Visit"
},
"End_Wellness_Visit": {
"type": "EncounterEnd",
"direct_transition": "Potential_Infection"
}
},
"gmf_version": 1
}

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src/main/resources/modules/cerebral_palsy.json Normal file
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src/main/resources/modules/chronic_ischaemic_heart_disease.json Normal file
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{
"name": "Chronic Ischaemic Heart Disease",
"remarks": [
"Chronic ischaemic heart disease (IHD) refers to reduced blood supply to the heart muscle due to coronary artery disease.",
"It is characterized by atherosclerotic plaque buildup in coronary arteries, leading to myocardial ischemia.",
"This module models the onset, progression, and management of chronic IHD, including stable angina and its complications.",
"Information on prevalence, progression, and treatment obtained from:",
"https://www.ncbi.nlm.nih.gov/books/NBK507846/",
"https://www.ahajournals.org/doi/10.1161/CIR.0000000000000757",
"https://www.nice.org.uk/guidance/ng185"
],
"states": {
"Initial": {
"type": "Initial",
"remarks": [
"======================================================================",
" INCIDENCE ",
"======================================================================",
"Chronic ischaemic heart disease affects approximately 3-4% of the general population.",
"It is more common in males, older adults, and those with risk factors like hypertension,",
"diabetes, hyperlipidemia, smoking, and family history of premature CAD."
],
"direct_transition": "Risk_Factor_Check"
},
"Risk_Factor_Check": {
"type": "Simple",
"complex_transition": [
{
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Gender",
"gender": "M"
},
{
"condition_type": "Age",
"operator": ">=",
"quantity": 45,
"unit": "years"
}
]
},
"distributions": [
{
"distribution": 0.08,
"transition": "Delay_For_IHD_Onset"
},
{
"distribution": 0.92,
"transition": "Terminal"
}
]
},
{
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Gender",
"gender": "F"
},
{
"condition_type": "Age",
"operator": ">=",
"quantity": 55,
"unit": "years"
}
]
},
"distributions": [
{
"distribution": 0.06,
"transition": "Delay_For_IHD_Onset"
},
{
"distribution": 0.94,
"transition": "Terminal"
}
]
},
{
"distributions": [
{
"distribution": 0.02,
"transition": "Delay_For_IHD_Onset"
},
{
"distribution": 0.98,
"transition": "Terminal"
}
]
}
]
},
"Delay_For_IHD_Onset": {
"type": "Delay",
"range": {
"low": 1,
"high": 10,
"unit": "years"
},
"direct_transition": "Chronic_IHD_Onset"
},
"Chronic_IHD_Onset": {
"type": "ConditionOnset",
"target_encounter": "IHD_Diagnosis_Encounter",
"assign_to_attribute": "ihd",
"codes": [
{
"system": "SNOMED-CT",
"code": "413838009",
"display": "Chronic ischemic heart disease (disorder)"
},
{
"system": "ICD-10-CM",
"code": "I25.9",
"display": "Chronic ischemic heart disease, unspecified"
}
],
"direct_transition": "Set_Angina_Status"
},
"Set_Angina_Status": {
"type": "SetAttribute",
"attribute": "angina_status",
"value": "asymptomatic",
"direct_transition": "IHD_Diagnosis_Encounter"
},
"IHD_Diagnosis_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "ihd",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem (procedure)"
}
],
"direct_transition": "Chest_Pain_Symptom"
},
"Chest_Pain_Symptom": {
"type": "Symptom",
"symptom": "chest pain",
"cause": "ihd",
"range": {
"low": 0,
"high": 30
},
"direct_transition": "Dyspnea_Symptom"
},
"Dyspnea_Symptom": {
"type": "Symptom",
"symptom": "dyspnea",
"cause": "ihd",
"range": {
"low": 0,
"high": 30
},
"direct_transition": "Fatigue_Symptom"
},
"Fatigue_Symptom": {
"type": "Symptom",
"symptom": "fatigue",
"cause": "ihd",
"range": {
"low": 0,
"high": 40
},
"direct_transition": "BP_Measurement"
},
"BP_Measurement": {
"type": "Observation",
"category": "vital-signs",
"unit": "mm[Hg]",
"codes": [
{
"system": "LOINC",
"code": "8480-6",
"display": "Systolic blood pressure"
}
],
"range": {
"low": 120,
"high": 160
},
"direct_transition": "ECG"
},
"ECG": {
"type": "Procedure",
"reason": "ihd",
"codes": [
{
"system": "SNOMED-CT",
"code": "29303009",
"display": "Electrocardiogram (procedure)"
}
],
"direct_transition": "ECG_Findings"
},
"ECG_Findings": {
"type": "Observation",
"category": "procedure",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "76547-9",
"display": "EKG impression narrative"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": "164865005",
"display": "ECG: ischaemic changes (finding)"
},
"direct_transition": "Lipid_Panel"
},
"Lipid_Panel": {
"type": "Procedure",
"reason": "ihd",
"codes": [
{
"system": "SNOMED-CT",
"code": "14698002",
"display": "Lipid panel (procedure)"
}
],
"direct_transition": "LDL_Test"
},
"LDL_Test": {
"type": "Observation",
"category": "laboratory",
"unit": "mg/dL",
"codes": [
{
"system": "LOINC",
"code": "18262-6",
"display": "Cholesterol in LDL [Mass/volume] in Serum or Plasma"
}
],
"range": {
"low": 120,
"high": 190
},
"direct_transition": "HDL_Test"
},
"HDL_Test": {
"type": "Observation",
"category": "laboratory",
"unit": "mg/dL",
"codes": [
{
"system": "LOINC",
"code": "2085-9",
"display": "Cholesterol in HDL [Mass/volume] in Serum or Plasma"
}
],
"range": {
"low": 30,
"high": 50
},
"direct_transition": "Stress_Test_Decision"
},
"Stress_Test_Decision": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.8,
"transition": "Exercise_Stress_Test"
},
{
"distribution": 0.2,
"transition": "Coronary_Angiography_Decision"
}
]
},
"Exercise_Stress_Test": {
"type": "Procedure",
"reason": "ihd",
"codes": [
{
"system": "SNOMED-CT",
"code": "251269002",
"display": "Exercise stress test (procedure)"
}
],
"duration": {
"low": 30,
"high": 45,
"unit": "minutes"
},
"direct_transition": "Stress_Test_Results"
},
"Stress_Test_Results": {
"type": "Observation",
"category": "procedure",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "69066-4",
"display": "Exercise stress test Study observation"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": "164873001",
"display": "Exercise ECG positive (finding)"
},
"direct_transition": "Coronary_Angiography_Decision"
},
"Coronary_Angiography_Decision": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.6,
"transition": "Coronary_Angiography"
},
{
"distribution": 0.4,
"transition": "Treatment_Plan"
}
]
},
"Coronary_Angiography": {
"type": "Procedure",
"reason": "ihd",
"codes": [
{
"system": "SNOMED-CT",
"code": "33367005",
"display": "Coronary arteriography (procedure)"
}
],
"duration": {
"low": 45,
"high": 90,
"unit": "minutes"
},
"direct_transition": "Angiography_Results"
},
"Angiography_Results": {
"type": "Observation",
"category": "procedure",
"unit": "",
"codes": [
{
"system": "LOINC",
"code": "79378-6",
"display": "Coronary angiography Narrative"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": "233817007",
"display": "Coronary artery stenosis (disorder)"
},
"direct_transition": "Update_IHD_Condition"
},
"Update_IHD_Condition": {
"type": "ConditionEnd",
"condition_onset": "ihd",
"direct_transition": "Specific_IHD_Diagnosis"
},
"Specific_IHD_Diagnosis": {
"type": "ConditionOnset",
"target_encounter": "IHD_Diagnosis_Encounter",
"assign_to_attribute": "ihd",
"codes": [
{
"system": "SNOMED-CT",
"code": "413838009",
"display": "Chronic ischemic heart disease (disorder)"
},
{
"system": "ICD-10-CM",
"code": "I25.1",
"display": "Atherosclerotic heart disease of native coronary artery"
}
],
"direct_transition": "Treatment_Plan"
},
"Treatment_Plan": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.9,
"transition": "Medical_Management"
},
{
"distribution": 0.1,
"transition": "Revascularization_Decision"
}
]
},
"Medical_Management": {
"type": "Simple",
"direct_transition": "Aspirin_Therapy"
},
"Aspirin_Therapy": {
"type": "MedicationOrder",
"assign_to_attribute": "aspirin",
"reason": "ihd",
"codes": [
{
"system": "RxNorm",
"code": "1191",
"display": "Aspirin 81 MG Oral Tablet"
}
],
"direct_transition": "Statin_Therapy"
},
"Statin_Therapy": {
"type": "MedicationOrder",
"assign_to_attribute": "statin",
"reason": "ihd",
"codes": [
{
"system": "RxNorm",
"code": "617311",
"display": "Atorvastatin 20 MG Oral Tablet"
}
],
"direct_transition": "Beta_Blocker_Decision"
},
"Beta_Blocker_Decision": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.7,
"transition": "Beta_Blocker_Therapy"
},
{
"distribution": 0.3,
"transition": "ACE_Inhibitor_Decision"
}
]
},
"Beta_Blocker_Therapy": {
"type": "MedicationOrder",
"assign_to_attribute": "beta_blocker",
"reason": "ihd",
"codes": [
{
"system": "RxNorm",
"code": "866924",
"display": "Metoprolol Tartrate 25 MG Oral Tablet"
}
],
"direct_transition": "ACE_Inhibitor_Decision"
},
"ACE_Inhibitor_Decision": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.6,
"transition": "ACE_Inhibitor_Therapy"
},
{
"distribution": 0.4,
"transition": "Nitrate_Decision"
}
]
},
"ACE_Inhibitor_Therapy": {
"type": "MedicationOrder",
"assign_to_attribute": "ace_inhibitor",
"reason": "ihd",
"codes": [
{
"system": "RxNorm",
"code": "1299896",
"display": "Lisinopril 10 MG Oral Tablet"
}
],
"direct_transition": "Nitrate_Decision"
},
"Nitrate_Decision": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.5,
"transition": "Nitrate_Therapy"
},
{
"distribution": 0.5,
"transition": "IHD_CarePlan"
}
]
}}}

464
src/main/resources/modules/chronic_kidney_disease.json Normal file
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{
"name": "Chronic Kidney Disease",
"remarks": [],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Initial_Kidney_Health"
},
"Initial_Kidney_Health": {
"type": "SetAttribute",
"attribute": "ckd",
"value": 0,
"distributed_transition": [
{
"transition": "Guard_for_Htn_or_DM",
"distribution": 0.998
},
{
"transition": "Nephropathy_Progression",
"distribution": 0.001
},
{
"transition": "Renal Dysplasia",
"distribution": 0.001
}
]
},
"Guard_for_Htn_or_DM": {
"type": "Guard",
"allow": {
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "hypertension",
"operator": "is not nil"
},
{
"condition_type": "Attribute",
"attribute": "diabetes",
"operator": "is not nil"
}
]
},
"direct_transition": "Nephropathy_Progression"
},
"Nephropathy_Progression": {
"type": "Delay",
"exact": {
"quantity": 1,
"unit": "months"
},
"remarks": [
"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4727808/",
"There are 5 defined stages of kidney disease; stage 5 is End-stage where dialysis is necessary",
"Prevalence of Nephropathy is 34.5% - http://link.springer.com/chapter/10.1007%2F978-1-4939-0793-9_2",
"Prevalence of microalbuminuria is ~ 28.8% - https://www.ncbi.nlm.nih.gov/pubmed/11877563",
"Prevalence of End stage renal disease is ~ .78% - ",
"https://www.cdc.gov/diabetes/pdfs/data/2014-report-estimates-of-diabetes-and-its-burden-in-the-united-states.pdf"
],
"complex_transition": [
{
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "veteran",
"operator": "is not nil"
},
{
"condition_type": "Attribute",
"attribute": "ckd",
"operator": "==",
"value": 0
}
]
},
"distributions": [
{
"distribution": 0.99,
"transition": "Nephropathy_Progression"
},
{
"distribution": 0.01,
"transition": "Set_CKD_1 Damage"
}
]
},
{
"condition": {
"condition_type": "Attribute",
"attribute": "ckd",
"operator": "==",
"value": 0
},
"distributions": [
{
"distribution": 0.9982,
"transition": "Nephropathy_Progression"
},
{
"distribution": 0.0018,
"transition": "Set_CKD_1 Damage"
}
]
},
{
"condition": {
"condition_type": "Attribute",
"attribute": "ckd",
"operator": "==",
"value": 1
},
"distributions": [
{
"distribution": 0.98,
"transition": "Set_CKD_1 Damage"
},
{
"distribution": 0.02,
"transition": "Set_CKD_2 Damage"
}
]
},
{
"condition": {
"condition_type": "Attribute",
"attribute": "ckd",
"operator": "==",
"value": 2
},
"distributions": [
{
"distribution": 0.99,
"transition": "Set_CKD_2 Damage"
},
{
"distribution": 0.01,
"transition": "Set_CKD_3 Damage"
}
]
},
{
"condition": {
"condition_type": "Attribute",
"attribute": "ckd",
"operator": "==",
"value": 3
},
"distributions": [
{
"distribution": 0.99,
"transition": "Set_CKD_3 Damage"
},
{
"distribution": 0.01,
"transition": "Set_CKD_4 Damage"
}
]
},
{
"condition": {
"condition_type": "Attribute",
"attribute": "ckd",
"operator": "==",
"value": 4
},
"distributions": [
{
"distribution": 0.99,
"transition": "Set_CKD_4 Damage"
},
{
"distribution": 0.01,
"transition": "Expected_Lifespan_for_ESRD"
}
]
},
{
"condition": {
"condition_type": "Attribute",
"attribute": "ckd",
"operator": "==",
"value": 5
},
"transition": "Expected_Lifespan_for_ESRD"
}
]
},
"Set_Nephropathy": {
"type": "SetAttribute",
"attribute": "nephropathy",
"value": true,
"direct_transition": "CKD1_Symptom_1"
},
"Set_Microalbuminuria": {
"type": "SetAttribute",
"attribute": "microalbuminuria",
"value": true,
"direct_transition": "CKD2_Symptom_1"
},
"Set_Proteinuria": {
"type": "SetAttribute",
"attribute": "proteinuria",
"value": true,
"direct_transition": "CKD3_Symptom_1"
},
"Expected_Lifespan_for_ESRD": {
"type": "Death",
"range": {
"low": 4,
"high": 10,
"unit": "years"
},
"codes": [
{
"system": "SNOMED-CT",
"code": "46177005",
"display": "End-stage renal disease (disorder)"
}
],
"remarks": [
"Life expectency depends on many factors, but for patients > 40 it's generally less than 10 years with dialysis",
"http://link.springer.com/article/10.1007/s00467-016-3383-8 (Table 2"
],
"direct_transition": "Set_CKD_5 Damage"
},
"Loop_back_to_Start": {
"type": "Simple",
"direct_transition": "Nephropathy_Progression"
},
"Set_CKD_1 Damage": {
"type": "SetAttribute",
"attribute": "ckd",
"direct_transition": "Set_Nephropathy",
"value": 1
},
"Set_CKD_2 Damage": {
"type": "SetAttribute",
"attribute": "ckd",
"direct_transition": "Set_Microalbuminuria",
"value": 2
},
"Set_CKD_3 Damage": {
"type": "SetAttribute",
"attribute": "ckd",
"value": 3,
"direct_transition": "Set_Proteinuria"
},
"Set_CKD_4 Damage": {
"type": "SetAttribute",
"attribute": "ckd",
"value": 4,
"direct_transition": "CKD4_Symptom_1"
},
"Set_CKD_5 Damage": {
"type": "SetAttribute",
"attribute": "ckd",
"direct_transition": "CKD5_Symptom_1",
"value": 5
},
"CKD1_Symptom_1": {
"type": "Symptom",
"symptom": "Hunger",
"range": {
"low": 1,
"high": 100
},
"direct_transition": "CKD1_Symptom_2"
},
"CKD2_Symptom_1": {
"type": "Symptom",
"symptom": "Hunger",
"range": {
"low": 20,
"high": 100
},
"direct_transition": "CKD2_Symptom_2"
},
"CKD2_Symptom_2": {
"type": "Symptom",
"symptom": "Fatigue",
"range": {
"low": 20,
"high": 100
},
"direct_transition": "CKD2_Symptom_3"
},
"CKD2_Symptom_3": {
"type": "Symptom",
"symptom": "Frequent Urination",
"range": {
"low": 20,
"high": 100
},
"direct_transition": "CKD2_Symptom_4"
},
"CKD2_Symptom_4": {
"type": "Symptom",
"symptom": "Thirst",
"range": {
"low": 20,
"high": 100
},
"direct_transition": "Loop_back_to_Start"
},
"CKD1_Symptom_2": {
"type": "Symptom",
"symptom": "Fatigue",
"range": {
"low": 1,
"high": 100
},
"direct_transition": "CKD1_Symptom_3"
},
"CKD1_Symptom_3": {
"type": "Symptom",
"symptom": "Frequent Urination",
"range": {
"low": 1,
"high": 100
},
"direct_transition": "CKD1_Symptom_4"
},
"CKD1_Symptom_4": {
"type": "Symptom",
"symptom": "Thirst",
"range": {
"low": 1,
"high": 100
},
"direct_transition": "Loop_back_to_Start"
},
"CKD3_Symptom_1": {
"type": "Symptom",
"symptom": "Hunger",
"range": {
"low": 40,
"high": 100
},
"direct_transition": "CKD3_Symptom_2"
},
"CKD3_Symptom_2": {
"type": "Symptom",
"symptom": "Fatigue",
"range": {
"low": 40,
"high": 100
},
"direct_transition": "CKD3_Symptom_3"
},
"CKD3_Symptom_3": {
"type": "Symptom",
"symptom": "Frequent Urination",
"range": {
"low": 40,
"high": 100
},
"direct_transition": "CKD3_Symptom_4"
},
"CKD3_Symptom_4": {
"type": "Symptom",
"symptom": "Thirst",
"range": {
"low": 40,
"high": 100
},
"direct_transition": "Loop_back_to_Start"
},
"CKD5_Symptom_1": {
"type": "Symptom",
"symptom": "Hunger",
"range": {
"low": 50,
"high": 100
},
"remarks": [
"Without intervention, 20-40 percent of patients with type 2 diabetes/microalbuminuria, will evolve to macroalbuminuria.",
"Shlipak, Michael. 'Clinical Evidence Handbook: Diabetic Nephropathy: Preventing Progression - American Family Physician'. www.aafp.org."
],
"direct_transition": "CKD5_Symptom_2"
},
"CKD5_Symptom_2": {
"type": "Symptom",
"symptom": "Fatigue",
"range": {
"low": 50,
"high": 100
},
"direct_transition": "CKD5_Symptom_3"
},
"CKD5_Symptom_3": {
"type": "Symptom",
"symptom": "Frequent Urination",
"range": {
"low": 50,
"high": 100
},
"direct_transition": "CKD5_Symptom_4"
},
"CKD5_Symptom_4": {
"type": "Symptom",
"symptom": "Thirst",
"range": {
"low": 50,
"high": 100
},
"direct_transition": "Loop_back_to_Start"
},
"CKD4_Symptom_1": {
"type": "Symptom",
"symptom": "Hunger",
"cause": "",
"direct_transition": "CKD4_Symptom_2",
"range": {
"low": 45,
"high": 2
}
},
"CKD4_Symptom_2": {
"type": "Symptom",
"symptom": "Fatigue",
"cause": "",
"direct_transition": "CKD4_Symptom_3",
"range": {
"low": 45,
"high": 100
}
},
"CKD4_Symptom_3": {
"type": "Symptom",
"symptom": "Frequent Urination",
"cause": "",
"direct_transition": "CKD4_Symptom_4",
"range": {
"low": 45,
"high": 100
}
},
"CKD4_Symptom_4": {
"type": "Symptom",
"symptom": "Thirst",
"cause": "",
"direct_transition": "Loop_back_to_Start",
"range": {
"low": 45,
"high": 100
}
},
"Renal Dysplasia": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "204949001",
"display": "Renal dysplasia (disorder)"
}
],
"direct_transition": "Expected_Lifespan_for_ESRD"
}
},
"gmf_version": 1
}

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src/main/resources/modules/colorectal_cancer.json Normal file
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401
src/main/resources/modules/common_cold.json Normal file
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{
"name": "Common Cold",
"remarks": [
"This module simulates the progression of the common cold (acute nasopharyngitis).",
"The common cold is a viral infectious disease of the upper respiratory tract that primarily affects the nose.",
"Symptoms include coughing, sore throat, runny nose, sneezing, headache, and fever.",
"Most people recover within 7-10 days, though some symptoms can last up to three weeks.",
"This module includes risk factors, diagnosis, treatment, and potential complications.",
"ICD-10 code: J00",
"Category: Respiratory"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Age_Guard"
},
"Age_Guard": {
"type": "Guard",
"allow": {
"condition_type": "Age",
"operator": ">=",
"quantity": 0,
"unit": "years"
},
"distributed_transition": [
{
"distribution": 0.95,
"transition": "Potential_Cold_Onset"
},
{
"distribution": 0.05,
"transition": "Terminal"
}
]
},
"Potential_Cold_Onset": {
"type": "Delay",
"remarks": [
"Common colds are more frequent in fall and winter seasons"
],
"range": {
"low": 3,
"high": 12,
"unit": "months"
},
"distributed_transition": [
{
"distribution": 0.7,
"transition": "Cold_Onset"
},
{
"distribution": 0.3,
"transition": "Potential_Cold_Onset"
}
]
},
"Cold_Onset": {
"type": "ConditionOnset",
"target_encounter": "Cold_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "82272006",
"display": "Common cold (disorder)"
}
],
"direct_transition": "Cold_Symptoms"
},
"Cold_Symptoms": {
"type": "Symptom",
"symptom": "Nasal Congestion",
"range": {
"low": 50,
"high": 100
},
"direct_transition": "Sore_Throat_Symptom"
},
"Sore_Throat_Symptom": {
"type": "Symptom",
"symptom": "Sore Throat",
"range": {
"low": 30,
"high": 70
},
"direct_transition": "Cough_Symptom"
},
"Cough_Symptom": {
"type": "Symptom",
"symptom": "Cough",
"range": {
"low": 40,
"high": 90
},
"direct_transition": "Headache_Symptom"
},
"Headache_Symptom": {
"type": "Symptom",
"symptom": "Headache",
"range": {
"low": 20,
"high": 60
},
"direct_transition": "Fever_Symptom"
},
"Fever_Symptom": {
"type": "Symptom",
"symptom": "Fever",
"range": {
"low": 0,
"high": 40
},
"direct_transition": "Fatigue_Symptom"
},
"Fatigue_Symptom": {
"type": "Symptom",
"symptom": "Fatigue",
"range": {
"low": 30,
"high": 70
},
"direct_transition": "Decide_To_Visit_Doctor"
},
"Decide_To_Visit_Doctor": {
"type": "Delay",
"range": {
"low": 1,
"high": 3,
"unit": "days"
},
"distributed_transition": [
{
"distribution": 0.3,
"transition": "Cold_Encounter"
},
{
"distribution": 0.7,
"transition": "Self_Care"
}
]
},
"Self_Care": {
"type": "Delay",
"range": {
"low": 5,
"high": 10,
"unit": "days"
},
"direct_transition": "Cold_Recovery"
},
"Cold_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Cold_Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "185345009",
"display": "Encounter for symptom"
}
],
"direct_transition": "Cold_Diagnosis"
},
"Cold_Diagnosis": {
"type": "Procedure",
"target_encounter": "Cold_Encounter",
"reason": "Cold_Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "162673000",
"display": "General examination of patient (procedure)"
}
],
"direct_transition": "Record_Cold_Diagnosis"
},
"Record_Cold_Diagnosis": {
"type": "DiagnosticReport",
"number_of_observations": 0,
"codes": [
{
"system": "SNOMED-CT",
"code": "162673000",
"display": "General examination of patient (procedure)"
}
],
"direct_transition": "Prescribe_Treatment"
},
"Prescribe_Treatment": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.5,
"transition": "Prescribe_Acetaminophen"
},
{
"distribution": 0.3,
"transition": "Prescribe_Ibuprofen"
},
{
"distribution": 0.2,
"transition": "Prescribe_Decongestant"
}
]
},
"Prescribe_Acetaminophen": {
"type": "MedicationOrder",
"target_encounter": "Cold_Encounter",
"reason": "Cold_Onset",
"codes": [
{
"system": "RxNorm",
"code": "313782",
"display": "Acetaminophen 325 MG Oral Tablet"
}
],
"direct_transition": "Cold_Encounter_End"
},
"Prescribe_Ibuprofen": {
"type": "MedicationOrder",
"target_encounter": "Cold_Encounter",
"reason": "Cold_Onset",
"codes": [
{
"system": "RxNorm",
"code": "197806",
"display": "Ibuprofen 200 MG Oral Tablet"
}
],
"direct_transition": "Cold_Encounter_End"
},
"Prescribe_Decongestant": {
"type": "MedicationOrder",
"target_encounter": "Cold_Encounter",
"reason": "Cold_Onset",
"codes": [
{
"system": "RxNorm",
"code": "1020137",
"display": "Pseudoephedrine Hydrochloride 30 MG Oral Tablet"
}
],
"direct_transition": "Cold_Encounter_End"
},
"Cold_Encounter_End": {
"type": "EncounterEnd",
"direct_transition": "Check_For_Complications"
},
"Check_For_Complications": {
"type": "Delay",
"range": {
"low": 3,
"high": 7,
"unit": "days"
},
"distributed_transition": [
{
"distribution": 0.05,
"transition": "Develop_Sinusitis"
},
{
"distribution": 0.03,
"transition": "Develop_Ear_Infection"
},
{
"distribution": 0.92,
"transition": "Cold_Recovery"
}
]
},
"Develop_Sinusitis": {
"type": "ConditionOnset",
"target_encounter": "Complication_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "36971009",
"display": "Sinusitis (disorder)"
}
],
"direct_transition": "Complication_Encounter"
},
"Develop_Ear_Infection": {
"type": "ConditionOnset",
"target_encounter": "Complication_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "65363002",
"display": "Otitis media (disorder)"
}
],
"direct_transition": "Complication_Encounter"
},
"Complication_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"codes": [
{
"system": "SNOMED-CT",
"code": "185345009",
"display": "Encounter for symptom"
}
],
"direct_transition": "Treat_Complication"
},
"Treat_Complication": {
"type": "MedicationOrder",
"target_encounter": "Complication_Encounter",
"codes": [
{
"system": "RxNorm",
"code": "1658139",
"display": "Amoxicillin 500 MG Oral Tablet"
}
],
"direct_transition": "Complication_Encounter_End"
},
"Complication_Encounter_End": {
"type": "EncounterEnd",
"direct_transition": "Complication_Recovery"
},
"Complication_Recovery": {
"type": "Delay",
"range": {
"low": 7,
"high": 14,
"unit": "days"
},
"direct_transition": "End_Complication"
},
"End_Complication": {
"type": "ConditionEnd",
"direct_transition": "Cold_Recovery"
},
"Cold_Recovery": {
"type": "Delay",
"range": {
"low": 1,
"high": 3,
"unit": "days"
},
"direct_transition": "End_Cold_Symptoms"
},
"End_Cold_Symptoms": {
"type": "Symptom",
"symptom": "Nasal Congestion",
"exact": {
"quantity": 0
},
"direct_transition": "End_Sore_Throat"
},
"End_Sore_Throat": {
"type": "Symptom",
"symptom": "Sore Throat",
"exact": {
"quantity": 0
},
"direct_transition": "End_Cough"
},
"End_Cough": {
"type": "Symptom",
"symptom": "Cough",
"exact": {
"quantity": 0
},
"direct_transition": "End_Headache"
},
"End_Headache": {
"type": "Symptom",
"symptom": "Headache",
"exact": {
"quantity": 0
},
"direct_transition": "End_Fever"
},
"End_Fever": {
"type": "Symptom",
"symptom": "Fever",
"exact": {
"quantity": 0
},
"direct_transition": "End_Fatigue"
},
"End_Fatigue": {
"type": "Symptom",
"symptom": "Fatigue",
"exact": {
"quantity": 0
},
"direct_transition": "End_Cold"
},
"End_Cold": {
"type": "ConditionEnd",
"condition_onset": "Cold_Onset",
"direct_transition": "Potential_Cold_Onset"
},
"Terminal": {
"type": "Terminal"
}
}
}

485
src/main/resources/modules/common_cold.json.fixed.raw Normal file
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{
"name": "Common Cold",
"remarks": [
"This module simulates the onset, progression, and management of the common cold (acute nasopharyngitis).",
"The common cold is a viral infection of the upper respiratory tract that primarily affects the nose and throat.",
"It is one of the most frequent infectious diseases in humans with most adults experiencing 2-3 colds per year.",
"While generally self-limiting, it can occasionally lead to complications, especially in vulnerable populations."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Age_Guard"
},
"Age_Guard": {
"type": "Guard",
"allow": {
"condition_type": "Age",
"operator": ">=",
"quantity": 0,
"unit": "years"
},
"direct_transition": "Cold_Incidence"
},
"Cold_Incidence": {
"type": "Delay",
"range": {
"low": 3,
"high": 24,
"unit": "months"
},
"direct_transition": "Season_Check"
},
"Season_Check": {
"type": "Simple",
"complex_transition": [
{
"condition": {
"condition_type": "Date",
"operator": "in",
"month_range": [10, 11, 12, 1, 2, 3]
},
"distributions": [
{
"distribution": 0.7,
"transition": "Cold_Onset"
},
{
"distribution": 0.3,
"transition": "No_Cold"
}
]
},
{
"distributions": [
{
"distribution": 0.3,
"transition": "Cold_Onset"
},
{
"distribution": 0.7,
"transition": "No_Cold"
}
]
}
]
},
"No_Cold": {
"type": "Simple",
"direct_transition": "Cold_Incidence"
},
"Cold_Onset": {
"type": "ConditionOnset",
"target_encounter": "Cold_Encounter",
"assign_to_attribute": "active_cold",
"codes": [
{
"system": "SNOMED-CT",
"code": "82272006",
"display": "Common cold (disorder)"
}
],
"direct_transition": "Cold_Symptoms"
},
"Cold_Symptoms": {
"type": "Symptom",
"symptom": "Nasal Congestion",
"range": {
"low": 50,
"high": 100
},
"direct_transition": "Sore_Throat_Symptom"
},
"Sore_Throat_Symptom": {
"type": "Symptom",
"symptom": "Sore Throat",
"range": {
"low": 30,
"high": 90
},
"direct_transition": "Cough_Symptom"
},
"Cough_Symptom": {
"type": "Symptom",
"symptom": "Cough",
"range": {
"low": 20,
"high": 80
},
"direct_transition": "Headache_Symptom"
},
"Headache_Symptom": {
"type": "Symptom",
"symptom": "Headache",
"range": {
"low": 10,
"high": 60
},
"direct_transition": "Fatigue_Symptom"
},
"Fatigue_Symptom": {
"type": "Symptom",
"symptom": "Fatigue",
"range": {
"low": 20,
"high": 70
},
"direct_transition": "Fever_Check"
},
"Fever_Check": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.3,
"transition": "Fever_Symptom"
},
{
"distribution": 0.7,
"transition": "Decide_Seek_Care"
}
]
},
"Fever_Symptom": {
"type": "Symptom",
"symptom": "Fever",
"range": {
"low": 20,
"high": 60
},
"direct_transition": "Decide_Seek_Care"
},
"Decide_Seek_Care": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.3,
"transition": "Cold_Encounter"
},
{
"distribution": 0.7,
"transition": "Self_Care"
}
]
},
"Self_Care": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.7,
"transition": "OTC_Medication"
},
{
"distribution": 0.3,
"transition": "No_Treatment"
}
]
},
"OTC_Medication": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.4,
"transition": "Acetaminophen"
},
{
"distribution": 0.3,
"transition": "Ibuprofen"
},
{
"distribution": 0.3,
"transition": "Cold_Medicine"
}
]
},
"Acetaminophen": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": "313782",
"display": "Acetaminophen 325 MG Oral Tablet"
}
],
"direct_transition": "Recovery_Period"
},
"Ibuprofen": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": "197806",
"display": "Ibuprofen 200 MG Oral Tablet"
}
],
"direct_transition": "Recovery_Period"
},
"Cold_Medicine": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": "1049630",
"display": "Acetaminophen 325 MG / Dextromethorphan Hydrobromide 10 MG / Phenylephrine Hydrochloride 5 MG Oral Tablet"
}
],
"direct_transition": "Recovery_Period"
},
"No_Treatment": {
"type": "Simple",
"direct_transition": "Recovery_Period"
},
"Cold_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "active_cold",
"codes": [
{
"system": "SNOMED-CT",
"code": "185345009",
"display": "Encounter for symptom"
}
],
"direct_transition": "Cold_Diagnosis"
},
"Cold_Diagnosis": {
"type": "Procedure",
"target_encounter": "Cold_Encounter",
"reason": "active_cold",
"codes": [
{
"system": "SNOMED-CT",
"code": "162673000",
"display": "General examination of patient (procedure)"
}
],
"direct_transition": "Check_Complications"
},
"Check_Complications": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.05,
"transition": "Sinusitis_Complication"
},
{
"distribution": 0.03,
"transition": "Ear_Infection_Complication"
},
{
"distribution": 0.92,
"transition": "Prescribe_Treatment"
}
]
},
"Sinusitis_Complication": {
"type": "ConditionOnset",
"target_encounter": "Cold_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "36971009",
"display": "Sinusitis (disorder)"
}
],
"direct_transition": "Prescribe_Antibiotics"
},
"Ear_Infection_Complication": {
"type": "ConditionOnset",
"target_encounter": "Cold_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "65363002",
"display": "Otitis media (disorder)"
}
],
"direct_transition": "Prescribe_Antibiotics"
},
"Prescribe_Antibiotics": {
"type": "MedicationOrder",
"target_encounter": "Cold_Encounter",
"codes": [
{
"system": "RxNorm",
"code": "1658139",
"display": "Amoxicillin 500 MG Oral Tablet"
}
],
"direct_transition": "Prescribe_Treatment"
},
"Prescribe_Treatment": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.5,
"transition": "Prescribe_Acetaminophen"
},
{
"distribution": 0.3,
"transition": "Prescribe_Ibuprofen"
},
{
"distribution": 0.2,
"transition": "Prescribe_Cold_Medicine"
}
]
},
"Prescribe_Acetaminophen": {
"type": "MedicationOrder",
"target_encounter": "Cold_Encounter",
"codes": [
{
"system": "RxNorm",
"code": "313782",
"display": "Acetaminophen 325 MG Oral Tablet"
}
],
"direct_transition": "Cold_Encounter_End"
},
"Prescribe_Ibuprofen": {
"type": "MedicationOrder",
"target_encounter": "Cold_Encounter",
"codes": [
{
"system": "RxNorm",
"code": "197806",
"display": "Ibuprofen 200 MG Oral Tablet"
}
],
"direct_transition": "Cold_Encounter_End"
},
"Prescribe_Cold_Medicine": {
"type": "MedicationOrder",
"target_encounter": "Cold_Encounter",
"codes": [
{
"system": "RxNorm",
"code": "1049630",
"display": "Acetaminophen 325 MG / Dextromethorphan Hydrobromide 10 MG / Phenylephrine Hydrochloride 5 MG Oral Tablet"
}
],
"direct_transition": "Cold_Encounter_End"
},
"Cold_Encounter_End": {
"type": "EncounterEnd",
"direct_transition": "Recovery_Period"
},
"Recovery_Period": {
"type": "Delay",
"range": {
"low": 5,
"high": 14,
"unit": "days"
},
"direct_transition": "Resolve_Cold"
},
"Resolve_Cold": {
"type": "ConditionEnd",
"referenced_by_attribute": "active_cold",
"direct_transition": "Symptom_Resolve"
},
"Symptom_Resolve": {
"type": "Symptom",
"symptom": "Nasal Congestion",
"exact": {
"quantity": 0
},
"direct_transition": "Sore_Throat_Resolve"
},
"Sore_Throat_Resolve": {
"type": "Symptom",
"symptom": "Sore Throat",
"exact": {
"quantity": 0
},
"direct_transition": "Cough_Resolve"
},
"Cough_Resolve": {
"type": "Symptom",
"symptom": "Cough",
"exact": {
"quantity": 0
},
"direct_transition": "Headache_Resolve"
},
"Headache_Resolve": {
"type": "Symptom",
"symptom": "Headache",
"exact": {
"quantity": 0
},
"direct_transition": "Fatigue_Resolve"
},
"Fatigue_Resolve": {
"type": "Symptom",
"symptom": "Fatigue",
"exact": {
"quantity": 0
},
"direct_transition": "Fever_Resolve"
},
"Fever_Resolve": {
"type": "Symptom",
"symptom": "Fever",
"exact": {
"quantity": 0
},
"direct_transition": "End_Medications"
},
"End_Medications": {
"type": "Simple",
"conditional_transition": [
{
"condition": {
"condition_type": "Active Medication",
"codes": [
{
"system": "RxNorm",
"code": "313782",
"display": "Acetaminophen 325 MG Oral Tablet"
}
]
},
"transition": "End_Acetaminophen"
},
{
"condition": {
"condition_type": "Active Medication",
"codes": [
{
"system": "RxNorm",
"code": "197806",
"display": "Ibuprofen 200 MG Oral Tablet"
}
]
},
"transition": "End_Ibuprofen"
},
{
"condition": {
"condition_type": "Active Medication",
"codes": [
{
"system": "RxNorm",
"code": "1049630",
"display": "Acetaminophen 325 MG / Dextromethorphan Hydrobromide 10 MG / Phenylephrine Hydrochloride 5 MG Oral Tablet"
}
]
},
"transition": "End_Cold_Medicine"
},
{
"condition": {
"condition_type": "Active Medication",
"codes": [
{
"system": "RxNorm",
"code": "1658139",
"display": "Amoxicillin 500 MG Oral Tablet"
}
]
},
"transition": "End_Antibiotics"
},
{
"transition": "

399
src/main/resources/modules/common_cold.json.raw Normal file
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@@ -0,0 +1,399 @@
{
"name": "Common Cold",
"remarks": [
"This module simulates the progression of the common cold (acute nasopharyngitis).",
"The common cold is a viral infectious disease of the upper respiratory tract that primarily affects the nose.",
"Symptoms include coughing, sore throat, runny nose, sneezing, headache, and fever.",
"Most people recover within 7-10 days, though some symptoms can last up to three weeks.",
"This module includes risk factors, diagnosis, treatment, and potential complications."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Age_Guard"
},
"Age_Guard": {
"type": "Guard",
"allow": {
"condition_type": "Age",
"operator": ">=",
"quantity": 0,
"unit": "years"
},
"distributed_transition": [
{
"distribution": 0.95,
"transition": "Potential_Cold_Onset"
},
{
"distribution": 0.05,
"transition": "Terminal"
}
]
},
"Potential_Cold_Onset": {
"type": "Delay",
"remarks": [
"Common colds are more frequent in fall and winter seasons"
],
"range": {
"low": 3,
"high": 12,
"unit": "months"
},
"distributed_transition": [
{
"distribution": 0.7,
"transition": "Cold_Onset"
},
{
"distribution": 0.3,
"transition": "Potential_Cold_Onset"
}
]
},
"Cold_Onset": {
"type": "ConditionOnset",
"target_encounter": "Cold_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "82272006",
"display": "Common cold (disorder)"
}
],
"direct_transition": "Cold_Symptoms"
},
"Cold_Symptoms": {
"type": "Symptom",
"symptom": "Nasal Congestion",
"range": {
"low": 50,
"high": 100
},
"direct_transition": "Sore_Throat_Symptom"
},
"Sore_Throat_Symptom": {
"type": "Symptom",
"symptom": "Sore Throat",
"range": {
"low": 30,
"high": 70
},
"direct_transition": "Cough_Symptom"
},
"Cough_Symptom": {
"type": "Symptom",
"symptom": "Cough",
"range": {
"low": 40,
"high": 90
},
"direct_transition": "Headache_Symptom"
},
"Headache_Symptom": {
"type": "Symptom",
"symptom": "Headache",
"range": {
"low": 20,
"high": 60
},
"direct_transition": "Fever_Symptom"
},
"Fever_Symptom": {
"type": "Symptom",
"symptom": "Fever",
"range": {
"low": 0,
"high": 40
},
"direct_transition": "Fatigue_Symptom"
},
"Fatigue_Symptom": {
"type": "Symptom",
"symptom": "Fatigue",
"range": {
"low": 30,
"high": 70
},
"direct_transition": "Decide_To_Visit_Doctor"
},
"Decide_To_Visit_Doctor": {
"type": "Delay",
"range": {
"low": 1,
"high": 3,
"unit": "days"
},
"distributed_transition": [
{
"distribution": 0.3,
"transition": "Cold_Encounter"
},
{
"distribution": 0.7,
"transition": "Self_Care"
}
]
},
"Self_Care": {
"type": "Delay",
"range": {
"low": 5,
"high": 10,
"unit": "days"
},
"direct_transition": "Cold_Recovery"
},
"Cold_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Cold_Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "185345009",
"display": "Encounter for symptom"
}
],
"direct_transition": "Cold_Diagnosis"
},
"Cold_Diagnosis": {
"type": "Procedure",
"target_encounter": "Cold_Encounter",
"reason": "Cold_Onset",
"codes": [
{
"system": "SNOMED-CT",
"code": "162673000",
"display": "General examination of patient (procedure)"
}
],
"direct_transition": "Record_Cold_Diagnosis"
},
"Record_Cold_Diagnosis": {
"type": "DiagnosticReport",
"number_of_observations": 0,
"codes": [
{
"system": "SNOMED-CT",
"code": "162673000",
"display": "General examination of patient (procedure)"
}
],
"direct_transition": "Prescribe_Treatment"
},
"Prescribe_Treatment": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.5,
"transition": "Prescribe_Acetaminophen"
},
{
"distribution": 0.3,
"transition": "Prescribe_Ibuprofen"
},
{
"distribution": 0.2,
"transition": "Prescribe_Decongestant"
}
]
},
"Prescribe_Acetaminophen": {
"type": "MedicationOrder",
"target_encounter": "Cold_Encounter",
"reason": "Cold_Onset",
"codes": [
{
"system": "RxNorm",
"code": "313782",
"display": "Acetaminophen 325 MG Oral Tablet"
}
],
"direct_transition": "Cold_Encounter_End"
},
"Prescribe_Ibuprofen": {
"type": "MedicationOrder",
"target_encounter": "Cold_Encounter",
"reason": "Cold_Onset",
"codes": [
{
"system": "RxNorm",
"code": "197806",
"display": "Ibuprofen 200 MG Oral Tablet"
}
],
"direct_transition": "Cold_Encounter_End"
},
"Prescribe_Decongestant": {
"type": "MedicationOrder",
"target_encounter": "Cold_Encounter",
"reason": "Cold_Onset",
"codes": [
{
"system": "RxNorm",
"code": "1020137",
"display": "Pseudoephedrine Hydrochloride 30 MG Oral Tablet"
}
],
"direct_transition": "Cold_Encounter_End"
},
"Cold_Encounter_End": {
"type": "EncounterEnd",
"direct_transition": "Check_For_Complications"
},
"Check_For_Complications": {
"type": "Delay",
"range": {
"low": 3,
"high": 7,
"unit": "days"
},
"distributed_transition": [
{
"distribution": 0.05,
"transition": "Develop_Sinusitis"
},
{
"distribution": 0.03,
"transition": "Develop_Ear_Infection"
},
{
"distribution": 0.92,
"transition": "Cold_Recovery"
}
]
},
"Develop_Sinusitis": {
"type": "ConditionOnset",
"target_encounter": "Complication_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "36971009",
"display": "Sinusitis (disorder)"
}
],
"direct_transition": "Complication_Encounter"
},
"Develop_Ear_Infection": {
"type": "ConditionOnset",
"target_encounter": "Complication_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "65363002",
"display": "Otitis media (disorder)"
}
],
"direct_transition": "Complication_Encounter"
},
"Complication_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"codes": [
{
"system": "SNOMED-CT",
"code": "185345009",
"display": "Encounter for symptom"
}
],
"direct_transition": "Treat_Complication"
},
"Treat_Complication": {
"type": "MedicationOrder",
"target_encounter": "Complication_Encounter",
"codes": [
{
"system": "RxNorm",
"code": "1658139",
"display": "Amoxicillin 500 MG Oral Tablet"
}
],
"direct_transition": "Complication_Encounter_End"
},
"Complication_Encounter_End": {
"type": "EncounterEnd",
"direct_transition": "Complication_Recovery"
},
"Complication_Recovery": {
"type": "Delay",
"range": {
"low": 7,
"high": 14,
"unit": "days"
},
"direct_transition": "End_Complication"
},
"End_Complication": {
"type": "ConditionEnd",
"direct_transition": "Cold_Recovery"
},
"Cold_Recovery": {
"type": "Delay",
"range": {
"low": 1,
"high": 3,
"unit": "days"
},
"direct_transition": "End_Cold_Symptoms"
},
"End_Cold_Symptoms": {
"type": "Symptom",
"symptom": "Nasal Congestion",
"exact": {
"quantity": 0
},
"direct_transition": "End_Sore_Throat"
},
"End_Sore_Throat": {
"type": "Symptom",
"symptom": "Sore Throat",
"exact": {
"quantity": 0
},
"direct_transition": "End_Cough"
},
"End_Cough": {
"type": "Symptom",
"symptom": "Cough",
"exact": {
"quantity": 0
},
"direct_transition": "End_Headache"
},
"End_Headache": {
"type": "Symptom",
"symptom": "Headache",
"exact": {
"quantity": 0
},
"direct_transition": "End_Fever"
},
"End_Fever": {
"type": "Symptom",
"symptom": "Fever",
"exact": {
"quantity": 0
},
"direct_transition": "End_Fatigue"
},
"End_Fatigue": {
"type": "Symptom",
"symptom": "Fatigue",
"exact": {
"quantity": 0
},
"direct_transition": "End_Cold"
},
"End_Cold": {
"type": "ConditionEnd",
"condition_onset": "Cold_Onset",
"direct_transition": "Potential_Cold_Onset"
},
"Terminal": {
"type": "Terminal"
}
}
}

492
src/main/resources/modules/complications_and_ill_defined_descriptions_of_heart_disease.json Normal file
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{
"name": "Complications and ill-defined descriptions of heart disease",
"remarks": [
"This module models complications and ill-defined descriptions of heart disease (ICD-10 code I51).",
"This category includes various cardiac complications and conditions that don't fit into more specific categories.",
"Common conditions include cardiac tamponade, myocardial fibrosis, and other ill-defined heart disorders.",
"Information on prevalence, progression, and treatment obtained from:",
"https://www.ahajournals.org/doi/10.1161/CIRCULATIONAHA.121.056856",
"https://www.ncbi.nlm.nih.gov/books/NBK559228/",
"https://www.heart.org/en/health-topics/heart-failure/what-is-heart-failure"
],
"states": {
"Initial": {
"type": "Initial",
"remarks": [
"======================================================================",
" INCIDENCE ",
"======================================================================",
"Ill-defined heart conditions affect approximately 1-3% of the general population.",
"Risk increases with age, particularly after 60 years old.",
"Often occurs as a complication of other cardiac conditions or systemic diseases."
],
"direct_transition": "Age_Guard"
},
"Age_Guard": {
"type": "Guard",
"allow": {
"condition_type": "Age",
"operator": ">=",
"quantity": 40,
"unit": "years"
},
"direct_transition": "Risk_Assessment"
},
"Risk_Assessment": {
"type": "Simple",
"complex_transition": [
{
"condition": {
"condition_type": "Age",
"operator": ">=",
"quantity": 70,
"unit": "years"
},
"distributions": [
{
"distribution": 0.08,
"transition": "Cardiac_Complication_Onset"
},
{
"distribution": 0.92,
"transition": "Terminal"
}
]
},
{
"condition": {
"condition_type": "Age",
"operator": ">=",
"quantity": 60,
"unit": "years"
},
"distributions": [
{
"distribution": 0.05,
"transition": "Cardiac_Complication_Onset"
},
{
"distribution": 0.95,
"transition": "Terminal"
}
]
},
{
"condition": {
"condition_type": "Age",
"operator": ">=",
"quantity": 50,
"unit": "years"
},
"distributions": [
{
"distribution": 0.03,
"transition": "Cardiac_Complication_Onset"
},
{
"distribution": 0.97,
"transition": "Terminal"
}
]
},
{
"distributions": [
{
"distribution": 0.01,
"transition": "Cardiac_Complication_Onset"
},
{
"distribution": 0.99,
"transition": "Terminal"
}
]
}
]
},
"Cardiac_Complication_Onset": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.3,
"transition": "Myocardial_Fibrosis_Onset"
},
{
"distribution": 0.2,
"transition": "Cardiac_Tamponade_Onset"
},
{
"distribution": 0.5,
"transition": "Other_Heart_Disorder_Onset"
}
]
},
"Myocardial_Fibrosis_Onset": {
"type": "ConditionOnset",
"target_encounter": "Diagnosis_Encounter",
"assign_to_attribute": "cardiac_complication",
"codes": [
{
"system": "SNOMED-CT",
"code": "233917008",
"display": "Myocardial fibrosis (disorder)"
},
{
"system": "ICD-10-CM",
"code": "I51.5",
"display": "Myocardial degeneration"
}
],
"direct_transition": "Set_Complication_Type_Fibrosis"
},
"Set_Complication_Type_Fibrosis": {
"type": "SetAttribute",
"attribute": "complication_type",
"value": "fibrosis",
"direct_transition": "Diagnosis_Encounter"
},
"Cardiac_Tamponade_Onset": {
"type": "ConditionOnset",
"target_encounter": "Diagnosis_Encounter",
"assign_to_attribute": "cardiac_complication",
"codes": [
{
"system": "SNOMED-CT",
"code": "42251007",
"display": "Cardiac tamponade (disorder)"
},
{
"system": "ICD-10-CM",
"code": "I31.9",
"display": "Disease of pericardium, unspecified"
}
],
"direct_transition": "Set_Complication_Type_Tamponade"
},
"Set_Complication_Type_Tamponade": {
"type": "SetAttribute",
"attribute": "complication_type",
"value": "tamponade",
"direct_transition": "Diagnosis_Encounter"
},
"Other_Heart_Disorder_Onset": {
"type": "ConditionOnset",
"target_encounter": "Diagnosis_Encounter",
"assign_to_attribute": "cardiac_complication",
"codes": [
{
"system": "SNOMED-CT",
"code": "84114007",
"display": "Heart disorder (disorder)"
},
{
"system": "ICD-10-CM",
"code": "I51.9",
"display": "Heart disease, unspecified"
}
],
"direct_transition": "Set_Complication_Type_Other"
},
"Set_Complication_Type_Other": {
"type": "SetAttribute",
"attribute": "complication_type",
"value": "other",
"direct_transition": "Diagnosis_Encounter"
},
"Diagnosis_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "cardiac_complication",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem (procedure)"
}
],
"direct_transition": "Symptom_Selection"
},
"Symptom_Selection": {
"type": "Simple",
"conditional_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "complication_type",
"operator": "==",
"value": "fibrosis"
},
"transition": "Fibrosis_Symptoms"
},
{
"condition": {
"condition_type": "Attribute",
"attribute": "complication_type",
"operator": "==",
"value": "tamponade"
},
"transition": "Tamponade_Symptoms"
},
{
"transition": "Other_Cardiac_Symptoms"
}
]
},
"Fibrosis_Symptoms": {
"type": "Symptom",
"symptom": "Dyspnea",
"cause": "cardiac_complication",
"range": {
"low": 30,
"high": 70
},
"direct_transition": "Fibrosis_Fatigue"
},
"Fibrosis_Fatigue": {
"type": "Symptom",
"symptom": "Fatigue",
"cause": "cardiac_complication",
"range": {
"low": 40,
"high": 80
},
"direct_transition": "Fibrosis_Palpitations"
},
"Fibrosis_Palpitations": {
"type": "Symptom",
"symptom": "Palpitations",
"cause": "cardiac_complication",
"range": {
"low": 20,
"high": 60
},
"direct_transition": "Vital_Signs"
},
"Tamponade_Symptoms": {
"type": "Symptom",
"symptom": "Chest Pain",
"cause": "cardiac_complication",
"range": {
"low": 60,
"high": 90
},
"direct_transition": "Tamponade_Dyspnea"
},
"Tamponade_Dyspnea": {
"type": "Symptom",
"symptom": "Dyspnea",
"cause": "cardiac_complication",
"range": {
"low": 70,
"high": 95
},
"direct_transition": "Tamponade_Tachycardia"
},
"Tamponade_Tachycardia": {
"type": "Symptom",
"symptom": "Tachycardia",
"cause": "cardiac_complication",
"range": {
"low": 50,
"high": 90
},
"direct_transition": "Vital_Signs"
},
"Other_Cardiac_Symptoms": {
"type": "Symptom",
"symptom": "Fatigue",
"cause": "cardiac_complication",
"range": {
"low": 30,
"high": 70
},
"direct_transition": "Other_Dyspnea"
},
"Other_Dyspnea": {
"type": "Symptom",
"symptom": "Dyspnea",
"cause": "cardiac_complication",
"range": {
"low": 20,
"high": 60
},
"direct_transition": "Other_Edema"
},
"Other_Edema": {
"type": "Symptom",
"symptom": "Peripheral Edema",
"cause": "cardiac_complication",
"range": {
"low": 10,
"high": 50
},
"direct_transition": "Vital_Signs"
},
"Vital_Signs": {
"type": "Simple",
"conditional_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "complication_type",
"operator": "==",
"value": "tamponade"
},
"transition": "Tamponade_BP"
},
{
"transition": "Normal_BP"
}
]
},
"Tamponade_BP": {
"type": "Observation",
"category": "vital-signs",
"unit": "mm[Hg]",
"codes": [
{
"system": "LOINC",
"code": "8480-6",
"display": "Systolic blood pressure"
}
],
"range": {
"low": 70,
"high": 100
},
"direct_transition": "Tamponade_HR"
},
"Tamponade_HR": {
"type": "Observation",
"category": "vital-signs",
"unit": "/min",
"codes": [
{
"system": "LOINC",
"code": "8867-4",
"display": "Heart rate"
}
],
"range": {
"low": 100,
"high": 140
},
"direct_transition": "Diagnostic_Tests"
},
"Normal_BP": {
"type": "Observation",
"category": "vital-signs",
"unit": "mm[Hg]",
"codes": [
{
"system": "LOINC",
"code": "8480-6",
"display": "Systolic blood pressure"
}
],
"range": {
"low": 110,
"high": 140
},
"direct_transition": "Normal_HR"
},
"Normal_HR": {
"type": "Observation",
"category": "vital-signs",
"unit": "/min",
"codes": [
{
"system": "LOINC",
"code": "8867-4",
"display": "Heart rate"
}
],
"range": {
"low": 70,
"high": 100
},
"direct_transition": "Diagnostic_Tests"
},
"Diagnostic_Tests": {
"type": "Simple",
"direct_transition": "ECG"
},
"ECG": {
"type": "Procedure",
"reason": "cardiac_complication",
"codes": [
{
"system": "SNOMED-CT",
"code": "29303009",
"display": "Electrocardiogram (procedure)"
}
],
"duration": {
"low": 10,
"high": 15,
"unit": "minutes"
},
"direct_transition": "Echocardiogram"
},
"Echocardiogram": {
"type": "Procedure",
"reason": "cardiac_complication",
"codes": [
{
"system": "SNOMED-CT",
"code": "40701008",
"display": "Echocardiography (procedure)"
}
],
"duration": {
"low": 20,
"high": 30,
"unit": "minutes"
},
"direct_transition": "Cardiac_Biomarkers"
},
"Cardiac_Biomarkers": {
"type": "Procedure",
"reason": "cardiac_complication",
"codes": [
{
"system": "SNOMED-CT",
"code": "252275004",
"display": "Cardiac enzyme measurement (procedure)"
}
],
"direct_transition": "Troponin_Test"
},
"Troponin_Test": {
"type": "Observation",
"category": "laboratory",
"unit": "ng/mL",
"codes": [
{
"system": "LOINC",
"code": "6598-7",
"display": "Troponin T [Mass/volume] in Serum or Plasma"
}
],
"range": {
"low": 0.01,
"high": 0.1
},
"direct_transition": "BNP_Test"
},
"BNP_Test": {
"type": "Observation",
"category": "laboratory",
"unit": "pg/mL",
"codes": [
{
"system": "LOINC",
"code": "33762-6",
"display": "Natriuretic peptide B [Mass/volume] in Serum or Plasma"
}
],
"range": {
"low": 100,
"high": 500
},
"direct_transition": "Treatment_Decision"
}}}

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src/main/resources/modules/congestive_heart_failure.json Normal file
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src/main/resources/modules/contraceptive_maintenance.json Normal file
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{
"name": "Contraceptive Maintenance",
"remarks": [
"Three types of contraceptives require periodic renewal to be effective: ",
"1. 'iud' - requires replacement every 5-10 years ",
"2. 'implant' - requires replacement every 3-4 years ",
"3. 'injectable' - requires another injection every 3 months ",
"Each of these contraceptives is initially implanted/injected by the prescribing ",
"submodule. Subsequent renewal or removal of these contraceptives is handled ",
"by this maintenance module.",
"Contraceptive maintenance automatically cancelled if either: ",
"1. 'pregnant' == true ",
"2. 'contraceptive_type' == nil "
],
"states": {
"Initial": {
"type": "Initial",
"conditional_transition": [
{
"condition": {
"condition_type": "Gender",
"gender": "M"
},
"transition": "Terminal"
},
{
"transition": "Contraception_Care_Reason"
}
]
},
"Clear_Contraceptive": {
"type": "CallSubmodule",
"submodule": "contraceptives/clear_contraceptive",
"direct_transition": "Contraceptive_Type_Guard"
},
"Contraceptive_Type_Guard": {
"type": "Guard",
"allow": {
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "contraceptive_type",
"operator": "==",
"value": "iud"
},
{
"condition_type": "Attribute",
"attribute": "contraceptive_type",
"operator": "==",
"value": "implant"
},
{
"condition_type": "Attribute",
"attribute": "contraceptive_type",
"operator": "==",
"value": "injectable"
}
]
},
"conditional_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "contraceptive_type",
"operator": "==",
"value": "iud"
},
"transition": "IUD_Maintenance"
},
{
"condition": {
"condition_type": "Attribute",
"attribute": "contraceptive_type",
"operator": "==",
"value": "implant"
},
"transition": "Implant_Maintenance"
},
{
"condition": {
"condition_type": "Attribute",
"attribute": "contraceptive_type",
"operator": "==",
"value": "injectable"
},
"transition": "Injectable_Maintenance"
}
]
},
"IUD_Maintenance": {
"type": "Guard",
"remarks": [
"======================================================================",
" IUD CONTRACEPTIVE MAINTENANCE ",
"======================================================================",
"Allow module progression if the IUD's lifetime is up (~4 years) ",
"or if the patient becomes pregnant."
],
"allow": {
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "pregnant",
"operator": "==",
"value": true
},
{
"condition_type": "Attribute",
"attribute": "contraceptive_type",
"operator": "is nil"
},
{
"condition_type": "And",
"conditions": [
{
"condition_type": "Not",
"condition": {
"condition_type": "PriorState",
"name": "Contraceptive_Type_Guard",
"within": {
"quantity": 5,
"unit": "years"
}
}
},
{
"condition_type": "Not",
"condition": {
"condition_type": "PriorState",
"name": "IUD_Replacement",
"within": {
"quantity": 5,
"unit": "years"
}
}
}
]
}
]
},
"conditional_transition": [
{
"condition": {
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "pregnant",
"operator": "==",
"value": true
},
{
"condition_type": "Attribute",
"attribute": "contraceptive_type",
"operator": "is nil"
}
]
},
"transition": "Remove_IUD_Encounter"
},
{
"transition": "Renew_IUD_Encounter"
}
]
},
"Renew_IUD_Encounter": {
"type": "Encounter",
"encounter_class": "outpatient",
"codes": [
{
"system": "SNOMED-CT",
"code": "308335008",
"display": "Patient encounter procedure (procedure)"
}
],
"direct_transition": "IUD_Replacement",
"reason": "contraception_care_reason"
},
"IUD_Replacement": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "46706006",
"display": "Replacement of contraceptive intrauterine device (procedure)"
}
],
"duration": {
"low": 40,
"high": 70,
"unit": "minutes"
},
"direct_transition": "End_IUD_Replacement_Encounter"
},
"End_IUD_Replacement_Encounter": {
"type": "EncounterEnd",
"direct_transition": "IUD_Maintenance"
},
"Remove_IUD_Encounter": {
"type": "Encounter",
"encounter_class": "outpatient",
"codes": [
{
"system": "SNOMED-CT",
"code": "308335008",
"display": "Patient encounter procedure (procedure)"
}
],
"direct_transition": "IUD_Removal",
"reason": "contraception_care_reason"
},
"IUD_Removal": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "1263416007",
"display": "Removal of intrauterine contraceptive device (procedure)"
}
],
"duration": {
"low": 40,
"high": 70,
"unit": "minutes"
},
"direct_transition": "End_IUD_Removal_Encounter"
},
"End_IUD_Removal_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Clear_Contraceptive"
},
"Implant_Maintenance": {
"type": "Guard",
"remarks": [
"======================================================================",
" IMPLANT CONTRACEPTIVE MAINTENANCE ",
"======================================================================",
"Every 3-4 years the implant must be removed or replaced."
],
"allow": {
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "pregnant",
"operator": "==",
"value": true
},
{
"condition_type": "Attribute",
"attribute": "contraceptive_type",
"operator": "is nil"
},
{
"condition_type": "And",
"conditions": [
{
"condition_type": "Not",
"condition": {
"condition_type": "PriorState",
"name": "Contraceptive_Type_Guard",
"within": {
"quantity": 4,
"unit": "years"
}
}
},
{
"condition_type": "Not",
"condition": {
"condition_type": "PriorState",
"name": "Replace_Contraceptive_Implant",
"within": {
"quantity": 4,
"unit": "years"
}
}
}
]
}
]
},
"conditional_transition": [
{
"condition": {
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "pregnant",
"operator": "==",
"value": true
},
{
"condition_type": "Attribute",
"attribute": "contraceptive_type",
"operator": "is nil"
}
]
},
"transition": "Remove_Implant_Encounter"
},
{
"transition": "Renew_Implant_Encounter"
}
]
},
"Renew_Implant_Encounter": {
"type": "Encounter",
"encounter_class": "outpatient",
"codes": [
{
"system": "SNOMED-CT",
"code": "308335008",
"display": "Patient encounter procedure (procedure)"
}
],
"direct_transition": "Remove_Implant_Before_Replacement",
"reason": "contraception_care_reason"
},
"End_Renew_Implant_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Implant_Maintenance"
},
"Remove_Implant_Encounter": {
"type": "Encounter",
"encounter_class": "outpatient",
"codes": [
{
"system": "SNOMED-CT",
"code": "308335008",
"display": "Patient encounter procedure (procedure)"
}
],
"direct_transition": "Remove_Implant",
"reason": "contraception_care_reason"
},
"Remove_Implant": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "301807007",
"display": "Removal of subcutaneous contraceptive (procedure)"
}
],
"duration": {
"low": 20,
"high": 40,
"unit": "minutes"
},
"direct_transition": "End_Remove_Implant_Encounter"
},
"End_Remove_Implant_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Clear_Contraceptive"
},
"Injectable_Maintenance": {
"type": "Guard",
"remarks": [
"======================================================================",
" INJECTABLE CONTRACEPTIVE MAINTENANCE ",
"======================================================================",
"Every 3 months an additional dose is given. If the age limit for the current ",
"age bracket is reached, no more additional doses are given."
],
"allow": {
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "pregnant",
"operator": "==",
"value": true
},
{
"condition_type": "Attribute",
"attribute": "contraceptive_type",
"operator": "is nil"
},
{
"condition_type": "And",
"conditions": [
{
"condition_type": "Not",
"condition": {
"condition_type": "PriorState",
"name": "Contraceptive_Type_Guard",
"within": {
"quantity": 3,
"unit": "months"
}
}
},
{
"condition_type": "Not",
"condition": {
"condition_type": "PriorState",
"name": "Regular_Injection_Encounter",
"within": {
"quantity": 3,
"unit": "months"
}
}
}
]
}
]
},
"conditional_transition": [
{
"condition": {
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "pregnant",
"operator": "==",
"value": true
},
{
"condition_type": "Attribute",
"attribute": "contraceptive_type",
"operator": "is nil"
}
]
},
"transition": "Clear_Contraceptive"
},
{
"transition": "Regular_Injection_Encounter"
}
]
},
"Regular_Injection_Encounter": {
"type": "Encounter",
"encounter_class": "outpatient",
"codes": [
{
"system": "SNOMED-CT",
"code": "308335008",
"display": "Patient encounter procedure (procedure)"
}
],
"direct_transition": "Regular_Contraceptive_Injection",
"reason": "contraception_care_reason"
},
"Regular_Contraceptive_Injection": {
"type": "Procedure",
"duration": {
"low": 10,
"high": 20,
"unit": "minutes"
},
"codes": [
{
"system": "SNOMED-CT",
"code": "76601001",
"display": "Intramuscular injection (procedure)"
}
],
"direct_transition": "End_Regular_Injection_Encounter"
},
"End_Regular_Injection_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Injectable_Maintenance"
},
"Terminal": {
"type": "Terminal"
},
"Replace_Contraceptive_Implant": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "169553002",
"display": "Insertion of subcutaneous contraceptive (procedure)"
}
],
"duration": {
"low": 20,
"high": 40,
"unit": "minutes"
},
"direct_transition": "End_Renew_Implant_Encounter"
},
"Remove_Implant_Before_Replacement": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "301807007",
"display": "Removal of subcutaneous contraceptive (procedure)"
}
],
"duration": {
"low": 20,
"high": 40,
"unit": "minutes"
},
"direct_transition": "Replace_Contraceptive_Implant"
},
"Contraception_Care_Reason": {
"type": "SetAttribute",
"attribute": "contraception_care_reason",
"direct_transition": "Contraceptive_Type_Guard",
"value_code": {
"system": "SNOMED-CT",
"code": "408969000",
"display": "Contraception care management (procedure)"
}
}
},
"gmf_version": 1
}

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{
"name": "Contraceptives",
"remarks": [
"This module prescribes many types of contraceptives to all potentially reproductive ",
"age groups. The availablility of different medicines and methods is historically ",
"accurate by year, based on these articles: ",
"http://www.ourbodiesourselves.org/health-info/a-brief-history-of-birth-control/",
"http://www.pbs.org/wnet/need-to-know/health/a-brief-history-of-the-birth-control-pill/480/",
"Hormonal contraceptives cause a slightly elevated risk of blood clots, heart attack, and ",
"stroke (1.6x) in females, especially in heavy smokers over the age of 35. No change was ",
"made to the existing cardiovascular disease module.",
"While male sterilization is used as a contraceptive method (8%), it's not modeled here. ",
"Instead, the 8% is folded into the female sterilization incidence. However, 6% of males ",
"age 30 - 55 are selected for sterilization to create accurate male patient records.",
"The use of a diaphragm and emergency contraceptives (e.g. Plan B) is not modeled here. ",
"Diaphragms are not modeled due to a lack of usage data and popularity, and emergency ",
"contraceptives are out-of-scope."
],
"states": {
"Initial": {
"type": "Initial",
"conditional_transition": [
{
"condition": {
"condition_type": "Gender",
"gender": "F"
},
"transition": "Delay_Until_Reproductive_Age"
},
{
"condition": {
"condition_type": "Gender",
"gender": "M"
},
"transition": "Select_For_Male_Sterilization"
}
]
},
"Delay_Until_Reproductive_Age": {
"type": "Delay",
"exact": {
"quantity": 14,
"unit": "years"
},
"direct_transition": "Female_Contraceptive_Use"
},
"Select_For_Male_Sterilization": {
"type": "Simple",
"remarks": [
"======================================================================",
" MALE STERLIZATION ",
"======================================================================",
"Male sterilization accounts for 8% of all contraceptive use, predominantly ",
"in older males. However, this does not mean 8% of all males are sterilized. ",
"According to the NIH, 6% of males have had a vasectomy. Source: ",
"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784091/",
"The percentage of males seeking vasectomies has remained approximately the ",
"same for the last 40 years. Vasectomies were first used as a form of ",
"contraceptive starting around WWII."
],
"distributed_transition": [
{
"distribution": 0.06,
"transition": "Delay_For_Male_Sterilization"
},
{
"distribution": 0.94,
"transition": "Terminal"
}
]
},
"Delay_For_Male_Sterilization": {
"type": "Delay",
"range": {
"low": 30,
"high": 55,
"unit": "years"
},
"conditional_transition": [
{
"condition": {
"condition_type": "Date",
"operator": ">",
"year": 1945
},
"transition": "Male_Sterilization_Procedure"
},
{
"transition": "Terminal"
}
]
},
"Male_Sterilization_Procedure": {
"type": "CallSubmodule",
"submodule": "contraceptives/male_sterilization",
"direct_transition": "Terminal"
},
"Female_Contraceptive_Use": {
"type": "SetAttribute",
"attribute": "contraception_care_reason",
"conditional_transition": [
{
"condition": {
"condition_type": "Age",
"operator": "<",
"quantity": 25,
"unit": "years"
},
"transition": "Young_Contraceptive_Use"
},
{
"condition": {
"condition_type": "Age",
"operator": "<",
"quantity": 35,
"unit": "years"
},
"transition": "Mid_Contraceptive_Use"
},
{
"condition": {
"condition_type": "Age",
"operator": "<",
"quantity": 50,
"unit": "years"
},
"transition": "Mature_Contraceptive_Use"
},
{
"transition": "Terminal"
}
],
"remarks": [
"======================================================================",
" FEMALE CONTRACEPTIVE USE ",
"======================================================================",
"Female use of contraceptives is recomputed 3 times in a patient's life, ",
"once for each major reproductive age bracket: ",
"1. Young (teen/20's) contraceptive users, age 14 - 24 ",
"2. Mid-age contraceptive users, age 25 - 34 ",
"3. Mature contraceptive users, age 35+ (limited by menopause at age 50) ",
"Combined with sexual_activity, this yields a full range of contraceptive ",
"users and outcomes, from those who never use contraceptives (and who likely ",
"have several children as a result), to lifetime contraceptive users with ",
"no children.",
"Whenever a woman becomes pregnancy her current contraceptive method is stopped. ",
"After the pregnancy terminates, she is re-routed here to re-up her contraceptive ",
"(or not)."
],
"value_code": {
"system": "SNOMED-CT",
"code": "389095005",
"display": "Contraception care (regime/therapy)"
}
},
"Young_Contraceptive_Use": {
"type": "Simple",
"remarks": [
"======================================================================",
" TEEN/20'S CONTRACEPTIVE USE ",
"======================================================================",
"18% of teens do not use any contraceptive method. The majority use a ",
"short-term solution such as withdrawal, condoms, or the pill. A select ",
"few use an IUD or long-acting contraceptive like an implant. A statistically ",
"insignificant number use sterilization, so it's omitted for this age group. ",
"Source: https://www.guttmacher.org/fact-sheet/contraceptive-use-united-states",
"There is significant overlap between those using a condom and those ",
"using a hormonal method (e.g. pill, patch, ring). The incidence of ",
"condom use below therefore represents those using ONLY a condom."
],
"distributed_transition": [
{
"distribution": 0.35,
"transition": "Using_Oral_Contraceptive"
},
{
"distribution": 0.2,
"transition": "Using_Withdrawal"
},
{
"distribution": 0.18,
"transition": "Using_No_Contraceptive"
},
{
"distribution": 0.18,
"transition": "Using_Condom_Only"
},
{
"distribution": 0.03,
"transition": "Using_Injectable"
},
{
"distribution": 0.02,
"transition": "Using_Ring"
},
{
"distribution": 0.02,
"transition": "Using_IUD"
},
{
"distribution": 0.01,
"transition": "Using_Implant"
},
{
"distribution": 0.01,
"transition": "Using_Patch"
}
]
},
"Mid_Contraceptive_Use": {
"type": "Simple",
"remarks": [
"======================================================================",
" MID-LIFE CONTRACEPTIVE USE ",
"======================================================================",
"In the 25 - 35 age bracket, more women are intentionally trying to get ",
"pregnant as they start families. For those not trying to become pregnant, ",
"long-acting contraceptives or sterilization are favored. Source: ",
"https://www.cdc.gov/nchs/data/databriefs/db173.pdf"
],
"distributed_transition": [
{
"distribution": 0.283,
"transition": "Using_No_Contraceptive"
},
{
"distribution": 0.169,
"transition": "Using_Oral_Contraceptive"
},
{
"distribution": 0.146,
"transition": "Using_Sterilization"
},
{
"distribution": 0.115,
"transition": "Using_Condom_Only"
},
{
"distribution": 0.099,
"transition": "Using_Withdrawal"
},
{
"distribution": 0.07,
"transition": "Using_IUD"
},
{
"distribution": 0.047,
"transition": "Using_Implant"
},
{
"distribution": 0.045,
"transition": "Using_Injectable"
},
{
"distribution": 0.016,
"transition": "Using_Ring"
},
{
"distribution": 0.01,
"transition": "Using_Patch"
}
]
},
"Mature_Contraceptive_Use": {
"type": "Simple",
"remarks": [
"======================================================================",
" MATURE CONTRACEPTIVE USE ",
"======================================================================",
"Most women in this age bracket are done having children and are seeking ",
"a long-term or permanent solution. The highest percentage of sterilization ",
"is in this category. (Again, note that 8% of the sterilization incidence ",
"in this category is male sterilization folded into female)."
],
"distributed_transition": [
{
"distribution": 0.39,
"transition": "Using_Sterilization"
},
{
"distribution": 0.209,
"transition": "Using_Oral_Contraceptive"
},
{
"distribution": 0.113,
"transition": "Using_Condom_Only"
},
{
"distribution": 0.052,
"transition": "Using_No_Contraceptive"
},
{
"distribution": 0.048,
"transition": "Using_Withdrawal"
},
{
"distribution": 0.07,
"transition": "Using_IUD"
},
{
"distribution": 0.047,
"transition": "Using_Implant"
},
{
"distribution": 0.045,
"transition": "Using_Injectable"
},
{
"distribution": 0.016,
"transition": "Using_Ring"
},
{
"distribution": 0.01,
"transition": "Using_Patch"
}
]
},
"Using_No_Contraceptive": {
"type": "SetAttribute",
"remarks": [
"======================================================================",
" CONTRACEPTIVE PRESCRIPTIONS ",
"======================================================================",
"These contraceptive prescriptions do not require maintenance. Fire and forget."
],
"attribute": "contraceptive_type",
"value": "none",
"direct_transition": "Route_To_Guard"
},
"Using_Withdrawal": {
"type": "SetAttribute",
"attribute": "contraceptive_type",
"value": "withdrawal",
"direct_transition": "Route_To_Guard"
},
"Using_Condom_Only": {
"type": "SetAttribute",
"attribute": "contraceptive_type",
"value": "condom",
"direct_transition": "Route_To_Guard"
},
"Using_Oral_Contraceptive": {
"type": "CallSubmodule",
"submodule": "contraceptives/oral_contraceptive",
"direct_transition": "Contraceptive_Prescribed?"
},
"Using_Sterilization": {
"type": "Simple",
"remarks": [
"This is the combination male-female sterilization incidence.",
"While only female patients are routed to this state, a portion ",
"are identified as using sterilization as a contraceptive method ",
"even though they are not given the sterilization procedure.",
"The ratio of female:male sterilization is 3:1.",
"NOTE: Only do this if age is at a transition year to avoid resampling after pregnancy.",
" Otherwise, go back to Female_Contraceptive_Use and sample again."
],
"complex_transition": [
{
"condition": {
"condition_type": "Or",
"conditions": [
{
"condition_type": "Age",
"operator": "==",
"quantity": 25,
"unit": "years"
},
{
"condition_type": "Age",
"operator": "==",
"quantity": 35,
"unit": "years"
}
]
},
"distributions": [
{
"distribution": 0.75,
"transition": "Using_Female_Sterilization"
},
{
"distribution": 0.25,
"transition": "Using_Male_Sterilization"
}
]
},
{
"distributions": [
{
"distribution": 1,
"transition": "Female_Contraceptive_Use"
}
]
}
]
},
"Using_Male_Sterilization": {
"type": "SetAttribute",
"remarks": [
"No female sterilization procedure is performed in this case."
],
"attribute": "contraceptive_type",
"value": "sterilization",
"direct_transition": "Route_To_Guard"
},
"Using_Female_Sterilization": {
"type": "CallSubmodule",
"submodule": "contraceptives/female_sterilization",
"direct_transition": "Terminal"
},
"Using_Ring": {
"type": "CallSubmodule",
"submodule": "contraceptives/ring_contraceptive",
"direct_transition": "Contraceptive_Prescribed?"
},
"Using_Patch": {
"type": "CallSubmodule",
"submodule": "contraceptives/patch_contraceptive",
"direct_transition": "Contraceptive_Prescribed?"
},
"Using_IUD": {
"type": "CallSubmodule",
"remarks": [
"======================================================================",
" CONTRACEPTIVES REQUIRING MAINTENANCE ",
"======================================================================",
"IUDs, implants, and injectables require periodic maintenance during a ",
"given age bracket. IUDs must be replaced every 5-10 years, implants every ",
"3 years, and injectables every 3 months. Maintenance is handled internally ",
"within the submodules.",
"These submodules are also 'self guarded', meaning they do not need the ",
"regular age guards to ensure the correct timing for the next age bracket ",
"(since they do so internally)."
],
"submodule": "contraceptives/intrauterine_device",
"direct_transition": "Contraceptive_Prescribed?"
},
"Using_Implant": {
"type": "CallSubmodule",
"submodule": "contraceptives/implant_contraceptive",
"direct_transition": "Contraceptive_Prescribed?"
},
"Using_Injectable": {
"type": "CallSubmodule",
"submodule": "contraceptives/injectable_contraceptive",
"direct_transition": "Contraceptive_Prescribed?"
},
"Contraceptive_Prescribed?": {
"type": "Simple",
"remarks": [
"If a contraceptive wasn't prescribed by the submodule (for example, because ",
"none was available for the current year of the simulation) both contraceptive ",
"attributes will be nill. ",
"Since no contraceptive was prescribed, default to the historically avaialable ",
"set of contraceptives."
],
"conditional_transition": [
{
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "contraceptive",
"operator": "is nil"
},
{
"condition_type": "Attribute",
"attribute": "contraceptive_type",
"operator": "is nil"
}
]
},
"transition": "Historical_Contraceptive_Use"
},
{
"transition": "Route_To_Guard"
}
]
},
"Historical_Contraceptive_Use": {
"type": "Simple",
"remarks": [
"These were available methods prior to the 1960's."
],
"distributed_transition": [
{
"distribution": 0.2,
"transition": "Using_No_Contraceptive"
},
{
"distribution": 0.4,
"transition": "Using_Withdrawal"
},
{
"distribution": 0.4,
"transition": "Using_Condom_Only"
}
]
},
"Route_To_Guard": {
"exact": {
"quantity": 12,
"unit": "months"
},
"type": "Delay",
"direct_transition": "Reset_Contraceptive_Use",
"remarks": [
"Using an annual delay causes resampling of contraception more frequently",
"and distributes the babies more evenly across the female population"
]
},
"Reset_Contraceptive_Use": {
"type": "CallSubmodule",
"remarks": [
"Prior to setting a new contraceptive, the previous contraceptive ",
"method is cleared."
],
"submodule": "contraceptives/clear_contraceptive",
"conditional_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "pregnant",
"operator": "==",
"value": true
},
"transition": "Pregnant_Guard"
},
{
"condition": {
"condition_type": "Age",
"operator": ">=",
"quantity": 50,
"unit": "years"
},
"transition": "Menopause_Reached"
},
{
"transition": "Female_Contraceptive_Use"
}
]
},
"Pregnant_Guard": {
"type": "Guard",
"remarks": [
"Once a female is no longer pregnant, she will re-select a contraceptive type."
],
"allow": {
"condition_type": "Attribute",
"attribute": "pregnant",
"operator": "==",
"value": false
},
"direct_transition": "Female_Contraceptive_Use"
},
"Menopause_Reached": {
"type": "Simple",
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

53
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{
"name": "Clear Contraceptive",
"remarks": [
"This submodule ends any active contraceptive medication assigned to the ",
"'contraceptive' attribute and clears the 'contraceptive_type' attribute ",
"for reassignment."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Clear_Contraceptive_Med"
},
"Clear_Contraceptive_Med": {
"type": "Simple",
"remarks": [
"If the 'contraceptive' attribute is currently set, the medication it ",
"references will be active."
],
"conditional_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "contraceptive",
"operator": "is not nil"
},
"transition": "End_Contraceptive_Med"
},
{
"transition": "Clear_Contraceptive_Type"
}
]
},
"End_Contraceptive_Med": {
"type": "MedicationEnd",
"referenced_by_attribute": "contraceptive",
"direct_transition": "Clear_Contraceptive"
},
"Clear_Contraceptive": {
"type": "SetAttribute",
"attribute": "contraceptive",
"direct_transition": "Clear_Contraceptive_Type"
},
"Clear_Contraceptive_Type": {
"type": "SetAttribute",
"attribute": "contraceptive_type",
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

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{
"name": "Female Sterilization",
"remarks": [
"This submodule performs a female sterilization procedure. This procedure ",
"is not reversible."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Set_Contraceptive_Type"
},
"Set_Contraceptive_Type": {
"type": "SetAttribute",
"attribute": "contraceptive_type",
"value": "sterilization",
"direct_transition": "Sterilization Requested"
},
"Consultation_Encounter": {
"type": "Encounter",
"encounter_class": "outpatient",
"codes": [
{
"system": "SNOMED-CT",
"code": "698314001",
"display": "Consultation for treatment (procedure)"
}
],
"direct_transition": "Consultation",
"reason": "Sterilization Requested"
},
"End_Consultation": {
"type": "EncounterEnd",
"direct_transition": "Delay_For_Procedure"
},
"Delay_For_Procedure": {
"type": "Delay",
"range": {
"low": 1,
"high": 3,
"unit": "weeks"
},
"direct_transition": "Tubal_Ligation_Surgery_Encounter"
},
"Tubal_Ligation_Surgery_Encounter": {
"type": "Encounter",
"encounter_class": "inpatient",
"codes": [
{
"system": "SNOMED-CT",
"code": "305408004",
"display": "Admission to surgical department (procedure)"
}
],
"direct_transition": "Tubal_Ligation_Procedure",
"reason": "Sterilization Requested"
},
"Tubal_Ligation_Procedure": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "287664005",
"display": "Ligation of bilateral fallopian tubes (procedure)"
}
],
"duration": {
"low": 2,
"high": 3,
"unit": "hours"
},
"direct_transition": "Sterilization Complete",
"reason": "Sterilization Requested"
},
"Become_Infertile": {
"type": "SetAttribute",
"attribute": "infertile",
"value": true,
"direct_transition": "Post_Surgery_Care"
},
"Post_Surgery_Care": {
"type": "CarePlanStart",
"codes": [
{
"system": "SNOMED-CT",
"code": "737471002",
"display": "Minor surgery care management (procedure)"
}
],
"activities": [
{
"system": "SNOMED-CT",
"code": "183051005",
"display": "Recommendation to rest (procedure)"
},
{
"system": "SNOMED-CT",
"code": "243077000",
"display": "Recommendation to limit sexual activity (procedure)"
}
],
"direct_transition": "Postoperative Care",
"reason": "History_of_Tubal_Ligation"
},
"End_Surgery_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Recovery_Period"
},
"Recovery_Period": {
"type": "Delay",
"range": {
"low": 2,
"high": 3,
"unit": "weeks"
},
"direct_transition": "End_Post_Surgery_Care"
},
"End_Post_Surgery_Care": {
"type": "CarePlanEnd",
"careplan": "Post_Surgery_Care",
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
},
"Consultation": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "268533009",
"display": "Sterilization education (procedure)"
}
],
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 60,
"low": 45
}
},
"unit": "minutes",
"direct_transition": "End_Consultation"
},
"Postoperative Care": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "133899007",
"display": "Postoperative care (regime/therapy)"
}
],
"distribution": {
"kind": "EXPONENTIAL",
"parameters": {
"mean": 5
}
},
"unit": "hours",
"direct_transition": "End_Surgery_Encounter",
"reason": "History_of_Tubal_Ligation"
},
"History_of_Tubal_Ligation": {
"type": "ConditionOnset",
"target_encounter": "Tubal_Ligation_Surgery_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "267020005",
"display": "History of tubal ligation (situation)"
}
],
"direct_transition": "Become_Infertile"
},
"Sterilization Requested": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "183996000",
"display": "Sterilization requested (situation)"
}
],
"direct_transition": "Consultation_Encounter",
"target_encounter": "Consultation_Encounter"
},
"Sterilization Complete": {
"type": "ConditionEnd",
"direct_transition": "History_of_Tubal_Ligation",
"condition_onset": "Sterilization Requested"
}
},
"gmf_version": 1
}

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{
"name": "Implant Contraceptive",
"remarks": [
"This submodule prescribes a long-acting, implanted contraceptive if one is ",
"available for the current year of the simulation. The first implanted ",
"contraceptive was available in 1990, marketed as Norplant. Norplant was ",
"discontinued in 2002 in favor of newer alternatives, but implants remain ",
"available today.",
"Implants must be readministered once every 3-4 years. The Contraceptive ",
"Maintenance module handles that.",
"Sources for historical availability: ",
"http://www.ourbodiesourselves.org/health-info/a-brief-history-of-birth-control/",
"http://www.pbs.org/wnet/need-to-know/health/a-brief-history-of-the-birth-control-pill/480/"
],
"states": {
"Initial": {
"type": "Initial",
"remarks": [
"Males, pregnant females, and those arriving here before the year 1991 ",
"do not get implant contraceptives."
],
"conditional_transition": [
{
"condition": {
"condition_type": "Gender",
"gender": "M"
},
"transition": "Terminal"
},
{
"condition": {
"condition_type": "Attribute",
"attribute": "pregnant",
"operator": "==",
"value": true
},
"transition": "Terminal"
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 1991
},
"transition": "Terminal"
},
{
"transition": "Set_Contraceptive_Type"
}
]
},
"Set_Contraceptive_Type": {
"type": "SetAttribute",
"attribute": "contraceptive_type",
"value": "implant",
"direct_transition": "Implant_Contraceptive_Encounter"
},
"Implant_Contraceptive_Encounter": {
"type": "Encounter",
"remarks": [
"======================================================================",
" NEW IMPLANT PRESCRIPTION ",
"======================================================================"
],
"encounter_class": "outpatient",
"codes": [
{
"system": "SNOMED-CT",
"code": "698314001",
"display": "Consultation for treatment (procedure)"
}
],
"direct_transition": "Prescribe_Implant_Contraceptive",
"reason": "contraception_care_reason"
},
"Prescribe_Implant_Contraceptive": {
"type": "Simple",
"remarks": [
"Norplant was available in January 1991. The original production ended ",
"in 2002, with supplies available until 2004-ish. Implanon became available ",
"in 2006 and an improvement, Nexplanon, in 2011. Implanon was taken off the ",
"market in 2012, so Nexplanon remains the only currently available implant ",
"in the United States.",
"While not *technically* historically accurate, the use of Norplant is stretched ",
"until 2006 to maintain continuity."
],
"complex_transition": [
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 2006
},
"distributions": [
{
"distribution": 1,
"transition": "Prescribe_Norplant"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 2011
},
"distributions": [
{
"distribution": 1,
"transition": "Prescribe_Implanon"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 2012
},
"distributions": [
{
"distribution": 0.8,
"transition": "Prescribe_Nexplanon"
},
{
"distribution": 0.8,
"transition": "Prescribe_Implanon"
}
]
},
{
"distributions": [
{
"distribution": 1,
"transition": "Prescribe_Nexplanon"
}
]
}
]
},
"Prescribe_Norplant": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "1366343",
"display": "Levonorgestrel 0.00354 MG/HR Drug Implant"
}
],
"direct_transition": "Initial_Implant",
"administration": true
},
"Prescribe_Implanon": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "389221",
"display": "Etonogestrel 68 MG Drug Implant"
}
],
"direct_transition": "Initial_Implant",
"administration": true
},
"Prescribe_Nexplanon": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "389221",
"display": "Etonogestrel 68 MG Drug Implant"
}
],
"direct_transition": "Initial_Implant",
"administration": true
},
"Initial_Implant": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "169553002",
"display": "Insertion of subcutaneous contraceptive (procedure)"
}
],
"duration": {
"low": 20,
"high": 40,
"unit": "minutes"
},
"direct_transition": "End_Initial_Encounter"
},
"End_Initial_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

161
src/main/resources/modules/contraceptives/injectable_contraceptive.json Normal file
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{
"name": "Injectable Contraceptive",
"remarks": [
"This submodule prescribes a long-acting, injectable contraceptive if one is ",
"available for the current year of the simulation. The first injectable ",
"contraceptive was available in 1992, marketed as Depo-Provera. Depo remains ",
"the only available injectable option in the U.S.",
"Injectables must be readministered once every 3 months. The Contraceptive ",
"Maintenance module handles that.",
"Sources for historical availability: ",
"http://www.ourbodiesourselves.org/health-info/a-brief-history-of-birth-control/",
"http://www.pbs.org/wnet/need-to-know/health/a-brief-history-of-the-birth-control-pill/480/"
],
"states": {
"Initial": {
"type": "Initial",
"remarks": [
"Males, pregnant females, and those arriving here before the year 1992 ",
"do not get injectable contraceptives."
],
"conditional_transition": [
{
"condition": {
"condition_type": "Gender",
"gender": "M"
},
"transition": "Terminal"
},
{
"condition": {
"condition_type": "Attribute",
"attribute": "pregnant",
"operator": "==",
"value": true
},
"transition": "Terminal"
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 1992
},
"transition": "Terminal"
},
{
"transition": "Set_Contraceptive_Type"
}
]
},
"Set_Contraceptive_Type": {
"type": "SetAttribute",
"attribute": "contraceptive_type",
"value": "injectable",
"direct_transition": "Injectable_Contraceptive_Encounter"
},
"Injectable_Contraceptive_Encounter": {
"type": "Encounter",
"remarks": [
"======================================================================",
" NEW PRESCRIPTION ",
"======================================================================"
],
"encounter_class": "outpatient",
"codes": [
{
"system": "SNOMED-CT",
"code": "698314001",
"display": "Consultation for treatment (procedure)"
}
],
"direct_transition": "Prescribe_Injectable_Contraceptive",
"reason": "contraception_care_reason"
},
"Prescribe_Injectable_Contraceptive": {
"type": "Simple",
"remarks": [
"Depo-Provera (150 mg/mL MPA) became available in 1992. A lower-dose, ",
"subcutaneous version became available in Dec. 2004 as Depo-SubQ Provera ",
"(104 mg/0.65 mL MPA)."
],
"complex_transition": [
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 2005
},
"distributions": [
{
"distribution": 1,
"transition": "Prescribe_Depo_Provera"
}
]
},
{
"distributions": [
{
"distribution": 0.7,
"transition": "Prescribe_Depo_Provera"
},
{
"distribution": 0.3,
"transition": "Prescribe_Depo_SubQ"
}
]
}
]
},
"Prescribe_Depo_Provera": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "1000126",
"display": "1 ML medroxyprogesterone acetate 150 MG/ML Injection"
}
],
"direct_transition": "Initial_Injection_By_Physician",
"administration": true
},
"Prescribe_Depo_SubQ": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "1000126",
"display": "1 ML medroxyPROGESTERone acetate 150 MG/ML Injection"
}
],
"direct_transition": "Initial_Injection_By_Physician",
"administration": true
},
"Initial_Injection_By_Physician": {
"type": "Procedure",
"duration": {
"low": 10,
"high": 20,
"unit": "minutes"
},
"codes": [
{
"system": "SNOMED-CT",
"code": "76601001",
"display": "Intramuscular injection (procedure)"
}
],
"direct_transition": "End_Consultation_Encounter"
},
"End_Consultation_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

337
src/main/resources/modules/contraceptives/intrauterine_device.json Normal file
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{
"name": "Intrauterine Device",
"remarks": [
"This submodule prescribes an intrauterine device (IUD) for contraception.",
"FDA approval of IUDs in the U.S. was in 1968. Early designs were flexible ",
"thermoplastic. Copper IUDs were introduced in the 1970's. One IUD in particular ",
"was problematic - the Dalkon Shield caused infections in 200k women and 10 ",
"deaths. It was discontinued in 1974. This caused widespread abandonment and ",
"distrust of IUDs in the 1980's.",
"Modern IUDs are again becoming popular. They are copper or combine low-dose ",
"hormones with plastic.",
"IUDs must be removed or replaced every 5-10 years. This is handled by the ",
"Contraceptive Maintenance module.",
"Sources for availability: ",
"https://www.wired.com/2011/07/ff_iud/",
"http://kff.org/womens-health-policy/fact-sheet/intrauterine-devices-iuds-access-for-women-in-the-u-s/"
],
"states": {
"Initial": {
"type": "Initial",
"remarks": [
"Males, pregnant females, and those arriving here before the year 1968 ",
"do not get IUDs."
],
"conditional_transition": [
{
"condition": {
"condition_type": "Gender",
"gender": "M"
},
"transition": "Terminal"
},
{
"condition": {
"condition_type": "Attribute",
"attribute": "pregnant",
"operator": "==",
"value": true
},
"transition": "Terminal"
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 1968
},
"transition": "Terminal"
},
{
"transition": "Set_Contraceptive_Type"
}
]
},
"Set_Contraceptive_Type": {
"type": "SetAttribute",
"attribute": "contraceptive_type",
"value": "iud",
"direct_transition": "IUD_Consultation_Encounter"
},
"IUD_Consultation_Encounter": {
"type": "Encounter",
"remarks": [
"======================================================================",
" NEW PRESCRIPTION ",
"======================================================================"
],
"encounter_class": "outpatient",
"codes": [
{
"system": "SNOMED-CT",
"code": "698314001",
"display": "Consultation for treatment (procedure)"
}
],
"direct_transition": "Prescribe_IUD",
"reason": "contraception_care_reason"
},
"Prescribe_IUD": {
"type": "Simple",
"remarks": [
"Unfortunately, RxNorm codes are not available for: ",
"Lippes Lopp, Safe-T-Coil, Copper 7, Dalkon Shield, or Paragard ",
"However, the contraceptive_type attribute remains set and the ",
"incidence of pregnancy will reflect that the woman is using an IUD."
],
"complex_transition": [
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 1971
},
"distributions": [
{
"distribution": 0.5,
"transition": "Prescribe_Lippes_Loop"
},
{
"distribution": 0.5,
"transition": "Prescribe_Safe_T_Coil"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 1975
},
"distributions": [
{
"distribution": 0.34,
"transition": "Prescribe_Lippes_Loop"
},
{
"distribution": 0.33,
"transition": "Prescribe_Safe_T_Coil"
},
{
"distribution": 0.33,
"transition": "Prescribe_Dalkon_Shield"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 1986
},
"distributions": [
{
"distribution": 0.3,
"transition": "Prescribe_Lippes_Loop"
},
{
"distribution": 0.3,
"transition": "Prescribe_Safe_T_Coil"
},
{
"distribution": 0.4,
"transition": "Prescribe_Copper_7"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 2001
},
"remarks": [
"Because of the Dalkon Shield scare, all IUDs but one (Paragard) ",
"were taken off the market by 1986."
],
"distributions": [
{
"distribution": 1,
"transition": "Prescribe_Paragard"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 2015
},
"distributions": [
{
"distribution": 0.4,
"transition": "Prescribe_Paragard"
},
{
"distribution": 0.6,
"transition": "Prescribe_Mirena"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 2016
},
"remarks": [
"Hormonal, plastic IUDs were introduced in 2001."
],
"distributions": [
{
"distribution": 0.3,
"transition": "Prescribe_Paragard"
},
{
"distribution": 0.3,
"transition": "Prescribe_Mirena"
},
{
"distribution": 0.4,
"transition": "Prescribe_Liletta"
}
]
},
{
"distributions": [
{
"distribution": 0.25,
"transition": "Prescribe_Paragard"
},
{
"distribution": 0.25,
"transition": "Prescribe_Mirena"
},
{
"distribution": 0.25,
"transition": "Prescribe_Liletta"
},
{
"distribution": 0.25,
"transition": "Prescribe_Kyleena"
}
]
}
]
},
"Prescribe_Lippes_Loop": {
"type": "Simple",
"direct_transition": "End_Consultation_Encounter"
},
"Prescribe_Safe_T_Coil": {
"type": "Simple",
"direct_transition": "End_Consultation_Encounter"
},
"Prescribe_Dalkon_Shield": {
"type": "Simple",
"direct_transition": "End_Consultation_Encounter"
},
"Prescribe_Copper_7": {
"type": "Simple",
"direct_transition": "End_Consultation_Encounter"
},
"Prescribe_Paragard": {
"type": "Simple",
"direct_transition": "End_Consultation_Encounter"
},
"Prescribe_Mirena": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "807283",
"display": "Mirena 52 MG Intrauterine System"
}
],
"direct_transition": "End_Consultation_Encounter",
"administration": true
},
"Prescribe_Liletta": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "1605257",
"display": "Liletta 52 MG Intrauterine System"
}
],
"direct_transition": "End_Consultation_Encounter",
"administration": true
},
"Prescribe_Kyleena": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "1856546",
"display": "Kyleena 19.5 MG Intrauterine System"
}
],
"direct_transition": "End_Consultation_Encounter",
"administration": true
},
"End_Consultation_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Delay_For_IUD_Insertion"
},
"Delay_For_IUD_Insertion": {
"type": "Delay",
"range": {
"low": 2,
"high": 5,
"unit": "days"
},
"direct_transition": "Initial_IUD_Insertion_Encounter"
},
"Initial_IUD_Insertion_Encounter": {
"type": "Encounter",
"encounter_class": "outpatient",
"codes": [
{
"system": "SNOMED-CT",
"code": "308335008",
"display": "Patient encounter procedure (procedure)"
}
],
"direct_transition": "IUD_Insertion",
"reason": "contraception_care_reason"
},
"IUD_Insertion": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "65200003",
"display": "Insertion of intrauterine contraceptive device (procedure)"
}
],
"duration": {
"low": 40,
"high": 70,
"unit": "minutes"
},
"direct_transition": "End_IUD_Insertion_Encounter"
},
"End_IUD_Insertion_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

140
src/main/resources/modules/contraceptives/male_sterilization.json Normal file
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{
"name": "Male Sterilization",
"remarks": [
"This submodule performs a male sterilization (vasectomy) procedure."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Sterilization_Requested"
},
"Consultation_Encounter": {
"type": "Encounter",
"encounter_class": "outpatient",
"codes": [
{
"system": "SNOMED-CT",
"code": "698314001",
"display": "Consultation for treatment (procedure)"
}
],
"direct_transition": "End_Consultation",
"reason": "Sterilization_Requested"
},
"End_Consultation": {
"type": "EncounterEnd",
"direct_transition": "Delay_For_Procedure"
},
"Delay_For_Procedure": {
"type": "Delay",
"range": {
"low": 1,
"high": 3,
"unit": "weeks"
},
"direct_transition": "Vasectomy_Encounter"
},
"Vasectomy_Encounter": {
"type": "Encounter",
"encounter_class": "outpatient",
"remarks": [
"Male vasectomies are typically performed right in the doctor's office. ",
"Unlike female sterilization, male sterilization is a relatively simple ",
"procedure."
],
"codes": [
{
"system": "SNOMED-CT",
"code": "308335008",
"display": "Patient encounter procedure (procedure)"
}
],
"direct_transition": "Vasectomy",
"reason": "Sterilization_Requested"
},
"Vasectomy": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "22523008",
"display": "Vasectomy (procedure)"
}
],
"duration": {
"low": 1,
"high": 2,
"unit": "hours"
},
"direct_transition": "Become_Infertile"
},
"Become_Infertile": {
"type": "SetAttribute",
"attribute": "infertile",
"value": true,
"direct_transition": "Post_Procedure_Care"
},
"Post_Procedure_Care": {
"type": "CarePlanStart",
"codes": [
{
"system": "SNOMED-CT",
"code": "737471002",
"display": "Minor surgery care management (procedure)"
}
],
"activities": [
{
"system": "SNOMED-CT",
"code": "183051005",
"display": "Recommendation to rest (procedure)"
},
{
"system": "SNOMED-CT",
"code": "243077000",
"display": "Recommendation to limit sexual activity (procedure)"
}
],
"direct_transition": "End_Sterilization_Requested"
},
"End_Vasectomy_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Delay_For_Recovery"
},
"Delay_For_Recovery": {
"type": "Delay",
"range": {
"low": 1,
"high": 2,
"unit": "weeks"
},
"direct_transition": "End_Vasectomy_Care"
},
"End_Vasectomy_Care": {
"type": "CarePlanEnd",
"careplan": "Post_Procedure_Care",
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
},
"Sterilization_Requested": {
"type": "ConditionOnset",
"target_encounter": "Consultation_Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "183996000",
"display": "Sterilization requested (situation)"
}
],
"direct_transition": "Consultation_Encounter"
},
"End_Sterilization_Requested": {
"type": "ConditionEnd",
"direct_transition": "End_Vasectomy_Encounter",
"condition_onset": "Sterilization_Requested"
}
},
"gmf_version": 1
}

511
src/main/resources/modules/contraceptives/oral_contraceptive.json Normal file
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{
"name": "Oral Contraceptive",
"remarks": [
"This module prescribes an oral, hormonal contraceptive if one is available ",
"for the current year of the simulation. There are 2 classes of oral contraceptives: ",
"1. Combination (estrogen, progestin), either monophasic and triphasic ",
"2. Minipill (progestin-only)",
"Combination pills may be either monophasic (same dosage, all month long) or triphasic ",
"(dosage increases progressively throughout the month). Potential side-effects of oral ",
"contraceptives include nausea, breast tenderness, mood swings, headaches, weight gain, ",
"spotting, and decreased libido. None of these side-effects are currently modeled.",
"Smoking, especially over the age of 35, significantly increases the risk of: ",
"1. Blood clots (1.6x with minipill, 2x with estrogen) ",
"2. Myocardial Infarction (1.6x) ",
"3. Ischemic Stroke (1.7x) ",
"Source: https://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0079002/",
"No changes were made to the cardiovascular disease module.",
"Minipill (progestin-only) contraceptives are safe for smokers, those at risk of ",
"heart disease, and new mothers who are breastfeeding. They carry a slightly elevated ",
"risk of ectopic pregnancy, are less effective than combination pills (91 - 99% effective), ",
"and must be taken very consistently to be effective. Source: ",
"http://www.feministcenter.org/en/health-wellness-services/comprehensive-gyn/birth-control-options/birth-control-information/101-mini-pills",
"The majority of women taking oral contraceptives take the combination pill.",
"Sources for historical availability: ",
"http://www.ourbodiesourselves.org/health-info/a-brief-history-of-birth-control/",
"http://www.pbs.org/wnet/need-to-know/health/a-brief-history-of-the-birth-control-pill/480/"
],
"states": {
"Initial": {
"type": "Initial",
"remarks": [
"Males, pregnant females, and those arriving here before the year 1960 ",
"do not get oral contraceptives."
],
"conditional_transition": [
{
"condition": {
"condition_type": "Gender",
"gender": "M"
},
"transition": "Terminal"
},
{
"condition": {
"condition_type": "Attribute",
"attribute": "pregnant",
"operator": "==",
"value": true
},
"transition": "Terminal"
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 1960
},
"transition": "Terminal"
},
{
"transition": "Set_Contraceptive_Type"
}
]
},
"Set_Contraceptive_Type": {
"type": "SetAttribute",
"attribute": "contraceptive_type",
"value": "pill",
"direct_transition": "Encounter_For_Oral_Contraceptive"
},
"Encounter_For_Oral_Contraceptive": {
"type": "Encounter",
"encounter_class": "outpatient",
"codes": [
{
"system": "SNOMED-CT",
"code": "698314001",
"display": "Consultation for treatment (procedure)"
}
],
"direct_transition": "Combination_Or_Minipill",
"reason": "contraception_care_reason"
},
"Combination_Or_Minipill": {
"type": "Simple",
"remarks": [
"If the patient has a high BMI (>30), was recently pregnant (w/in 6 months), smokes, ",
"or has high blood pressure (systolic > 130) the minipill is prescribed. Otherwise, a ",
"combination pill is prescribed.",
"TODO: Check if the patient was recently pregnant. We need a 'Prior Condition', or ",
"'Prior Event' condition to check for this. If the mother is breastfeeding, the ",
"combination pill should not be used."
],
"conditional_transition": [
{
"condition": {
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "smoker",
"operator": "==",
"value": true
},
{
"condition_type": "Vital Sign",
"vital_sign": "BMI",
"operator": ">",
"value": 30
},
{
"condition_type": "Vital Sign",
"vital_sign": "Systolic Blood Pressure",
"operator": ">",
"value": 130
}
]
},
"transition": "Prescribe_Minipill"
},
{
"transition": "Prescribe_Combination_Pill"
}
]
},
"Prescribe_Minipill": {
"type": "Simple",
"remarks": [
"======================================================================",
" MINIPILL ",
"======================================================================",
"What type of pill is prescribed (if any) depends on the current year ",
"of the simulation."
],
"complex_transition": [
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 2002
},
"remarks": [
"If before 2002, the patient instead gets prescribed a combination pill.",
"This will have averse affects on that patient's health if they meet one ",
"of the conditions above."
],
"distributions": [
{
"distribution": 1,
"transition": "Prescribe_Combination_Pill"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 2003
},
"distributions": [
{
"distribution": 1,
"transition": "Prescribe_Camila"
}
]
},
{
"distributions": [
{
"distribution": 0.3,
"transition": "Prescribe_Camila"
},
{
"distribution": 0.3,
"transition": "Prescribe_Errin"
},
{
"distribution": 0.4,
"transition": "Prescribe_Jolivette"
}
]
}
]
},
"Prescribe_Camila": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "748962",
"display": "Camila 28 Day Pack"
}
],
"direct_transition": "End_Encounter"
},
"Prescribe_Errin": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "831533",
"display": "Errin 28 Day Pack"
}
],
"direct_transition": "End_Encounter"
},
"Prescribe_Jolivette": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "757594",
"display": "Jolivette 28 Day Pack"
}
],
"direct_transition": "End_Encounter"
},
"Prescribe_Combination_Pill": {
"type": "Simple",
"remarks": [
"======================================================================",
" COMBINATION PILL ",
"======================================================================",
"What type of pill is prescribed (if any) depends on the current year ",
"of the simulation."
],
"complex_transition": [
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 1974
},
"remarks": [
"Enovid got FDA approval in May, 1960 for contraceptive use.",
"10mg mestranol/noretynodrel, high-dose hormone pill."
],
"distributions": [
{
"distribution": 1,
"transition": "Prescribe_Enovid"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 1988
},
"remarks": [
"Use of the high dose 10mg mestranol/noretynodrel (Enovid) steadily grew. ",
"The first documented case of blood clots (likely in a smoker), were in ",
"1961. Norinyl (norethindrone-ethinyl estradiol) was introduced in 1974."
],
"distributions": [
{
"distribution": 0.5,
"transition": "Prescribe_Enovid"
},
{
"distribution": 0.5,
"transition": "Prescribe_Norinyl"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 1989
},
"remarks": [
"Enovid was taken off the market in 1988 in favor of low-dose alternatives."
],
"distributions": [
{
"distribution": 1,
"transition": "Prescribe_Norinyl"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 1998
},
"remarks": [
"Ortho-Tri Cyclen was introduced in 1989."
],
"distributions": [
{
"distribution": 0.4,
"transition": "Prescribe_Norinyl"
},
{
"distribution": 0.6,
"transition": "Prescribe_Ortho_Tri_Cyclen"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 2003
},
"remarks": [
"Estrostep introduced in 1997, Ortho-Novum 1998 (same composition as Norinyl)."
],
"distributions": [
{
"distribution": 0.3,
"transition": "Prescribe_Norinyl"
},
{
"distribution": 0.2,
"transition": "Prescribe_Ortho_Tri_Cyclen"
},
{
"distribution": 0.3,
"transition": "Prescribe_Estrostep"
}
]
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 2010
},
"remarks": [
"Trinessa and Seasonique (2003), Yaz (2006)."
],
"distributions": [
{
"distribution": 0.2,
"transition": "Prescribe_Ortho_Tri_Cyclen"
},
{
"distribution": 0.2,
"transition": "Prescribe_Estrostep"
},
{
"distribution": 0.2,
"transition": "Prescribe_Trinessa"
},
{
"distribution": 0.2,
"transition": "Prescribe_Seasonique"
},
{
"distribution": 0.2,
"transition": "Prescribe_Yaz"
}
]
},
{
"remarks": [
"Natazia (2010), Levora (2016)."
],
"distributions": [
{
"distribution": 0.2,
"transition": "Prescribe_Trinessa"
},
{
"distribution": 0.2,
"transition": "Prescribe_Seasonique"
},
{
"distribution": 0.2,
"transition": "Prescribe_Yaz"
},
{
"distribution": 0.2,
"transition": "Prescribe_Natazia"
},
{
"distribution": 0.2,
"transition": "Prescribe_Levora"
}
]
}
]
},
"Prescribe_Enovid": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "235389",
"display": "Mestranol / Norethynodrel"
}
],
"direct_transition": "End_Encounter"
},
"Prescribe_Norinyl": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "749882",
"display": "Norinyl 1+50 28 Day Pack"
}
],
"direct_transition": "End_Encounter"
},
"Prescribe_Estrostep": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "1359133",
"display": "Estrostep Fe 28 Day Pack"
}
],
"direct_transition": "End_Encounter"
},
"Prescribe_Ortho_Tri_Cyclen": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "749785",
"display": "Ortho Tri-Cyclen 28 Day Pack"
}
],
"direct_transition": "End_Encounter"
},
"Prescribe_Trinessa": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "751905",
"display": "Trinessa 28 Day Pack"
}
],
"direct_transition": "End_Encounter"
},
"Prescribe_Seasonique": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"remarks": [
"These are long-term, low-dose hormones that cause only 4 menstruations per year."
],
"codes": [
{
"system": "RxNorm",
"code": "749762",
"display": "Seasonique 91 Day Pack"
}
],
"direct_transition": "End_Encounter"
},
"Prescribe_Yaz": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "748856",
"display": "Yaz 28 Day Pack"
}
],
"direct_transition": "End_Encounter"
},
"Prescribe_Natazia": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "978950",
"display": "Natazia 28 Day Pack"
}
],
"direct_transition": "End_Encounter"
},
"Prescribe_Levora": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "748879",
"display": "Levora 0.15/30 28 Day Pack"
}
],
"direct_transition": "End_Encounter"
},
"End_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

87
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{
"name": "Patch Contraceptive",
"remarks": [
"This module prescribes a hormonal patch if one is available ",
"for the current year of the simulation.",
"Sources for historical availability: ",
"http://www.ourbodiesourselves.org/health-info/a-brief-history-of-birth-control/",
"http://www.pbs.org/wnet/need-to-know/health/a-brief-history-of-the-birth-control-pill/480/"
],
"states": {
"Initial": {
"type": "Initial",
"remarks": [
"Males, pregnant females, and those arriving here before the year 2002 ",
"do not get patch contraceptives."
],
"conditional_transition": [
{
"condition": {
"condition_type": "Gender",
"gender": "M"
},
"transition": "Terminal"
},
{
"condition": {
"condition_type": "Attribute",
"attribute": "pregnant",
"operator": "==",
"value": true
},
"transition": "Terminal"
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 2002
},
"transition": "Terminal"
},
{
"transition": "Set_Contraceptive_Type"
}
]
},
"Set_Contraceptive_Type": {
"type": "SetAttribute",
"attribute": "contraceptive_type",
"value": "patch",
"direct_transition": "Patch_Contraceptive_Consultation"
},
"Patch_Contraceptive_Consultation": {
"type": "Encounter",
"encounter_class": "outpatient",
"codes": [
{
"system": "SNOMED-CT",
"code": "698314001",
"display": "Consultation for treatment (procedure)"
}
],
"direct_transition": "Prescribe_Xulane",
"reason": "contraception_care_reason"
},
"Prescribe_Xulane": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "1534809",
"display": "168 HR Ethinyl Estradiol 0.00146 MG/HR / norelgestromin 0.00625 MG/HR Transdermal System"
}
],
"direct_transition": "End_Consultation_Encounter"
},
"End_Consultation_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

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src/main/resources/modules/contraceptives/ring_contraceptive.json Normal file
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{
"name": "Vaginal Ring Contraceptive",
"remarks": [
"This submodule prescribes a hormonal contraceptive ring if one ",
"is available for the current year of the simulation. The ring is ",
"inserted into the vagina and may be removed at will, or for short ",
"periods of time during sexual intercourse."
],
"states": {
"Initial": {
"type": "Initial",
"remarks": [
"Males, pregnant females, and those arriving here before the year 2001 ",
"do not get ring contraceptives."
],
"conditional_transition": [
{
"condition": {
"condition_type": "Gender",
"gender": "M"
},
"transition": "Terminal"
},
{
"condition": {
"condition_type": "Attribute",
"attribute": "pregnant",
"operator": "==",
"value": true
},
"transition": "Terminal"
},
{
"condition": {
"condition_type": "Date",
"operator": "<",
"year": 2001
},
"transition": "Terminal"
},
{
"transition": "Set_Contraceptive_Type"
}
]
},
"Set_Contraceptive_Type": {
"type": "SetAttribute",
"attribute": "contraceptive_type",
"value": "ring",
"direct_transition": "Ring_Contraceptive_Consultation"
},
"Ring_Contraceptive_Consultation": {
"type": "Encounter",
"encounter_class": "outpatient",
"codes": [
{
"system": "SNOMED-CT",
"code": "698314001",
"display": "Consultation for treatment (procedure)"
}
],
"direct_transition": "Prescribe_Nuvaring",
"reason": "contraception_care_reason"
},
"Prescribe_Nuvaring": {
"type": "MedicationOrder",
"assign_to_attribute": "contraceptive",
"codes": [
{
"system": "RxNorm",
"code": "1367439",
"display": "NuvaRing 0.12/0.015 MG per 24HR 21 Day Vaginal System"
}
],
"direct_transition": "End_Consultation_Encounter"
},
"End_Consultation_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

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{
"name": "covid19",
"remarks": [
"This is module for the treatment of COVID-19 has estimates for rates of infection, rates of admission, and probabilities.",
"",
"Treatments are based on many sources, many of which are updating. Many pathways are missing.",
"",
"Daily lab values and measurements are missing."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Wait Until Exposure"
},
"Terminal": {
"type": "Terminal"
},
"Wait Until Exposure": {
"type": "Delay",
"exact": {
"quantity": 4,
"unit": "days"
},
"lookup_table_transition": [
{
"transition": "Wait Until Exposure",
"default_probability": 1,
"lookup_table_name": "covid19_prob.csv"
},
{
"transition": "Check Vaccine Status",
"default_probability": 0,
"lookup_table_name": "covid19_prob.csv"
},
{
"transition": "Terminal",
"default_probability": 0,
"lookup_table_name": "covid19_prob.csv"
}
]
},
"Call Infection Submodule": {
"submodule": "covid19/infection",
"type": "CallSubmodule",
"direct_transition": "Terminal"
},
"Check Vaccine Status": {
"type": "Simple",
"complex_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "C19_FULLY_VACCINATED",
"operator": "==",
"value": true
},
"distributions": [
{
"transition": "Call Infection Submodule",
"distribution": 0.01
},
{
"transition": "Wait Until Exposure",
"distribution": 0.99
}
]
},
{
"transition": "Call Infection Submodule"
}
]
}
},
"gmf_version": 2
}

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src/main/resources/modules/covid19/determine_risk.json Normal file
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{
"name": "determine_risk",
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Determine Risk",
"remarks": [
"Assess patient comorbidities and set attribute (covid19_risk):",
" - (high) if patient has comorbidity impacting risks",
" - (low) if patient has no comorbidity impacting risks"
]
},
"Terminal": {
"type": "Terminal"
},
"Determine Risk": {
"type": "Simple",
"conditional_transition": [
{
"transition": "High Risk of Severe Disease",
"condition": {
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "diabetes",
"operator": "==",
"value": true
},
{
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "hypertension",
"operator": "==",
"value": true
},
{
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "copd_variant",
"operator": "is not nil"
},
{
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "Cystic_Fibrosis",
"operator": "is not nil"
},
{
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "asthma_condition",
"operator": "is not nil"
},
{
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "smoker",
"operator": "==",
"value": true
},
{
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "coronary_heart_disease",
"operator": "==",
"value": true
},
{
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "chf",
"operator": "is not nil"
},
{
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "homelessness_category",
"operator": "==",
"value": "chronic"
},
{
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "lung_cancer",
"operator": "==",
"value": true
},
{
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "colorectal_cancer_stage",
"operator": "is not nil"
},
{
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "breast_cancer_condition",
"operator": "is not nil"
},
{
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "lupus_careplan",
"operator": "is not nil"
},
{
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "ra_careplan",
"operator": "is not nil"
},
{
"condition_type": "Vital Sign",
"vital_sign": "BMI",
"operator": ">=",
"value": 40
}
]
}
]
}
]
}
]
}
]
}
]
}
]
}
]
}
]
}
]
}
]
}
]
}
]
}
]
}
},
{
"transition": "Low Risk of Severe Disease"
}
]
},
"High Risk of Severe Disease": {
"type": "SetAttribute",
"attribute": "covid19_risk",
"direct_transition": "Determine Severity",
"value": "high"
},
"Low Risk of Severe Disease": {
"type": "SetAttribute",
"attribute": "covid19_risk",
"direct_transition": "Determine Severity",
"value": "low"
},
"Determine Severity": {
"type": "Simple",
"lookup_table_transition": [
{
"transition": "Negative Severity",
"lookup_table_name": "covid-19-severity-outcomes.csv",
"default_probability": 0.85
},
{
"transition": "General Severity",
"lookup_table_name": "covid-19-severity-outcomes.csv",
"default_probability": 0.05
},
{
"transition": "Severe Severity",
"lookup_table_name": "covid-19-severity-outcomes.csv",
"default_probability": 0.05
},
{
"transition": "Critical Severity",
"default_probability": 0.05,
"lookup_table_name": "covid-19-severity-outcomes.csv"
}
]
},
"Negative Severity": {
"type": "SetAttribute",
"attribute": "covid19_severity",
"direct_transition": "Survival: Survivor",
"value": "negative"
},
"Severe Severity": {
"type": "SetAttribute",
"attribute": "covid19_severity",
"direct_transition": "Determine Survival",
"value": "severe"
},
"Determine Survival": {
"type": "Simple",
"lookup_table_transition": [
{
"transition": "Survival: Survivor",
"lookup_table_name": "covid-19-survival-outcomes.csv",
"default_probability": 0.8
},
{
"transition": "Survival: Non-Survivor",
"lookup_table_name": "covid-19-survival-outcomes.csv",
"default_probability": 0.2
}
]
},
"Survival: Survivor": {
"type": "SetAttribute",
"attribute": "covid19_death",
"direct_transition": "Terminal",
"value": false
},
"Survival: Non-Survivor": {
"type": "SetAttribute",
"attribute": "covid19_death",
"direct_transition": "Terminal",
"value": true
},
"General Severity": {
"type": "SetAttribute",
"attribute": "covid19_severity",
"direct_transition": "Determine Survival",
"value": "general"
},
"Critical Severity": {
"type": "SetAttribute",
"attribute": "covid19_severity",
"direct_transition": "Determine Survival",
"value": "critical"
}
},
"remarks": [
"This submodule determines covid19 risk, severity, and death."
],
"gmf_version": 1
}

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src/main/resources/modules/covid19/diagnose_bacterial_infection.json Normal file
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{
"name": "diagnose_bacterial_infection",
"remarks": [
"Zhou shows that only 15% (survivors + non-survivors) of patients had a secondary bacterial infection (positive culture). Given a daily probability of 2.5%, this should result around 13% for survivors and 18% for non-survivors, based on length of stay."
],
"states": {
"Initial": {
"type": "Initial",
"conditional_transition": [
{
"transition": "Check for Bacterial Infection",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_bacterial_infection",
"operator": "is nil"
}
},
{
"transition": "Terminal"
}
]
},
"Terminal": {
"type": "Terminal"
},
"Check for Bacterial Infection": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.025,
"transition": "Take Culture"
},
{
"transition": "Terminal",
"distribution": 0.9750000000000001
}
]
},
"Bacterial Infection": {
"type": "ConditionOnset",
"assign_to_attribute": "covid19_bacterial_infection",
"codes": [
{
"system": "SNOMED-CT",
"code": "87628006",
"display": "Bacterial infectious disease (disorder)"
}
],
"direct_transition": "Terminal"
},
"Take Culture": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "61594008",
"display": "Microbial culture (procedure)"
}
],
"duration": {
"low": 5,
"high": 10,
"unit": "minutes"
},
"direct_transition": "Bacterial Infection"
}
},
"gmf_version": 1
}

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src/main/resources/modules/covid19/diagnose_blood_clot.json Normal file
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{
"name": "diagnose_blood_clot",
"remarks": [
"At some point, both patients on the floor and ICU should develop a clot (i.e. the following diagnoses)",
"•\tAcute pulmonary embolism (PE) ",
"•\tAcute deep venous thrombosis (VT)",
"**Coagulopathy is not sufficient, see discussion below. ",
"",
"Suggestion would be to have individuals with higher d-dimers develop clots since d-dimer increases are associated with clot formation. Normal d-dimer range is 0.0 - 0.49.",
""
],
"states": {
"Initial": {
"type": "Initial",
"conditional_transition": [
{
"transition": "Initialize",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_diagnosed_clot",
"operator": "is nil"
}
},
{
"transition": "Terminal",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_diagnosed_clot",
"operator": "==",
"value": true
}
},
{
"transition": "Check D-Dimer"
}
]
},
"Terminal": {
"type": "Terminal"
},
"Initialize": {
"type": "Simple",
"direct_transition": "No Diagnosed Clots"
},
"Check D-Dimer": {
"type": "Simple",
"conditional_transition": [
{
"transition": "Diagnose Clot",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_ddimer",
"operator": ">=",
"value": 0.5
}
},
{
"transition": "Terminal"
}
]
},
"Diagnose Clot": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Diagnose Acute Pulmonary Embolism",
"distribution": 0.1
},
{
"transition": "Diagnose Acute Deep Venous Thrombosis",
"distribution": 0.1
},
{
"transition": "Terminal",
"distribution": 0.8
}
]
},
"Diagnose Acute Pulmonary Embolism": {
"type": "ConditionOnset",
"assign_to_attribute": "covid19_clot",
"codes": [
{
"system": "SNOMED-CT",
"code": "706870000",
"display": "Acute pulmonary embolism (disorder)"
}
],
"direct_transition": "Diagnosed Clots"
},
"Diagnose Acute Deep Venous Thrombosis": {
"type": "ConditionOnset",
"assign_to_attribute": "covid19_clot",
"codes": [
{
"system": "SNOMED-CT",
"code": "132281000119108",
"display": "Acute deep venous thrombosis (disorder)"
}
],
"direct_transition": "Diagnosed Clots"
},
"Diagnosed Clots": {
"type": "SetAttribute",
"attribute": "covid19_diagnosed_clot",
"direct_transition": "Terminal",
"value": true
},
"No Diagnosed Clots": {
"type": "SetAttribute",
"attribute": "covid19_diagnosed_clot",
"value": false,
"direct_transition": "Check D-Dimer"
}
},
"gmf_version": 1
}

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{
"name": "end_outcomes",
"remarks": [
"This module ends patient outcomes from covid19 according to Table 2 from https://doi.org/10.1016/S0140-6736(20)30566-3"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "End ARDS"
},
"Terminal": {
"type": "Terminal"
},
"End Pneumonia": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "233604007",
"display": "Pneumonia (disorder)"
}
],
"direct_transition": "End Hypoxemia"
},
"End ARDS": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "67782005",
"display": "Acute respiratory distress syndrome (disorder)"
}
],
"direct_transition": "End Acute Cardiac Injury"
},
"End Sepsis": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "770349000",
"display": "Sepsis caused by virus (disorder)"
}
],
"direct_transition": "End Septic Shock"
},
"End Septic Shock": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "76571007",
"display": "Septic shock (disorder)"
}
],
"direct_transition": "End Covid19"
},
"End Heart Failure": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "84114007",
"display": "Heart failure (disorder)"
}
],
"direct_transition": "End Pneumonia"
},
"End Acute Cardiac Injury": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "86175003",
"display": "Injury of heart (disorder)"
}
],
"direct_transition": "End Acute Kidney Injury"
},
"End Acute Kidney Injury": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "40095003",
"display": "Injury of kidney (disorder)"
}
],
"direct_transition": "End Coagulopathy"
},
"End Coagulopathy": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "234466008",
"display": "Acquired coagulation disorder (disorder)"
}
],
"direct_transition": "End Pulmonary Embolism"
},
"End Mild Respiratory Distress": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "271825005",
"display": "Respiratory distress (finding)"
}
],
"direct_transition": "End Respiratory Failure"
},
"End Respiratory Failure": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "65710008",
"display": "Acute respiratory failure (disorder)"
}
],
"remarks": [
"67 of 173 (38.7% round up to 40%) severe patients required mechanical ventilation."
],
"direct_transition": "End Sepsis"
},
"End Covid19": {
"type": "ConditionEnd",
"direct_transition": "Terminal",
"referenced_by_attribute": "covid19"
},
"End Pulmonary Embolism": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "706870000",
"display": "Acute pulmonary embolism (disorder)"
}
],
"direct_transition": "End Venous Thrombosis"
},
"End Venous Thrombosis": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "132281000119108",
"display": "Acute deep venous thrombosis (disorder)"
}
],
"direct_transition": "End Heart Failure"
},
"End Hypoxemia": {
"type": "ConditionEnd",
"direct_transition": "End Mild Respiratory Distress",
"codes": [
{
"system": "SNOMED-CT",
"code": "389087006",
"display": "Hypoxemia (disorder)"
}
]
}
},
"gmf_version": 1
}

217
src/main/resources/modules/covid19/end_symptoms.json Normal file
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{
"name": "end_symptoms",
"remarks": [
"This submodule ends symptoms of COVID19 according to the rates documented in Table 1 of https://www.nejm.org/doi/full/10.1056/NEJMoa2002032",
"",
"Loss of taste from Table 2 of ",
"https://jamanetwork.com/journals/jama/fullarticle/2765183"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Chills End"
},
"Terminal": {
"type": "Terminal"
},
"Conjunctival Congestion End": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "246677007",
"display": "Passive conjunctival congestion (finding)"
}
],
"direct_transition": "Cough End"
},
"Nasal Congestion End": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "68235000",
"display": "Nasal congestion (finding)"
}
],
"direct_transition": "Nausea End"
},
"Headache End": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "25064002",
"display": "Headache (finding)"
}
],
"direct_transition": "Hemoptysis End"
},
"Cough End": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "49727002",
"display": "Cough (finding)"
}
],
"direct_transition": "Diarrhea End"
},
"Sore Throat End": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "267102003",
"display": "Sore throat (finding)"
}
],
"direct_transition": "Sputum Production End"
},
"Sputum Production End": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "248595008",
"display": "Sputum finding (finding)"
}
],
"direct_transition": "Vomiting End"
},
"Fatigue End": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "84229001",
"display": "Fatigue (finding)"
}
],
"direct_transition": "Fever End"
},
"Hemoptysis End": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "66857006",
"display": "Hemoptysis (finding)"
}
],
"direct_transition": "Joint Pain End"
},
"Shortness of Breath End": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "267036007",
"display": "Dyspnea (finding)"
}
],
"direct_transition": "Wheezing End"
},
"Nausea End": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "422587007",
"display": "Nausea (finding)"
}
],
"direct_transition": "Shortness of Breath End"
},
"Vomiting End": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "249497008",
"display": "Vomiting symptom (finding)"
}
],
"direct_transition": "Loss of Taste End"
},
"Diarrhea End": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "267060006",
"display": "Diarrhea symptom (finding)"
}
],
"direct_transition": "Fatigue End"
},
"Muscle Pain End": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "68962001",
"display": "Muscle pain (finding)"
}
],
"direct_transition": "Nasal Congestion End"
},
"Joint Pain End": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "57676002",
"display": "Joint pain (finding)"
}
],
"direct_transition": "Muscle Pain End"
},
"Chills End": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "43724002",
"display": "Chill (finding)"
}
],
"direct_transition": "Conjunctival Congestion End"
},
"Fever End": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "386661006",
"display": "Fever (finding)"
}
],
"direct_transition": "Headache End"
},
"Loss of Taste End": {
"type": "ConditionEnd",
"direct_transition": "Terminal",
"codes": [
{
"system": "SNOMED-CT",
"code": "36955009",
"display": "Loss of taste (finding)"
}
]
},
"Wheezing End": {
"type": "ConditionEnd",
"codes": [
{
"system": "SNOMED-CT",
"code": "56018004",
"display": "Wheezing (finding)"
}
],
"direct_transition": "Sore Throat End"
}
},
"gmf_version": 1
}

1253
src/main/resources/modules/covid19/infection.json Normal file
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932
src/main/resources/modules/covid19/measurements_daily.json Normal file
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{
"name": "measurements_daily",
"remarks": [
"Daily observations and labs during hospitalization and ICU."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Record Vitals"
},
"Terminal": {
"type": "Terminal"
},
"CBC": {
"type": "DiagnosticReport",
"codes": [
{
"system": "LOINC",
"code": "58410-2",
"display": "CBC panel - Blood by Automated count"
}
],
"observations": [
{
"category": "laboratory",
"unit": "10*3/uL",
"codes": [
{
"system": "LOINC",
"code": "6690-2",
"display": "Leukocytes [#/volume] in Blood by Automated count"
}
],
"range": {
"low": 3,
"high": 4
}
},
{
"category": "laboratory",
"unit": "10*6/uL",
"codes": [
{
"system": "LOINC",
"code": "789-8",
"display": "Erythrocytes [#/volume] in Blood by Automated count"
}
],
"range": {
"low": 3.77,
"high": 5.8
}
},
{
"category": "laboratory",
"unit": "g/dL",
"codes": [
{
"system": "LOINC",
"code": "718-7",
"display": "Hemoglobin [Mass/volume] in Blood"
}
],
"range": {
"low": 11.1,
"high": 14.1
}
},
{
"category": "laboratory",
"unit": "%",
"codes": [
{
"system": "LOINC",
"code": "4544-3",
"display": "Hematocrit [Volume Fraction] of Blood by Automated count"
}
],
"range": {
"low": 37.5,
"high": 46.6
}
},
{
"category": "laboratory",
"unit": "fL",
"codes": [
{
"system": "LOINC",
"code": "787-2",
"display": "MCV [Entitic volume] by Automated count"
}
],
"range": {
"low": 79,
"high": 97
}
},
{
"category": "laboratory",
"unit": "pg",
"codes": [
{
"system": "LOINC",
"code": "785-6",
"display": "MCH [Entitic mass] by Automated count"
}
],
"range": {
"low": 26.6,
"high": 33
}
},
{
"category": "laboratory",
"unit": "g/dL",
"codes": [
{
"system": "LOINC",
"code": "786-4",
"display": "MCHC [Mass/volume] by Automated count"
}
],
"range": {
"low": 31.5,
"high": 35.7
}
},
{
"category": "laboratory",
"unit": "%",
"codes": [
{
"system": "LOINC",
"code": "788-0",
"display": "Erythrocyte distribution width [Ratio] by Automated count"
}
],
"range": {
"low": 12.3,
"high": 15.4
}
},
{
"category": "laboratory",
"unit": "10*3/uL",
"codes": [
{
"system": "LOINC",
"code": "777-3",
"display": "Platelets [#/volume] in Blood by Automated count"
}
],
"range": {
"low": 99,
"high": 150
}
}
],
"remarks": [
"In the most severe patients, white-cell counts should be less than 4000 per mm3",
"In the most severe patients, platelet counts should also trend towards being less than 150K per mm3",
"In the most severe patients, median hemoglobin should be around 12.8 g/dL"
],
"direct_transition": "CBC_Differential"
},
"CBC_Differential": {
"type": "DiagnosticReport",
"codes": [
{
"system": "LOINC",
"code": "57023-4",
"display": "Auto Differential panel - Blood"
}
],
"observations": [
{
"category": "laboratory",
"unit": "%",
"codes": [
{
"system": "LOINC",
"code": "770-8",
"display": "Neutrophils/100 leukocytes in Blood by Automated count"
}
],
"range": {
"low": 10,
"high": 45
}
},
{
"category": "laboratory",
"unit": "%",
"codes": [
{
"system": "LOINC",
"code": "736-9",
"display": "Lymphocytes/100 leukocytes in Blood by Automated count"
}
],
"range": {
"low": 5,
"high": 25
}
},
{
"category": "laboratory",
"unit": "%",
"codes": [
{
"system": "LOINC",
"code": "5905-5",
"display": "Monocytes/100 leukocytes in Blood by Automated count"
}
],
"range": {
"low": 5,
"high": 15
}
},
{
"category": "laboratory",
"unit": "%",
"codes": [
{
"system": "LOINC",
"code": "713-8",
"display": "Eosinophils/100 leukocytes in Blood by Automated count"
}
],
"range": {
"low": 3,
"high": 6
}
},
{
"category": "laboratory",
"unit": "%",
"codes": [
{
"system": "LOINC",
"code": "706-2",
"display": "Basophils/100 leukocytes in Blood by Automated count"
}
],
"range": {
"low": 2,
"high": 4
}
},
{
"category": "laboratory",
"unit": "10*3/uL",
"codes": [
{
"system": "LOINC",
"code": "751-8",
"display": "Neutrophils [#/volume] in Blood by Automated count"
}
],
"range": {
"low": 1.4,
"high": 4
}
},
{
"category": "laboratory",
"unit": "10*3/uL",
"codes": [
{
"system": "LOINC",
"code": "731-0",
"display": "Lymphocytes [#/volume] in Blood by Automated count"
}
],
"attribute": "covid19_lymphocytes"
},
{
"category": "laboratory",
"unit": "10*3/uL",
"codes": [
{
"system": "LOINC",
"code": "742-7",
"display": "Monocytes [#/volume] in Blood by Automated count"
}
],
"range": {
"low": 0.5,
"high": 1.4
}
},
{
"category": "laboratory",
"unit": "10*3/uL",
"codes": [
{
"system": "LOINC",
"code": "711-2",
"display": "Eosinophils [#/volume] in Blood by Automated count"
}
],
"range": {
"low": 0.2,
"high": 0.6
}
},
{
"category": "laboratory",
"unit": "10*3/uL",
"codes": [
{
"system": "LOINC",
"code": "704-7",
"display": "Basophils [#/volume] in Blood by Automated count"
}
],
"range": {
"low": 0.2,
"high": 0.4
}
}
],
"remarks": [
"Viral infection should show DECREASES in neutro and lymph, and INCREASES in mono, eosino, and baso."
],
"conditional_transition": [
{
"condition": {
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "ckd",
"operator": "is not nil"
},
{
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "40095003",
"display": "Injury of kidney (disorder)"
}
]
}
]
},
"transition": "Comprehensive Metabolic Panel with Kidney Damage"
},
{
"transition": "Comprehensive Metabolic Panel with Normal Kidney"
}
]
},
"Ventilation Check": {
"type": "Simple",
"conditional_transition": [
{
"transition": "Arterial Blood Gas",
"condition": {
"condition_type": "Or",
"conditions": [
{
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "65710008",
"display": "Acute respiratory failure (disorder)"
}
]
},
{
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "76571007",
"display": "Septic shock (disorder)"
}
]
}
]
}
},
{
"transition": "Terminal"
}
]
},
"Arterial Blood Gas": {
"type": "DiagnosticReport",
"codes": [
{
"system": "LOINC",
"code": "24336-0",
"display": "Gas panel - Arterial blood"
}
],
"observations": [
{
"category": "laboratory",
"unit": "[pH]",
"codes": [
{
"system": "LOINC",
"code": "2744-1",
"display": "pH of Arterial blood"
}
],
"range": {
"low": 6.8,
"high": 7.3
}
},
{
"category": "laboratory",
"unit": "mm[Hg]",
"codes": [
{
"system": "LOINC",
"code": "2019-8",
"display": "Carbon dioxide [Partial pressure] in Arterial blood"
}
],
"range": {
"low": 35,
"high": 45
}
},
{
"category": "laboratory",
"unit": "mm[Hg]",
"codes": [
{
"system": "LOINC",
"code": "2703-7",
"display": "Oxygen [Partial pressure] in Arterial blood"
}
],
"attribute": "covid19_pao2"
},
{
"category": "laboratory",
"unit": "mmol/L",
"codes": [
{
"system": "LOINC",
"code": "1960-4",
"display": "Bicarbonate [Moles/volume] in Arterial blood"
}
],
"range": {
"low": 22,
"high": 27
}
},
{
"category": "vital-signs",
"unit": "%",
"codes": [
{
"system": "LOINC",
"code": "2708-6",
"display": "Oxygen saturation in Arterial blood"
},
{
"system": "LOINC",
"code": "59408-5",
"display": "Oxygen saturation in Arterial blood by Pulse oximetry"
}
],
"vital_sign": "Oxygen Saturation"
}
],
"direct_transition": "Record FiO2"
},
"Comprehensive Metabolic Panel with Normal Kidney": {
"type": "DiagnosticReport",
"codes": [
{
"system": "LOINC",
"code": "24323-8",
"display": "Comprehensive metabolic 2000 panel - Serum or Plasma"
}
],
"observations": [
{
"category": "laboratory",
"vital_sign": "Glucose",
"codes": [
{
"system": "LOINC",
"code": "2345-7",
"display": "Glucose [Mass/volume] in Serum or Plasma"
}
],
"unit": "mg/dL"
},
{
"category": "laboratory",
"vital_sign": "Urea Nitrogen",
"codes": [
{
"system": "LOINC",
"code": "3094-0",
"display": "Urea nitrogen [Mass/volume] in Serum or Plasma"
}
],
"unit": "mg/dL"
},
{
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "2160-0",
"display": "Creatinine [Mass/volume] in Serum or Plasma"
}
],
"unit": "mg/dL",
"vital_sign": "Creatinine"
},
{
"category": "laboratory",
"vital_sign": "Calcium",
"codes": [
{
"system": "LOINC",
"code": "17861-6",
"display": "Calcium [Mass/volume] in Serum or Plasma"
}
],
"unit": "mg/dL"
},
{
"category": "laboratory",
"vital_sign": "Sodium",
"codes": [
{
"system": "LOINC",
"code": "2951-2",
"display": "Sodium [Moles/volume] in Serum or Plasma"
}
],
"unit": "mmol/L"
},
{
"category": "laboratory",
"vital_sign": "Potassium",
"codes": [
{
"system": "LOINC",
"code": "2823-3",
"display": "Potassium [Moles/volume] in Serum or Plasma"
}
],
"unit": "mmol/L"
},
{
"category": "laboratory",
"vital_sign": "Chloride",
"codes": [
{
"system": "LOINC",
"code": "2075-0",
"display": "Chloride [Moles/volume] in Serum or Plasma"
}
],
"unit": "mmol/L"
},
{
"category": "laboratory",
"vital_sign": "Carbon Dioxide",
"codes": [
{
"system": "LOINC",
"code": "2028-9",
"display": "Carbon dioxide, total [Moles/volume] in Serum or Plasma"
}
],
"unit": "mmol/L"
},
{
"category": "laboratory",
"unit": "mL/min",
"codes": [
{
"system": "LOINC",
"code": "33914-3",
"display": "Glomerular filtration rate/1.73 sq M.predicted [Volume Rate/Area] in Serum or Plasma by Creatinine-based formula (MDRD)"
}
],
"vital_sign": "EGFR"
},
{
"category": "laboratory",
"unit": "g/dL",
"codes": [
{
"system": "LOINC",
"code": "2885-2",
"display": "Protein [Mass/volume] in Serum or Plasma"
}
],
"range": {
"low": 5.5,
"high": 8
}
},
{
"category": "laboratory",
"unit": "g/dL",
"codes": [
{
"system": "LOINC",
"code": "1751-7",
"display": "Albumin [Mass/volume] in Serum or Plasma"
}
],
"range": {
"low": 3.5,
"high": 5.5
}
},
{
"category": "laboratory",
"unit": "mg/dL",
"codes": [
{
"system": "LOINC",
"code": "1975-2",
"display": "Bilirubin.total [Mass/volume] in Serum or Plasma"
}
],
"range": {
"low": 0.3,
"high": 1.2
}
},
{
"category": "laboratory",
"unit": "U/L",
"codes": [
{
"system": "LOINC",
"code": "6768-6",
"display": "Alkaline phosphatase [Enzymatic activity/volume] in Serum or Plasma"
}
],
"range": {
"low": 39,
"high": 117
}
},
{
"category": "laboratory",
"unit": "U/L",
"codes": [
{
"system": "LOINC",
"code": "1742-6",
"display": "Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma"
}
],
"range": {
"low": 0,
"high": 44
}
},
{
"category": "laboratory",
"unit": "U/L",
"codes": [
{
"system": "LOINC",
"code": "1920-8",
"display": "Aspartate aminotransferase [Enzymatic activity/volume] in Serum or Plasma"
}
],
"range": {
"low": 0,
"high": 40
}
}
],
"direct_transition": "Ventilation Check"
},
"Comprehensive Metabolic Panel with Kidney Damage": {
"type": "DiagnosticReport",
"codes": [
{
"system": "LOINC",
"code": "24323-8",
"display": "Comprehensive metabolic 2000 panel - Serum or Plasma"
}
],
"observations": [
{
"category": "laboratory",
"vital_sign": "Glucose",
"codes": [
{
"system": "LOINC",
"code": "2345-7",
"display": "Glucose [Mass/volume] in Serum or Plasma"
}
],
"unit": "mg/dL"
},
{
"category": "laboratory",
"vital_sign": "Urea Nitrogen",
"codes": [
{
"system": "LOINC",
"code": "3094-0",
"display": "Urea nitrogen [Mass/volume] in Serum or Plasma"
}
],
"unit": "mg/dL"
},
{
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "2160-0",
"display": "Creatinine [Mass/volume] in Serum or Plasma"
}
],
"unit": "mg/dL",
"range": {
"low": 2.5,
"high": 3
}
},
{
"category": "laboratory",
"vital_sign": "Calcium",
"codes": [
{
"system": "LOINC",
"code": "17861-6",
"display": "Calcium [Mass/volume] in Serum or Plasma"
}
],
"unit": "mg/dL"
},
{
"category": "laboratory",
"vital_sign": "Sodium",
"codes": [
{
"system": "LOINC",
"code": "2951-2",
"display": "Sodium [Moles/volume] in Serum or Plasma"
}
],
"unit": "mmol/L"
},
{
"category": "laboratory",
"vital_sign": "Potassium",
"codes": [
{
"system": "LOINC",
"code": "2823-3",
"display": "Potassium [Moles/volume] in Serum or Plasma"
}
],
"unit": "mmol/L"
},
{
"category": "laboratory",
"vital_sign": "Chloride",
"codes": [
{
"system": "LOINC",
"code": "2075-0",
"display": "Chloride [Moles/volume] in Serum or Plasma"
}
],
"unit": "mmol/L"
},
{
"category": "laboratory",
"vital_sign": "Carbon Dioxide",
"codes": [
{
"system": "LOINC",
"code": "2028-9",
"display": "Carbon dioxide, total [Moles/volume] in Serum or Plasma"
}
],
"unit": "mmol/L"
},
{
"category": "laboratory",
"unit": "mL/min",
"codes": [
{
"system": "LOINC",
"code": "33914-3",
"display": "Glomerular filtration rate/1.73 sq M.predicted [Volume Rate/Area] in Serum or Plasma by Creatinine-based formula (MDRD)"
}
],
"range": {
"low": 5,
"high": 14
}
},
{
"category": "laboratory",
"unit": "g/dL",
"codes": [
{
"system": "LOINC",
"code": "2885-2",
"display": "Protein [Mass/volume] in Serum or Plasma"
}
],
"range": {
"low": 5.5,
"high": 8
}
},
{
"category": "laboratory",
"unit": "g/dL",
"codes": [
{
"system": "LOINC",
"code": "1751-7",
"display": "Albumin [Mass/volume] in Serum or Plasma"
}
],
"range": {
"low": 3.5,
"high": 5.5
}
},
{
"category": "laboratory",
"unit": "mg/dL",
"codes": [
{
"system": "LOINC",
"code": "1975-2",
"display": "Bilirubin.total [Mass/volume] in Serum or Plasma"
}
],
"range": {
"low": 6,
"high": 15
}
},
{
"category": "laboratory",
"unit": "U/L",
"codes": [
{
"system": "LOINC",
"code": "6768-6",
"display": "Alkaline phosphatase [Enzymatic activity/volume] in Serum or Plasma"
}
],
"range": {
"low": 39,
"high": 117
}
},
{
"category": "laboratory",
"unit": "U/L",
"codes": [
{
"system": "LOINC",
"code": "1742-6",
"display": "Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma"
}
],
"range": {
"low": 0,
"high": 44
}
},
{
"category": "laboratory",
"unit": "U/L",
"codes": [
{
"system": "LOINC",
"code": "1920-8",
"display": "Aspartate aminotransferase [Enzymatic activity/volume] in Serum or Plasma"
}
],
"range": {
"low": 0,
"high": 40
}
}
],
"direct_transition": "Ventilation Check"
},
"Record FiO2": {
"type": "Observation",
"category": "laboratory",
"unit": "%",
"codes": [
{
"system": "LOINC",
"code": "19994-3",
"display": "Oxygen/Total gas setting [Volume Fraction] Ventilator"
}
],
"direct_transition": "Terminal",
"range": {
"low": 30,
"high": 100
}
},
"Record Vitals": {
"type": "CallSubmodule",
"submodule": "covid19/measurements_vitals",
"direct_transition": "CBC"
}
},
"gmf_version": 1
}

222
src/main/resources/modules/covid19/measurements_frequent.json Normal file
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{
"name": "measurements_frequent",
"remarks": [
"Frequent observations and labs during hospitalization and ICU."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "D_Dimer"
},
"Terminal": {
"type": "Terminal"
},
"D_Dimer": {
"type": "Observation",
"category": "laboratory",
"unit": "ug/mL",
"codes": [
{
"system": "LOINC",
"code": "48065-7",
"display": "Fibrin D-dimer FEU [Mass/volume] in Platelet poor plasma"
}
],
"attribute": "covid19_ddimer",
"conditional_transition": [
{
"transition": "Interleukin_6_Rarely_Used_Clinical_Trial_Patients_Only",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_clinical_trial",
"operator": "==",
"value": "toclizumab"
}
},
{
"transition": "Serum_Ferritin"
}
]
},
"Interleukin_6_Rarely_Used_Clinical_Trial_Patients_Only": {
"type": "DiagnosticReport",
"codes": [
{
"system": "LOINC",
"code": "82335-1",
"display": "Cytokines panel - Serum or Plasma"
}
],
"observations": [
{
"category": "laboratory",
"unit": "pg/mL",
"codes": [
{
"system": "LOINC",
"code": "26881-3",
"display": "Interleukin 6 [Mass/volume] in Serum or Plasma"
}
],
"attribute": "covid19_interleukin6"
}
],
"remarks": [
"Small percentage of patients will have this. 3%"
],
"direct_transition": "Serum_Ferritin"
},
"Serum_Ferritin": {
"type": "DiagnosticReport",
"codes": [
{
"system": "LOINC",
"code": "75689-0",
"display": "Iron panel - Serum or Plasma"
}
],
"observations": [
{
"category": "laboratory",
"unit": "ug/L",
"codes": [
{
"system": "LOINC",
"code": "2276-4",
"display": "Ferritin [Mass/volume] in Serum or Plasma"
}
],
"attribute": "covid19_ferritin"
}
],
"direct_transition": "High_Sensitivity_Cardiac_Troponin_I"
},
"High_Sensitivity_Cardiac_Troponin_I": {
"type": "DiagnosticReport",
"codes": [
{
"system": "LOINC",
"code": "89577-1",
"display": "Troponin I.cardiac panel - Serum or Plasma by High sensitivity method"
}
],
"observations": [
{
"category": "laboratory",
"unit": "pg/mL",
"codes": [
{
"system": "LOINC",
"code": "89579-7",
"display": "Troponin I.cardiac [Mass/volume] in Serum or Plasma by High sensitivity method"
}
],
"attribute": "covid19_cardiac_troponin"
}
],
"direct_transition": "Lactate_Dehydrogenase"
},
"Lactate_Dehydrogenase": {
"type": "Observation",
"category": "laboratory",
"unit": "U/L",
"codes": [
{
"system": "LOINC",
"code": "14804-9",
"display": "Lactate dehydrogenase [Enzymatic activity/volume] in Serum or Plasma by Lactate to pyruvate reaction"
},
{
"system": "LOINC",
"code": "2532-0",
"display": "Lactate dehydrogenase [Enzymatic activity/volume] in Serum or Plasma"
}
],
"attribute": "covid19_lactate_dehydrogenase",
"remarks": [
"TODO: Should be part of the Panel 42929-0 Lactate dehydrogenase panel - Serum or Plasma, but there are too many other required values that we do not know the ranges for."
],
"direct_transition": "Creatine Kinase"
},
"C-Reactive Protein": {
"type": "Observation",
"category": "laboratory",
"unit": "mg/L",
"codes": [
{
"system": "LOINC",
"code": "1988-5",
"display": "C reactive protein [Mass/volume] in Serum or Plasma"
}
],
"direct_transition": "Prothrombin_Time",
"attribute": "covid19_c_reactive_protein"
},
"Creatine Kinase": {
"type": "Observation",
"category": "laboratory",
"unit": "U/L",
"codes": [
{
"system": "LOINC",
"code": "2157-6",
"display": "Creatine kinase [Enzymatic activity/volume] in Serum or Plasma"
}
],
"direct_transition": "C-Reactive Protein",
"attribute": "covid19_creatine_kinase"
},
"Prothrombin_Time": {
"type": "DiagnosticReport",
"codes": [
{
"system": "LOINC",
"code": "34528-0",
"display": "PT panel - Platelet poor plasma by Coagulation assay"
}
],
"observations": [
{
"category": "laboratory",
"unit": "s",
"codes": [
{
"system": "LOINC",
"code": "5902-2",
"display": "Prothrombin time (PT)"
}
],
"attribute": "covid19_pt"
},
{
"category": "laboratory",
"unit": "{INR}",
"codes": [
{
"system": "LOINC",
"code": "6301-6",
"display": "INR in Platelet poor plasma by Coagulation assay"
}
],
"attribute": "covid19_inr"
}
],
"direct_transition": "Procalcitonin"
},
"Procalcitonin": {
"type": "Observation",
"category": "laboratory",
"unit": "ng/mL",
"codes": [
{
"system": "LOINC",
"code": "33959-8",
"display": "Procalcitonin [Mass/volume] in Serum or Plasma"
}
],
"direct_transition": "Terminal",
"attribute": "covid19_procalcitonin"
}
},
"gmf_version": 1
}

143
src/main/resources/modules/covid19/measurements_vitals.json Normal file
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{
"name": "measurements_vitals",
"remarks": [
"Vitals taken in the covid19 module."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Temperature"
},
"Terminal": {
"type": "Terminal"
},
"Temperature": {
"type": "Observation",
"category": "vital-signs",
"unit": "Cel",
"codes": [
{
"system": "LOINC",
"code": "8310-5",
"display": "Body temperature"
},
{
"system": "LOINC",
"code": "8331-1",
"display": "Oral temperature"
}
],
"range": {
"low": 37.7,
"high": 42.2
},
"direct_transition": "Respiratory Rate"
},
"Oxygen Saturation": {
"type": "Observation",
"category": "vital-signs",
"unit": "%",
"codes": [
{
"system": "LOINC",
"code": "2708-6",
"display": "Oxygen saturation in Arterial blood"
},
{
"system": "LOINC",
"code": "59408-5",
"display": "Oxygen saturation in Arterial blood by Pulse oximetry"
}
],
"vital_sign": "Oxygen Saturation",
"direct_transition": "Blood Pressure"
},
"Blood Pressure": {
"type": "MultiObservation",
"category": "vital-signs",
"codes": [
{
"system": "LOINC",
"code": "85354-9",
"display": "Blood pressure panel with all children optional"
}
],
"observations": [
{
"category": "vital-signs",
"vital_sign": "Systolic Blood Pressure",
"codes": [
{
"system": "LOINC",
"code": "8480-6",
"display": "Systolic Blood Pressure"
}
],
"unit": "mm[Hg]"
},
{
"category": "vital-signs",
"vital_sign": "Diastolic Blood Pressure",
"codes": [
{
"system": "LOINC",
"code": "8462-4",
"display": "Diastolic Blood Pressure"
}
],
"unit": "mm[Hg]"
}
],
"direct_transition": "Body Weight"
},
"Body Weight": {
"type": "Observation",
"category": "vital-signs",
"vital_sign": "Weight",
"codes": [
{
"system": "LOINC",
"code": "29463-7",
"display": "Body Weight"
}
],
"unit": "kg",
"direct_transition": "Terminal"
},
"Respiratory Rate": {
"type": "Observation",
"category": "vital-signs",
"unit": "/min",
"codes": [
{
"system": "LOINC",
"code": "9279-1",
"display": "Respiratory rate"
}
],
"direct_transition": "Heart Rate",
"range": {
"low": 12,
"high": 40
}
},
"Heart Rate": {
"type": "Observation",
"category": "vital-signs",
"unit": "/min",
"codes": [
{
"system": "LOINC",
"code": "8867-4",
"display": "Heart rate"
}
],
"direct_transition": "Oxygen Saturation",
"range": {
"low": 50,
"high": 200
}
}
},
"gmf_version": 1
}

1054
src/main/resources/modules/covid19/medications.json Normal file
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514
src/main/resources/modules/covid19/nonsurvivor_lab_values.json Normal file
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{
"name": "nonsurvivor_lab_values",
"remarks": [
"Based on Figure 2 from https://doi.org/10.1016/S0140-6736(20)30566-3"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Set Creatine Kinase"
},
"Terminal": {
"type": "Terminal"
},
"Day": {
"type": "Simple",
"conditional_transition": [
{
"transition": "DDimer_4",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_admission_days",
"operator": "<",
"value": 7
}
},
{
"transition": "DDimer_7",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_admission_days",
"operator": "<",
"value": 10
}
},
{
"transition": "DDimer_10",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_admission_days",
"operator": "<",
"value": 13
}
},
{
"transition": "DDimer_13",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_admission_days",
"operator": "<",
"value": 16
}
},
{
"transition": "DDimer_16",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_admission_days",
"operator": "<",
"value": 19
}
},
{
"transition": "DDimer_19",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_admission_days",
"operator": "==",
"value": 22
}
},
{
"transition": "DDimer_22"
}
]
},
"DDimer_4": {
"type": "SetAttribute",
"attribute": "covid19_ddimer",
"range": {
"low": 1,
"high": 2
},
"direct_transition": "Lymphocytes_4"
},
"DDimer_7": {
"type": "SetAttribute",
"attribute": "covid19_ddimer",
"range": {
"low": 2,
"high": 3
},
"direct_transition": "Lymphocytes_7"
},
"DDimer_10": {
"type": "SetAttribute",
"attribute": "covid19_ddimer",
"range": {
"low": 12,
"high": 16
},
"direct_transition": "Lymphocytes_10"
},
"DDimer_13": {
"type": "SetAttribute",
"attribute": "covid19_ddimer",
"range": {
"low": 14,
"high": 19
},
"direct_transition": "Lymphocytes_13"
},
"DDimer_16": {
"type": "SetAttribute",
"attribute": "covid19_ddimer",
"range": {
"low": 20,
"high": 26
},
"direct_transition": "Lymphocytes_16"
},
"DDimer_19": {
"type": "SetAttribute",
"attribute": "covid19_ddimer",
"range": {
"low": 33,
"high": 38
},
"direct_transition": "Lymphocytes_19"
},
"DDimer_22": {
"type": "SetAttribute",
"attribute": "covid19_ddimer",
"range": {
"low": 39,
"high": 45
},
"direct_transition": "Lymphocytes_22"
},
"Lymphocytes_4": {
"type": "SetAttribute",
"attribute": "covid19_lymphocytes",
"direct_transition": "Interleukin6_4",
"range": {
"low": 0.4,
"high": 0.8
}
},
"Lymphocytes_19": {
"type": "SetAttribute",
"attribute": "covid19_lymphocytes",
"range": {
"low": 0.3,
"high": 0.6
},
"direct_transition": "Interleukin6_19"
},
"Lymphocytes_16": {
"type": "SetAttribute",
"attribute": "covid19_lymphocytes",
"range": {
"low": 0.3,
"high": 0.6
},
"direct_transition": "Interleukin6_16"
},
"Lymphocytes_13": {
"type": "SetAttribute",
"attribute": "covid19_lymphocytes",
"range": {
"low": 0.4,
"high": 0.6
},
"direct_transition": "Interleukin6_13"
},
"Lymphocytes_10": {
"type": "SetAttribute",
"attribute": "covid19_lymphocytes",
"range": {
"low": 0.4,
"high": 0.7
},
"direct_transition": "Interleukin6_10"
},
"Lymphocytes_7": {
"type": "SetAttribute",
"attribute": "covid19_lymphocytes",
"range": {
"low": 0.5,
"high": 0.8
},
"direct_transition": "Interleukin6_7"
},
"Interleukin6_4": {
"type": "SetAttribute",
"attribute": "covid19_interleukin6",
"direct_transition": "Ferritin_4",
"range": {
"low": 7.5,
"high": 11.5
}
},
"Lymphocytes_22": {
"type": "SetAttribute",
"attribute": "covid19_lymphocytes",
"range": {
"low": 0.3,
"high": 0.5
},
"direct_transition": "Interleukin6_22"
},
"Interleukin6_22": {
"type": "SetAttribute",
"attribute": "covid19_interleukin6",
"range": {
"low": 26,
"high": 30
},
"direct_transition": "Ferritin_22"
},
"Interleukin6_19": {
"type": "SetAttribute",
"attribute": "covid19_interleukin6",
"range": {
"low": 24,
"high": 28
},
"direct_transition": "Ferritin_19"
},
"Interleukin6_16": {
"type": "SetAttribute",
"attribute": "covid19_interleukin6",
"range": {
"low": 15,
"high": 19
},
"direct_transition": "Ferritin_16"
},
"Interleukin6_13": {
"type": "SetAttribute",
"attribute": "covid19_interleukin6",
"range": {
"low": 9,
"high": 13
},
"direct_transition": "Ferritin_13"
},
"Interleukin6_10": {
"type": "SetAttribute",
"attribute": "covid19_interleukin6",
"range": {
"low": 8,
"high": 12
},
"direct_transition": "Ferritin_10"
},
"Interleukin6_7": {
"type": "SetAttribute",
"attribute": "covid19_interleukin6",
"range": {
"low": 10,
"high": 14
},
"direct_transition": "Ferritin_7"
},
"Ferritin_4": {
"type": "SetAttribute",
"attribute": "covid19_ferritin",
"direct_transition": "Cardiac_Troponin_4",
"range": {
"low": 800,
"high": 1200
}
},
"Ferritin_22": {
"type": "SetAttribute",
"attribute": "covid19_ferritin",
"value": 2000,
"direct_transition": "Cardiac_Troponin_22"
},
"Ferritin_19": {
"type": "SetAttribute",
"attribute": "covid19_ferritin",
"value": 2000,
"direct_transition": "Cardiac_Troponin_19"
},
"Ferritin_16": {
"type": "SetAttribute",
"attribute": "covid19_ferritin",
"range": {
"low": 1800,
"high": 2000
},
"direct_transition": "Cardiac_Troponin_16"
},
"Ferritin_13": {
"type": "SetAttribute",
"attribute": "covid19_ferritin",
"range": {
"low": 1500,
"high": 1900
},
"direct_transition": "Cardiac_Troponin_13"
},
"Ferritin_10": {
"type": "SetAttribute",
"attribute": "covid19_ferritin",
"range": {
"low": 1400,
"high": 1800
},
"direct_transition": "Cardiac_Troponin_10"
},
"Ferritin_7": {
"type": "SetAttribute",
"attribute": "covid19_ferritin",
"range": {
"low": 1400,
"high": 1800
},
"direct_transition": "Cardiac_Troponin_7"
},
"Cardiac_Troponin_4": {
"type": "SetAttribute",
"attribute": "covid19_cardiac_troponin",
"direct_transition": "Lactate_Dehydrogenase_4",
"range": {
"low": 6,
"high": 10
}
},
"Cardiac_Troponin_22": {
"type": "SetAttribute",
"attribute": "covid19_cardiac_troponin",
"range": {
"low": 250,
"high": 350
},
"direct_transition": "Lactate_Dehydrogenase_22"
},
"Cardiac_Troponin_19": {
"type": "SetAttribute",
"attribute": "covid19_cardiac_troponin",
"range": {
"low": 130,
"high": 160
},
"direct_transition": "Lactate_Dehydrogenase_19"
},
"Cardiac_Troponin_16": {
"type": "SetAttribute",
"attribute": "covid19_cardiac_troponin",
"range": {
"low": 55,
"high": 65
},
"direct_transition": "Lactate_Dehydrogenase_16"
},
"Cardiac_Troponin_13": {
"type": "SetAttribute",
"attribute": "covid19_cardiac_troponin",
"range": {
"low": 50,
"high": 60
},
"direct_transition": "Lactate_Dehydrogenase_13"
},
"Cardiac_Troponin_10": {
"type": "SetAttribute",
"attribute": "covid19_cardiac_troponin",
"range": {
"low": 20,
"high": 24
},
"direct_transition": "Lactate_Dehydrogenase_10"
},
"Cardiac_Troponin_7": {
"type": "SetAttribute",
"attribute": "covid19_cardiac_troponin",
"range": {
"low": 22,
"high": 26
},
"direct_transition": "Lactate_Dehydrogenase_7"
},
"Lactate_Dehydrogenase_4": {
"type": "SetAttribute",
"attribute": "covid19_lactate_dehydrogenase",
"direct_transition": "Terminal",
"range": {
"low": 315,
"high": 345
}
},
"Lactate_Dehydrogenase_22": {
"type": "SetAttribute",
"attribute": "covid19_lactate_dehydrogenase",
"range": {
"low": 500,
"high": 600
},
"direct_transition": "Terminal"
},
"Lactate_Dehydrogenase_19": {
"type": "SetAttribute",
"attribute": "covid19_lactate_dehydrogenase",
"range": {
"low": 390,
"high": 430
},
"direct_transition": "Terminal"
},
"Lactate_Dehydrogenase_16": {
"type": "SetAttribute",
"attribute": "covid19_lactate_dehydrogenase",
"range": {
"low": 370,
"high": 390
},
"direct_transition": "Terminal"
},
"Lactate_Dehydrogenase_13": {
"type": "SetAttribute",
"attribute": "covid19_lactate_dehydrogenase",
"range": {
"low": 390,
"high": 410
},
"direct_transition": "Terminal"
},
"Lactate_Dehydrogenase_10": {
"type": "SetAttribute",
"attribute": "covid19_lactate_dehydrogenase",
"range": {
"low": 380,
"high": 400
},
"direct_transition": "Terminal"
},
"Lactate_Dehydrogenase_7": {
"type": "SetAttribute",
"attribute": "covid19_lactate_dehydrogenase",
"range": {
"low": 300,
"high": 330
},
"direct_transition": "Terminal"
},
"Set Creatine Kinase": {
"type": "SetAttribute",
"attribute": "covid19_creatine_kinase",
"direct_transition": "Set C-Reactive Protein",
"range": {
"low": 20,
"high": 204
}
},
"Set C-Reactive Protein": {
"type": "SetAttribute",
"attribute": "covid19_c_reactive_protein",
"direct_transition": "Set PT",
"range": {
"low": 8,
"high": 18
}
},
"Set PT": {
"type": "SetAttribute",
"attribute": "covid19_pt",
"range": {
"low": 11,
"high": 14
},
"direct_transition": "Set INR"
},
"Set INR": {
"type": "SetAttribute",
"attribute": "covid19_inr",
"range": {
"low": 3,
"high": 5
},
"direct_transition": "Set Procalitonin"
},
"Set Procalitonin": {
"type": "SetAttribute",
"attribute": "covid19_procalcitonin",
"direct_transition": "Poor Oxygen Saturation",
"range": {
"low": 0,
"high": 0.5
}
},
"Poor Oxygen Saturation": {
"type": "VitalSign",
"vital_sign": "Oxygen Saturation",
"unit": "%",
"range": {
"low": 75,
"high": 89
},
"direct_transition": "Set PaO2"
},
"Set PaO2": {
"type": "SetAttribute",
"attribute": "covid19_pao2",
"direct_transition": "Day",
"range": {
"low": 37,
"high": 60
}
}
},
"gmf_version": 1
}

421
src/main/resources/modules/covid19/outcomes.json Normal file
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{
"name": "outcomes",
"remarks": [
"This module determines patient outcomes from covid19 according to Table 2 from https://doi.org/10.1016/S0140-6736(20)30566-3"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Pneumonia"
},
"Terminal": {
"type": "Terminal"
},
"Pneumonia": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "233604007",
"display": "Pneumonia (disorder)"
}
],
"direct_transition": "Hypoxemia",
"target_encounter": "Hospital Inpatient Admission"
},
"ARDS": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "67782005",
"display": "Acute respiratory distress syndrome (disorder)"
}
],
"direct_transition": "Check Heart Failure",
"target_encounter": "ICU Admission"
},
"Sepsis": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "770349000",
"display": "Sepsis caused by virus (disorder)"
}
],
"complex_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_death",
"operator": "==",
"value": true
},
"distributions": [
{
"transition": "Septic Shock",
"distribution": 0.7
},
{
"transition": "Terminal",
"distribution": 0.3
}
]
},
{
"transition": "Terminal"
}
],
"target_encounter": "Hospital Inpatient Admission"
},
"Septic Shock": {
"assign_to_attribute": "Ventilator Reason",
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "76571007",
"display": "Septic shock (disorder)"
}
],
"direct_transition": "Terminal",
"target_encounter": "ICU Admission"
},
"Check Heart Failure": {
"type": "Simple",
"complex_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_death",
"operator": "==",
"value": true
},
"distributions": [
{
"transition": "Heart Failure",
"distribution": 0.52
},
{
"transition": "Check Acute Cardiac Injury",
"distribution": 0.48
}
]
},
{
"distributions": [
{
"transition": "Heart Failure",
"distribution": 0.12
},
{
"transition": "Check Acute Cardiac Injury",
"distribution": 0.88
}
]
}
]
},
"Heart Failure": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "84114007",
"display": "Heart failure (disorder)"
}
],
"direct_transition": "Check Acute Cardiac Injury",
"target_encounter": "ICU Admission"
},
"Acute Cardiac Injury": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "86175003",
"display": "Injury of heart (disorder)"
}
],
"direct_transition": "Check Acute Kidney Injury",
"target_encounter": "ICU Admission"
},
"Check Acute Cardiac Injury": {
"type": "Simple",
"complex_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_death",
"operator": "==",
"value": true
},
"distributions": [
{
"transition": "Acute Cardiac Injury",
"distribution": 0.5
},
{
"transition": "Check Acute Kidney Injury",
"distribution": 0.5
}
]
},
{
"distributions": [
{
"transition": "Acute Cardiac Injury",
"distribution": 0.01
},
{
"transition": "Check Acute Kidney Injury",
"distribution": 1
}
]
}
]
},
"Check Acute Kidney Injury": {
"type": "Simple",
"complex_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_death",
"operator": "==",
"value": true
},
"distributions": [
{
"transition": "Acute Kidney Injury",
"distribution": 0.5
},
{
"transition": "Check Coagulopathy",
"distribution": 0.5
}
]
},
{
"distributions": [
{
"transition": "Acute Kidney Injury",
"distribution": 0.01
},
{
"transition": "Check Coagulopathy",
"distribution": 0.99
}
]
}
]
},
"Check Coagulopathy": {
"type": "Simple",
"complex_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_death",
"operator": "==",
"value": true
},
"distributions": [
{
"transition": "Coagulopathy",
"distribution": 0.5
},
{
"transition": "Determine Sepsis",
"distribution": 0.5
}
]
},
{
"distributions": [
{
"transition": "Coagulopathy",
"distribution": 0.07
},
{
"transition": "Determine Sepsis",
"distribution": 0.9299999999999999
}
]
}
]
},
"Acute Kidney Injury": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "40095003",
"display": "Injury of kidney (disorder)"
}
],
"direct_transition": "Check Coagulopathy",
"target_encounter": "ICU Admission"
},
"Coagulopathy": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "234466008",
"display": "Acquired coagulation disorder (disorder)"
}
],
"direct_transition": "Determine Sepsis",
"target_encounter": "ICU Admission"
},
"Determine Sepsis": {
"type": "Simple",
"conditional_transition": [
{
"transition": "Sepsis",
"condition": {
"condition_type": "Or",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "covid19_death",
"operator": "==",
"value": true
},
{
"condition_type": "Or",
"conditions": [
{
"condition_type": "PriorState",
"name": "ARDS"
},
{
"condition_type": "Or",
"conditions": [
{
"condition_type": "PriorState",
"name": "Heart Failure"
},
{
"condition_type": "PriorState",
"name": "Coagulopathy"
}
]
}
]
}
]
}
},
{
"transition": "Terminal"
}
]
},
"Respiratory Failure": {
"assign_to_attribute": "Ventilator Reason",
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "65710008",
"display": "Acute respiratory failure (disorder)"
}
],
"remarks": [
"67 of 173 (38.7% round up to 40%) severe patients required mechanical ventilation."
],
"complex_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_death",
"operator": "==",
"value": true
},
"distributions": [
{
"transition": "ARDS",
"distribution": 0.94
},
{
"transition": "Check Heart Failure",
"distribution": 0.06
}
]
},
{
"distributions": [
{
"transition": "ARDS",
"distribution": 0.18
},
{
"transition": "Check Heart Failure",
"distribution": 0.8200000000000001
}
]
}
],
"target_encounter": "Hospital Inpatient Admission"
},
"Mild Respiratory Distress": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "271825005",
"display": "Respiratory distress (finding)"
}
],
"complex_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_death",
"operator": "==",
"value": true
},
"distributions": [
{
"transition": "Respiratory Failure",
"distribution": 0.98
},
{
"transition": "Check Heart Failure",
"distribution": 0.02
}
]
},
{
"distributions": [
{
"transition": "Respiratory Failure",
"distribution": 0.36
},
{
"transition": "Check Heart Failure",
"distribution": 0.64
}
]
}
],
"target_encounter": "Hospital Inpatient Admission"
},
"Hypoxemia": {
"type": "ConditionOnset",
"target_encounter": "Hospital Inpatient Admission",
"codes": [
{
"system": "SNOMED-CT",
"code": "389087006",
"display": "Hypoxemia (disorder)"
}
],
"direct_transition": "Mild Respiratory Distress"
}
},
"gmf_version": 1
}

100
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{
"name": "Supplies - Hospitalization",
"remarks": [
"This module includes the supplies needed during daily treatment of COVID-19 in a basic hospital inpatient setting, not the ICU.",
"",
"Daily Hospitalization Assumptions: For continency capacity for the daily hospitalization, the following assumptions apply per patient per 24-hour period: ",
"•\tBasic strategy:",
"o\tAdministrative and engineering measures have already been implemented (e.g. reducing visitors, excluding non-essential personnel, and cohorting patients, etc.)",
"o\tNursing staff uses a bundling care model (e.g. vitals/assessments, etc. done at once) and assists with meal tray delivery and basic environmental services to reduce room entry. ",
"o\tConsulting physicians/APPs rely on the physical examination of the primary physician/APP to reduce room entry.",
"•\tPPE Strategy for encounters with all COVID/PUI patients:",
"o\tSingle-use isolation gowns: changed with each room entry",
"o\tGloves: changed with each room entry",
"o\tFace shields: approved for extended wear with a max of 1 per physician/APP and nurse per 24 hours. ",
"o\tN95s: approved for extended wear with a max of 1 per physician/APP and nurse per 24 hours. ",
"•\tRoom entry assumptions: ",
"o\tPhysician/APP staff maximum room entry per 24 hours is 3.",
"o\tPrimary nurse maximum room entry per 24 hours is 6.",
"o\tAdditional nursing staff maximum room entry per 24 hours is 2.",
"o\tAllied staff maximum room entry per 24 hours is 1",
"",
"",
"| Staff Type | Assumed Ratios* | N95Mask** | Face shield** | Gowns*** | Wipes*** | Gloves*** | Alcohol*** |",
"|-----------------------------------------|-----------------|------------|----------------|----------|-----------|-----------|------------|",
"| Primary Physician or APP | 16:1 | 2 | 2 | 3 | 2 | 6 | |",
"| Primary Nurse | 4:1 | 2 | 2 | 6 | 2 | 12 | |",
"| Additional Nursing Staff | 6:1 | 2 | 2 | 2 | 2 | 4 | |",
"| Other allied health and ancillary staff | 25:1 | 2 | 2 | 1 | 2 | 2 | |",
"| Quantity for supply list | N/A | 2 | 2 | 12 | 8 | 24 | 1 |",
"",
"*Ratios crowdsourced with colleagues across the country (MD, RNs, CNA, Nurse Techs)",
"** When calculating total PPE use, these items are not 1:1 with patients, but are determined based on the number of each staff present caring for COVID/PUI patients each 24 hours. (i.e. # staff type X 2)",
"*** When calculating total PPE use, these items are 1:1 for patients for every 24 hours (i.e. every COVID patient uses 8 gowns, 4 wipes, etc. every 24 hours)",
""
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Precautions_Baseline"
},
"Precautions_Baseline": {
"type": "SupplyList",
"supplies": [
{
"quantity": 2,
"code": {
"system": "SNOMED-CT",
"code": "409533008",
"display": "Air-purifying respirator (physical object)"
}
},
{
"quantity": 24,
"code": {
"system": "SNOMED-CT",
"code": "713779008",
"display": "Nitrile examination/treatment glove, non-powdered, sterile (physical object)"
}
},
{
"quantity": 12,
"code": {
"system": "SNOMED-CT",
"code": "1141679000",
"display": "Isolation gown (physical object)"
}
},
{
"quantity": 2,
"code": {
"system": "SNOMED-CT",
"code": "706724001",
"display": "Face shield (physical object)"
}
},
{
"quantity": 1,
"code": {
"system": "SNOMED-CT",
"code": "419343004",
"display": "Alcohol disinfectant (substance)"
}
},
{
"quantity": 8,
"code": {
"system": "SNOMED-CT",
"code": "470618009",
"display": "Antiseptic towelette (physical object)"
}
}
],
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

99
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{
"name": "Supplies - ICU",
"remarks": [
"This module includes the supplies needed during daily treatment of COVID-19 in an intensive care setting. These supplies offer a higher level of protection to the health care provider than the general inpatient setting. ",
"",
"Daily ICU Assumptions:",
"•\tBasic strategy = Same as hospitalization",
"•\tPPE strategy = Same as hospitalization, with the exception of gowns. ",
"o\tReusable isolation gowns are approved for extended wear with a max of 2 per patient per 24 hours (i.e. one for day shift nurse and one for night shift nurse) ",
"•\tRoom entry assumptions:",
"o\tICU physician maximum room entry per 24 hours is 4",
"o\tICU nurse maximum room entry per 24 hours is 12",
"o\tRespiratory therapist maximum room entry per 24 hours is 4",
"o\tAllied health/support maximum room entry per 24 hours is 2",
"",
"| Staff Type | Assumed Ratios | N95 Mask** | Face shield** | Gowns Reusable*** | Gowns single use*** | Wipes*** | Gloves*** | Alcohol*** |",
"|---------------------------------|-----------------|------------|---------------|-------------------|---------------------|----------|------------|------------|",
"| ICU physician | 1:10 | 2 | 2 | 0 | 4 | 4 | 8 | |",
"| ICU Nurse | 2:1 | 2 | 2 | 2 | 0 | 5 | 24 | |",
"| Respiratory Therapist | 5:1 | 2 | 2 | 0 | 4 | 5 | 8 | |",
"| Allied Health/care team support | 24:1 | 2 | 2 | 0 | 2 | 2 | 4 | |",
"| Quantity for supply list | | 2 | 2 | 2 | 10 | 16 | 44 | 2 |",
"",
"** When calculating total PPE use, these items are not 1:1 with patients, but are determined based on the number of each staff present caring for COVID/PUI patients each 24 hours. (i.e. # staff type X 2)",
"*** When calculating total PPE use, these items are 1:1 for patients for every 24 hours (i.e. every COVID patient uses 8 gowns, 4 wipes, etc. every 24 hours)"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Precautions_Aerosol"
},
"Precautions_Aerosol": {
"type": "SupplyList",
"supplies": [
{
"quantity": 44,
"code": {
"system": "SNOMED-CT",
"code": "713779008",
"display": "Nitrile examination/treatment glove, non-powdered, sterile (physical object)"
}
},
{
"quantity": 2,
"code": {
"system": "SNOMED-CT",
"code": "1141679000",
"display": "Isolation gown (physical object)"
}
},
{
"quantity": 10,
"code": {
"system": "SNOMED-CT",
"code": "1141679000",
"display": "Isolation gown (physical object)"
}
},
{
"quantity": 2,
"code": {
"system": "SNOMED-CT",
"code": "409533008",
"display": "Air-purifying respirator (physical object)"
}
},
{
"quantity": 2,
"code": {
"system": "SNOMED-CT",
"code": "706724001",
"display": "Face shield (physical object)"
}
},
{
"quantity": 2,
"code": {
"system": "SNOMED-CT",
"code": "419343004",
"display": "Alcohol disinfectant (substance)"
}
},
{
"quantity": 16,
"code": {
"system": "SNOMED-CT",
"code": "470618009",
"display": "Antiseptic towelette (physical object)"
}
}
],
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

201
src/main/resources/modules/covid19/supplies_intubation.json Normal file
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{
"name": "Supplies - Intubation",
"remarks": [
"This module includes the supplies needed during an intubation (i.e, an aerosolizing procedures) in support of the treatment of COVID-19. These are the supplies offering the highest level of protection to the health care provider, as well as the required supplies for the procedure itself. This submodule should be considered additional to the other supplies submodules as it only considers a single procedure, not the entire day. This also considers the inclusion of a respiratory therapist in addition to the 1 doctor and 1 nurse.",
"",
"Patient",
"- no additional supplies",
"",
"HCP",
" - Nurse and RT wear same as ICU PPE:",
" - gloves",
" - isolation gown",
" - glasses/goggles/shield",
"- physician:",
" - wears OR gown instead of isolation gown",
" - surgical cap",
" - extra set of gloves",
"",
""
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Ventilator"
},
"Supplies_Intubation": {
"type": "SupplyList",
"supplies": [
{
"quantity": 8,
"code": {
"system": "SNOMED-CT",
"code": "713779008",
"display": "Nitrile examination/treatment glove, non-powdered, sterile (physical object)"
}
},
{
"quantity": 2,
"code": {
"system": "SNOMED-CT",
"code": "1141679000",
"display": "Isolation gown (physical object)"
}
},
{
"quantity": 1,
"code": {
"system": "SNOMED-CT",
"code": "463696005",
"display": "Operating room laundry bag (physical object)"
}
},
{
"quantity": 1,
"code": {
"system": "SNOMED-CT",
"code": "736143005",
"display": "Radial surgical retractor seal cap (physical object)"
}
},
{
"quantity": 3,
"code": {
"system": "SNOMED-CT",
"code": "409533008",
"display": "Air-purifying respirator (physical object)"
}
},
{
"quantity": 3,
"code": {
"system": "SNOMED-CT",
"code": "38126007",
"display": "Protective glasses, device (physical object)"
}
},
{
"quantity": 1,
"code": {
"system": "SNOMED-CT",
"code": "419343004",
"display": "Alcohol disinfectant (substance)"
}
},
{
"quantity": 1,
"code": {
"system": "SNOMED-CT",
"code": "470618009",
"display": "Antiseptic towelette (physical object)"
}
},
{
"quantity": 1,
"code": {
"system": "SNOMED-CT",
"code": "285698002",
"display": "Laryngoscope blade (physical object)"
}
},
{
"quantity": 1,
"code": {
"system": "SNOMED-CT",
"code": "26412008",
"display": "Endotracheal tube, device (physical object)"
}
},
{
"quantity": 1,
"code": {
"system": "SNOMED-CT",
"code": "725095003",
"display": "Endotracheal tube introducer (physical object)"
}
},
{
"quantity": 2,
"code": {
"system": "SNOMED-CT",
"code": "61968008",
"display": "Syringe, device (physical object)"
}
},
{
"quantity": 1,
"code": {
"system": "SNOMED-CT",
"code": "706092000",
"display": "Suction system (physical object)"
}
},
{
"quantity": 1,
"code": {
"system": "SNOMED-CT",
"code": "706774004",
"display": "Lubricant (physical object)"
}
},
{
"quantity": 1,
"code": {
"system": "SNOMED-CT",
"code": "468601005",
"display": "Endotracheal tube holder (physical object)"
}
},
{
"quantity": 1,
"code": {
"system": "SNOMED-CT",
"code": "701434005",
"display": "Viral filter (physical object)"
}
},
{
"quantity": 1,
"code": {
"system": "SNOMED-CT",
"code": "827149008",
"display": "Carbon dioxide breath analyzer (physical object)"
}
},
{
"quantity": 1,
"code": {
"system": "SNOMED-CT",
"code": "17102003",
"display": "Nasogastric tube, device (physical object)"
}
}
],
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
},
"Ventilator": {
"type": "Device",
"code": {
"system": "SNOMED-CT",
"code": "449071006",
"display": "Mechanical ventilator (physical object)"
},
"direct_transition": "Laryngoscope",
"assign_to_attribute": "covid19_ventilator"
},
"Laryngoscope": {
"type": "Device",
"code": {
"system": "SNOMED-CT",
"code": "448907002",
"display": "Videolaryngoscope (physical object)"
},
"direct_transition": "Supplies_Intubation",
"assign_to_attribute": "covid19_laryngoscope"
}
},
"gmf_version": 1
}

562
src/main/resources/modules/covid19/survivor_lab_values.json Normal file
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{
"name": "survivor_lab_values",
"remarks": [
"Based on Figure 2 from https://doi.org/10.1016/S0140-6736(20)30566-3"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Set_Creatine_Kinase"
},
"Terminal": {
"type": "Terminal"
},
"Day": {
"type": "Simple",
"conditional_transition": [
{
"transition": "DDimer_4",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_admission_days",
"operator": "<",
"value": 7
}
},
{
"transition": "DDimer_7",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_admission_days",
"operator": "<",
"value": 10
}
},
{
"transition": "DDimer_10",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_admission_days",
"operator": "<",
"value": 13
}
},
{
"transition": "DDimer_13",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_admission_days",
"operator": "<",
"value": 16
}
},
{
"transition": "DDimer_16",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_admission_days",
"operator": "<",
"value": 19
}
},
{
"transition": "DDimer_19",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_admission_days",
"operator": "==",
"value": 22
}
},
{
"transition": "DDimer_22"
}
]
},
"DDimer_4": {
"type": "SetAttribute",
"attribute": "covid19_ddimer",
"range": {
"low": 0.2,
"high": 0.4
},
"direct_transition": "Lymphocytes_4"
},
"DDimer_7": {
"type": "SetAttribute",
"attribute": "covid19_ddimer",
"range": {
"low": 0.4,
"high": 0.6
},
"direct_transition": "Lymphocytes_7"
},
"DDimer_10": {
"type": "SetAttribute",
"attribute": "covid19_ddimer",
"range": {
"low": 0.5,
"high": 0.7
},
"direct_transition": "Lymphocytes_10"
},
"DDimer_13": {
"type": "SetAttribute",
"attribute": "covid19_ddimer",
"range": {
"low": 0.5,
"high": 0.7
},
"direct_transition": "Lymphocytes_13"
},
"DDimer_16": {
"type": "SetAttribute",
"attribute": "covid19_ddimer",
"range": {
"low": 0.6,
"high": 0.8
},
"direct_transition": "Lymphocytes_16"
},
"DDimer_19": {
"type": "SetAttribute",
"attribute": "covid19_ddimer",
"range": {
"low": 0.9,
"high": 1.1
},
"direct_transition": "Lymphocytes_19"
},
"DDimer_22": {
"type": "SetAttribute",
"attribute": "covid19_ddimer",
"range": {
"low": 0.4,
"high": 0.6
},
"direct_transition": "Lymphocytes_22"
},
"Lymphocytes_4": {
"type": "SetAttribute",
"attribute": "covid19_lymphocytes",
"direct_transition": "Interleukin6_4",
"range": {
"low": 1,
"high": 1.1
}
},
"Lymphocytes_19": {
"type": "SetAttribute",
"attribute": "covid19_lymphocytes",
"range": {
"low": 1.3,
"high": 1.5
},
"direct_transition": "Interleukin6_19"
},
"Lymphocytes_16": {
"type": "SetAttribute",
"attribute": "covid19_lymphocytes",
"range": {
"low": 1.1,
"high": 1.3
},
"direct_transition": "Interleukin6_16"
},
"Lymphocytes_13": {
"type": "SetAttribute",
"attribute": "covid19_lymphocytes",
"range": {
"low": 1.1,
"high": 1.2
},
"direct_transition": "Interleukin6_13"
},
"Lymphocytes_10": {
"type": "SetAttribute",
"attribute": "covid19_lymphocytes",
"range": {
"low": 0.9,
"high": 1.1
},
"direct_transition": "Interleukin6_10"
},
"Lymphocytes_7": {
"type": "SetAttribute",
"attribute": "covid19_lymphocytes",
"range": {
"low": 0.8,
"high": 1
},
"direct_transition": "Interleukin6_7"
},
"Interleukin6_4": {
"type": "SetAttribute",
"attribute": "covid19_interleukin6",
"direct_transition": "Ferritin_4",
"range": {
"low": 4,
"high": 6
}
},
"Lymphocytes_22": {
"type": "SetAttribute",
"attribute": "covid19_lymphocytes",
"range": {
"low": 1.3,
"high": 1.5
},
"direct_transition": "Interleukin6_22"
},
"Interleukin6_22": {
"type": "SetAttribute",
"attribute": "covid19_interleukin6",
"range": {
"low": 5,
"high": 7
},
"direct_transition": "Ferritin_22"
},
"Interleukin6_19": {
"type": "SetAttribute",
"attribute": "covid19_interleukin6",
"range": {
"low": 5,
"high": 7
},
"direct_transition": "Ferritin_19"
},
"Interleukin6_16": {
"type": "SetAttribute",
"attribute": "covid19_interleukin6",
"range": {
"low": 5,
"high": 7
},
"direct_transition": "Ferritin_16"
},
"Interleukin6_13": {
"type": "SetAttribute",
"attribute": "covid19_interleukin6",
"range": {
"low": 5,
"high": 7
},
"direct_transition": "Ferritin_13"
},
"Interleukin6_10": {
"type": "SetAttribute",
"attribute": "covid19_interleukin6",
"range": {
"low": 5,
"high": 7
},
"direct_transition": "Ferritin_10"
},
"Interleukin6_7": {
"type": "SetAttribute",
"attribute": "covid19_interleukin6",
"range": {
"low": 5,
"high": 7
},
"direct_transition": "Ferritin_7"
},
"Ferritin_4": {
"type": "SetAttribute",
"attribute": "covid19_ferritin",
"direct_transition": "Cardiac_Troponin_4",
"range": {
"low": 300,
"high": 500
}
},
"Ferritin_22": {
"type": "SetAttribute",
"attribute": "covid19_ferritin",
"range": {
"low": 300,
"high": 450
},
"direct_transition": "Cardiac_Troponin_22"
},
"Ferritin_19": {
"type": "SetAttribute",
"attribute": "covid19_ferritin",
"range": {
"low": 400,
"high": 500
},
"direct_transition": "Cardiac_Troponin_19"
},
"Ferritin_16": {
"type": "SetAttribute",
"attribute": "covid19_ferritin",
"range": {
"low": 400,
"high": 500
},
"direct_transition": "Cardiac_Troponin_16"
},
"Ferritin_13": {
"type": "SetAttribute",
"attribute": "covid19_ferritin",
"range": {
"low": 550,
"high": 650
},
"direct_transition": "Cardiac_Troponin_13"
},
"Ferritin_10": {
"type": "SetAttribute",
"attribute": "covid19_ferritin",
"range": {
"low": 450,
"high": 600
},
"direct_transition": "Cardiac_Troponin_10"
},
"Ferritin_7": {
"type": "SetAttribute",
"attribute": "covid19_ferritin",
"range": {
"low": 450,
"high": 550
},
"direct_transition": "Cardiac_Troponin_7"
},
"Cardiac_Troponin_4": {
"type": "SetAttribute",
"attribute": "covid19_cardiac_troponin",
"direct_transition": "Lactate_Dehydrogenase_4",
"range": {
"low": 1.5,
"high": 3.5
}
},
"Cardiac_Troponin_22": {
"type": "SetAttribute",
"attribute": "covid19_cardiac_troponin",
"range": {
"low": 3,
"high": 4
},
"direct_transition": "Lactate_Dehydrogenase_22"
},
"Cardiac_Troponin_19": {
"type": "SetAttribute",
"attribute": "covid19_cardiac_troponin",
"range": {
"low": 2,
"high": 3
},
"direct_transition": "Lactate_Dehydrogenase_19"
},
"Cardiac_Troponin_16": {
"type": "SetAttribute",
"attribute": "covid19_cardiac_troponin",
"range": {
"low": 2,
"high": 3
},
"direct_transition": "Lactate_Dehydrogenase_16"
},
"Cardiac_Troponin_13": {
"type": "SetAttribute",
"attribute": "covid19_cardiac_troponin",
"range": {
"low": 4,
"high": 5
},
"direct_transition": "Lactate_Dehydrogenase_13"
},
"Cardiac_Troponin_10": {
"type": "SetAttribute",
"attribute": "covid19_cardiac_troponin",
"range": {
"low": 3,
"high": 5
},
"direct_transition": "Lactate_Dehydrogenase_10"
},
"Cardiac_Troponin_7": {
"type": "SetAttribute",
"attribute": "covid19_cardiac_troponin",
"range": {
"low": 2,
"high": 4
},
"direct_transition": "Lactate_Dehydrogenase_7"
},
"Lactate_Dehydrogenase_4": {
"type": "SetAttribute",
"attribute": "covid19_lactate_dehydrogenase",
"direct_transition": "Terminal",
"range": {
"low": 200,
"high": 250
}
},
"Lactate_Dehydrogenase_22": {
"type": "SetAttribute",
"attribute": "covid19_lactate_dehydrogenase",
"range": {
"low": 180,
"high": 220
},
"direct_transition": "Terminal"
},
"Lactate_Dehydrogenase_19": {
"type": "SetAttribute",
"attribute": "covid19_lactate_dehydrogenase",
"range": {
"low": 200,
"high": 250
},
"direct_transition": "Terminal"
},
"Lactate_Dehydrogenase_16": {
"type": "SetAttribute",
"attribute": "covid19_lactate_dehydrogenase",
"range": {
"low": 200,
"high": 300
},
"direct_transition": "Terminal"
},
"Lactate_Dehydrogenase_13": {
"type": "SetAttribute",
"attribute": "covid19_lactate_dehydrogenase",
"range": {
"low": 250,
"high": 350
},
"direct_transition": "Terminal"
},
"Lactate_Dehydrogenase_10": {
"type": "SetAttribute",
"attribute": "covid19_lactate_dehydrogenase",
"range": {
"low": 250,
"high": 350
},
"direct_transition": "Terminal"
},
"Lactate_Dehydrogenase_7": {
"type": "SetAttribute",
"attribute": "covid19_lactate_dehydrogenase",
"range": {
"low": 225,
"high": 250
},
"direct_transition": "Terminal"
},
"Set_Creatine_Kinase": {
"type": "SetAttribute",
"attribute": "covid19_creatine_kinase",
"range": {
"low": 12,
"high": 53
},
"direct_transition": "Set_C_Reactive_Protein"
},
"Set_C_Reactive_Protein": {
"type": "SetAttribute",
"attribute": "covid19_c_reactive_protein",
"range": {
"low": 8,
"high": 12
},
"direct_transition": "Set_PT"
},
"Set_PT": {
"type": "SetAttribute",
"attribute": "covid19_pt",
"range": {
"low": 10,
"high": 13
},
"direct_transition": "Set_INR"
},
"Set_INR": {
"type": "SetAttribute",
"attribute": "covid19_inr",
"range": {
"low": 1,
"high": 3
},
"direct_transition": "Set_Procalitonin"
},
"Set_Procalitonin": {
"type": "SetAttribute",
"attribute": "covid19_procalcitonin",
"range": {
"low": 0,
"high": 0.2
},
"conditional_transition": [
{
"transition": "Recovered Oxygen Saturation",
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "covid19_icu_days",
"operator": "is not nil"
},
{
"condition_type": "Attribute",
"attribute": "covid19_icu_days",
"operator": "<",
"value": 2
}
]
}
},
{
"transition": "Poor Oxygen Saturation"
}
]
},
"Poor Oxygen Saturation": {
"type": "VitalSign",
"vital_sign": "Oxygen Saturation",
"unit": "%",
"direct_transition": "Set Poor PaO2",
"range": {
"low": 75,
"high": 89
}
},
"Recovered Oxygen Saturation": {
"type": "VitalSign",
"vital_sign": "Oxygen Saturation",
"unit": "%",
"direct_transition": "Set Recovered PaO2",
"range": {
"low": 90,
"high": 100
}
},
"Set Poor PaO2": {
"type": "SetAttribute",
"attribute": "covid19_pao2",
"range": {
"low": 37,
"high": 60
},
"direct_transition": "Day"
},
"Set Recovered PaO2": {
"type": "SetAttribute",
"attribute": "covid19_pao2",
"range": {
"low": 60,
"high": 98
},
"direct_transition": "Day"
}
},
"gmf_version": 1
}

1050
src/main/resources/modules/covid19/symptoms.json Normal file
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src/main/resources/modules/covid19/treat_blood_clot.json Normal file
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{
"name": "treat_blood_clot",
"remarks": [
"All patients admitted to the hospital should be placed on prophylaxis for venous thromboembolism (blood clots).",
"",
"At some point, both patients on the floor and ICU should develop a clot (see the diagnose_blood_clot submodule), at which point they should be treated differently."
],
"states": {
"Initial": {
"type": "Initial",
"conditional_transition": [
{
"transition": "Terminal",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_diagnosed_clot",
"operator": "is nil"
}
},
{
"transition": "Blood Clot Treatment",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_diagnosed_clot",
"operator": "==",
"value": true
}
},
{
"transition": "Blood Clot Prophylaxis",
"condition": {
"condition_type": "Attribute",
"attribute": "covid19_diagnosed_clot",
"operator": "==",
"value": false
}
},
{
"transition": "Terminal"
}
]
},
"Terminal": {
"type": "Terminal"
},
"Blood Clot Prophylaxis": {
"type": "Simple",
"conditional_transition": [
{
"transition": "Heparin",
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "ckd",
"operator": "is not nil"
},
{
"condition_type": "Attribute",
"attribute": "ckd",
"operator": ">=",
"value": 4
}
]
}
},
{
"transition": "Enoxaparin 30",
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "40095003",
"display": "Injury of kidney (disorder)"
}
]
}
},
{
"transition": "Enoxaparin 40"
}
]
},
"Blood Clot Treatment": {
"type": "Simple",
"conditional_transition": [
{
"transition": "Heparin Single Dose",
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "ckd",
"operator": "is not nil"
},
{
"condition_type": "Attribute",
"attribute": "ckd",
"operator": ">=",
"value": 4
}
]
}
},
{
"transition": "Enoxaparin",
"condition": {
"condition_type": "Active Condition",
"codes": [
{
"system": "SNOMED-CT",
"code": "40095003",
"display": "Injury of kidney (disorder)"
}
]
}
},
{
"transition": "Enoxaparin Double"
}
]
},
"Heparin": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 1659263,
"display": "1 ML heparin sodium, porcine 5000 UNT/ML Injection"
}
],
"direct_transition": "Terminal",
"administration": true,
"prescription": {
"dosage": {
"amount": 1,
"frequency": 1,
"period": 1,
"unit": "days"
},
"duration": {
"quantity": 1,
"unit": "days"
},
"refills": 2
}
},
"Enoxaparin 30": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 854228,
"display": "0.3 ML Enoxaparin sodium 100 MG/ML Prefilled Syringe"
}
],
"direct_transition": "Terminal",
"administration": true,
"prescription": {
"dosage": {
"amount": 1,
"frequency": 1,
"period": 1,
"unit": "days"
},
"duration": {
"quantity": 1,
"unit": "days"
},
"refills": 2
}
},
"Enoxaparin 40": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 854235,
"display": "0.4 ML Enoxaparin sodium 100 MG/ML Prefilled Syringe"
}
],
"administration": true,
"direct_transition": "Terminal"
},
"Heparin Infusion": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "103746007",
"display": "Heparin therapy (procedure)"
},
{
"system": "SNOMED-CT",
"code": "36576007",
"display": "Infusion (procedure)"
}
],
"direct_transition": "Terminal",
"reason": "covid19_clot"
},
"Heparin Single Dose": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 1659263,
"display": "1 ML heparin sodium, porcine 5000 UNT/ML Injection"
}
],
"direct_transition": "Heparin Infusion",
"administration": true,
"reason": "covid19_clot"
},
"Enoxaparin Double": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 854252,
"display": "1 ML Enoxaparin sodium 150 MG/ML Prefilled Syringe"
}
],
"direct_transition": "Terminal",
"administration": true,
"prescription": {
"dosage": {
"amount": 1,
"frequency": 1,
"period": 1,
"unit": "days"
},
"duration": {
"quantity": 1,
"unit": "days"
},
"refills": 2
},
"reason": "covid19_clot"
},
"Enoxaparin": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 854252,
"display": "1 ML Enoxaparin sodium 150 MG/ML Prefilled Syringe"
}
],
"administration": true,
"reason": "covid19_clot",
"direct_transition": "Terminal"
}
},
"gmf_version": 1
}

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src/main/resources/modules/cystic_fibrosis.json Normal file
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src/main/resources/modules/dementia.json Normal file
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{
"name": "Dementia",
"remarks": [
"right now this is just Alzheimer's but there are other dementias that could be adapted into this model"
],
"states": {
"Initial": {
"type": "Initial",
"distributed_transition": [
{
"distribution": 0.4,
"transition": "AlzheimersGene"
},
{
"distribution": 0.6,
"transition": "Terminal"
}
],
"remarks": [
"Alzheimer's has been shown to be significantly based on genetics, and there are specific genes to point to for early-onset:",
"https://www.nia.nih.gov/alzheimers/publication/alzheimers-disease-genetics-fact-sheet",
"Since Synthea does not currently model at the level of individual genes",
"we'll use a simple probability to differentiate the population into who will and won't get alzheimers.",
"The 40% chance does seem high, but the key factor here is the delay in when it appears.",
"38% of people over age 85 have alzheimer's. ( http://www.alzheimers.net/resources/alzheimers-statistics/ )"
]
},
"AlzheimersGene": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.95,
"transition": "PreAlzheimers"
},
{
"distribution": 0.05,
"transition": "PreEarlyOnsetAlzheimers"
}
],
"remarks": [
"Early onset Alzheimers affects roughly 5% of people with Alzheimer's. http://www.mayoclinic.org/diseases-conditions/alzheimers-disease/in-depth/alzheimers/art-20048356"
]
},
"PreAlzheimers": {
"type": "Delay",
"range": {
"low": 64,
"high": 80,
"unit": "years"
},
"remarks": [
"There is evidence that higher education leads to a delay in the onset of alzheimers."
],
"conditional_transition": [
{
"condition": {
"condition_type": "Socioeconomic Status",
"category": "High"
},
"transition": "EducationDelay"
},
{
"transition": "AlzheimersOnset"
}
]
},
"EducationDelay": {
"type": "Delay",
"range": {
"low": 5,
"high": 10,
"unit": "years"
},
"direct_transition": "AlzheimersOnset"
},
"AlzheimersOnset": {
"type": "ConditionOnset",
"target_encounter": "DiagnosisEncounter",
"assign_to_attribute": "Type of Alzheimer's",
"codes": [
{
"system": "SNOMED-CT",
"code": "26929004",
"display": "Alzheimer's disease (disorder)"
}
],
"direct_transition": "Eventual_Hospice_Reason"
},
"PreEarlyOnsetAlzheimers": {
"type": "Delay",
"range": {
"low": 40,
"high": 64,
"unit": "years"
},
"direct_transition": "EarlyOnsetAlzheimersOnset"
},
"EarlyOnsetAlzheimersOnset": {
"type": "ConditionOnset",
"target_encounter": "DiagnosisEncounter",
"assign_to_attribute": "Type of Alzheimer's",
"codes": [
{
"system": "SNOMED-CT",
"code": "230265002",
"display": "Familial Alzheimer's disease of early onset (disorder)"
}
],
"direct_transition": "Eventual_Hospice_Reason"
},
"NoImpairment": {
"type": "Delay",
"range": {
"low": 12,
"high": 36,
"unit": "months"
},
"remarks": [
"1. Normal"
],
"direct_transition": "VeryMildDecline"
},
"VeryMildDecline": {
"type": "Delay",
"range": {
"low": 12,
"high": 36,
"unit": "months"
},
"remarks": [
"2. Very mild decline, also considered normal aged forgetfulness"
],
"direct_transition": "DecreasedCommunication"
},
"DecreasedCommunication": {
"type": "Symptom",
"symptom": "Decreased Communication",
"range": {
"low": 0,
"high": 50
},
"direct_transition": "DecreasedAttentiveness"
},
"DecreasedAttentiveness": {
"type": "Symptom",
"symptom": "Decreased Attentiveness",
"range": {
"low": 0,
"high": 50
},
"direct_transition": "DecreasedJudgment"
},
"DecreasedJudgment": {
"type": "Symptom",
"symptom": "Decreased in Judgement",
"range": {
"low": 0,
"high": 50
},
"direct_transition": "DecreasedVisualPerception"
},
"DecreasedVisualPerception": {
"type": "Symptom",
"symptom": "Decreased Visual Perception",
"range": {
"low": 0,
"high": 50
},
"direct_transition": "Confusion"
},
"Confusion": {
"type": "Symptom",
"symptom": "Confusion",
"range": {
"low": 0,
"high": 50
},
"direct_transition": "MildMemoryLoss"
},
"MildMemoryLoss": {
"type": "Symptom",
"symptom": "Memory Loss",
"range": {
"low": 0,
"high": 50
},
"direct_transition": "MildDecline"
},
"MildDecline": {
"type": "Delay",
"range": {
"low": 6,
"high": 12,
"unit": "months"
},
"remarks": [
"3. Mild decline, aka mild cognitive impairment (MCI) progresses to the next stage in generally 2-4 years",
"Persons at this stage display subtle deficits which are noted by others close to the subject",
"https://www.alzinfo.org/understand-alzheimers/clinical-stages-of-alzheimers/"
],
"conditional_transition": [
{
"condition": {
"condition_type": "Symptom",
"symptom": "Memory Loss",
"operator": ">",
"value": 40
},
"transition": "DiagnosisEncounter",
"remarks": [
"if the symptom is sufficiently noticeable enough people can be diagnosed in this stage, if not they will be diagnosed in the next stage"
]
},
{
"condition": {
"condition_type": "Symptom",
"symptom": "Memory Loss",
"operator": ">",
"value": 30
},
"transition": "ModerateDecline"
},
{
"transition": "MildMemoryLoss"
}
]
},
"DiagnosisEncounter": {
"type": "Encounter",
"wellness": true,
"remarks": [
"This is the enounter where alzheimer's is diagnosed. ",
"Typical life expectancy after an Alzheimer’s diagnosis is 4-to-8 years. (Alzheimer’s Association)"
],
"direct_transition": "Diagnosis_MMSE_Score",
"reason": "Type of Alzheimer's"
},
"Diagnosis_MMSE_Score": {
"type": "Observation",
"category": "survey",
"range": {
"low": 18,
"high": 25
},
"remarks": [
"The maximum MMSE score is 30 points. A score of 20 to 24 suggests mild dementia, ",
"13 to 20 suggests moderate dementia, and less than 12 indicates severe dementia",
"http://www.alz.org/alzheimers_disease_steps_to_diagnosis.asp",
"also available is the Clinical Dementia Rating (CDR)",
"http://alzheimer.wustl.edu/cdr/cdr.htm"
],
"unit": "{score}",
"codes": [
{
"system": "LOINC",
"code": "72106-8",
"display": "Total score [MMSE]"
}
],
"direct_transition": "Dementia_CarePlan"
},
"Dementia_CarePlan": {
"type": "CarePlanStart",
"reason": "Type of Alzheimer's",
"codes": [
{
"system": "SNOMED-CT",
"code": "386257007",
"display": "Dementia management (regime/therapy)"
}
],
"activities": [
{
"system": "SNOMED-CT",
"code": "311401005",
"display": "Patient education (procedure)"
},
{
"system": "SNOMED-CT",
"code": "710125008",
"display": "Promotion of use of memory skills (procedure)"
},
{
"system": "SNOMED-CT",
"code": "315043002",
"display": "Long term social support (regime/therapy)"
}
],
"direct_transition": "FirstPrescription"
},
"FirstPrescription": {
"type": "Simple",
"conditional_transition": [
{
"condition": {
"condition_type": "Date",
"operator": ">",
"year": 2001
},
"transition": "FirstPrescription1",
"remarks": [
"galantamine(razadyne) fda approved in 2001"
]
},
{
"condition": {
"condition_type": "Date",
"operator": ">",
"year": 1996
},
"transition": "FirstPrescription2",
"remarks": [
"donepezil(aricept) fda approved in 1996"
]
},
{
"condition": {
"condition_type": "Date",
"operator": ">",
"year": 1993
},
"transition": "FirstPrescription3",
"remarks": [
"tarine first available in 1993"
]
},
{
"transition": "End_Diagnosis_Encounter",
"remarks": [
"before 1993 there were no specific drugs approved for Alzheimer’s by the fda"
]
}
]
},
"FirstPrescription1": {
"type": "MedicationOrder",
"assign_to_attribute": "Alzheimer's Medication",
"reason": "Type of Alzheimer's",
"codes": [
{
"system": "RxNorm",
"code": "310436",
"display": "Galantamine 4 MG Oral Tablet"
}
],
"direct_transition": "End_Diagnosis_Encounter"
},
"FirstPrescription2": {
"type": "MedicationOrder",
"assign_to_attribute": "Alzheimer's Medication",
"reason": "Type of Alzheimer's",
"codes": [
{
"system": "RxNorm",
"code": "997223",
"display": "Donepezil hydrochloride 10 MG Oral Tablet"
}
],
"direct_transition": "End_Diagnosis_Encounter"
},
"FirstPrescription3": {
"type": "MedicationOrder",
"assign_to_attribute": "Alzheimer's Medication",
"reason": "Type of Alzheimer's",
"codes": [
{
"system": "RxNorm",
"code": "313185",
"display": "Tacrine 10 MG Oral Capsule"
}
],
"direct_transition": "End_Diagnosis_Encounter"
},
"ModerateDecline": {
"type": "Delay",
"range": {
"low": 5,
"high": 7,
"unit": "months"
},
"remarks": [
"4. Moderate decline, or mild alzheimer's has a mean duration of 2 years.",
"The diagnosis of alzheimer's can be made with considerable accuracy in this stage",
"https://www.alzinfo.org/understand-alzheimers/clinical-stages-of-alzheimers/"
],
"conditional_transition": [
{
"condition": {
"condition_type": "Not",
"condition": {
"condition_type": "PriorState",
"name": "DiagnosisEncounter"
}
},
"transition": "DiagnosisEncounter"
},
{
"condition": {
"condition_type": "Symptom",
"symptom": "Memory Loss",
"operator": ">",
"value": 70
},
"transition": "ModeratelySevere_Encounter"
},
{
"transition": "ModerateMemoryLoss"
}
]
},
"ModerateMemoryLoss": {
"type": "Symptom",
"symptom": "Memory Loss",
"range": {
"low": 50,
"high": 100
},
"remarks": [
"These numbers do not map to any real data, they are just picked mathematically to get the %s right"
],
"direct_transition": "ModerateDecline"
},
"ModeratelySevere_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Type of Alzheimer's",
"telemedicine_possibility": "possible",
"codes": [
{
"system": "SNOMED-CT",
"code": "316744009",
"display": "Office Visit"
}
],
"direct_transition": "ModeratelySevere_MMSE_Score"
},
"ModeratelySevere_MMSE_Score": {
"type": "Observation",
"category": "survey",
"codes": [
{
"system": "LOINC",
"code": "72106-8",
"display": "Total score [MMSE]"
}
],
"range": {
"low": 12,
"high": 18
},
"remarks": [
"The maximum MMSE score is 30 points. A score of 20 to 24 suggests mild dementia, ",
"13 to 20 suggests moderate dementia, and less than 12 indicates severe dementia",
"http://www.alz.org/alzheimers_disease_steps_to_diagnosis.asp"
],
"unit": "{score}",
"conditional_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "Alzheimer's Medication",
"operator": "is not nil"
},
"transition": "EndFirstPrescription"
},
{
"transition": "SecondPrescription"
}
]
},
"EndFirstPrescription": {
"type": "MedicationEnd",
"referenced_by_attribute": "Alzheimer's Medication",
"direct_transition": "SecondPrescription"
},
"SecondPrescription": {
"type": "Simple",
"conditional_transition": [
{
"condition": {
"condition_type": "Date",
"operator": ">",
"year": 2014
},
"transition": "SecondPrescription1",
"remarks": [
"memantine+donepezil(namzaric) fda approved in 2014"
]
},
{
"condition": {
"condition_type": "Date",
"operator": ">",
"year": 2003
},
"transition": "SecondPrescription2",
"remarks": [
"memantine(namenda) fda approved in 2003"
]
},
{
"condition": {
"condition_type": "Date",
"operator": ">",
"year": 1996
},
"transition": "SecondPrescription3",
"remarks": [
"donepezil(aricept) fda approved in 1996"
]
},
{
"transition": "End_ModeratelySevere_Encounter"
}
]
},
"SecondPrescription1": {
"type": "MedicationOrder",
"reason": "Type of Alzheimer's",
"codes": [
{
"system": "RxNorm",
"code": "1599803",
"display": "24 HR Donepezil hydrochloride 10 MG / Memantine hydrochloride 28 MG Extended Release Oral Capsule"
}
],
"direct_transition": "End_ModeratelySevere_Encounter"
},
"SecondPrescription2": {
"type": "MedicationOrder",
"reason": "Type of Alzheimer's",
"codes": [
{
"system": "RxNorm",
"code": "996740",
"display": "Memantine hydrochloride 2 MG/ML Oral Solution"
}
],
"direct_transition": "End_ModeratelySevere_Encounter"
},
"SecondPrescription3": {
"type": "MedicationOrder",
"reason": "Type of Alzheimer's",
"codes": [
{
"system": "RxNorm",
"code": "1100184",
"display": "Donepezil hydrochloride 23 MG Oral Tablet"
}
],
"direct_transition": "End_ModeratelySevere_Encounter"
},
"End_ModeratelySevere_Encounter": {
"type": "EncounterEnd",
"direct_transition": "ModeratelySevereDecline"
},
"ModeratelySevereDecline": {
"type": "Delay",
"range": {
"low": 12,
"high": 24,
"unit": "months"
},
"remarks": [
"5. Moderately severe decline, aka mid-stage or moderate alzheimer's has a mean duration about 1.5 yrs",
"https://www.alzinfo.org/understand-alzheimers/clinical-stages-of-alzheimers/"
],
"direct_transition": "Severe_Encounter"
},
"Severe_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Type of Alzheimer's",
"codes": [
{
"system": "SNOMED-CT",
"code": "316744009",
"display": "Office Visit"
}
],
"direct_transition": "Severe_MMSE_Score"
},
"Severe_MMSE_Score": {
"type": "Observation",
"category": "survey",
"codes": [
{
"system": "LOINC",
"code": "72106-8",
"display": "Total score [MMSE]"
}
],
"range": {
"low": 6,
"high": 12
},
"remarks": [
"The maximum MMSE score is 30 points. A score of 20 to 24 suggests mild dementia, ",
"13 to 20 suggests moderate dementia, and less than 12 indicates severe dementia",
"http://www.alz.org/alzheimers_disease_steps_to_diagnosis.asp"
],
"unit": "{score}",
"direct_transition": "End_Severe_Encounter"
},
"End_Severe_Encounter": {
"type": "EncounterEnd",
"direct_transition": "SevereDecline"
},
"SevereDecline": {
"type": "Delay",
"range": {
"low": 20,
"high": 40,
"unit": "months"
},
"remarks": [
"6. Severe decline, or moderately severe Alzheimer's contains 5 defined substages, the total duration approximately 2.5 yrs"
],
"direct_transition": "VerySevere_Encounter"
},
"VerySevere_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Type of Alzheimer's",
"codes": [
{
"system": "SNOMED-CT",
"code": "316744009",
"display": "Office Visit"
}
],
"direct_transition": "VerySevere_MMSE_Score"
},
"VerySevere_MMSE_Score": {
"type": "Observation",
"category": "survey",
"codes": [
{
"system": "LOINC",
"code": "72106-8",
"display": "Total score [MMSE]"
}
],
"range": {
"low": 0,
"high": 6
},
"remarks": [
"The maximum MMSE score is 30 points. A score of 20 to 24 suggests mild dementia, ",
"13 to 20 suggests moderate dementia, and less than 12 indicates severe dementia",
"http://www.alz.org/alzheimers_disease_steps_to_diagnosis.asp"
],
"unit": "{score}",
"direct_transition": "End_VerySevere_Encounter"
},
"End_VerySevere_Encounter": {
"type": "EncounterEnd",
"direct_transition": "VerySevereDecline"
},
"VerySevereDecline": {
"type": "Delay",
"range": {
"low": 6,
"high": 12,
"unit": "months"
},
"remarks": [
"7. Very severe decline, aka late-stage or severe alzheimer's contains 6 functional substages, each with a mean duration ~1 yr",
"https://www.alzinfo.org/understand-alzheimers/clinical-stages-of-alzheimers/"
],
"distributed_transition": [
{
"distribution": 0.16,
"transition": "Pneumonia"
},
{
"distribution": 0.16,
"transition": "Death"
},
{
"distribution": 0.68,
"transition": "VerySevereDecline"
}
]
},
"Pneumonia": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "233604007",
"display": "Pneumonia (disorder)"
}
],
"remarks": [
"Pneumonia is one of the most common causes of death among Alzheimer’s patients"
],
"direct_transition": "PneumoniaEncounter",
"assign_to_attribute": "hospice_reason",
"target_encounter": "PneumoniaEncounter"
},
"PneumoniaEncounter": {
"type": "Encounter",
"encounter_class": "emergency",
"reason": "Pneumonia",
"codes": [
{
"system": "SNOMED-CT",
"code": "4525004",
"display": "Emergency department patient visit (procedure)"
}
],
"direct_transition": "Emergency Time"
},
"PneumoniaDeath": {
"type": "Death",
"range": {
"low": 4,
"high": 14,
"unit": "days"
},
"condition_onset": "Pneumonia",
"direct_transition": "Admit to Hospice"
},
"Death": {
"type": "Death",
"referenced_by_attribute": "Type of Alzheimer's",
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
},
"End_Diagnosis_Encounter": {
"type": "EncounterEnd",
"direct_transition": "ModerateDecline"
},
"Eventual_Hospice_Reason": {
"type": "SetAttribute",
"attribute": "hospice_reason",
"direct_transition": "NoImpairment",
"value_attribute": "Type of Alzheimer's"
},
"Admit to Hospice": {
"type": "SetAttribute",
"attribute": "hospice",
"direct_transition": "Terminal",
"value": true
},
"Emergency Time": {
"type": "Delay",
"distribution": {
"kind": "EXPONENTIAL",
"parameters": {
"mean": 3
}
},
"unit": "hours",
"direct_transition": "End Emergency Visit"
},
"End Emergency Visit": {
"type": "EncounterEnd",
"direct_transition": "PneumoniaDeath",
"discharge_disposition": {
"system": "NUBC",
"code": 50,
"display": "Discharged/transferred to Hospice - home"
}
}
},
"gmf_version": 1
}

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src/main/resources/modules/dental_and_oral_examination.json Normal file
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src/main/resources/modules/dentures.json Normal file
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{
"name": "Dentures",
"remarks": [
"This model may be triggered based upon the number of 'missing_teeth' a person has. Missing teeth are set in the 'dental_and_oral_examination' module.",
"",
"A number of \"comorbid\" conditions are included, because the related surgeries to address these conditions are not covered by Medicare reimbursement in 2023 when it is related the are related to dentures: frenectomy (effects 5% of population), ridge reconstruction, palate bone growth (effects 30% of the population), and mandible bone growth (effects 2.7% of the population).",
"",
"Dentures last 7-10 years before replacement.",
"",
"References:",
"- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1949218/",
"- https://my.clevelandclinic.org/health/articles/10900-dentures",
"- https://my.clevelandclinic.org/health/diseases/24829-torus-palatinus",
"- https://my.clevelandclinic.org/health/diseases/24830-mandibular-tori",
"- https://www.centerfordentalreconstruction.com/oral-surgery-services/bone-grafting/ridge-augmentation",
"- https://www.cms.gov/Regulations-and-Guidance/Guidance/Manuals/Downloads/bp102c15.pdf"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Wait for Missing Teeth"
},
"Wait for Missing Teeth": {
"type": "Guard",
"allow": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "missing_teeth",
"operator": "is not nil"
},
{
"condition_type": "Attribute",
"attribute": "missing_teeth",
"operator": ">=",
"value": 2
}
]
},
"direct_transition": "Check A"
},
"Initial Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Loss of teeth",
"telemedicine_possibility": "none",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem (procedure)"
}
],
"direct_transition": "Dental_consultation_and_report"
},
"Dental_consultation_and_report": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "34043003",
"display": "Dental consultation and report (procedure)"
}
],
"distribution": {
"kind": "GAUSSIAN",
"parameters": {
"min": 5,
"mean": 30,
"standardDeviation": 10
}
},
"unit": "minutes",
"direct_transition": "Dental_x_ray_system",
"reason": "Loss of teeth"
},
"Dental_x_ray_system": {
"type": "Device",
"code": {
"system": "SNOMED-CT",
"code": "706298007",
"display": "Dental x-ray system (physical object)"
},
"direct_transition": "Dental_X_ray"
},
"Dental_X_ray": {
"type": "ImagingStudy",
"procedure_code": {
"system": "SNOMED-CT",
"code": "241046008",
"display": "Dental plain X-ray bitewing (procedure)"
},
"series": [
{
"body_site": {
"system": "SNOMED-CT",
"code": "700016008",
"display": "Structure of region of internal part of mouth (body structure)"
},
"modality": {
"system": "DICOM-DCM",
"code": "DX",
"display": "Digital Radiography"
},
"instances": [
{
"title": "Digital Intra-Oral X-Ray Image",
"sop_class": {
"system": "DICOM-SOP",
"code": "1.2.840.10008.5.1.4.1.1.1.3",
"display": "Digital Intra-Oral X-Ray Image Storage - For Presentation"
}
}
]
}
],
"direct_transition": "Finish_Dental_x_ray_system"
},
"Finish_Dental_x_ray_system": {
"type": "DeviceEnd",
"device": "Dental x-ray system",
"direct_transition": "Dental Impression Supplies"
},
"Dental Impression Supplies": {
"type": "SupplyList",
"supplies": [
{
"quantity": 1,
"code": {
"system": "SNOMED-CT",
"code": "706390002",
"display": "Dental impression material (physical object)"
}
},
{
"quantity": 1,
"code": {
"system": "SNOMED-CT",
"code": "468277001",
"display": "Dental impression tray material (physical object)"
}
}
],
"direct_transition": "Dental Impression"
},
"Dental Impression": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "234745004",
"display": "Take oral or dental impression (procedure)"
},
{
"system": "SNOMED-CT",
"code": "234754001",
"display": "Take impression for orthodontic appliance (procedure)"
}
],
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 60,
"low": 30
}
},
"unit": "minutes",
"direct_transition": "End Initial Encounter",
"reason": "Loss of teeth"
},
"End Initial Encounter": {
"type": "EncounterEnd",
"direct_transition": "Check for Related Surgeries"
},
"Check for Related Surgeries": {
"type": "Simple",
"conditional_transition": [
{
"transition": "Wait for Surgery",
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Not",
"condition": {
"condition_type": "PriorState",
"name": "Wait for Surgery"
}
},
{
"condition_type": "Or",
"conditions": [
{
"condition_type": "Or",
"conditions": [
{
"condition_type": "PriorState",
"name": "Needs Frenectomy"
},
{
"condition_type": "PriorState",
"name": "Needs Torus Palatinus Removed"
}
]
},
{
"condition_type": "Or",
"conditions": [
{
"condition_type": "PriorState",
"name": "Needs Torus Mandibularis Removed"
},
{
"condition_type": "PriorState",
"name": "Needs Ridge Reconstruction"
}
]
}
]
}
]
}
},
{
"transition": "No Surgery"
}
]
},
"No Surgery": {
"type": "Delay",
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 4,
"low": 2
}
},
"unit": "weeks",
"direct_transition": "Fitting Encounter"
},
"Fitting Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Loss of teeth",
"telemedicine_possibility": "none",
"codes": [
{
"system": "SNOMED-CT",
"code": "390906007",
"display": "Follow-up encounter (procedure)"
}
],
"conditional_transition": [
{
"transition": "End Previous Dentures",
"condition": {
"condition_type": "PriorState",
"name": "Dentures"
}
},
{
"transition": "Dentures"
}
]
},
"Dentures": {
"type": "Device",
"code": {
"system": "SNOMED-CT",
"code": "8060009",
"display": "Denture, device (physical object)"
},
"direct_transition": "Fitting of dentures",
"assign_to_attribute": "dentures"
},
"Fitting of dentures": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "1269321004",
"display": "Fitting of denture (procedure)"
}
],
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 60,
"low": 15
}
},
"unit": "minutes",
"direct_transition": "End Fitting",
"reason": "Loss of teeth"
},
"End Fitting": {
"type": "EncounterEnd",
"direct_transition": "Wait for Replacement"
},
"Wait for Replacement": {
"type": "Delay",
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 10,
"low": 7
}
},
"unit": "years",
"direct_transition": "Initial Encounter"
},
"Loss of teeth": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "37320007",
"display": "Loss of teeth (disorder)"
}
],
"direct_transition": "Initial Encounter",
"target_encounter": "Initial Encounter"
},
"End Comorbidity Checks": {
"type": "Simple",
"direct_transition": "Loss of teeth"
},
"Needs Frenectomy": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "67787004",
"display": "Tongue tie (disorder)"
}
],
"direct_transition": "Check D",
"target_encounter": "Initial Encounter",
"assign_to_attribute": "denture_surgery_reason"
},
"Needs Torus Palatinus Removed": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "46752004",
"display": "Torus palatinus (disorder)"
}
],
"direct_transition": "Check B",
"target_encounter": "Initial Encounter",
"assign_to_attribute": "denture_surgery_reason"
},
"Needs Torus Mandibularis Removed": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "11625007",
"display": "Torus mandibularis (disorder)"
}
],
"direct_transition": "End Comorbidity Checks",
"target_encounter": "Initial Encounter",
"assign_to_attribute": "denture_surgery_reason"
},
"Needs Ridge Reconstruction": {
"type": "ConditionOnset",
"codes": [
{
"system": "SNOMED-CT",
"code": "1255252008",
"display": "Resorption of alveolar process due to dental trauma (disorder)"
}
],
"direct_transition": "Check C",
"target_encounter": "Initial Encounter",
"assign_to_attribute": "denture_surgery_reason"
},
"Wait for Surgery": {
"type": "Delay",
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 21,
"low": 7
}
},
"unit": "days",
"direct_transition": "Surgery Encounter"
},
"Excision of maxillary torus palatinus": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "79345008",
"display": "Excision of maxillary torus palatinus (procedure)"
}
],
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 60,
"low": 30
}
},
"unit": "minutes",
"direct_transition": "End Torus Palatinus",
"reason": "Needs Torus Palatinus Removed"
},
"Excision of lingual torus": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "23183008",
"display": "Excision of lingual torus (procedure)"
}
],
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 60,
"low": 30
}
},
"unit": "minutes",
"reason": "Needs Torus Mandibularis Removed",
"direct_transition": "End Torus Mandibularis"
},
"Surgery Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "denture_surgery_reason",
"telemedicine_possibility": "none",
"codes": [
{
"system": "SNOMED-CT",
"code": "390906007",
"display": "Follow-up encounter (procedure)"
}
],
"direct_transition": "Operating_room"
},
"Check A": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Needs Torus Palatinus Removed",
"distribution": 0.3
},
{
"transition": "Check B",
"distribution": 0.7
}
]
},
"Check B": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Needs Ridge Reconstruction",
"distribution": 0.3
},
{
"transition": "Check C",
"distribution": 0.7
}
]
},
"Check D": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Needs Torus Mandibularis Removed",
"distribution": 0.027
},
{
"transition": "End Comorbidity Checks",
"distribution": 0.973
}
]
},
"Check C": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Needs Frenectomy",
"distribution": 0.05
},
{
"transition": "Check D",
"distribution": 0.95
}
]
},
"End_Surgery": {
"type": "EncounterEnd",
"direct_transition": "Wait for Fitting"
},
"Wait for Fitting": {
"type": "Delay",
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 14,
"low": 3
}
},
"unit": "days",
"direct_transition": "Fitting Encounter"
},
"Operating_room": {
"type": "Device",
"code": {
"system": "SNOMED-CT",
"code": "225738002",
"display": "Operating room (environment)"
},
"direct_transition": "Dental_Anesthesia"
},
"Exit_Operating_room": {
"type": "DeviceEnd",
"device": "Operating room",
"direct_transition": "Postoperative_care_for_dental_procedure"
},
"Postoperative_care_for_dental_procedure": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": 456191000124101,
"display": "Postoperative care for dental procedure (regime/therapy)"
}
],
"distribution": {
"kind": "GAUSSIAN",
"parameters": {
"min": 5,
"mean": 60,
"standardDeviation": 15
}
},
"unit": "minutes",
"reason": "dental_surgery_reason",
"direct_transition": "End_Surgery"
},
"Dental_Anesthesia": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "3802001",
"display": "Dental application of desensitizing medicament (procedure)"
}
],
"distribution": {
"kind": "GAUSSIAN",
"parameters": {
"min": 5,
"mean": 60,
"standardDeviation": 15
}
},
"unit": "minutes",
"reason": "dental_surgery_reason",
"direct_transition": "Dental_surgical_procedure"
},
"Dental_surgical_procedure": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "81733005",
"display": "Dental surgical procedure (procedure)"
}
],
"distribution": {
"kind": "GAUSSIAN",
"parameters": {
"min": 5,
"mean": 10,
"standardDeviation": 5
}
},
"unit": "minutes",
"reason": "dental_surgery_reason",
"direct_transition": "Surgery A"
},
"Excision of lingual frenum": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "23933004",
"display": "Excision of lingual frenum (procedure)"
}
],
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 60,
"low": 30
}
},
"unit": "minutes",
"reason": "Needs Frenectomy",
"direct_transition": "End Tongue Tied"
},
"Grafting of periodontal bone defect": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "234687006",
"display": "Grafting of periodontal bone defect (procedure)"
}
],
"distribution": {
"kind": "UNIFORM",
"parameters": {
"high": 60,
"low": 30
}
},
"unit": "minutes",
"direct_transition": "End Ridge Defect",
"reason": "Needs Ridge Reconstruction"
},
"Surgery A": {
"type": "Simple",
"conditional_transition": [
{
"transition": "Excision of maxillary torus palatinus",
"condition": {
"condition_type": "PriorState",
"name": "Needs Torus Palatinus Removed"
}
},
{
"transition": "Surgery B"
}
]
},
"Surgery B": {
"type": "Simple",
"conditional_transition": [
{
"transition": "Grafting of periodontal bone defect",
"condition": {
"condition_type": "PriorState",
"name": "Needs Ridge Reconstruction"
}
},
{
"transition": "Surgery C"
}
]
},
"Surgery C": {
"type": "Simple",
"conditional_transition": [
{
"transition": "Excision of lingual frenum",
"condition": {
"condition_type": "PriorState",
"name": "Needs Frenectomy"
}
},
{
"transition": "Surgery D"
}
]
},
"Surgery D": {
"type": "Simple",
"conditional_transition": [
{
"transition": "Excision of lingual torus",
"condition": {
"condition_type": "PriorState",
"name": "Needs Torus Mandibularis Removed"
}
},
{
"transition": "Exit_Operating_room"
}
]
},
"End Torus Palatinus": {
"type": "ConditionEnd",
"direct_transition": "Surgery B",
"condition_onset": "Needs Torus Palatinus Removed"
},
"End Ridge Defect": {
"type": "ConditionEnd",
"direct_transition": "Surgery C",
"condition_onset": "Needs Ridge Reconstruction"
},
"End Tongue Tied": {
"type": "ConditionEnd",
"direct_transition": "Surgery D",
"condition_onset": "Needs Frenectomy"
},
"End Torus Mandibularis": {
"type": "ConditionEnd",
"direct_transition": "Exit_Operating_room",
"condition_onset": "Needs Torus Mandibularis Removed"
},
"End Previous Dentures": {
"type": "DeviceEnd",
"direct_transition": "Dentures",
"device": "Dentures"
}
},
"gmf_version": 2
}

692
src/main/resources/modules/dermatitis.json Normal file
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{
"name": "Dermatitis",
"remarks": [
"Source: https://nationaleczema.org/research/eczema-prevalence/",
"Known colloquially as Eczema. About 10.7% of children develop dermatitis ",
"and dermatitis is found in about 10.2% of adults. 31.6M adults overall ",
"have eczema. 17.8M have moderate to severe cases, usually atopic dermatitis (AD).",
"Atopic dermatitis usually appears in childhood. 1/3 of all children with AD ",
"have severe cases. Up to 3% of adults are also living with severe AD, suggesting ",
"that AD is typically a lifelong condition.",
"The remaining patients with dermatitis typically have contact dermatitis (CD), ",
"aggravated by specific substances such as nickel, latex, and chromium. ",
"2x as many females develop CD as males."
],
"states": {
"Initial": {
"type": "Initial",
"remarks": [
"======================================================================",
" INCIDENCE ",
"======================================================================"
],
"direct_transition": "Delay_For_Atopy"
},
"Delay_For_Atopy": {
"type": "Delay",
"remarks": [
"The Atopy module must be processed before any of the allergy modules so ",
"atopy can appropriately influence allergies. Delaying the smallest possible ",
"time step to ensure this happens."
],
"exact": {
"quantity": 1,
"unit": "weeks"
},
"conditional_transition": [
{
"condition": {
"condition_type": "Attribute",
"attribute": "atopic",
"operator": "is not nil"
},
"transition": "Atopic"
},
{
"transition": "Not_Atopic"
}
]
},
"Atopic": {
"type": "Simple",
"remarks": [
"35% of all atopic patients develop AD. See the Atopy model for more info."
],
"distributed_transition": [
{
"distribution": 0.35,
"transition": "Atopic_Dermatitis_Incidence"
},
{
"distribution": 0.65,
"transition": "Terminal"
}
]
},
"Not_Atopic": {
"type": "Simple",
"remarks": [
"There is a small possibility that non-atopic patients still develop AD.",
"More commonly however, non-atopic patients instead develop contact ",
"dermatitis sometime during adulthood, often from a person's occupation.",
"For example, occupational contact dermatitis is common in: ",
"Metalworkers, Hair Dressers, Healthcare Professionals, Cleaners, ",
"Construction Workers, Painters, and those in Food Manufacturing."
],
"distributed_transition": [
{
"distribution": 0.003125,
"transition": "Atopic_Dermatitis_Incidence"
},
{
"distribution": 0.043125,
"transition": "Delay_Until_Adulthood"
},
{
"distribution": 0.95375,
"transition": "Terminal"
}
]
},
"Atopic_Dermatitis_Incidence": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.5,
"transition": "Early_Childhood_AD"
},
{
"distribution": 0.45,
"transition": "Mid_Childhood_AD"
},
{
"distribution": 0.05,
"transition": "Late_Childhood_AD"
}
]
},
"Early_Childhood_AD": {
"type": "Delay",
"remarks": [
"Children <1 year old. Early childhood AD is widspread and found ",
"mainly on the face and extremities."
],
"range": {
"low": 0,
"high": 11,
"unit": "months"
},
"direct_transition": "Childhood_Atopic_Dermatitis"
},
"Mid_Childhood_AD": {
"type": "Delay",
"remarks": [
"Children <5 years old. AD found in older children (not infants) is ",
"typically found at the limb flexures, such as the elbow and knee."
],
"range": {
"low": 12,
"high": 59,
"unit": "months"
},
"direct_transition": "Childhood_Atopic_Dermatitis"
},
"Late_Childhood_AD": {
"type": "Delay",
"remarks": [
"Children <10 years old. AD found in older children (not infants) is ",
"typically found at the limb flexures, such as the elbow and knee."
],
"range": {
"low": 60,
"high": 120,
"unit": "months"
},
"direct_transition": "Childhood_Atopic_Dermatitis"
},
"Delay_Until_Adulthood": {
"type": "Delay",
"range": {
"low": 18,
"high": 35,
"unit": "years"
},
"direct_transition": "Adult_Contact_Dermatitis"
},
"Childhood_Atopic_Dermatitis": {
"type": "ConditionOnset",
"target_encounter": "PCP_Encounter",
"assign_to_attribute": "dermatitis",
"codes": [
{
"system": "SNOMED-CT",
"code": "24079001",
"display": "Atopic dermatitis (disorder)"
}
],
"direct_transition": "PCP_Encounter"
},
"Adult_Contact_Dermatitis": {
"type": "ConditionOnset",
"target_encounter": "PCP_Encounter",
"assign_to_attribute": "dermatitis",
"codes": [
{
"system": "SNOMED-CT",
"code": "40275004",
"display": "Contact dermatitis (disorder)"
}
],
"direct_transition": "PCP_Encounter"
},
"PCP_Encounter": {
"type": "Encounter",
"remarks": [
"The rashes and sensitivity caused by dermatitis are bad enough to drive ",
"any sensible parents to bring their child to the doctor. The PCP will then ",
"refer the child to an allergist and/or dermatologist. 1/3 of all AD cases ",
"are considered 'severe'. Moderate and severe cases are first referred to ",
"a dermatologist, followed by an allergist."
],
"encounter_class": "ambulatory",
"reason": "dermatitis",
"telemedicine_possibility": "possible",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem (procedure)"
}
],
"direct_transition": "Dermatitis_Symptom1"
},
"Dermatitis_Symptom1": {
"type": "Symptom",
"symptom": "Itchiness",
"range": {
"low": 0,
"high": 20
},
"direct_transition": "Dermatitis_Symptom2"
},
"Dermatitis_Symptom2": {
"type": "Symptom",
"symptom": "Red Skin",
"range": {
"low": 0,
"high": 20
},
"direct_transition": "Dermatitis_Symptom3"
},
"Dermatitis_Symptom3": {
"type": "Symptom",
"symptom": "Rash",
"range": {
"low": 0,
"high": 20
},
"direct_transition": "Dermatitis_Careplan"
},
"Dermatitis_Careplan": {
"type": "CarePlanStart",
"remarks": [
"Treatment of eczema is all about self care. Typically all a patient can ",
"do is treat the symptoms and avoid allergens and irritants. Allergy ",
"tests and specialized treatment by an allergist really didn't exist ",
"before 1975 - 1980."
],
"reason": "dermatitis",
"codes": [
{
"system": "SNOMED-CT",
"code": "711282006",
"display": "Skin condition care (regime/therapy)"
}
],
"activities": [
{
"system": "SNOMED-CT",
"code": "225130001",
"display": "Application of moisturizer to skin (procedure)"
}
],
"direct_transition": "End_Diagnosis_Encounter"
},
"End_Diagnosis_Encounter": {
"type": "EncounterEnd",
"distributed_transition": [
{
"distribution": 0.33,
"remarks": [
"The mild cases of eczema receive no further treatment unless they get worse."
],
"transition": "Living_With_Dermatitis"
},
{
"distribution": 0.67,
"transition": "Delay_For_Dermatologist"
}
]
},
"Delay_For_Dermatologist": {
"type": "Delay",
"range": {
"low": 1,
"high": 7,
"unit": "days"
},
"direct_transition": "Dermatologist_Visit"
},
"Dermatologist_Visit": {
"type": "Encounter",
"remarks": [
"1/3 of all eczema cases are severe. 0.5 * 0.67 ~= 0.33"
],
"encounter_class": "ambulatory",
"telemedicine_possibility": "possible",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem (procedure)"
}
],
"complex_transition": [
{
"condition": {
"condition_type": "PriorState",
"name": "Early_Childhood_AD"
},
"distributions": [
{
"distribution": 0.5,
"transition": "Early_Childhood_AD_Moderate_Observations"
},
{
"distribution": 0.5,
"transition": "Early_Childhood_AD_Severe_Observations"
}
]
},
{
"condition": {
"condition_type": "PriorState",
"name": "Mid_Childhood_AD"
},
"distributions": [
{
"distribution": 0.5,
"transition": "Mid_Childhood_AD_Moderate_Observations"
},
{
"distribution": 0.5,
"transition": "Mid_Childhood_AD_Severe_Observations"
}
]
},
{
"condition": {
"condition_type": "PriorState",
"name": "Adult_Contact_Dermatitis"
},
"distributions": [
{
"distribution": 0.67,
"transition": "Moderate_Contact_Dermatitis_Observations"
},
{
"distribution": 0.33,
"transition": "Severe_Contact_Dermatitis_Observations"
}
]
}
],
"reason": "dermatitis"
},
"Early_Childhood_AD_Moderate_Observations": {
"type": "CallSubmodule",
"submodule": "dermatitis/early_moderate_eczema_obs",
"direct_transition": "Advise_To_Visit_Allergist"
},
"Early_Childhood_AD_Severe_Observations": {
"type": "CallSubmodule",
"submodule": "dermatitis/early_severe_eczema_obs",
"direct_transition": "Advise_To_Visit_Allergist"
},
"Mid_Childhood_AD_Moderate_Observations": {
"type": "CallSubmodule",
"submodule": "dermatitis/mid_moderate_eczema_obs",
"direct_transition": "Advise_To_Visit_Allergist"
},
"Mid_Childhood_AD_Severe_Observations": {
"type": "CallSubmodule",
"submodule": "dermatitis/mid_severe_eczema_obs",
"direct_transition": "Advise_To_Visit_Allergist"
},
"Moderate_Contact_Dermatitis_Observations": {
"type": "CallSubmodule",
"submodule": "dermatitis/moderate_cd_obs",
"direct_transition": "Prescribe_Corticosteroid"
},
"Severe_Contact_Dermatitis_Observations": {
"type": "CallSubmodule",
"submodule": "dermatitis/severe_cd_obs",
"direct_transition": "Prescribe_Corticosteroid"
},
"Prescribe_Corticosteroid": {
"type": "MedicationOrder",
"remarks": [
"These are only prescribed to adults or older children."
],
"reason": "dermatitis",
"codes": [
{
"system": "RxNorm",
"code": "106258",
"display": "Hydrocortisone 10 MG/ML Topical Cream"
}
],
"prescription": {
"as_needed": true
},
"direct_transition": "Advise_To_Visit_Allergist"
},
"Advise_To_Visit_Allergist": {
"type": "SetAttribute",
"attribute": "visit_allergist",
"value": true,
"direct_transition": "End_Dermatologist_Visit"
},
"End_Dermatologist_Visit": {
"type": "EncounterEnd",
"direct_transition": "Living_With_Dermatitis"
},
"Living_With_Dermatitis": {
"type": "Delay",
"remarks": [
"======================================================================",
" LIVING WITH DERMATITS ",
"======================================================================"
],
"range": {
"low": 8,
"high": 16,
"unit": "months"
},
"conditional_transition": [
{
"condition": {
"condition_type": "PriorState",
"name": "Adult_Contact_Dermatitis"
},
"transition": "Potential_CD_Resolves"
},
{
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "PriorState",
"name": "Childhood_Atopic_Dermatitis"
},
{
"condition_type": "Not",
"condition": {
"condition_type": "PriorState",
"name": "Potentially_Outgrow_AD"
}
},
{
"condition_type": "Age",
"operator": ">",
"quantity": 16,
"unit": "years"
}
]
},
"transition": "Potentially_Outgrow_AD"
},
{
"transition": "Potential_AD_Flare_Up"
}
]
},
"Potentially_Outgrow_AD": {
"type": "Simple",
"remarks": [
"About 75% of children with Atopic Dermatitis outgrow it by adolescence."
],
"distributed_transition": [
{
"distribution": 0.75,
"transition": "Dermatitis_Resolves"
},
{
"distribution": 0.25,
"transition": "Potential_AD_Flare_Up"
}
]
},
"Potential_AD_Flare_Up": {
"type": "Simple",
"remarks": [
"A 'flare-up' is a heightening of the symptoms from Atopic Dermatitis, including ",
"very itchy skin, spreading rashes, and sensitivity. For older children (>12) and ",
"adults an immunosuppressant and topical corticosteroid are prescribed to control ",
"the symptoms. ",
"Only patients with moderate to severe AD paid a visit to the Dermatologist."
],
"complex_transition": [
{
"condition": {
"condition_type": "PriorState",
"name": "Dermatologist_Visit"
},
"distributions": [
{
"distribution": 0.1,
"transition": "AD_Flare_Up"
},
{
"distribution": 0.9,
"transition": "Living_With_Dermatitis"
}
]
},
{
"distributions": [
{
"distribution": 1,
"transition": "Living_With_Dermatitis"
}
]
}
]
},
"AD_Flare_Up": {
"type": "Delay",
"remarks": [
"A flare-up is bad enough to seek treatment. Usually another visit to the dermatologist ",
"will suffice."
],
"range": {
"low": 1,
"high": 7,
"unit": "days"
},
"direct_transition": "Dermatologist_Visit_For_Flare_Up"
},
"Dermatologist_Visit_For_Flare_Up": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "dermatitis",
"telemedicine_possibility": "possible",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem (procedure)"
}
],
"conditional_transition": [
{
"condition": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Age",
"operator": ">",
"quantity": 16,
"unit": "years"
},
{
"condition_type": "Date",
"operator": ">=",
"year": 1983
}
]
},
"transition": "Prescribe_Immunosuppressant"
},
{
"transition": "Prescribe_Corticosteroid_For_Flare_Up"
}
]
},
"Prescribe_Immunosuppressant": {
"type": "MedicationOrder",
"reason": "dermatitis",
"remarks": [
"Immunosuppressants like cyclosporine were invented in the late 1970's ",
"and came to market in the early 1980s. Cyclosporine was available starting ",
"in 1983."
],
"codes": [
{
"system": "RxNorm",
"code": "241834",
"display": "cycloSPORINE, modified 100 MG Oral Capsule"
}
],
"prescription": {
"dosage": {
"amount": 1,
"frequency": 1,
"period": 1,
"unit": "days"
},
"duration": {
"quantity": 2,
"unit": "weeks"
}
},
"direct_transition": "Prescribe_Corticosteroid_For_Flare_Up"
},
"Prescribe_Corticosteroid_For_Flare_Up": {
"type": "MedicationOrder",
"reason": "dermatitis",
"codes": [
{
"system": "RxNorm",
"code": "106258",
"display": "Hydrocortisone 10 MG/ML Topical Cream"
}
],
"prescription": {
"as_needed": true
},
"direct_transition": "End_Flare_Up_Encounter"
},
"Treating_Flare_Up": {
"type": "Delay",
"range": {
"low": 2,
"high": 4,
"unit": "weeks"
},
"conditional_transition": [
{
"condition": {
"condition_type": "Active Medication",
"codes": [
{
"system": "RxNorm",
"code": "241834",
"display": "cycloSPORINE, modified 100 MG Oral Capsule"
}
]
},
"transition": "End_Immunosuppressant"
},
{
"transition": "End_Corticosteroid"
}
]
},
"End_Immunosuppressant": {
"type": "MedicationEnd",
"medication_order": "Prescribe_Immunosuppressant",
"direct_transition": "End_Corticosteroid"
},
"End_Corticosteroid": {
"type": "MedicationEnd",
"medication_order": "Prescribe_Corticosteroid_For_Flare_Up",
"direct_transition": "Living_With_Dermatitis"
},
"Potential_CD_Resolves": {
"type": "Simple",
"distributed_transition": [
{
"distribution": 0.75,
"transition": "Dermatitis_Resolves"
},
{
"distribution": 0.25,
"transition": "Living_With_Dermatitis"
}
]
},
"Dermatitis_Resolves": {
"type": "ConditionEnd",
"referenced_by_attribute": "dermatitis",
"direct_transition": "End_Dermatitis_CarePlan"
},
"End_Dermatitis_CarePlan": {
"type": "CarePlanEnd",
"careplan": "Dermatitis_Careplan",
"direct_transition": "Dermatitis_Symptom1_Ends"
},
"Dermatitis_Symptom1_Ends": {
"type": "Symptom",
"symptom": "Itchiness",
"exact": {
"quantity": 0
},
"direct_transition": "Dermatitis_Symptom2_Ends"
},
"Dermatitis_Symptom2_Ends": {
"type": "Symptom",
"symptom": "Red Skin",
"exact": {
"quantity": 0
},
"direct_transition": "Dermatitis_Symptom3_Ends"
},
"Dermatitis_Symptom3_Ends": {
"type": "Symptom",
"symptom": "Rash",
"exact": {
"quantity": 0
},
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
},
"End_Flare_Up_Encounter": {
"type": "EncounterEnd",
"direct_transition": "Treating_Flare_Up"
}
},
"gmf_version": 1
}

88
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{
"name": "Early Childhood Moderate Eczema Observations",
"remarks": [
"A series of observations regarding the prevalence of eczema ",
"on different portions of the body. In this case the eczema is ",
"found to be mild/moderate and confined to the face and limbs, as is ",
"commonly seen in young children. See: ",
"http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2230.2012.04336.x/full"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Eczema_Obs_Head_And_Neck"
},
"Eczema_Obs_Head_And_Neck": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66519-0",
"display": "Percentage area affected by eczema Head and Neck [PhenX]"
}
],
"range": {
"low": 10,
"high": 40
},
"unit": "%",
"direct_transition": "Eczema_Obs_Trunk"
},
"Eczema_Obs_Trunk": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66529-9",
"display": "Percentage area affected by eczema Trunk [PhenX]"
}
],
"range": {
"low": 0,
"high": 10
},
"unit": "%",
"direct_transition": "Eczema_Obs_Upper_Extremities"
},
"Eczema_Obs_Upper_Extremities": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66524-0",
"display": "Percentage area affected by eczema Upper extremity - bilateral [PhenX]"
}
],
"range": {
"low": 0,
"high": 10
},
"unit": "%",
"direct_transition": "Eczema_Obs_Lower_Extremities"
},
"Eczema_Obs_Lower_Extremities": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66534-9",
"display": "Percentage area affected by eczema Lower extremity - bilateral [PhenX]"
}
],
"range": {
"low": 0,
"high": 10
},
"unit": "%",
"direct_transition": "Eczema_Obs_Terminal"
},
"Eczema_Obs_Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

88
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{
"name": "Early Childhood Severe Eczema Observations",
"remarks": [
"A series of observations regarding the prevalence of eczema ",
"on different portions of the body. In this case the eczema is ",
"found to be severe but confined to the face and limbs, as is ",
"commonly seen in young children. See: ",
"http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2230.2012.04336.x/full"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Eczema_Obs_Head_And_Neck"
},
"Eczema_Obs_Head_And_Neck": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66519-0",
"display": "Percentage area affected by eczema Head and Neck [PhenX]"
}
],
"range": {
"low": 40,
"high": 60
},
"unit": "%",
"direct_transition": "Eczema_Obs_Trunk"
},
"Eczema_Obs_Trunk": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66529-9",
"display": "Percentage area affected by eczema Trunk [PhenX]"
}
],
"range": {
"low": 0,
"high": 20
},
"unit": "%",
"direct_transition": "Eczema_Obs_Upper_Extremities"
},
"Eczema_Obs_Upper_Extremities": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66524-0",
"display": "Percentage area affected by eczema Upper extremity - bilateral [PhenX]"
}
],
"range": {
"low": 0,
"high": 20
},
"unit": "%",
"direct_transition": "Eczema_Obs_Lower_Extremities"
},
"Eczema_Obs_Lower_Extremities": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66534-9",
"display": "Percentage area affected by eczema Lower extremity - bilateral [PhenX]"
}
],
"range": {
"low": 0,
"high": 20
},
"unit": "%",
"direct_transition": "Eczema_Obs_Terminal"
},
"Eczema_Obs_Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

88
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{
"name": "Mid Childhood Moderate Eczema Observations",
"remarks": [
"A series of observations regarding the prevalence of eczema ",
"on different portions of the body. In this case the eczema is ",
"found to be mild/moderate and primarilly in the joint flexures, ",
"as is commonly seen in older children. See: ",
"http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2230.2012.04336.x/full"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Eczema_Obs_Head_And_Neck"
},
"Eczema_Obs_Head_And_Neck": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66519-0",
"display": "Percentage area affected by eczema Head and Neck [PhenX]"
}
],
"range": {
"low": 0,
"high": 15
},
"unit": "%",
"direct_transition": "Eczema_Obs_Trunk"
},
"Eczema_Obs_Trunk": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66529-9",
"display": "Percentage area affected by eczema Trunk [PhenX]"
}
],
"range": {
"low": 0,
"high": 10
},
"unit": "%",
"direct_transition": "Eczema_Obs_Upper_Extremities"
},
"Eczema_Obs_Upper_Extremities": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66524-0",
"display": "Percentage area affected by eczema Upper extremity - bilateral [PhenX]"
}
],
"range": {
"low": 0,
"high": 20
},
"unit": "%",
"direct_transition": "Eczema_Obs_Lower_Extremities"
},
"Eczema_Obs_Lower_Extremities": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66534-9",
"display": "Percentage area affected by eczema Lower extremity - bilateral [PhenX]"
}
],
"range": {
"low": 0,
"high": 20
},
"unit": "%",
"direct_transition": "Eczema_Obs_Terminal"
},
"Eczema_Obs_Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

88
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{
"name": "Mid Childhood Severe Eczema Observations",
"remarks": [
"A series of observations regarding the prevalence of eczema ",
"on different portions of the body. In this case the eczema is ",
"found to be severe and primarilly in the joint flexures, ",
"as is commonly seen in older children. See: ",
"http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2230.2012.04336.x/full"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Eczema_Obs_Head_And_Neck"
},
"Eczema_Obs_Head_And_Neck": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66519-0",
"display": "Percentage area affected by eczema Head and Neck [PhenX]"
}
],
"range": {
"low": 0,
"high": 15
},
"unit": "%",
"direct_transition": "Eczema_Obs_Trunk"
},
"Eczema_Obs_Trunk": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66529-9",
"display": "Percentage area affected by eczema Trunk [PhenX]"
}
],
"range": {
"low": 0,
"high": 20
},
"unit": "%",
"direct_transition": "Eczema_Obs_Upper_Extremities"
},
"Eczema_Obs_Upper_Extremities": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66524-0",
"display": "Percentage area affected by eczema Upper extremity - bilateral [PhenX]"
}
],
"range": {
"low": 0,
"high": 40
},
"unit": "%",
"direct_transition": "Eczema_Obs_Lower_Extremities"
},
"Eczema_Obs_Lower_Extremities": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66534-9",
"display": "Percentage area affected by eczema Lower extremity - bilateral [PhenX]"
}
],
"range": {
"low": 0,
"high": 40
},
"unit": "%",
"direct_transition": "Eczema_Obs_Terminal"
},
"Eczema_Obs_Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

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{
"name": "Moderate Contact Dermatitis Observations",
"remarks": [
"A series of observations regarding the prevalence of eczema ",
"on different portions of the body. In this case the eczema is ",
"found to be moderate and confined to the extremities as is commonly ",
"seen with contact dermatitis."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Eczema_Obs_Head_And_Neck"
},
"Eczema_Obs_Head_And_Neck": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66519-0",
"display": "Percentage area affected by eczema Head and Neck [PhenX]"
}
],
"exact": {
"quantity": 0
},
"unit": "%",
"direct_transition": "Eczema_Obs_Trunk"
},
"Eczema_Obs_Trunk": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66529-9",
"display": "Percentage area affected by eczema Trunk [PhenX]"
}
],
"exact": {
"quantity": 0
},
"unit": "%",
"direct_transition": "Eczema_Obs_Upper_Extremities"
},
"Eczema_Obs_Upper_Extremities": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66524-0",
"display": "Percentage area affected by eczema Upper extremity - bilateral [PhenX]"
}
],
"range": {
"low": 10,
"high": 40
},
"unit": "%",
"direct_transition": "Eczema_Obs_Lower_Extremities"
},
"Eczema_Obs_Lower_Extremities": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66534-9",
"display": "Percentage area affected by eczema Lower extremity - bilateral [PhenX]"
}
],
"range": {
"low": 0,
"high": 15
},
"unit": "%",
"direct_transition": "Eczema_Obs_Terminal"
},
"Eczema_Obs_Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

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{
"name": "Severe Contact Dermatitis Observations",
"remarks": [
"A series of observations regarding the prevalence of eczema ",
"on different portions of the body. In this case the eczema is ",
"found to be severe and confined to the extremities as is commonly ",
"seen with contact dermatitis."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Eczema_Obs_Head_And_Neck"
},
"Eczema_Obs_Head_And_Neck": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66519-0",
"display": "Percentage area affected by eczema Head and Neck [PhenX]"
}
],
"exact": {
"quantity": 0
},
"unit": "%",
"direct_transition": "Eczema_Obs_Trunk"
},
"Eczema_Obs_Trunk": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66529-9",
"display": "Percentage area affected by eczema Trunk [PhenX]"
}
],
"exact": {
"quantity": 0
},
"unit": "%",
"direct_transition": "Eczema_Obs_Upper_Extremities"
},
"Eczema_Obs_Upper_Extremities": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66524-0",
"display": "Percentage area affected by eczema Upper extremity - bilateral [PhenX]"
}
],
"range": {
"low": 30,
"high": 75
},
"unit": "%",
"direct_transition": "Eczema_Obs_Lower_Extremities"
},
"Eczema_Obs_Lower_Extremities": {
"type": "Observation",
"category": "exam",
"codes": [
{
"system": "LOINC",
"code": "66534-9",
"display": "Percentage area affected by eczema Lower extremity - bilateral [PhenX]"
}
],
"range": {
"low": 0,
"high": 35
},
"unit": "%",
"direct_transition": "Eczema_Obs_Terminal"
},
"Eczema_Obs_Terminal": {
"type": "Terminal"
}
},
"gmf_version": 1
}

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{
"name": "Diabetes",
"gmf_version": 2,
"remarks": [
"Basic module for Diabetes",
"Auto-generated as a placeholder",
"Reference: https://www.cdc.gov/diabetes/basics/",
"Reference: https://www.mayoclinic.org/diseases-conditions/diabetes/diagnosis-treatment/drc-20371451"
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "Diagnosis"
},
"Diagnosis": {
"type": "ConditionOnset",
"target_encounter": "Encounter",
"codes": [
{
"system": "SNOMED-CT",
"code": "73211009",
"display": "Diabetes mellitus"
},
{
"system": "ICD-10-CM",
"code": "E11.9",
"display": "Type 2 diabetes mellitus without complications"
}
],
"direct_transition": "Encounter"
},
"Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"reason": "Diagnosis",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for diabetes mellitus"
}
],
"direct_transition": "Medication"
},
"Medication": {
"type": "MedicationOrder",
"reason": "Diagnosis",
"codes": [
{
"system": "RxNorm",
"code": "860975",
"display": "24 HR Metformin hydrochloride 500 MG Extended Release Oral Tablet"
}
],
"direct_transition": "Terminal"
},
"Terminal": {
"type": "Terminal"
}
}
}

762
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{
"name": "Dialysis",
"remarks": [
"Dialysis Encounter for patients with level 4 Chronic Kidney Disease (CKD)."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "CKD guard"
},
"3 day delay": {
"type": "Delay",
"exact": {
"quantity": 3,
"unit": "days"
},
"conditional_transition": [
{
"transition": "CKD guard",
"condition": {
"condition_type": "Attribute",
"attribute": "ckd",
"operator": "<",
"value": 4
}
},
{
"transition": "Dialysis_Encounter"
}
]
},
"Dialysis_Encounter": {
"type": "Encounter",
"encounter_class": "ambulatory",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem (procedure)"
}
],
"direct_transition": "Dialysis",
"reason": "dialysis_reason"
},
"Dialysis": {
"type": "Procedure",
"codes": [
{
"system": "SNOMED-CT",
"code": "265764009",
"display": "Renal dialysis (procedure)"
}
],
"duration": {
"low": 2,
"high": 4,
"unit": "hours"
},
"conditional_transition": [
{
"transition": "Prescribe_EPOGEN Ref-RxNorm",
"condition": {
"condition_type": "Attribute",
"attribute": "anemia",
"operator": "is not nil"
}
},
{
"transition": "Dialysis weight record"
}
],
"reason": "dialysis_reason"
},
"end dialysis": {
"type": "EncounterEnd",
"conditional_transition": [
{
"transition": "3 day delay",
"condition": {
"condition_type": "PriorState",
"name": "Physician Monthly Enc",
"within": {
"quantity": 30,
"unit": "days"
}
}
},
{
"transition": "Physician Monthly Enc"
}
]
},
"Physician Monthly Enc": {
"type": "Encounter",
"encounter_class": "ambulatory",
"codes": [
{
"system": "SNOMED-CT",
"code": "185347001",
"display": "Encounter for problem (procedure)"
}
],
"direct_transition": "Record_CMP",
"reason": "dialysis_reason"
},
"end encounter": {
"type": "EncounterEnd",
"direct_transition": "3 day delay"
},
"CKD guard": {
"type": "Guard",
"allow": {
"condition_type": "And",
"conditions": [
{
"condition_type": "Attribute",
"attribute": "ckd",
"operator": "is not nil"
},
{
"condition_type": "Attribute",
"attribute": "ckd",
"operator": ">=",
"value": 4
}
]
},
"distributed_transition": [
{
"transition": "Check_Anemia_Exist",
"distribution": 0.534
},
{
"transition": "3 day delay",
"distribution": 0.466
}
],
"remarks": [
"The prevalence of anemia increased with stage of CKD, from 8.4% at stage 1 to 53.4% at stage 5\". Dialysis is needed at stage 5 - ps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3879360/",
""
]
},
"Dialysis weight record": {
"type": "Observation",
"category": "vital-signs",
"unit": "kg",
"codes": [
{
"system": "LOINC",
"code": "74006-8",
"display": "Weight difference [Mass difference] --pre dialysis - post dialysis"
}
],
"direct_transition": "Pain_Vital",
"range": {
"low": 1,
"high": 5
}
},
"Dialysis CarePlan": {
"type": "CarePlanStart",
"codes": [
{
"system": "SNOMED-CT",
"code": "736690008",
"display": "Dialysis care plan (record artifact)"
}
],
"direct_transition": "end encounter",
"activities": [
{
"system": "SNOMED-CT",
"code": "183063000",
"display": "Low salt diet education (procedure)"
},
{
"system": "SNOMED-CT",
"code": "229152003",
"display": "Lower limb exercises (regime/therapy)"
},
{
"system": "SNOMED-CT",
"code": "11816003",
"display": "Diet education (procedure)"
}
]
},
"Record_CMP": {
"type": "DiagnosticReport",
"codes": [
{
"system": "LOINC",
"code": "24323-8",
"display": "Comprehensive metabolic 2000 panel - Serum or Plasma"
}
],
"observations": [
{
"category": "laboratory",
"vital_sign": "Glucose",
"codes": [
{
"system": "LOINC",
"code": "2339-0",
"display": "Glucose [Mass/volume] in Blood"
}
],
"unit": "mg/dL"
},
{
"category": "laboratory",
"vital_sign": "Urea Nitrogen",
"codes": [
{
"system": "LOINC",
"code": "6299-2",
"display": "Urea nitrogen [Mass/volume] in Blood"
}
],
"unit": "mg/dL"
},
{
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "38483-4",
"display": "Creatinine [Mass/volume] in Blood"
}
],
"unit": "mg/dL",
"range": {
"low": 2.5,
"high": 3.5
}
},
{
"category": "laboratory",
"vital_sign": "Calcium",
"codes": [
{
"system": "LOINC",
"code": "49765-1",
"display": "Calcium [Mass/volume] in Blood"
}
],
"unit": "mg/dL"
},
{
"category": "laboratory",
"vital_sign": "Sodium",
"codes": [
{
"system": "LOINC",
"code": "2947-0",
"display": "Sodium [Moles/volume] in Blood"
}
],
"unit": "mmol/L"
},
{
"category": "laboratory",
"vital_sign": "Potassium",
"codes": [
{
"system": "LOINC",
"code": "6298-4",
"display": "Potassium [Moles/volume] in Blood"
}
],
"unit": "mmol/L"
},
{
"category": "laboratory",
"vital_sign": "Chloride",
"codes": [
{
"system": "LOINC",
"code": "2069-3",
"display": "Chloride [Moles/volume] in Blood"
}
],
"unit": "mmol/L"
},
{
"category": "laboratory",
"vital_sign": "Carbon Dioxide",
"codes": [
{
"system": "LOINC",
"code": "20565-8",
"display": "Carbon dioxide, total [Moles/volume] in Blood"
}
],
"unit": "mmol/L"
},
{
"category": "laboratory",
"unit": "mL/min",
"codes": [
{
"system": "LOINC",
"code": "33914-3",
"display": "Glomerular filtration rate/1.73 sq M.predicted [Volume Rate/Area] in Serum or Plasma by Creatinine-based formula (MDRD)"
}
],
"range": {
"low": 4,
"high": 29
}
},
{
"category": "laboratory",
"unit": "g/dL",
"codes": [
{
"system": "LOINC",
"code": "2885-2",
"display": "Protein [Mass/volume] in Serum or Plasma"
}
],
"range": {
"low": 6,
"high": 8
}
},
{
"category": "laboratory",
"unit": "g/dL",
"codes": [
{
"system": "LOINC",
"code": "1751-7",
"display": "Albumin [Mass/volume] in Serum or Plasma"
}
],
"range": {
"low": 3.5,
"high": 5.5
}
},
{
"category": "laboratory",
"unit": "g/L",
"codes": [
{
"system": "LOINC",
"code": "10834-0",
"display": "Globulin [Mass/volume] in Serum by calculation"
}
],
"range": {
"low": 2,
"high": 3.5
}
},
{
"category": "laboratory",
"unit": "mg/dL",
"codes": [
{
"system": "LOINC",
"code": "1975-2",
"display": "Bilirubin.total [Mass/volume] in Serum or Plasma"
}
],
"range": {
"low": 0.1,
"high": 1.2
}
},
{
"category": "laboratory",
"unit": "U/L",
"codes": [
{
"system": "LOINC",
"code": "6768-6",
"display": "Alkaline phosphatase [Enzymatic activity/volume] in Serum or Plasma"
}
],
"range": {
"low": 20,
"high": 140
}
},
{
"category": "laboratory",
"unit": "U/L",
"codes": [
{
"system": "LOINC",
"code": "1742-6",
"display": "Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma"
}
],
"range": {
"low": 20,
"high": 60
}
},
{
"category": "laboratory",
"unit": "U/L",
"codes": [
{
"system": "LOINC",
"code": "1920-8",
"display": "Aspartate aminotransferase [Enzymatic activity/volume] in Serum or Plasma"
}
],
"range": {
"low": 6,
"high": 40
}
}
],
"direct_transition": "Record_Urinalysis"
},
"Record_Urinalysis": {
"type": "DiagnosticReport",
"codes": [
{
"system": "LOINC",
"code": "24357-6",
"display": "Urinalysis macro (dipstick) panel - Urine"
}
],
"observations": [
{
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "5767-9",
"display": "Appearance of Urine"
}
],
"unit": "{nominal}",
"value_code": {
"system": "SNOMED-CT",
"code": "7766007",
"display": "Cloudy urine (finding)"
}
},
{
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "34533-0",
"display": "Odor of Urine"
}
],
"unit": "{nominal}",
"value_code": {
"system": "SNOMED-CT",
"code": "167248002",
"display": "Urine smell ammoniacal (finding)"
}
},
{
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "32167-9",
"display": "Clarity of Urine"
}
],
"unit": "{nominal}",
"value_code": {
"system": "SNOMED-CT",
"code": "300828005",
"display": "Translucent (qualifier value)"
}
},
{
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "5778-6",
"display": "Color of Urine"
}
],
"unit": "{nominal}",
"value_code": {
"system": "SNOMED-CT",
"code": "371254008",
"display": "Brown color (qualifier value)"
}
},
{
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "5792-7",
"display": "Glucose [Mass/volume] in Urine by Test strip"
}
],
"unit": "mg/dL",
"range": {
"low": 0.5,
"high": 2.5
}
},
{
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "25428-4",
"display": "Glucose [Presence] in Urine by Test strip"
}
],
"unit": "{nominal}",
"value_code": {
"system": "SNOMED-CT",
"code": "167265006",
"display": "Urine glucose test = ++ (finding)"
}
},
{
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "20505-4",
"display": "Bilirubin.total [Mass/volume] in Urine by Test strip"
}
],
"unit": "mg/dL",
"range": {
"low": 0.2,
"high": 1.5
}
},
{
"category": "laboratory",
"codes": [
{
"system": "LOINC",
"code": "5770-3",
"display": "Bilirubin.total [Presence] in Urine by Test strip"
}
],
"unit": "{nominal}",
"value_code": {
"system": "SNOMED-CT",
"code": "275778006",
"display": "Finding of bilirubin in urine (finding)"
}
},
{
"category": "laboratory",
"unit": "mg/dL",
"codes": [
{
"system": "LOINC",
"code": "5797-6",
"display": "Ketones [Mass/volume] in Urine by Test strip"
}
],
"range": {
"low": 0,
"high": 20
}
},
{
"category": "laboratory",
"unit": "{nominal}",
"codes": [
{
"system": "LOINC",
"code": "2514-8",
"display": "Ketones [Presence] in Urine by Test strip"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": "167291007",
"display": "Urine ketone test = +++ (finding)"
}
},
{
"category": "laboratory",
"unit": "{nominal}",
"codes": [
{
"system": "LOINC",
"code": "5811-5",
"display": "Specific gravity of Urine by Test strip"
}
],
"range": {
"low": 1.001,
"high": 1.039
}
},
{
"category": "laboratory",
"unit": "pH",
"codes": [
{
"system": "LOINC",
"code": "5803-2",
"display": "pH of Urine by Test strip"
}
],
"range": {
"low": 5,
"high": 7
}
},
{
"category": "laboratory",
"unit": "mg/dL",
"codes": [
{
"system": "LOINC",
"code": "5804-0",
"display": "Protein [Mass/volume] in Urine by Test strip"
}
],
"range": {
"low": 250,
"high": 450
}
},
{
"category": "laboratory",
"unit": "{nominal}",
"codes": [
{
"system": "LOINC",
"code": "20454-5",
"display": "Protein [Presence] in Urine by Test strip"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": "167277001",
"display": "Urine protein test = +++ (finding)"
}
},
{
"category": "laboratory",
"unit": "{nominal}",
"codes": [
{
"system": "LOINC",
"code": "5802-4",
"display": "Nitrite [Presence] in Urine by Test strip"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": "314138001",
"display": "Nitrite not detected in urine (finding)"
}
},
{
"category": "laboratory",
"unit": "{nominal}",
"codes": [
{
"system": "LOINC",
"code": "5794-3",
"display": "Hemoglobin [Presence] in Urine by Test strip"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": "167297006",
"display": "Blood not detected in urine (finding)"
}
},
{
"category": "laboratory",
"unit": "{nominal}",
"codes": [
{
"system": "LOINC",
"code": "5799-2",
"display": "Leukocyte esterase [Presence] in Urine by Test strip"
}
],
"value_code": {
"system": "SNOMED-CT",
"code": "394717006",
"display": "Urine leukocytes not detected (finding)"
}
}
],
"direct_transition": "Dialysis CarePlan"
},
"Pain_Vital": {
"type": "Observation",
"category": "vital-signs",
"unit": "{score}",
"codes": [
{
"system": "LOINC",
"code": "72514-3",
"display": "Pain severity - 0-10 verbal numeric rating [Score] - Reported"
}
],
"range": {
"decimals": 0,
"low": 2,
"high": 6
},
"direct_transition": "end dialysis"
},
"Anemia_Submodule": {
"type": "CallSubmodule",
"submodule": "anemia/anemia_sub",
"direct_transition": "3 day delay"
},
"Check_Anemia_Exist": {
"type": "Simple",
"conditional_transition": [
{
"transition": "Anemia_Submodule",
"condition": {
"condition_type": "Attribute",
"attribute": "anemia",
"operator": "is nil"
}
},
{
"transition": "3 day delay"
}
]
},
"Prescribe_EPOGEN Ref-RxNorm": {
"type": "MedicationOrder",
"codes": [
{
"system": "RxNorm",
"code": 205923,
"display": "1 ML Epoetin Alfa 4000 UNT/ML Injection [Epogen]"
}
],
"direct_transition": "Epogen_Administered",
"remarks": [
"Recommended starting dose for adult patients is 50 to 100 Units/kg 3 times weekly. Reduce or interrupt the dose if hemoglobin level approaches or exceeds 11 g/dl - Ref: Section -For Adult Patients with CKD on Dialysis (https://www.rxlist.com/epogen-drug.htm#description)"
],
"assign_to_attribute": "anemia_medication",
"reason": "anemia",
"administration": true
},
"Epogen_Administered": {
"type": "MedicationEnd",
"direct_transition": "Dialysis weight record",
"referenced_by_attribute": "anemia_medication"
}
},
"gmf_version": 1
}

73
src/main/resources/modules/dme/wheelchair.json Normal file
View File

@@ -0,0 +1,73 @@
{
"name": "wheelchair",
"remarks": [
"Assigns a manual or power wheelchair and optional accessory according to probabilities calculated from ~500K wheelchair claim lines."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "End Previous Wheelchair"
},
"Terminal": {
"type": "Terminal"
},
"New Wheelchair": {
"type": "Device",
"code": {
"system": "SNOMED-CT",
"code": "228869008",
"display": "Manual wheelchair (physical object)"
},
"direct_transition": "Accessory Check",
"assign_to_attribute": "wheelchair"
},
"End Previous Wheelchair": {
"type": "CallSubmodule",
"submodule": "dme/wheelchair_end",
"distributed_transition": [
{
"transition": "New Wheelchair",
"distribution": 0.86
},
{
"transition": "New Power Wheelchair",
"distribution": 0.14
}
]
},
"New Power Wheelchair": {
"type": "Device",
"code": {
"system": "SNOMED-CT",
"code": "705427004",
"display": "Power-assisted wheelchair (physical object)"
},
"direct_transition": "Accessory Check",
"assign_to_attribute": "wheelchair"
},
"Accessory Check": {
"type": "Simple",
"distributed_transition": [
{
"transition": "Wheelchair Accessory",
"distribution": 0.73
},
{
"transition": "Terminal",
"distribution": 0.27
}
]
},
"Wheelchair Accessory": {
"type": "Device",
"code": {
"system": "SNOMED-CT",
"code": "705417005",
"display": "Wheelchair accessory (physical object)"
},
"direct_transition": "Terminal",
"assign_to_attribute": "wheelchair_accessory"
}
},
"gmf_version": 2
}

26
src/main/resources/modules/dme/wheelchair_end.json Normal file
View File

@@ -0,0 +1,26 @@
{
"name": "wheelchair_end",
"remarks": [
"Submodule to stop wheelchair and accessory devices."
],
"states": {
"Initial": {
"type": "Initial",
"direct_transition": "End Wheelchair"
},
"Terminal": {
"type": "Terminal"
},
"End Wheelchair": {
"type": "DeviceEnd",
"direct_transition": "End Accessory",
"referenced_by_attribute": "wheelchair"
},
"End Accessory": {
"type": "DeviceEnd",
"direct_transition": "Terminal",
"referenced_by_attribute": "wheelchair_accessory"
}
},
"gmf_version": 2
}

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