scd.json

{
  "name": "SCD",
  "remarks": [
    "Ragha Srinivasan ",
    "St. Jude Children's Research Hospital",
    "April 19, 2023",
    "* Test data in OMOP CDM format generation for KIDS23 BioHackathon **",
    "",
    "Synthetic Data Generation: ",
    "Establishment of a Synthetic Longitudinal Clinical Cohort of Pediatric and Adolescent Patients with Sickle Cell Disease (SCD)",
    "Patient Age Birth through 18 years",
    "",
    "List all SCD patients based on most prevalent Sickle cell genotype is based on the diagnosis in the medical record.",
    "",
    "References",
    "",
    "SNOMED CT BROWSER https://browser.ihtsdotools.org/?",
    "",
    "Synthea New Module Builder ",
    "https://synthetichealth.github.io/synthea/#technology-landing",
    "",
    "synthetichealth/synthea",
    "Synthea contains a framework for defining modules using JSON. These JSON modules describe a progression of states and the transitions between them. On each Synthea generation time-step, the generic framework processes states one at a time to trigger conditions, encounters, medications, and other clinical events. ",
    "he Module Builder is a web interface for clinicians and other healthcare professionals to design Synthea modules with no programming experience required. A short video introduction to the Module Builder is available on YouTube (linked below), and a Tutorial is available on this Wiki.",
    "https://github.com/synthetichealth/synthea/wiki/Generic-Module-Framework",
    "",
    "",
    "Thank you."
  ],
  "states": {
    "Initial": {
      "type": "Initial",
      "direct_transition": "Pediatric & Adoloscent"
    },
    "Terminal": {
      "type": "Terminal"
    },
    "Sickle Cell Disease": {
      "type": "Simple",
      "distributed_transition": [
        {
          "transition": "Sickle_Cell_Disease_1",
          "distribution": 0.25
        },
        {
          "transition": "Sickle_Cell_Disease_2",
          "distribution": 0.25
        },
        {
          "transition": "Sickle_Cell_Disease_3",
          "distribution": 0.25
        },
        {
          "transition": "Sickle_Cell_Disease_4",
          "distribution": 0.25
        }
      ]
    },
    "Pediatric & Adoloscent": {
      "type": "Delay",
      "distribution": {
        "kind": "UNIFORM",
        "parameters": {
          "high": 220,
          "low": 1
        }
      },
      "unit": "months",
      "direct_transition": "Wellness Encounter"
    },
    "Wellness Encounter": {
      "type": "Encounter",
      "reason": "",
      "telemedicine_possibility": "none",
      "wellness": true,
      "direct_transition": "CBC_with_Low_Hemoglobin"
    },
    "Penicillin Check": {
      "type": "Simple",
      "conditional_transition": [
        {
          "transition": "Daily Pencillin",
          "condition": {
            "condition_type": "And",
            "conditions": [
              {
                "condition_type": "Age",
                "operator": "<=",
                "quantity": 5,
                "unit": "years",
                "value": 0
              },
              {
                "condition_type": "Not",
                "condition": {
                  "condition_type": "Active Medication",
                  "codes": [
                    {
                      "system": "RxNorm",
                      "code": 834061,
                      "display": "penicillin V potassium 250 MG Oral Tablet"
                    }
                  ]
                }
              }
            ]
          }
        },
        {
          "transition": "Stop Pencillin",
          "condition": {
            "condition_type": "Age",
            "operator": ">",
            "quantity": 5,
            "unit": "years"
          }
        }
      ]
    },
    "Stop Pencillin": {
      "type": "MedicationEnd",
      "medication_order": "Daily Pencillin",
      "direct_transition": "End Encounter"
    },
    "End Encounter": {
      "type": "EncounterEnd",
      "conditional_transition": [
        {
          "transition": "Next Wellness Encounter",
          "condition": {
            "condition_type": "Active Medication",
            "codes": [
              {
                "system": "RxNorm",
                "code": 834061,
                "display": "penicillin V potassium 250 MG Oral Tablet"
              }
            ]
          }
        },
        {
          "transition": "Terminal"
        }
      ]
    },
    "Next Wellness Encounter": {
      "type": "Encounter",
      "reason": "",
      "telemedicine_possibility": "none",
      "direct_transition": "Penicillin Check",
      "wellness": true
    },
    "Daily Pencillin": {
      "type": "MedicationOrder",
      "codes": [
        {
          "system": "RxNorm",
          "code": 834061,
          "display": "penicillin V potassium 250 MG Oral Tablet"
        }
      ],
      "reason": "scd_diagnosis",
      "chronic": true,
      "prescription": {
        "dosage": {
          "amount": 1,
          "frequency": 1,
          "period": 1,
          "unit": "days"
        },
        "duration": {
          "quantity": 1,
          "unit": "days"
        },
        "as_needed": true
      },
      "direct_transition": "End Encounter",
      "assign_to_attribute": ""
    },
    "Daily Folic Acid": {
      "type": "MedicationOrder",
      "codes": [
        {
          "system": "RxNorm",
          "code": 285122,
          "display": "folic acid 0.8 MG Oral Tablet [Folacin]"
        }
      ],
      "reason": "scd_diagnosis",
      "chronic": true,
      "prescription": {
        "dosage": {
          "amount": 1,
          "frequency": 1,
          "period": 1,
          "unit": "days"
        },
        "duration": {
          "quantity": 1,
          "unit": "days"
        },
        "as_needed": true
      },
      "direct_transition": "Penicillin Check"
    },
    "CBC_with_Low_Hemoglobin": {
      "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": 6,
            "high": 8
          }
        },
        {
          "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": "Sickling Test"
    },
    "Sickle_Cell_Disease_2": {
      "type": "ConditionOnset",
      "codes": [
        {
          "system": "SNOMED-CT",
          "code": 35434009,
          "display": "Sickle cell-hemoglobin C disease (disorder)"
        }
      ],
      "assign_to_attribute": "scd_diagnosis",
      "direct_transition": "Daily Folic Acid"
    },
    "Sickle_Cell_Disease_3": {
      "type": "ConditionOnset",
      "codes": [
        {
          "system": "SNOMED-CT",
          "code": 417357006,
          "display": "Sickling disorder due to hemoglobin S (disorder)"
        }
      ],
      "assign_to_attribute": "scd_diagnosis",
      "direct_transition": "Daily Folic Acid"
    },
    "Sickle_Cell_Disease_4": {
      "type": "ConditionOnset",
      "codes": [
        {
          "system": "SNOMED-CT",
          "code": 127042006,
          "display": "Sickle cell beta plus thalassemia (disorder)"
        }
      ],
      "assign_to_attribute": "scd_diagnosis",
      "direct_transition": "Daily Folic Acid"
    },
    "Sickle_Cell_Disease_1": {
      "type": "ConditionOnset",
      "codes": [
        {
          "system": "SNOMED-CT",
          "code": 127040003,
          "display": "Sickle cell-hemoglobin SS disease (disorder)"
        }
      ],
      "assign_to_attribute": "scd_diagnosis",
      "direct_transition": "Daily Folic Acid"
    },
    "Sickling Test": {
      "type": "Procedure",
      "codes": [
        {
          "system": "SNOMED-CT",
          "code": 252289009,
          "display": "Sickling test (procedure)"
        }
      ],
      "distribution": {
        "kind": "UNIFORM",
        "parameters": {
          "high": 60,
          "low": 30
        }
      },
      "unit": "minutes",
      "direct_transition": "Sickle Cell Disease"
    }
  },
  "gmf_version": 2
}