MIMIC-IV example - patients with laparascopic cholecystectomy procedure

mimic_lc.py

from pathling import PathlingContext
import re

pc = PathlingContext.create()

data = pc.read.ndjson(
    "/tmp/mimic-iv-clinical-database-demo-on-fhir-2.1.0/fhir",
    file_name_mapper=lambda file_name: re.findall(
        r"Mimic(\w+?)(?:ED|ICU|"
        r"Chartevents|Datetimeevents|Labevents|MicroOrg|MicroSusc|MicroTest|"
        r"Outputevents|Lab|Mix|VitalSigns|VitalSignsED)?$",
        file_name,
    ),
)

patient = data.view(
    "Patient",
    select=[
        {
            "column": [
                {
                    "name": "patient_id",
                    "path": "getResourceKey()",
                    "description": "Unique identifier for the patient",
                }
            ]
        }
    ],
)

laparoscopic_cholecystectomy = data.view(
    "Procedure",
    select=[
        {
            "column": [
                {
                    "name": "condition_id",
                    "path": "getResourceKey()",
                    "description": "Unique identifier for the procedure",
                },
                {
                    "name": "patient_id",
                    "path": "subject.getReferenceKey()",
                    "description": "Reference to the patient who underwent the procedure",
                },
                {
                    "name": "performed_at",
                    "path": "performed.ofType(dateTime)",
                    "description": "Date and time when the procedure was performed",
                },
            ]
        },
        {
            "forEach": "code.coding",
            "column": [
                {
                    "name": "code_system",
                    "path": "system",
                    "description": "The code system that defines the procedure code",
                },
                {
                    "name": "code_code",
                    "path": "code",
                    "description": "The procedure code value",
                },
                {
                    "name": "code_display",
                    "path": "display",
                    "description": "Human-readable description of the procedure",
                },
            ],
        },
    ],
    where=[
        {
            "path": "code.coding.where(system = 'http://mimic.mit.edu/fhir/mimic/CodeSystem/mimic-procedure-icd9').exists(code = '5123' or code = '5124')",
            "description": "Filter for laparoscopic cholecystectomy procedures (ICD-9 codes 51.23 and 51.24)",
        }
    ],
)

result = patient.join(laparoscopic_cholecystectomy, on="patient_id")
result.show(truncate=False)

output.md

patient_id	condition_id	performed_at	code_system	code_code	code_display
Patient/8adbf3e4-47ff-561e-b1b6-746ee32e056d	Procedure/71664e0b-2062-5998-b88e-4b60f961aae8	2150-06-03T00:00:00-04:00	http://mimic.mit.edu/fhir/mimic/CodeSystem/mimic-procedure-icd9	5124	Laparoscopic partial cholecystectomy
Patient/568cb149-804c-59e8-bdf5-816e8151cd22	Procedure/69621df5-b36b-5959-a3df-d3081045754b	2196-06-14T00:00:00-04:00	http://mimic.mit.edu/fhir/mimic/CodeSystem/mimic-procedure-icd9	5123	Laparoscopic cholecystectomy