eICU-CRD tutorial¶

This notebook shows examples of how to use the cycquery tool on eicu-CRD.

Each query is limit to 100 rows (for quick results).

First, setup the eICU database according to the instructions in eicu-code.
The database is assumed to be hosted using postgres. Update the config parameters such as username and password, passed to EICUQuerier accordingly.

Imports and instantiate `EICUQuerier`¶

[1]:

"""eICU-CRD tutorial."""

import cycquery.ops as qo
from cycquery import EICUQuerier


querier = EICUQuerier(
    dbms="postgresql",
    port=5432,
    host="localhost",
    database="eicu",
    user="postgres",
    password="pwd",
)
# List all tables.
querier.list_tables("eicu_crd")

2024-11-20 05:43:00,894 INFO cycquery.orm    - Database setup, ready to run queries!

[1]:

['eicu_crd.admissiondrug',
 'eicu_crd.admissiondx',
 'eicu_crd.allergy',
 'eicu_crd.apacheapsvar',
 'eicu_crd.apachepatientresult',
 'eicu_crd.apachepredvar',
 'eicu_crd.careplancareprovider',
 'eicu_crd.careplaneol',
 'eicu_crd.careplangeneral',
 'eicu_crd.careplangoal',
 'eicu_crd.careplaninfectiousdisease',
 'eicu_crd.customlab',
 'eicu_crd.diagnosis',
 'eicu_crd.hospital',
 'eicu_crd.infusiondrug',
 'eicu_crd.intakeoutput',
 'eicu_crd.lab',
 'eicu_crd.medication',
 'eicu_crd.microlab',
 'eicu_crd.note',
 'eicu_crd.nurseassessment',
 'eicu_crd.nursecare',
 'eicu_crd.nursecharting',
 'eicu_crd.pasthistory',
 'eicu_crd.patient',
 'eicu_crd.physicalexam',
 'eicu_crd.respiratorycare',
 'eicu_crd.respiratorycharting',
 'eicu_crd.treatment',
 'eicu_crd.vitalaperiodic',
 'eicu_crd.vitalperiodic']

Example 1. Get all female patients discharged in 2014 (limit to 100 rows).¶

[2]:

ops = qo.Sequential(
    qo.ConditionEquals("hospitaldischargeyear", 2014),
    qo.ConditionEquals("gender", "Female"),
)
patients = querier.eicu_crd.patient()
patients = patients.ops(ops).run(limit=100)
print(f"{len(patients)} rows extracted!")

2024-11-20 05:43:01,944 INFO cycquery.orm    - Query returned successfully!

2024-11-20 05:43:01,946 INFO cycquery.utils.profile - Finished executing function run_query in 0.285067 s

100 rows extracted!

Example 2. Get all patient encounters with diagnoses (`schizophrenia` in `diagnosisstring`), discharged in the year 2015.¶

[3]:

patients = querier.eicu_crd.patient()
diagnoses = querier.eicu_crd.diagnosis()
diagnoses = diagnoses.ops(qo.ConditionSubstring("diagnosisstring", "schizophrenia"))
patient_diagnoses = patients.join(
    join_table=diagnoses,
    on="patientunitstayid",
)
patient_diagnoses = patient_diagnoses.run(limit=100)
print(f"{len(patient_diagnoses)} rows extracted!")

2024-11-20 05:43:06,716 INFO cycquery.orm    - Query returned successfully!

2024-11-20 05:43:06,718 INFO cycquery.utils.profile - Finished executing function run_query in 4.741402 s

100 rows extracted!

Example 3. Get potassium lab tests for patients discharged in the year 2014, for all teaching hospitals.¶

[4]:

hospitals = querier.eicu_crd.hospital()
hospitals = hospitals.ops(qo.ConditionEquals("teachingstatus", True))
patients = querier.eicu_crd.patient()
patients = patients.ops(qo.ConditionEquals("hospitaldischargeyear", 2015))
patients = patients.join(
    join_table=hospitals,
    on="hospitalid",
)
labs = querier.eicu_crd.lab()
labs = labs.ops(qo.ConditionEquals("labname", "potassium"))
patient_labs = patients.join(
    join_table=labs,
    on="patientunitstayid",
).run(limit=100)
print(f"{len(patient_labs)} rows extracted!")

2024-11-20 05:43:07,270 INFO cycquery.orm    - Query returned successfully!

2024-11-20 05:43:07,272 INFO cycquery.utils.profile - Finished executing function run_query in 0.506820 s

100 rows extracted!

Example 4. Get glucose medications (substring search) for female patients discharged in 2014.¶

[5]:

ops = qo.Sequential(
    qo.ConditionEquals("hospitaldischargeyear", 2014),
    qo.ConditionEquals("gender", "Female"),
)
patients = querier.eicu_crd.patient()
patients = patients.ops(ops)
medications = querier.eicu_crd.medication()
medications = medications.ops(qo.ConditionSubstring("drugname", "glucose"))
patient_medications = patients.join(
    join_table=medications,
    on="patientunitstayid",
).run(limit=100)
print(f"{len(patient_medications)} rows extracted!")

2024-11-20 05:43:09,861 INFO cycquery.orm    - Query returned successfully!

2024-11-20 05:43:09,863 INFO cycquery.utils.profile - Finished executing function run_query in 2.551167 s

100 rows extracted!