Tutorials

The cycquery tool allows you to query EHR databases. It is a Python API that that communicates with postgresql databases. It is a wrapper around the SQLAlchemy ORM and uses SQLAlchemy query objects and functions to build queries.

• MIMIC-III tutorial
  • Imports and instantiate MIMICIIIQuerier
  • Example 1. Get all male patients with a mortality outcome.
  • Example 2. Get all female patient encounters with diagnoses (gastroenteritis in ICD-9 long title).
  • Example 3. Get potassium lab tests for female patients.
  • Example 4. Get AaDO2 carevue chart events for male patients that have a valuenum of less than 20.
• MIMIC-IV tutorial
  • Imports and instantiate MIMICIVQuerier
  • Example 1. Get all patient admissions from 2021 or later (approx year of admission)
  • Example 2. Get all patient encounters with diagnoses (schizophrenia in ICD-10 long title), in the year 2015.
  • Example 3. Advanced - uses ConditionRegexMatch from cycquery.ops. Get all patient encounters with diagnoses (ICD-9 long title contains schizophrenia and chronic ), in the year 2015.
  • Example 4. Get routine vital signs for patients from year 2015.
  • Example 5. Get hemoglobin lab tests for patients from year 2009.
  • Example 6. Get radiology reports and filter on keywords lymphadenopathy and infectious occurring together from year 2009.
  • Example 7. Get all female patient encounters from year 2015, and return batches partitioned and indexed on subject_id.
  • Example 8. Running a raw SQL string.
• eICU-CRD tutorial
  • Imports and instantiate EICUQuerier
  • Example 1. Get all female patients discharged in 2014 (limit to 100 rows).
  • Example 2. Get all patient encounters with diagnoses (schizophrenia in diagnosisstring), discharged in the year 2015.
  • Example 3. Get potassium lab tests for patients discharged in the year 2014, for all teaching hospitals.
  • Example 4. Get glucose medications (substring search) for female patients discharged in 2014.
• OMOP tutorial
  • Imports and instantiate OMOPQuerier.
  • Example 1. Get all patient visits in or after 2010.
  • Example 2. Get measurements for all visits in or after 2020.
  • Imports and instantiate OMOPQuerier.
  • Example 1. Get all patient visits that ended in a mortality outcome in or after 2010.
  • Example 2. Get all measurements for female patient visits with sepsis diagnoses, that ended in a mortality outcome.
• GEMINI tutorial
  • Imports and instantiate GEMINIQuerier.
  • Example 1a. Create a table with only one hospitalization per patient, keeping the most recent encounter for each patient. Sort the dataset by patient_id_hashed and discharge_date_time, and then keep the recent record.
  • Example 1b. From the above set of encounters, take a subset of patients who were discharged between April 1, 2015 and March 31, 2016.
  • Example 1c. From the above set of encounters, get the total number of admissions for each hospital.
  • Example 2a. How many sodium tests were placed between Apr 1, 2015 and May 31, 2015 at hospital 101?