Mimic Skill

MIMIC-IV Data Extraction Skill

Extract intensive care data from the MIMIC-IV database. Provides SQL templates and Python code; users handle database connections themselves.

Connection Method

Users provide their own PostgreSQL connection parameters. This skill only provides query code.

Important Changes in MIMIC-IV (vs MIMIC-III)

⚠️ If you have used MIMIC-III, please note the following changes!

1. Table Name Changes

2. New Tables (MIMIC-IV)

3. New Modules (MIMIC-IV)

MIMIC-IV is now divided into 6 modules:

4. Field Name Conventions

✅ Correct (lowercase):

SELECT ce.subject_id, ce.stay_id, ce.itemid, ce.charttime
FROM chartevents ce
WHERE ce.stay_id = 100001

❌ Incorrect (camelCase or old field names):

SELECT ce.subjectId, ce.icustay_id  -- Field does not exist!
FROM chartevents ce

---

Supported Query Types

Workflow

1. Confirm the query type needed by the user
2. Read the corresponding references file to get SQL/Python templates
3. Adjust query conditions based on specific user requirements
4. Provide both SQL and Python implementations
5. Explain how to customize parameters (e.g., time range, itemid, etc.)

Key Conventions

• MIMIC-IV uses stay_id as the ICU stay identifier (not MIMIC-III's icustay_id)
• anchor_age is truncated (patients >89 are all set to 91)
• chartevents is linked via stay_id, labevents via hadm_id
• itemid comes from d_items (vital signs) and d_labitems (lab tests)
• Time representation: MIMIC-IV uses absolute timestamps (TIMESTAMP type), time functions can be used directly

---

Common Query Scenarios

1. Extract First Day Vital Signs in ICU

SELECT 
    ce.subject_id,
    ce.stay_id,
    ce.itemid,
    di.label,
    ce.charttime,
    ce.valuenum,
    ce.valueuom
FROM chartevents ce
INNER JOIN icustays ic ON ce.stay_id = ic.stay_id
INNER JOIN d_items di ON ce.itemid = di.itemid
WHERE ce.charttime >= ic.intime
  AND ce.charttime < ic.intime + INTERVAL '1 day'
  AND ce.itemid IN (220045, 220050, 220051, 220052, 223762, 220210, 220277, 223835)
  AND ce.valuenum IS NOT NULL
ORDER BY ce.stay_id, ce.charttime;

2. Extract First Day Laboratory Tests in ICU

SELECT 
    le.subject_id,
    le.hadm_id,
    le.itemid,
    dli.label,
    le.charttime,
    le.valuenum,
    le.valueuom
FROM labevents le
INNER JOIN admissions a ON le.hadm_id = a.hadm_id
INNER JOIN d_labitems dli ON le.itemid = dli.itemid
WHERE le.charttime >= a.admittime
  AND le.charttime < a.admittime + INTERVAL '1 day'
  AND le.itemid IN (50912, 51006, 50983, 50971, 50902, 50882)
  AND le.valuenum IS NOT NULL
ORDER BY le.subject_id, le.charttime;

3. Extract Patient Diagnoses (ICD Codes)

SELECT 
    d.subject_id,
    d.hadm_id,
    d.seq_num,
    d.icd_code,
    d.icd_version,
    did.long_title
FROM diagnoses_icd d
LEFT JOIN d_icd_diagnoses did
    ON d.icd_code = did.icd_code AND d.icd_version = did.icd_version
WHERE d.hadm_id = %(hadm_id)s
ORDER BY d.seq_num;

---

Notes

1. Table and Field Name Case Sensitivity

• All lowercase: All table and field names in MIMIC-IV are lowercase
• Use double quotes: If you must use uppercase or camelCase names, wrap them in double quotes (not recommended)

2. Time Handling

• Absolute timestamps: All time fields are TIMESTAMP type (UTC timezone)
• Time functions: You can directly use functions like EXTRACT, DATE_PART, INTERVAL
• Timezone conversion: Use AT TIME ZONE for local time conversion

-- Convert to local time (e.g., Eastern Time)
SELECT charttime AT TIME ZONE 'America/New_York'
FROM chartevents
WHERE stay_id = 100001;

3. Large Table Query Optimization

• The chartevents table has hundreds of millions of rows; when querying, be sure to:
  • Filter by stay_id
  • Limit the charttime range
  • Add a LIMIT clause (for testing)
  • Use EXPLAIN to analyze the query plan

4. Numeric vs Text Results

• valuenum: Numeric results (for calculations)
• value: Text results (for qualitative results, e.g., "Positive", "Negative")

-- Correct: Use valuenum for numeric results
SELECT AVG(valuenum) AS avg_creatinine
FROM labevents
WHERE itemid = 50912 AND valuenum IS NOT NULL;

-- Correct: Use value for text results
SELECT COUNT(*) AS num_positive
FROM labevents
WHERE itemid = 500061 AND value = 'Positive';

---

Reference Links

• MIMIC-IV Official Documentation: https://mimic.mit.edu/docs/IV/
• MIMIC-IV Data Introduction: https://physionet.org/content/mimiciv/3.1/
• MIMIC-IV-ED Data Introduction: https://physionet.org/content/mimic-iv-ed/2.0/
• MIMIC-IV-Note Data Introduction: https://physionet.org/content/mimic-iv-note/2.0/
• MIMIC-CXR Data Introduction: https://physionet.org/content/mimic-cxr/2.1/
• Access Application: https://physionet.org/register/
• MIMIC Code Repository: https://github.com/MIT-LCP/mimic-code

---

Last Updated: 2026-05-20
Updated by: 悟空（基于 MIMIC-IV 官方文档修正）