mimic-patient-analysis

name

mimic-patient-analysis

description

Comprehensive patient analysis using the MIMIC-IV clinical database. Use this skill whenever asked to analyze, summarize, or investigate a patient's medical history, hospital admissions, diagnoses, medications, procedures, or clinical course from a MIMIC-IV SQLite database. Triggers on prompts like "Analyze patient [ID]", "summarize patient history", "what happened to patient X", or any request to explore patient-level EHR data from MIMIC-IV tables.

MIMIC-IV Patient Analysis

Perform a comprehensive, systematic analysis of a patient's complete clinical record from the MIMIC-IV database by querying the SQLite database directly and efficiently.

Database Structure

The database has 27 tables. Key tables and their primary columns:

Core patient tables:

• hosp_patients — demographics: subject_id, gender, anchor_age, anchor_year, anchor_year_group, dod
• hosp_admissions — hospital stays: subject_id, hadm_id, admittime, dischtime, deathtime, admission_type, admission_location, discharge_location, insurance, language, marital_status, race, edregtime, edouttime, hospital_expire_flag

Clinical data (per admission):

• hosp_diagnoses_icd — ICD diagnoses: subject_id, hadm_id, seq_num, icd_code, icd_version
• hosp_d_icd_diagnoses — diagnosis dictionary: icd_code, icd_version, long_title
• hosp_procedures_icd — ICD procedures: subject_id, hadm_id, seq_num, chartdate, icd_code, icd_version
• hosp_d_icd_procedures — procedure dictionary: icd_code, icd_version, long_title
• hosp_drgcodes — DRG billing: subject_id, hadm_id, drg_type, drg_code, description, drg_severity, drg_mortality
• hosp_services — clinical service: subject_id, hadm_id, transfertime, prev_service, curr_service
• hosp_transfers — unit movements: subject_id, hadm_id, transfer_id, eventtype, careunit, intime, outtime

Medications:

• hosp_prescriptions — prescribed drugs: subject_id, hadm_id, starttime, stoptime, drug, drug_type, dose_val_rx, dose_unit_rx, route
• hosp_emar — administration record: subject_id, hadm_id, emar_id, charttime, medication, event_txt, scheduletime
• hosp_pharmacy — pharmacy fills: subject_id, hadm_id, pharmacy_id, drug, starttime, stoptime

Diagnostics:

• hosp_microbiologyevents — cultures: subject_id, hadm_id, charttime, spec_type_desc, test_name, org_name, interpretation, comments
• hosp_omr — vitals/anthropometrics: subject_id, chartdate, seq_num, result_name, result_value
• hosp_hcpcsevents — billing codes: subject_id, hadm_id, chartdate, hcpcs_cd, short_description
• hosp_d_hcpcs — HCPCS dictionary: code, category, long_description, short_description

Orders:

• hosp_poe — provider orders: subject_id, hadm_id, poe_id, ordertime, order_type, order_subtype, transaction_type, order_status

ICU tables (only present if patient had ICU stay):

• icu_icustays — ICU episodes: subject_id, hadm_id, stay_id, first_careunit, last_careunit, intime, outtime, los
• icu_inputevents, icu_outputevents, icu_procedureevents — ICU events by stay_id

Critical Column Name Pitfalls

Avoid these common errors that cause query failures:

Table	WRONG	CORRECT
hosp_transfers	transfertime	intime (sort by intime)
hosp_poe	order_time	ordertime
hosp_omr	charttime	chartdate
hosp_hcpcsevents JOIN hosp_d_hcpcs	ON h.hcpcs_cd = d.hcpcs_cd	ON h.hcpcs_cd = d.code

Analysis Workflow

Start with get_database_info to confirm table availability, then query directly — do not call describe_table before each query; use the column names listed above.

Step 1 — Patient demographics

SELECT * FROM hosp_patients WHERE subject_id = <patient_id>

Note: anchor_age is age in anchor_year (dates are shifted for privacy). If dod is not null, the patient died.

Step 2 — All hospital admissions

SELECT * FROM hosp_admissions WHERE subject_id = <patient_id> ORDER BY admittime

For each hadm_id, note: admission/discharge times, type, source, destination, insurance, hospital_expire_flag.

Step 3 — ICU stays

SELECT * FROM icu_icustays WHERE subject_id = <patient_id> ORDER BY intime

Empty result = no ICU. If ICU present, note care units and length of stay (los).

Step 4 — Diagnoses (with human-readable names)

SELECT d.icd_code, d.icd_version, d.long_title, diag.hadm_id, diag.seq_num
FROM hosp_diagnoses_icd diag
JOIN hosp_d_icd_diagnoses d ON diag.icd_code = d.icd_code AND diag.icd_version = d.icd_version
WHERE diag.subject_id = <patient_id>
ORDER BY diag.hadm_id, diag.seq_num

seq_num=1 is the primary diagnosis. Group by hadm_id to see diagnoses per admission.

Step 5 — Procedures

SELECT p.hadm_id, p.seq_num, p.chartdate, p.icd_code, proc.long_title
FROM hosp_procedures_icd p
JOIN hosp_d_icd_procedures proc ON p.icd_code = proc.icd_code AND p.icd_version = proc.icd_version
WHERE p.subject_id = <patient_id>
ORDER BY p.hadm_id, p.seq_num

Step 6 — Medications prescribed

SELECT hadm_id, drug, starttime, stoptime, dose_val_rx, dose_unit_rx, route
FROM hosp_prescriptions
WHERE subject_id = <patient_id>
ORDER BY hadm_id, starttime

Step 7 — Physical measurements (BMI, weight, height, BP)

SELECT chartdate, result_name, result_value
FROM hosp_omr
WHERE subject_id = <patient_id>
ORDER BY chartdate

Step 8 — Microbiology cultures

SELECT chartdate, spec_type_desc, test_name, org_name, interpretation, comments
FROM hosp_microbiologyevents
WHERE subject_id = <patient_id>
ORDER BY chartdate

org_name null with a comment like "< 10,000 CFU/mL" = negative culture.

Step 9 — Clinical service and transfers

-- Service
SELECT * FROM hosp_services WHERE subject_id = <patient_id> ORDER BY transfertime

-- Physical location movements
SELECT * FROM hosp_transfers WHERE hadm_id = <hadm_id> ORDER BY intime

Step 10 — DRG billing codes

SELECT * FROM hosp_drgcodes WHERE subject_id = <patient_id>

APR-DRG has severity (1-4) and mortality (1-4) scores.

Optional — Provider orders and eMAR

Query hosp_poe (by hadm_id, ORDER BY ordertime) to see what was ordered and when. Query hosp_emar (by hadm_id, ORDER BY charttime) to see which medications were actually administered vs "Not Given".

Synthesizing the Analysis

After gathering data, produce a structured summary covering:

1. Demographics — age, sex, race, insurance, vital status (alive/deceased + date if known)
2. Admission summary — number of admissions, dates, types, sources, discharge destinations
3. ICU course — whether ICU was needed, which units, duration
4. Primary diagnosis and DRG — main condition(s), billing classification, severity
5. Comorbidities — significant secondary diagnoses across admissions
6. Procedures — surgical and therapeutic interventions
7. Medications — key drug classes, notable transitions (e.g., anticoagulation changes), route
8. Diagnostics — culture results, physical measurements/trends
9. Clinical trajectory — how the patient's condition evolved across admissions
10. Key clinical insights — clinically meaningful patterns (e.g., discharge to rehab suggesting functional impairment, multiple laxatives suggesting immobility, sequential anticoagulants suggesting treatment adjustment)

End the analysis with FINISH: followed by the full summary.

Efficiency Tips

• Query all admissions first, then drill into individual hadm_id values for detailed data
• For patients with multiple admissions, query diagnoses and medications across all hadm_ids at once using subject_id
• If a query returns an error mentioning available columns, correct the column name immediately — do not call describe_table; instead consult the column reference above
• Use LIMIT when exploring eMAR/POE (large tables); paginate with OFFSET if needed
• The hosp_emar event_txt field distinguishes "Administered" from "Not Given" — this reveals medication compliance