MIMIC-IV3.0安装

1.软件准备

7-zip：配置环境变量（安装路径）

Postgressql：配置环境变量（安装路径/bin）

Navicat

2.文件夹准备

MIMIC-IV3.0数据：MIMIC-IV v3.0 (physionet.org)

MIMIC-IV3.0安装代码：https://github.com/MIT-LCP/mimic-code

简化流程（将所需sql都复制到MIMIC-IV3.0文件夹路径下），包括：create.sql, load_7z.sql, index.sql, function.sql 和 concepts_postgres文件夹

注意事项：更改create.sql中admissions里language VARCHAR(10)为language VARCHAR(100)

3.开始安装

打开Postgres依次运行以下代码

Drop database if exists mimiciv3;

create database mimiciv3 owner postgres;

\c mimiciv3;

\set mimic_data_dir '你的MIMIC数据存放路径'

\encoding 'utf8'

\i 代码存放路径/create.sql

\i 代码存放路径/load_7z.sql

\i 代码存放路径/index.sql

\i 代码存放路径/functions.sql

\i 代码存放路径/postgres-make-concepts.sql (先更改里面的路径与其本身存放路径一致)

4.单独运行icu_hourly, sofa, sepsis3.sql

先更改icu_hourly里面的代码为：

-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
DROP TABLE IF EXISTS mimiciv_derived.icustay_hourly; CREATE TABLE mimiciv_derived.icustay_hourly AS
/* This query generates a row for every hour the patient is in the ICU. */ /* The hours are based on clock-hours (i.e. 02:00, 03:00). */ /* The hour clock starts 24 hours before the first heart rate measurement. */ /* Note that the time of the first heart rate measurement is ceilinged to */ /* the hour. */ /* this query extracts the cohort and every possible hour they were in the ICU */ /* this table can be to other tables on stay_id and (ENDTIME - 1 hour,ENDTIME] */ /* get first/last measurement time */
WITH all_hours AS (
  SELECT
    it.stay_id, /* round the intime up to the nearest hour */
    CASE
      WHEN DATE_TRUNC('HOUR', it.intime_hr) = it.intime_hr
      THEN it.intime_hr
      ELSE DATE_TRUNC('HOUR', it.intime_hr) + INTERVAL '1 HOUR'
    END AS endtime, /* create integers for each charttime in hours from admission */ /* so 0 is admission time, 1 is one hour after admission, etc, */ /* up to ICU disch */ /*  we allow 24 hours before ICU admission (to grab labs before admit) */
    GENERATE_SERIES(-24, CAST(CEIL(EXTRACT(EPOCH FROM it.outtime_hr - it.intime_hr) / 3600.0) AS INT)) AS hrs /* noqa: L016 */
  FROM mimiciv_derived.icustay_times AS it
)
SELECT
  stay_id,
  CAST(hr_unnested AS BIGINT) AS hr,
  endtime + CAST(hr_unnested AS BIGINT) * INTERVAL '1 HOUR' AS endtime
FROM all_hours
CROSS JOIN UNNEST(ARRAY[all_hours.hrs]) AS _t(hr_unnested)

而后正常运行sofa和sepsis3