MIMIC-iv官方SQL概念语句标注——mimic_derived模块部分信息
1.mmic-iv与mimic-iii的区别之一就是前者分了3个模块，mimic_icu，mimic_hosp和mimic_core, 而在学习过程中我们还可以观察到另外一个模块mimic_derived, 而且这个模块仅存在与谷歌云的mimic数据库中, 本地建立的数据库中虽然有这个模块，但是没有内容（需要自己根据官方提供的代码生成，也是现在我们要查看的内容）。
由于mimic_derived 参与了很多内容的查询，熟悉这个模块的内容还是很有必要的，但是官方对这个模块缺乏详细的介绍。今天通过官方提供的源代码查看理解mimic_derived中各个表格的内容，记录在这里，供大家参考。
注：仅包含了作者认为重要的表格，并非全部。
- age，为患者入院（admission）时的年龄，存储在age列。
-- This query calculates the age of a patient on admission to the hospital.
-- The columns of the table patients: anchor_age, anchor_year, anchor_year_group
-- provide information regarding the actual patient year for the patient admission,
-- and the patient's age at that time.
-- anchor_year is a shifted year for the patient.
-- anchor_year_group is a range of years - the patient's anchor_year occurred during this range.
-- anchor_age is the patient's age in the anchor_year.
-- Example: a patient has an anchor_year of 2153,
-- anchor_year_group of 2008 - 2010, and an anchor_age of 60.
-- The year 2153 for the patient corresponds to 2008, 2009, or 2010.
-- The patient was 60 in the shifted year of 2153, i.e. they were 60 in 2008, 2009, or 2010.
-- A patient admission in 2154 will occur in 2009-2011,
-- an admission in 2155 will occur in 2010-2012, and so on.
-- Therefore, the age of a patient = hospital admission time - anchor_year + anchor_age
SELECT
ad.subject_id
, ad.hadm_id
, ad.admittime
, pa.anchor_age
, pa.anchor_year
, DATETIME_DIFF(ad.admittime, DATETIME(pa.anchor_year, 1, 1, 0, 0, 0), YEAR) + pa.anchor_age AS age
FROM `physionet-data.mimic_core.admissions` ad
INNER JOIN `physionet-data.mimic_core.patients` pa
ON ad.subject_id = pa.subject_id
;
- 令人惊喜的发现derived中的一个表格icustay_detail提供了多种结局的数据， 包括是否发生院内死亡（hospital_expire_flag）、住院时间（los_hospital）、住ICU时间(los_icu)以及是否是首次进入院，是否是首次进入ICU等，为提取部分患者结局变量提供了方便。
SELECT ie.subject_id, ie.hadm_id, ie.stay_id
-- patient level factors
, pat.gender, pat.dod
-- hospital level factors
, adm.admittime, adm.dischtime
, DATETIME_DIFF(adm.dischtime, adm.admittime, DAY) as los_hospital
, DATETIME_DIFF(adm.admittime, DATETIME(pat.anchor_year, 1, 1, 0, 0, 0), YEAR) + pat.anchor_age as admission_age
, adm.ethnicity
, adm.hospital_expire_flag
, DENSE_RANK() OVER (PARTITION BY adm.subject_id ORDER BY adm.admittime) AS hospstay_seq
, CASE
WHEN DENSE_RANK() OVER (PARTITION BY adm.subject_id ORDER BY adm.admittime) = 1 THEN True
ELSE False END AS first_hosp_stay
-- icu level factors
, ie.intime as icu_intime, ie.outtime as icu_outtime
, ROUND(DATETIME_DIFF(ie.outtime, ie.intime, HOUR)/24.0, 2) as los_icu
, DENSE_RANK() OVER (PARTITION BY ie.hadm_id ORDER BY ie.intime) AS icustay_seq
-- first ICU stay *for the current hospitalization*
, CASE
WHEN DENSE_RANK() OVER (PARTITION BY ie.hadm_id ORDER BY ie.intime) = 1 THEN True
ELSE False END AS first_icu_stay
FROM `physionet-data.mimic_icu.icustays` ie
INNER JOIN `physionet-data.mimic_core.admissions` adm
ON ie.hadm_id = adm.hadm_id
INNER JOIN `physionet-data.mimic_core.patients` pat
ON ie.subject_id = pat.subject_id
- weight_duration, ICU期间体重的变化，体重是反应患者营养状况的重要因素，常被纳入到预测因素中。
-- This query extracts weights for adult ICU patients with start/stop times
-- if an admission weight is given, then this is assigned from intime to outtime
WITH wt_stg as
(
SELECT
c.stay_id
, c.charttime
, case when c.itemid = 226512 then 'admit'
else 'daily' end as weight_type
-- TODO: eliminate obvious outliers if there is a reasonable weight
, c.valuenum as weight
FROM `physionet-data.mimic_icu.chartevents` c
WHERE c.valuenum IS NOT NULL
AND c.itemid in
(
226512 -- Admit Wt
, 224639 -- Daily Weight
)
AND c.valuenum > 0
)
-- assign ascending row number
, wt_stg1 as
(
select
stay_id
, charttime
, weight_type
, weight
, ROW_NUMBER() OVER (partition by stay_id, weight_type order by charttime) as rn
from wt_stg
WHERE weight IS NOT NULL
)
-- change charttime to intime for the first admission weight recorded
, wt_stg2 AS
(
SELECT
wt_stg1.stay_id
, ie.intime, ie.outtime
, wt_stg1.weight_type
, case when wt_stg1.weight_type = 'admit' and wt_stg1.rn = 1
then DATETIME_SUB(ie.intime, INTERVAL '2' HOUR)
else wt_stg1.charttime end as starttime
, wt_stg1.weight
from wt_stg1
INNER JOIN `physionet-data.mimic_icu.icustays` ie
on ie.stay_id = wt_stg1.stay_id
)
, wt_stg3 as
(
select
stay_id
, intime, outtime
, starttime
, coalesce(
LEAD(starttime) OVER (PARTITION BY stay_id ORDER BY starttime),
DATETIME_ADD(outtime, INTERVAL '2' HOUR)
) as endtime
, weight
, weight_type
from wt_stg2
)
-- this table is the start/stop times from admit/daily weight in charted data
, wt1 as
(
select
stay_id
, starttime
, coalesce(endtime,
LEAD(starttime) OVER (partition by stay_id order by starttime),
-- impute ICU discharge as the end of the final weight measurement
-- plus a 2 hour "fuzziness" window
DATETIME_ADD(outtime, INTERVAL '2' HOUR)
) as endtime
, weight
, weight_type
from wt_stg3
)
-- if the intime for the patient is < the first charted daily weight
-- then we will have a "gap" at the start of their stay
-- to prevent this, we look for these gaps and backfill the first weight
-- this adds (153255-149657)=3598 rows, meaning this fix helps for up to 3598 stay_id
, wt_fix as
(
select ie.stay_id
-- we add a 2 hour "fuzziness" window
, DATETIME_SUB(ie.intime, INTERVAL '2' HOUR) as starttime
, wt.starttime as endtime
, wt.weight
, wt.weight_type
from `physionet-data.mimic_icu.icustays` ie
inner join
-- the below subquery returns one row for each unique stay_id
-- the row contains: the first starttime and the corresponding weight
(
SELECT wt1.stay_id, wt1.starttime, wt1.weight
, weight_type
, ROW_NUMBER() OVER (PARTITION BY wt1.stay_id ORDER BY wt1.starttime) as rn
FROM wt1
) wt
ON ie.stay_id = wt.stay_id
AND wt.rn = 1
and ie.intime < wt.starttime
)
-- add the backfill rows to the main weight table
SELECT
wt1.stay_id
, wt1.starttime
, wt1.endtime
, wt1.weight
, wt1.weight_type
FROM wt1
UNION ALL
SELECT
wt_fix.stay_id
, wt_fix.starttime
, wt_fix.endtime
, wt_fix.weight
, wt_fix.weight_type
FROM wt_fix;
- bg (blood gas), 血气分析，代码注释中说来源是hosp模块的labevents，部分指标也和ICU相关。有个地方存疑，血气指标皆取了最大值，不知道这是否符合医学常识， 注释中解释为“simply collapse rows”（仅是为了压缩列），不一定符合实际中的需求，注意。
-- The aim of this query is to pivot entries related to blood gases
-- which were found in LABEVENTS
WITH bg AS
(
select
-- specimen_id only ever has 1 measurement for each itemid
-- so, we may simply collapse rows using MAX()
MAX(subject_id) AS subject_id
, MAX(hadm_id) AS hadm_id
, MAX(charttime) AS charttime
-- specimen_id *may* have different storetimes, so this is taking the latest
, MAX(storetime) AS storetime
, le.specimen_id
, MAX(CASE WHEN itemid = 52028 THEN value ELSE NULL END) AS specimen
, MAX(CASE WHEN itemid = 50801 THEN valuenum ELSE NULL END) AS aado2
, MAX(CASE WHEN itemid = 50802 THEN valuenum ELSE NULL END) AS baseexcess
, MAX(CASE WHEN itemid = 50803 THEN valuenum ELSE NULL END) AS bicarbonate
, MAX(CASE WHEN itemid = 50804 THEN valuenum ELSE NULL END) AS totalco2
, MAX(CASE WHEN itemid = 50805 THEN valuenum ELSE NULL END) AS carboxyhemoglobin
, MAX(CASE WHEN itemid = 50806 THEN valuenum ELSE NULL END) AS chloride
, MAX(CASE WHEN itemid = 50808 THEN valuenum ELSE NULL END) AS calcium
, MAX(CASE WHEN itemid = 50809 and valuenum <= 10000 THEN valuenum ELSE NULL END) AS glucose
, MAX(CASE WHEN itemid = 50810 and valuenum <= 100 THEN valuenum ELSE NULL END) AS hematocrit
, MAX(CASE WHEN itemid = 50811 THEN valuenum ELSE NULL END) AS hemoglobin
, MAX(CASE WHEN itemid = 50813 and valuenum <= 10000 THEN valuenum ELSE NULL END) AS lactate
, MAX(CASE WHEN itemid = 50814 THEN valuenum ELSE NULL END) AS methemoglobin
, MAX(CASE WHEN itemid = 50815 THEN valuenum ELSE NULL END) AS o2flow
-- fix a common unit conversion error for fio2
-- atmospheric o2 is 20.89%, so any value <= 20 is unphysiologic
-- usually this is a misplaced O2 flow measurement
, MAX(CASE WHEN itemid = 50816 THEN
CASE
WHEN valuenum > 20 AND valuenum <= 100 THEN valuenum
WHEN valuenum > 0.2 AND valuenum <= 1.0 THEN valuenum*100.0
ELSE NULL END
ELSE NULL END) AS fio2
, MAX(CASE WHEN itemid = 50817 AND valuenum <= 100 THEN valuenum ELSE NULL END) AS so2
, MAX(CASE WHEN itemid = 50818 THEN valuenum ELSE NULL END) AS pco2
, MAX(CASE WHEN itemid = 50819 THEN valuenum ELSE NULL END) AS peep
, MAX(CASE WHEN itemid = 50820 THEN valuenum ELSE NULL END) AS ph
, MAX(CASE WHEN itemid = 50821 THEN valuenum ELSE NULL END) AS po2
, MAX(CASE WHEN itemid = 50822 THEN valuenum ELSE NULL END) AS potassium
, MAX(CASE WHEN itemid = 50823 THEN valuenum ELSE NULL END) AS requiredo2
, MAX(CASE WHEN itemid = 50824 THEN valuenum ELSE NULL END) AS sodium
, MAX(CASE WHEN itemid = 50825 THEN valuenum ELSE NULL END) AS temperature
, MAX(CASE WHEN itemid = 50807 THEN value ELSE NULL END) AS comments
FROM mimic_hosp.labevents le
where le.ITEMID in
-- blood gases
(
52028 -- specimen
, 50801 -- aado2
, 50802 -- base excess
, 50803 -- bicarb
, 50804 -- calc tot co2
, 50805 -- carboxyhgb
, 50806 -- chloride
-- , 52390 -- chloride, WB CL-
, 50807 -- comments
, 50808 -- free calcium
, 50809 -- glucose
, 50810 -- hct
, 50811 -- hgb
, 50813 -- lactate
, 50814 -- methemoglobin
, 50815 -- o2 flow
, 50816 -- fio2
, 50817 -- o2 sat
, 50818 -- pco2
, 50819 -- peep
, 50820 -- pH
, 50821 -- pO2
, 50822 -- potassium
-- , 52408 -- potassium, WB K+
, 50823 -- required O2
, 50824 -- sodium
-- , 52411 -- sodium, WB NA +
, 50825 -- temperature
)
GROUP BY le.specimen_id
)
, stg_spo2 as
(
select subject_id, charttime
-- avg here is just used to group SpO2 by charttime
, AVG(valuenum) as SpO2
FROM mimic_icu.chartevents
where ITEMID = 220277 -- O2 saturation pulseoxymetry
and valuenum > 0 and valuenum <= 100
group by subject_id, charttime
)
, stg_fio2 as
(
select subject_id, charttime
-- pre-process the FiO2s to ensure they are between 21-100%
, max(
case
when valuenum > 0.2 and valuenum <= 1
then valuenum * 100
-- improperly input data - looks like O2 flow in litres
when valuenum > 1 and valuenum < 20
then null
when valuenum >= 20 and valuenum <= 100
then valuenum
else null end
) as fio2_chartevents
FROM mimic_icu.chartevents
where ITEMID = 223835 -- Inspired O2 Fraction (FiO2)
and valuenum > 0 and valuenum <= 100
group by subject_id, charttime
)
, stg2 as
(
select bg.*
, ROW_NUMBER() OVER (partition by bg.subject_id, bg.charttime order by s1.charttime DESC) as lastRowSpO2
, s1.spo2
from bg
left join stg_spo2 s1
-- same hospitalization
on bg.subject_id = s1.subject_id
-- spo2 occurred at most 2 hours before this blood gas
and s1.charttime between DATETIME_SUB(bg.charttime, INTERVAL 2 HOUR) and bg.charttime
where bg.po2 is not null
)
, stg3 as
(
select bg.*
, ROW_NUMBER() OVER (partition by bg.subject_id, bg.charttime order by s2.charttime DESC) as lastRowFiO2
, s2.fio2_chartevents
-- create our specimen prediction
, 1/(1+exp(-(-0.02544
+ 0.04598 * po2
+ coalesce(-0.15356 * spo2 , -0.15356 * 97.49420 + 0.13429)
+ coalesce( 0.00621 * fio2_chartevents , 0.00621 * 51.49550 + -0.24958)
+ coalesce( 0.10559 * hemoglobin , 0.10559 * 10.32307 + 0.05954)
+ coalesce( 0.13251 * so2 , 0.13251 * 93.66539 + -0.23172)
+ coalesce(-0.01511 * pco2 , -0.01511 * 42.08866 + -0.01630)
+ coalesce( 0.01480 * fio2 , 0.01480 * 63.97836 + -0.31142)
+ coalesce(-0.00200 * aado2 , -0.00200 * 442.21186 + -0.01328)
+ coalesce(-0.03220 * bicarbonate , -0.03220 * 22.96894 + -0.06535)
+ coalesce( 0.05384 * totalco2 , 0.05384 * 24.72632 + -0.01405)
+ coalesce( 0.08202 * lactate , 0.08202 * 3.06436 + 0.06038)
+ coalesce( 0.10956 * ph , 0.10956 * 7.36233 + -0.00617)
+ coalesce( 0.00848 * o2flow , 0.00848 * 7.59362 + -0.35803)
))) as specimen_prob
from stg2 bg
left join stg_fio2 s2
-- same patient
on bg.subject_id = s2.subject_id
-- fio2 occurred at most 4 hours before this blood gas
and s2.charttime between DATETIME_SUB(bg.charttime, INTERVAL 4 HOUR) and bg.charttime
AND s2.fio2_chartevents > 0
where bg.lastRowSpO2 = 1 -- only the row with the most recent SpO2 (if no SpO2 found lastRowSpO2 = 1)
)
select
stg3.subject_id
, stg3.hadm_id
, stg3.charttime
-- raw data indicating sample type
, specimen
-- prediction of specimen for obs missing the actual specimen
, case
when specimen is not null then specimen
when specimen_prob > 0.75 then 'ART.'
else null end as specimen_pred
, specimen_prob
-- oxygen related parameters
, so2
, po2
, pco2
, fio2_chartevents, fio2
, aado2
-- also calculate AADO2
, case
when po2 is null
OR pco2 is null
THEN NULL
WHEN fio2 IS NOT NULL
-- multiple by 100 because fio2 is in a % but should be a fraction
THEN (fio2/100) * (760 - 47) - (pco2/0.8) - po2
WHEN fio2_chartevents IS NOT NULL
THEN (fio2_chartevents/100) * (760 - 47) - (pco2/0.8) - po2
else null
end as aado2_calc
, case
when PO2 is null
THEN NULL
WHEN fio2 IS NOT NULL
-- multiply by 100 because fio2 is in a % but should be a fraction
then 100 * PO2/fio2
WHEN fio2_chartevents IS NOT NULL
-- multiply by 100 because fio2 is in a % but should be a fraction
then 100 * PO2/fio2_chartevents
else null
end as pao2fio2ratio
-- acid-base parameters
, ph, baseexcess
, bicarbonate, totalco2
-- blood count parameters
, hematocrit
, hemoglobin
, carboxyhemoglobin
, methemoglobin
-- chemistry
, chloride, calcium
, temperature
, potassium, sodium
, lactate
, glucose
-- ventilation stuff that's sometimes input
-- , intubated, tidalvolume, ventilationrate, ventilator
-- , peep, o2flow
-- , requiredo2
from stg3
where lastRowFiO2 = 1 -- only the most recent FiO2
;
- blood_differential, 血细胞分类
-- For reference, some common unit conversions:
-- 10^9/L == K/uL == 10^3/uL
WITH blood_diff AS
(
SELECT
MAX(subject_id) AS subject_id
, MAX(hadm_id) AS hadm_id
, MAX(charttime) AS charttime
, le.specimen_id
-- create one set of columns for percentages, and one set of columns for counts
-- we harmonize all count units into K/uL == 10^9/L
-- counts have an "_abs" suffix, percentages do not
-- absolute counts
, MAX(CASE WHEN itemid in (51300, 51301, 51755) THEN valuenum ELSE NULL END) AS wbc
, MAX(CASE WHEN itemid = 52069 THEN valuenum ELSE NULL END) AS basophils_abs
-- 52073 in K/uL, 51199 in #/uL
, MAX(CASE WHEN itemid = 52073 THEN valuenum WHEN itemid = 51199 THEN valuenum / 1000.0 ELSE NULL END) AS eosinophils_abs
-- 51133 in K/uL, 52769 in #/uL
, MAX(CASE WHEN itemid = 51133 THEN valuenum WHEN itemid = 52769 THEN valuenum / 1000.0 ELSE NULL END) AS lymphocytes_abs
-- 52074 in K/uL, 51253 in #/uL
, MAX(CASE WHEN itemid = 52074 THEN valuenum WHEN itemid = 51253 THEN valuenum / 1000.0 ELSE NULL END) AS monocytes_abs
, MAX(CASE WHEN itemid = 52075 THEN valuenum ELSE NULL END) AS neutrophils_abs
-- convert from #/uL to K/uL
, MAX(CASE WHEN itemid = 51218 THEN valuenum / 1000.0 ELSE NULL END) AS granulocytes_abs
-- percentages, equal to cell count / white blood cell count
, MAX(CASE WHEN itemid = 51146 THEN valuenum ELSE NULL END) AS basophils
, MAX(CASE WHEN itemid = 51200 THEN valuenum ELSE NULL END) AS eosinophils
, MAX(CASE WHEN itemid in (51244, 51245) THEN valuenum ELSE NULL END) AS lymphocytes
, MAX(CASE WHEN itemid = 51254 THEN valuenum ELSE NULL END) AS monocytes
, MAX(CASE WHEN itemid = 51256 THEN valuenum ELSE NULL END) AS neutrophils
-- other cell count percentages
, MAX(CASE WHEN itemid = 51143 THEN valuenum ELSE NULL END) AS atypical_lymphocytes
, MAX(CASE WHEN itemid = 51144 THEN valuenum ELSE NULL END) AS bands
, MAX(CASE WHEN itemid = 52135 THEN valuenum ELSE NULL END) AS immature_granulocytes
, MAX(CASE WHEN itemid = 51251 THEN valuenum ELSE NULL END) AS metamyelocytes
, MAX(CASE WHEN itemid = 51257 THEN valuenum ELSE NULL END) AS nrbc
-- utility flags which determine whether imputation is possible
, CASE
-- WBC is available
WHEN MAX(CASE WHEN itemid in (51300, 51301, 51755) THEN valuenum ELSE NULL END) > 0
-- and we have at least one percentage from the diff
-- sometimes the entire diff is 0%, which looks like bad data
AND SUM(CASE WHEN itemid IN (51146, 51200, 51244, 51245, 51254, 51256) THEN valuenum ELSE NULL END) > 0
THEN 1 ELSE 0 END AS impute_abs
FROM mimic_hosp.labevents le
WHERE le.itemid IN
(
51146, -- basophils
52069, -- Absolute basophil count
51199, -- Eosinophil Count
51200, -- Eosinophils
52073, -- Absolute Eosinophil count
51244, -- Lymphocytes
51245, -- Lymphocytes, Percent
51133, -- Absolute Lymphocyte Count
52769, -- Absolute Lymphocyte Count
51253, -- Monocyte Count
51254, -- Monocytes
52074, -- Absolute Monocyte Count
51256, -- Neutrophils
52075, -- Absolute Neutrophil Count
51143, -- Atypical lymphocytes
51144, -- Bands (%)
51218, -- Granulocyte Count
52135, -- Immature granulocytes (%)
51251, -- Metamyelocytes
51257, -- Nucleated Red Cells
-- wbc totals measured in K/uL
51300, 51301, 51755
-- 52220 (wbcp) is percentage
-- below are point of care tests which are extremely infrequent and usually low quality
-- 51697, -- Neutrophils (mmol/L)
-- below itemid do not have data as of MIMIC-IV v1.0
-- 51536, -- Absolute Lymphocyte Count
-- 51537, -- Absolute Neutrophil
-- 51690, -- Lymphocytes
-- 52151, -- NRBC
)
AND valuenum IS NOT NULL
-- differential values cannot be negative
AND valuenum >= 0
GROUP BY le.specimen_id
)
SELECT
subject_id, hadm_id, charttime, specimen_id
, wbc
-- impute absolute count if percentage & WBC is available
, ROUND(CASE
WHEN basophils_abs IS NULL AND basophils IS NOT NULL AND impute_abs = 1
THEN basophils * wbc
ELSE basophils_abs
END, 4) AS basophils_abs
, ROUND(CASE
WHEN eosinophils_abs IS NULL AND eosinophils IS NOT NULL AND impute_abs = 1
THEN eosinophils * wbc
ELSE eosinophils_abs
END, 4) AS eosinophils_abs
, ROUND(CASE
WHEN lymphocytes_abs IS NULL AND lymphocytes IS NOT NULL AND impute_abs = 1
THEN lymphocytes * wbc
ELSE lymphocytes_abs
END, 4) AS lymphocytes_abs
, ROUND(CASE
WHEN monocytes_abs IS NULL AND monocytes IS NOT NULL AND impute_abs = 1
THEN monocytes * wbc
ELSE monocytes_abs
END, 4) AS monocytes_abs
, ROUND(CASE
WHEN neutrophils_abs IS NULL AND neutrophils IS NOT NULL AND impute_abs = 1
THEN neutrophils * wbc
ELSE neutrophils_abs
END, 4) AS neutrophils_abs
, basophils
, eosinophils
, lymphocytes
, monocytes
, neutrophils
-- impute bands/blasts?
, atypical_lymphocytes
, bands
, immature_granulocytes
, metamyelocytes
, nrbc
FROM blood_diff
;
- cardiac_maker, 心脏标记物，三种酶
-- begin query that extracts the data
SELECT
MAX(subject_id) AS subject_id
, MAX(hadm_id) AS hadm_id
, MAX(charttime) AS charttime
, le.specimen_id
-- convert from itemid into a meaningful column
, MAX(CASE WHEN itemid = 51002 THEN value ELSE NULL END) AS troponin_i
, MAX(CASE WHEN itemid = 51003 THEN value ELSE NULL END) AS troponin_t
, MAX(CASE WHEN itemid = 50911 THEN valuenum ELSE NULL END) AS ck_mb
FROM mimic_hosp.labevents le
WHERE le.itemid IN
(
-- 51002, -- Troponin I (troponin-I is not measured in MIMIC-IV)
-- 52598, -- Troponin I, point of care, rare/poor quality
51003, -- Troponin T
50911 -- Creatinine Kinase, MB isoenzyme
)
GROUP BY le.specimen_id
;
-chemistry， 化学元素
-- extract chemistry labs
-- excludes point of care tests (very rare)
-- blood gas measurements are *not* included in this query
-- instead they are in bg.sql
SELECT
MAX(subject_id) AS subject_id
, MAX(hadm_id) AS hadm_id
, MAX(charttime) AS charttime
, le.specimen_id
-- convert from itemid into a meaningful column
, MAX(CASE WHEN itemid = 50862 AND valuenum <= 10 THEN valuenum ELSE NULL END) AS albumin
, MAX(CASE WHEN itemid = 50930 AND valuenum <= 10 THEN valuenum ELSE NULL END) AS globulin
, MAX(CASE WHEN itemid = 50976 AND valuenum <= 20 THEN valuenum ELSE NULL END) AS total_protein
, MAX(CASE WHEN itemid = 50868 AND valuenum <= 10000 THEN valuenum ELSE NULL END) AS aniongap
, MAX(CASE WHEN itemid = 50882 AND valuenum <= 10000 THEN valuenum ELSE NULL END) AS bicarbonate
, MAX(CASE WHEN itemid = 51006 AND valuenum <= 300 THEN valuenum ELSE NULL END) AS bun
, MAX(CASE WHEN itemid = 50893 AND valuenum <= 10000 THEN valuenum ELSE NULL END) AS calcium
, MAX(CASE WHEN itemid = 50902 AND valuenum <= 10000 THEN valuenum ELSE NULL END) AS chloride
, MAX(CASE WHEN itemid = 50912 AND valuenum <= 150 THEN valuenum ELSE NULL END) AS creatinine
, MAX(CASE WHEN itemid = 50931 AND valuenum <= 10000 THEN valuenum ELSE NULL END) AS glucose
, MAX(CASE WHEN itemid = 50983 AND valuenum <= 200 THEN valuenum ELSE NULL END) AS sodium
, MAX(CASE WHEN itemid = 50971 AND valuenum <= 30 THEN valuenum ELSE NULL END) AS potassium
FROM mimic_hosp.labevents le
WHERE le.itemid IN
(
-- comment is: LABEL | CATEGORY | FLUID | NUMBER OF ROWS IN LABEVENTS
50862, -- ALBUMIN | CHEMISTRY | BLOOD | 146697
50930, -- Globulin
50976, -- Total protein
50868, -- ANION GAP | CHEMISTRY | BLOOD | 769895
-- 52456, -- Anion gap, point of care test
50882, -- BICARBONATE | CHEMISTRY | BLOOD | 780733
50893, -- Calcium
50912, -- CREATININE | CHEMISTRY | BLOOD | 797476
-- 52502, Creatinine, point of care
50902, -- CHLORIDE | CHEMISTRY | BLOOD | 795568
50931, -- GLUCOSE | CHEMISTRY | BLOOD | 748981
-- 52525, Glucose, point of care
50971, -- POTASSIUM | CHEMISTRY | BLOOD | 845825
-- 52566, -- Potassium, point of care
50983, -- SODIUM | CHEMISTRY | BLOOD | 808489
-- 52579, -- Sodium, point of care
51006 -- UREA NITROGEN | CHEMISTRY | BLOOD | 791925
-- 52603, Urea, point of care
)
AND valuenum IS NOT NULL
-- lab values cannot be 0 and cannot be negative
-- .. except anion gap.
AND (valuenum > 0 OR itemid = 50868)
GROUP BY le.specimen_id
;
- GCS评分， 神经系统功能评分
-- This query extracts the Glasgow Coma Scale, a measure of neurological function.
-- The query has a few special rules:
-- (1) The verbal component can be set to 0 if the patient is ventilated.
-- This is corrected to 5 - the overall GCS is set to 15 in these cases.
-- (2) Often only one of three components is documented. The other components
-- are carried forward.
-- ITEMIDs used:
-- METAVISION
-- 223900 GCS - Verbal Response
-- 223901 GCS - Motor Response
-- 220739 GCS - Eye Opening
-- Note:
-- The GCS for sedated patients is defaulted to 15 in this code.
-- This is in line with how the data is meant to be collected.
-- e.g., from the SAPS II publication:
-- For sedated patients, the Glasgow Coma Score before sedation was used.
-- This was ascertained either from interviewing the physician who ordered the sedation,
-- or by reviewing the patient's medical record.
with base as
(
select
subject_id
, ce.stay_id, ce.charttime
-- pivot each value into its own column
, max(case when ce.ITEMID = 223901 then ce.valuenum else null end) as GCSMotor
, max(case
when ce.ITEMID = 223900 and ce.VALUE = 'No Response-ETT' then 0
when ce.ITEMID = 223900 then ce.valuenum
else null
end) as GCSVerbal
, max(case when ce.ITEMID = 220739 then ce.valuenum else null end) as GCSEyes
-- convert the data into a number, reserving a value of 0 for ET/Trach
, max(case
-- endotrach/vent is assigned a value of 0
-- flag it here to later parse specially
when ce.ITEMID = 223900 and ce.VALUE = 'No Response-ETT' then 1 -- metavision
else 0 end)
as endotrachflag
, ROW_NUMBER ()
OVER (PARTITION BY ce.stay_id ORDER BY ce.charttime ASC) as rn
from mimic_icu.chartevents ce
-- Isolate the desired GCS variables
where ce.ITEMID in
(
-- GCS components, Metavision
223900, 223901, 220739
)
group by ce.subject_id, ce.stay_id, ce.charttime
)
, gcs as (
select b.*
, b2.GCSVerbal as GCSVerbalPrev
, b2.GCSMotor as GCSMotorPrev
, b2.GCSEyes as GCSEyesPrev
-- Calculate GCS, factoring in special case when they are intubated and prev vals
-- note that the coalesce are used to implement the following if:
-- if current value exists, use it
-- if previous value exists, use it
-- otherwise, default to normal
, case
-- replace GCS during sedation with 15
when b.GCSVerbal = 0
then 15
when b.GCSVerbal is null and b2.GCSVerbal = 0
then 15
-- if previously they were intub, but they aren't now, do not use previous GCS values
when b2.GCSVerbal = 0
then
coalesce(b.GCSMotor,6)
+ coalesce(b.GCSVerbal,5)
+ coalesce(b.GCSEyes,4)
-- otherwise, add up score normally, imputing previous value if none available at current time
else
coalesce(b.GCSMotor,coalesce(b2.GCSMotor,6))
+ coalesce(b.GCSVerbal,coalesce(b2.GCSVerbal,5))
+ coalesce(b.GCSEyes,coalesce(b2.GCSEyes,4))
end as GCS
from base b
-- join to itself within 6 hours to get previous value
left join base b2
on b.stay_id = b2.stay_id
and b.rn = b2.rn+1
and b2.charttime > DATETIME_ADD(b.charttime, INTERVAL 6 HOUR)
)
-- combine components with previous within 6 hours
-- filter down to cohort which is not excluded
-- truncate charttime to the hour
, gcs_stg as
(
select
subject_id
, gs.stay_id, gs.charttime
, GCS
, coalesce(GCSMotor,GCSMotorPrev) as GCSMotor
, coalesce(GCSVerbal,GCSVerbalPrev) as GCSVerbal
, coalesce(GCSEyes,GCSEyesPrev) as GCSEyes
, case when coalesce(GCSMotor,GCSMotorPrev) is null then 0 else 1 end
+ case when coalesce(GCSVerbal,GCSVerbalPrev) is null then 0 else 1 end
+ case when coalesce(GCSEyes,GCSEyesPrev) is null then 0 else 1 end
as components_measured
, EndoTrachFlag
from gcs gs
)
-- priority is:
-- (i) complete data, (ii) non-sedated GCS, (iii) lowest GCS, (iv) charttime
, gcs_priority as
(
select
subject_id
, stay_id
, charttime
, gcs
, gcsmotor
, gcsverbal
, gcseyes
, EndoTrachFlag
, ROW_NUMBER() over
(
PARTITION BY stay_id, charttime
ORDER BY components_measured DESC, endotrachflag, gcs, charttime DESC
) as rn
from gcs_stg
)
select
gs.subject_id
, gs.stay_id
, gs.charttime
, GCS AS gcs
, GCSMotor AS gcs_motor
, GCSVerbal AS gcs_verbal
, GCSEyes AS gcs_eyes
, EndoTrachFlag AS gcs_unable
from gcs_priority gs
where rn = 1
;
- inflammation， C反应蛋白，炎症标记物
SELECT
MAX(subject_id) AS subject_id
, MAX(hadm_id) AS hadm_id
, MAX(charttime) AS charttime
, le.specimen_id
-- convert from itemid into a meaningful column
, MAX(CASE WHEN itemid = 50889 THEN valuenum ELSE NULL END) AS crp
-- , CAST(NULL AS NUMERIC) AS il6
-- , CAST(NULL AS NUMERIC) AS procalcitonin
FROM mimic_hosp.labevents le
WHERE le.itemid IN
(
50889 -- crp
-- 51652 -- high sensitivity CRP
)
AND valuenum IS NOT NULL
-- lab values cannot be 0 and cannot be negative
AND valuenum > 0
GROUP BY le.specimen_id
;
- vitalsign 包括心率、血压、血糖等
-- This query pivots the vital signs for the entire patient stay.
-- Vital signs include heart rate, blood pressure, respiration rate, and temperature
select
ce.subject_id
, ce.stay_id
, ce.charttime
, AVG(case when itemid in (220045) and valuenum > 0 and valuenum < 300 then valuenum else null end) as heart_rate
, AVG(case when itemid in (220179,220050) and valuenum > 0 and valuenum < 400 then valuenum else null end) as sbp
, AVG(case when itemid in (220180,220051) and valuenum > 0 and valuenum < 300 then valuenum else null end) as dbp
, AVG(case when itemid in (220052,220181,225312) and valuenum > 0 and valuenum < 300 then valuenum else null end) as mbp
, AVG(case when itemid = 220179 and valuenum > 0 and valuenum < 400 then valuenum else null end) as sbp_ni
, AVG(case when itemid = 220180 and valuenum > 0 and valuenum < 300 then valuenum else null end) as dbp_ni
, AVG(case when itemid = 220181 and valuenum > 0 and valuenum < 300 then valuenum else null end) as mbp_ni
, AVG(case when itemid in (220210,224690) and valuenum > 0 and valuenum < 70 then valuenum else null end) as resp_rate
, ROUND(
AVG(case when itemid in (223761) and valuenum > 70 and valuenum < 120 then (valuenum-32)/1.8 -- converted to degC in valuenum call
when itemid in (223762) and valuenum > 10 and valuenum < 50 then valuenum else null end)
, 2) as temperature
, MAX(CASE WHEN itemid = 224642 THEN value ELSE NULL END) AS temperature_site
, AVG(case when itemid in (220277) and valuenum > 0 and valuenum <= 100 then valuenum else null end) as spo2
, AVG(case when itemid in (225664,220621,226537) and valuenum > 0 then valuenum else null end) as glucose
FROM mimic_icu.chartevents ce
where ce.stay_id IS NOT NULL
and ce.itemid in
(
220045, -- Heart Rate
225309, -- ART BP Systolic
225310, -- ART BP Diastolic
225312, -- ART BP Mean
220050, -- Arterial Blood Pressure systolic
220051, -- Arterial Blood Pressure diastolic
220052, -- Arterial Blood Pressure mean
220179, -- Non Invasive Blood Pressure systolic
220180, -- Non Invasive Blood Pressure diastolic
220181, -- Non Invasive Blood Pressure mean
220210, -- Respiratory Rate
224690, -- Respiratory Rate (Total)
220277, -- SPO2, peripheral
-- GLUCOSE, both lab and fingerstick
225664, -- Glucose finger stick
220621, -- Glucose (serum)
226537, -- Glucose (whole blood)
-- TEMPERATURE
223762, -- "Temperature Celsius"
223761, -- "Temperature Fahrenheit"
224642 -- Temperature Site
-- 226329 -- Blood Temperature CCO (C)
)
group by ce.subject_id, ce.stay_id, ce.charttime
;
-crrt， 连续肾脏替代治疗
with crrt_settings as
(
select ce.stay_id, ce.charttime
, CASE WHEN ce.itemid = 227290 THEN ce.value END AS CRRT_mode
, CASE WHEN ce.itemid = 224149 THEN ce.valuenum ELSE NULL END AS AccessPressure
, CASE WHEN ce.itemid = 224144 THEN ce.valuenum ELSE NULL END AS BloodFlow -- (ml/min)
, CASE WHEN ce.itemid = 228004 THEN ce.valuenum ELSE NULL END AS Citrate -- (ACD-A)
, CASE WHEN ce.itemid = 225183 THEN ce.valuenum ELSE NULL END AS CurrentGoal
, CASE WHEN ce.itemid = 225977 THEN ce.value ELSE NULL END AS DialysateFluid
, CASE WHEN ce.itemid = 224154 THEN ce.valuenum ELSE NULL END AS DialysateRate
, CASE WHEN ce.itemid = 224151 THEN ce.valuenum ELSE NULL END AS EffluentPressure
, CASE WHEN ce.itemid = 224150 THEN ce.valuenum ELSE NULL END AS FilterPressure
, CASE WHEN ce.itemid = 225958 THEN ce.value ELSE NULL END AS HeparinConcentration -- (units/mL)
, CASE WHEN ce.itemid = 224145 THEN ce.valuenum ELSE NULL END AS HeparinDose -- (per hour)
-- below may not account for drug infusion/hyperalimentation/anticoagulants infused
, CASE WHEN ce.itemid = 224191 THEN ce.valuenum ELSE NULL END AS HourlyPatientFluidRemoval
, CASE WHEN ce.itemid = 228005 THEN ce.valuenum ELSE NULL END AS PrefilterReplacementRate
, CASE WHEN ce.itemid = 228006 THEN ce.valuenum ELSE NULL END AS PostFilterReplacementRate
, CASE WHEN ce.itemid = 225976 THEN ce.value ELSE NULL END AS ReplacementFluid
, CASE WHEN ce.itemid = 224153 THEN ce.valuenum ELSE NULL END AS ReplacementRate
, CASE WHEN ce.itemid = 224152 THEN ce.valuenum ELSE NULL END AS ReturnPressure
, CASE WHEN ce.itemid = 226457 THEN ce.valuenum END AS UltrafiltrateOutput
-- separate system integrity into sub components
-- need to do this as 224146 has multiple unique values for a single charttime
-- e.g. "Clots Present" and "Active" at same time
, CASE
WHEN ce.itemid = 224146
AND ce.value IN ('Active', 'Initiated', 'Reinitiated', 'New Filter')
THEN 1
WHEN ce.itemid = 224146
AND ce.value IN ('Recirculating', 'Discontinued')
THEN 0
ELSE NULL END as system_active
, CASE
WHEN ce.itemid = 224146
AND ce.value IN ('Clots Present', 'Clots Present')
THEN 1
WHEN ce.itemid = 224146
AND ce.value IN ('No Clot Present', 'No Clot Present')
THEN 0
ELSE NULL END as clots
, CASE
WHEN ce.itemid = 224146
AND ce.value IN ('Clots Increasing', 'Clot Increasing')
THEN 1
ELSE NULL END as clots_increasing
, CASE
WHEN ce.itemid = 224146
AND ce.value IN ('Clotted')
THEN 1
ELSE NULL END as clotted
from `physionet-data.mimic_icu.chartevents` ce
where ce.itemid in
(
-- MetaVision ITEMIDs
227290, -- CRRT Mode
224146, -- System Integrity
-- 225956, -- Reason for CRRT Filter Change
-- above itemid is one of: Clotted, Line Changed, Procedure
-- only ~200 rows, not super useful
224149, -- Access Pressure
224144, -- Blood Flow (ml/min)
228004, -- Citrate (ACD-A)
225183, -- Current Goal
225977, -- Dialysate Fluid
224154, -- Dialysate Rate
224151, -- Effluent Pressure
224150, -- Filter Pressure
225958, -- Heparin Concentration (units/mL)
224145, -- Heparin Dose (per hour)
224191, -- Hourly Patient Fluid Removal
228005, -- PBP (Prefilter) Replacement Rate
228006, -- Post Filter Replacement Rate
225976, -- Replacement Fluid
224153, -- Replacement Rate
224152, -- Return Pressure
226457 -- Ultrafiltrate Output
)
and ce.value is not null
)
-- use MAX() to collapse to a single row
-- there is only ever 1 row for unique combinations of stay_id/charttime/itemid
select stay_id
, charttime
, MAX(crrt_mode) AS crrt_mode
, MAX(AccessPressure) AS access_pressure
, MAX(BloodFlow) AS blood_flow
, MAX(Citrate) AS citrate
, MAX(CurrentGoal) AS current_goal
, MAX(DialysateFluid) AS dialysate_fluid
, MAX(DialysateRate) AS dialysate_rate
, MAX(EffluentPressure) AS effluent_pressure
, MAX(FilterPressure) AS filter_pressure
, MAX(HeparinConcentration) AS heparin_concentration
, MAX(HeparinDose) AS heparin_dose
, MAX(HourlyPatientFluidRemoval) AS hourly_patient_fluid_removal
, MAX(PrefilterReplacementRate) AS prefilter_replacement_rate
, MAX(PostFilterReplacementRate) AS postfilter_replacement_rate
, MAX(ReplacementFluid) AS replacement_fluid
, MAX(ReplacementRate) AS replacement_rate
, MAX(ReturnPressure) AS return_pressure
, MAX(UltrafiltrateOutput) AS ultrafiltrate_output
, MAX(system_active) AS system_active
, MAX(clots) AS clots
, MAX(clots_increasing) AS clots_increasing
, MAX(clotted) AS clotted
from crrt_settings
group by stay_id, charttime
- ventilation， 机械通气
-- Calculate duration of mechanical ventilation.
-- Some useful cases for debugging:
-- stay_id = 30019660 has a tracheostomy placed in the ICU
-- stay_id = 30000117 has explicit documentation of extubation
-- classify vent settings into modes
WITH tm AS
(
SELECT stay_id, charttime
FROM `physionet-data.mimic_derived.ventilator_setting`
UNION DISTINCT
SELECT stay_id, charttime
FROM `physionet-data.mimic_derived.oxygen_delivery`
)
, vs AS
(
SELECT tm.stay_id, tm.charttime
-- source data columns, here for debug
, o2_delivery_device_1
, COALESCE(ventilator_mode, ventilator_mode_hamilton) AS vent_mode
-- case statement determining the type of intervention
-- done in order of priority: trach > mech vent > NIV > high flow > o2
, CASE
-- tracheostomy
WHEN o2_delivery_device_1 IN
(
'Tracheostomy tube'
-- 'Trach mask ' -- 16435 observations
)
THEN 'Trach'
-- mechanical ventilation
WHEN o2_delivery_device_1 IN
(
'Endotracheal tube'
)
OR ventilator_mode IN
(
'(S) CMV',
'APRV',
'APRV/Biphasic+ApnPress',
'APRV/Biphasic+ApnVol',
'APV (cmv)',
'Ambient',
'Apnea Ventilation',
'CMV',
'CMV/ASSIST',
'CMV/ASSIST/AutoFlow',
'CMV/AutoFlow',
'CPAP/PPS',
'CPAP/PSV+Apn TCPL',
'CPAP/PSV+ApnPres',
'CPAP/PSV+ApnVol',
'MMV',
'MMV/AutoFlow',
'MMV/PSV',
'MMV/PSV/AutoFlow',
'P-CMV',
'PCV+',
'PCV+/PSV',
'PCV+Assist',
'PRES/AC',
'PRVC/AC',
'PRVC/SIMV',
'PSV/SBT',
'SIMV',
'SIMV/AutoFlow',
'SIMV/PRES',
'SIMV/PSV',
'SIMV/PSV/AutoFlow',
'SIMV/VOL',
'SYNCHRON MASTER',
'SYNCHRON SLAVE',
'VOL/AC'
)
OR ventilator_mode_hamilton IN
(
'APRV',
'APV (cmv)',
'Ambient',
'(S) CMV',
'P-CMV',
'SIMV',
'APV (simv)',
'P-SIMV',
'VS',
'ASV'
)
THEN 'InvasiveVent'
-- NIV
WHEN o2_delivery_device_1 IN
(
'Bipap mask ', -- 8997 observations
'CPAP mask ' -- 5568 observations
)
OR ventilator_mode_hamilton IN
(
'DuoPaP',
'NIV',
'NIV-ST'
)
THEN 'NonInvasiveVent'
-- high flow
when o2_delivery_device_1 IN
(
'High flow neb', -- 10785 observations
'High flow nasal cannula' -- 925 observations
)
THEN 'HighFlow'
-- normal oxygen delivery
WHEN o2_delivery_device_1 in
(
'Nasal cannula', -- 153714 observations
'Face tent', -- 24601 observations
'Aerosol-cool', -- 24560 observations
'Non-rebreather', -- 5182 observations
'Venti mask ', -- 1947 observations
'Medium conc mask ', -- 1888 observations
'T-piece', -- 1135 observations
'Ultrasonic neb', -- 9 observations
'Vapomist', -- 3 observations
'Oxymizer' -- 1301 observations
)
THEN 'Oxygen'
-- Not categorized:
-- 'Other', 'None'
ELSE NULL END AS ventilation_status
FROM tm
LEFT JOIN `physionet-data.mimic_derived.ventilator_setting` vs
ON tm.stay_id = vs.stay_id
AND tm.charttime = vs.charttime
LEFT JOIN `physionet-data.mimic_derived.oxygen_delivery` od
ON tm.stay_id = od.stay_id
AND tm.charttime = od.charttime
)
, vd0 AS
(
SELECT
stay_id, charttime
-- source data columns, here for debug
, o2_delivery_device_1
, vent_mode
-- carry over the previous charttime which had the same state
, LAG(charttime, 1) OVER (PARTITION BY stay_id, ventilation_status ORDER BY charttime) AS charttime_lag
-- bring back the next charttime, regardless of the state
-- this will be used as the end time for state transitions
, LEAD(charttime, 1) OVER w AS charttime_lead
, ventilation_status
, LAG(ventilation_status, 1) OVER w AS ventilation_status_lag
FROM vs
WHERE ventilation_status IS NOT NULL
WINDOW w AS (PARTITION BY stay_id ORDER BY charttime)
)
, vd1 as
(
SELECT
stay_id
-- source data columns, here for debug
, o2_delivery_device_1
, vent_mode
, charttime_lag
, charttime
, charttime_lead
, ventilation_status
-- calculate the time since the last event
, DATETIME_DIFF(charttime, charttime_lag, MINUTE)/60 as ventduration
-- now we determine if the current ventilation status is "new", or continuing the previous
, CASE
-- a 14 hour gap always initiates a new event
WHEN DATETIME_DIFF(charttime, charttime_lag, HOUR) >= 14 THEN 1
WHEN ventilation_status_lag IS NULL THEN 1
-- not a new event if identical to the last row
WHEN ventilation_status_lag != ventilation_status THEN 1
ELSE 0
END AS new_status
FROM vd0
)
, vd2 as
(
SELECT vd1.*
-- create a cumulative sum of the instances of new ventilation
-- this results in a monotonic integer assigned to each instance of ventilation
, SUM(new_status) OVER (PARTITION BY stay_id ORDER BY charttime) AS vent_num
FROM vd1
)
-- create the durations for each ventilation instance
SELECT stay_id
, MIN(charttime) AS starttime
-- for the end time of the ventilation event, the time of the *next* setting
-- i.e. if we go NIV -> O2, the end time of NIV is the first row with a documented O2 device
-- ... unless it's been over 14 hours, in which case it's the last row with a documented NIV.
, MAX(
CASE
WHEN charttime_lead IS NULL
OR DATETIME_DIFF(charttime_lead, charttime, HOUR) >= 14
THEN charttime
ELSE charttime_lead
END
) AS endtime
-- all rows with the same vent_num will have the same ventilation_status
-- for efficiency, we use an aggregate here, but we could equally well group by this column
, MAX(ventilation_status) AS ventilation_status
FROM vd2
GROUP BY stay_id, vent_num
HAVING min(charttime) != max(charttime)
;
-rrt 肾脏透析疗法
-- Creates a table with stay_id / time / dialysis type (if present)
with ce as
(
select ce.stay_id
, ce.charttime
-- when ce.itemid in (152,148,149,146,147,151,150) and value is not null then 1
-- when ce.itemid in (229,235,241,247,253,259,265,271) and value = 'Dialysis Line' then 1
-- when ce.itemid = 466 and value = 'Dialysis RN' then 1
-- when ce.itemid = 927 and value = 'Dialysis Solutions' then 1
-- when ce.itemid = 6250 and value = 'dialys' then 1
-- when ce.
-- when ce.itemid = 582 and value in ('CAVH Start','CAVH D/C','CVVHD Start','CVVHD D/C','Hemodialysis st','Hemodialysis end') then 1
, CASE
-- metavision itemids
-- checkboxes
WHEN ce.itemid IN
(
226118 -- | Dialysis Catheter placed in outside facility | Access Lines - Invasive | chartevents | Checkbox
, 227357 -- | Dialysis Catheter Dressing Occlusive | Access Lines - Invasive | chartevents | Checkbox
, 225725 -- | Dialysis Catheter Tip Cultured | Access Lines - Invasive | chartevents | Checkbox
) THEN 1
-- numeric data
WHEN ce.itemid IN
(
226499 -- | Hemodialysis Output | Dialysis
, 224154 -- | Dialysate Rate | Dialysis
, 225810 -- | Dwell Time (Peritoneal Dialysis) | Dialysis
, 225959 -- | Medication Added Amount #1 (Peritoneal Dialysis) | Dialysis
, 227639 -- | Medication Added Amount #2 (Peritoneal Dialysis) | Dialysis
, 225183 -- | Current Goal | Dialysis
, 227438 -- | Volume not removed | Dialysis
, 224191 -- | Hourly Patient Fluid Removal | Dialysis
, 225806 -- | Volume In (PD) | Dialysis
, 225807 -- | Volume Out (PD) | Dialysis
, 228004 -- | Citrate (ACD-A) | Dialysis
, 228005 -- | PBP (Prefilter) Replacement Rate | Dialysis
, 228006 -- | Post Filter Replacement Rate | Dialysis
, 224144 -- | Blood Flow (ml/min) | Dialysis
, 224145 -- | Heparin Dose (per hour) | Dialysis
, 224149 -- | Access Pressure | Dialysis
, 224150 -- | Filter Pressure | Dialysis
, 224151 -- | Effluent Pressure | Dialysis
, 224152 -- | Return Pressure | Dialysis
, 224153 -- | Replacement Rate | Dialysis
, 224404 -- | ART Lumen Volume | Dialysis
, 224406 -- | VEN Lumen Volume | Dialysis
, 226457 -- | Ultrafiltrate Output | Dialysis
) THEN 1
-- text fields
WHEN ce.itemid IN
(
224135 -- | Dialysis Access Site | Dialysis
, 224139 -- | Dialysis Site Appearance | Dialysis
, 224146 -- | System Integrity | Dialysis
, 225323 -- | Dialysis Catheter Site Appear | Access Lines - Invasive
, 225740 -- | Dialysis Catheter Discontinued | Access Lines - Invasive
, 225776 -- | Dialysis Catheter Dressing Type | Access Lines - Invasive
, 225951 -- | Peritoneal Dialysis Fluid Appearance | Dialysis
, 225952 -- | Medication Added #1 (Peritoneal Dialysis) | Dialysis
, 225953 -- | Solution (Peritoneal Dialysis) | Dialysis
, 225954 -- | Dialysis Access Type | Dialysis
, 225956 -- | Reason for CRRT Filter Change | Dialysis
, 225958 -- | Heparin Concentration (units/mL) | Dialysis
, 225961 -- | Medication Added Units #1 (Peritoneal Dialysis) | Dialysis
, 225963 -- | Peritoneal Dialysis Catheter Type | Dialysis
, 225965 -- | Peritoneal Dialysis Catheter Status | Dialysis
, 225976 -- | Replacement Fluid | Dialysis
, 225977 -- | Dialysate Fluid | Dialysis
, 227124 -- | Dialysis Catheter Type | Access Lines - Invasive
, 227290 -- | CRRT mode | Dialysis
, 227638 -- | Medication Added #2 (Peritoneal Dialysis) | Dialysis
, 227640 -- | Medication Added Units #2 (Peritoneal Dialysis) | Dialysis
, 227753 -- | Dialysis Catheter Placement Confirmed by X-ray | Access Lines - Invasive
) THEN 1
ELSE 0 END
AS dialysis_present
, CASE
WHEN ce.itemid = 225965 -- Peritoneal Dialysis Catheter Status
AND value = 'In use' THEN 1
WHEN ce.itemid IN
(
226499 -- | Hemodialysis Output | Dialysis
, 224154 -- | Dialysate Rate | Dialysis
, 225183 -- | Current Goal | Dialysis
, 227438 -- | Volume not removed | Dialysis
, 224191 -- | Hourly Patient Fluid Removal | Dialysis
, 225806 -- | Volume In (PD) | Dialysis
, 225807 -- | Volume Out (PD) | Dialysis
, 228004 -- | Citrate (ACD-A) | Dialysis
, 228005 -- | PBP (Prefilter) Replacement Rate | Dialysis
, 228006 -- | Post Filter Replacement Rate | Dialysis
, 224144 -- | Blood Flow (ml/min) | Dialysis
, 224145 -- | Heparin Dose (per hour) | Dialysis
, 224153 -- | Replacement Rate | Dialysis
, 226457 -- | Ultrafiltrate Output | Dialysis
) THEN 1
ELSE 0 END
AS dialysis_active
, CASE
-- dialysis mode
-- we try to set dialysis mode to one of:
-- CVVH
-- CVVHD
-- CVVHDF
-- SCUF
-- Peritoneal
-- IHD
-- these are the modes in itemid 227290
WHEN ce.itemid = 227290 THEN value
-- itemids which imply a certain dialysis mode
-- peritoneal dialysis
WHEN ce.itemid IN
(
225810 -- | Dwell Time (Peritoneal Dialysis) | Dialysis
, 225806 -- | Volume In (PD) | Dialysis
, 225807 -- | Volume Out (PD) | Dialysis
, 225810 -- | Dwell Time (Peritoneal Dialysis) | Dialysis
, 227639 -- | Medication Added Amount #2 (Peritoneal Dialysis) | Dialysis
, 225959 -- | Medication Added Amount #1 (Peritoneal Dialysis) | Dialysis
, 225951 -- | Peritoneal Dialysis Fluid Appearance | Dialysis
, 225952 -- | Medication Added #1 (Peritoneal Dialysis) | Dialysis
, 225961 -- | Medication Added Units #1 (Peritoneal Dialysis) | Dialysis
, 225953 -- | Solution (Peritoneal Dialysis) | Dialysis
, 225963 -- | Peritoneal Dialysis Catheter Type | Dialysis
, 225965 -- | Peritoneal Dialysis Catheter Status | Dialysis
, 227638 -- | Medication Added #2 (Peritoneal Dialysis) | Dialysis
, 227640 -- | Medication Added Units #2 (Peritoneal Dialysis) | Dialysis
)
THEN 'Peritoneal'
WHEN ce.itemid = 226499
THEN 'IHD'
ELSE NULL END as dialysis_type
from `physionet-data.mimic_icu.chartevents` ce
WHERE ce.itemid in
(
-- === MetaVision itemids === --
-- Checkboxes
226118 -- | Dialysis Catheter placed in outside facility | Access Lines - Invasive | chartevents | Checkbox
, 227357 -- | Dialysis Catheter Dressing Occlusive | Access Lines - Invasive | chartevents | Checkbox
, 225725 -- | Dialysis Catheter Tip Cultured | Access Lines - Invasive | chartevents | Checkbox
-- Numeric values
, 226499 -- | Hemodialysis Output | Dialysis | chartevents | Numeric
, 224154 -- | Dialysate Rate | Dialysis | chartevents | Numeric
, 225810 -- | Dwell Time (Peritoneal Dialysis) | Dialysis | chartevents | Numeric
, 227639 -- | Medication Added Amount #2 (Peritoneal Dialysis) | Dialysis | chartevents | Numeric
, 225183 -- | Current Goal | Dialysis | chartevents | Numeric
, 227438 -- | Volume not removed | Dialysis | chartevents | Numeric
, 224191 -- | Hourly Patient Fluid Removal | Dialysis | chartevents | Numeric
, 225806 -- | Volume In (PD) | Dialysis | chartevents | Numeric
, 225807 -- | Volume Out (PD) | Dialysis | chartevents | Numeric
, 228004 -- | Citrate (ACD-A) | Dialysis | chartevents | Numeric
, 228005 -- | PBP (Prefilter) Replacement Rate | Dialysis | chartevents | Numeric
, 228006 -- | Post Filter Replacement Rate | Dialysis | chartevents | Numeric
, 224144 -- | Blood Flow (ml/min) | Dialysis | chartevents | Numeric
, 224145 -- | Heparin Dose (per hour) | Dialysis | chartevents | Numeric
, 224149 -- | Access Pressure | Dialysis | chartevents | Numeric
, 224150 -- | Filter Pressure | Dialysis | chartevents | Numeric
, 224151 -- | Effluent Pressure | Dialysis | chartevents | Numeric
, 224152 -- | Return Pressure | Dialysis | chartevents | Numeric
, 224153 -- | Replacement Rate | Dialysis | chartevents | Numeric
, 224404 -- | ART Lumen Volume | Dialysis | chartevents | Numeric
, 224406 -- | VEN Lumen Volume | Dialysis | chartevents | Numeric
, 226457 -- | Ultrafiltrate Output | Dialysis | chartevents | Numeric
, 225959 -- | Medication Added Amount #1 (Peritoneal Dialysis) | Dialysis | chartevents | Numeric
-- Text values
, 224135 -- | Dialysis Access Site | Dialysis | chartevents | Text
, 224139 -- | Dialysis Site Appearance | Dialysis | chartevents | Text
, 224146 -- | System Integrity | Dialysis | chartevents | Text
, 225323 -- | Dialysis Catheter Site Appear | Access Lines - Invasive | chartevents | Text
, 225740 -- | Dialysis Catheter Discontinued | Access Lines - Invasive | chartevents | Text
, 225776 -- | Dialysis Catheter Dressing Type | Access Lines - Invasive | chartevents | Text
, 225951 -- | Peritoneal Dialysis Fluid Appearance | Dialysis | chartevents | Text
, 225952 -- | Medication Added #1 (Peritoneal Dialysis) | Dialysis | chartevents | Text
, 225953 -- | Solution (Peritoneal Dialysis) | Dialysis | chartevents | Text
, 225954 -- | Dialysis Access Type | Dialysis | chartevents | Text
, 225956 -- | Reason for CRRT Filter Change | Dialysis | chartevents | Text
, 225958 -- | Heparin Concentration (units/mL) | Dialysis | chartevents | Text
, 225961 -- | Medication Added Units #1 (Peritoneal Dialysis) | Dialysis | chartevents | Text
, 225963 -- | Peritoneal Dialysis Catheter Type | Dialysis | chartevents | Text
, 225965 -- | Peritoneal Dialysis Catheter Status | Dialysis | chartevents | Text
, 225976 -- | Replacement Fluid | Dialysis | chartevents | Text
, 225977 -- | Dialysate Fluid | Dialysis | chartevents | Text
, 227124 -- | Dialysis Catheter Type | Access Lines - Invasive | chartevents | Text
, 227290 -- | CRRT mode | Dialysis | chartevents | Text
, 227638 -- | Medication Added #2 (Peritoneal Dialysis) | Dialysis | chartevents | Text
, 227640 -- | Medication Added Units #2 (Peritoneal Dialysis) | Dialysis | chartevents | Text
, 227753 -- | Dialysis Catheter Placement Confirmed by X-ray | Access Lines - Invasive | chartevents | Text
)
AND ce.value IS NOT NULL
)
-- TODO:
-- charttime + dialysis_present + dialysis_active
-- for inputevents_cv, outputevents
-- for procedures_mv, left join and set the dialysis_type
, oe as
(
select stay_id
, charttime
, 1 AS dialysis_present
, 0 AS dialysis_active
, NULL AS dialysis_type
from `physionet-data.mimic_icu.outputevents`
where itemid in
(
40386 -- hemodialysis
)
and value > 0 -- also ensures it's not null
)
, mv_ranges as
(
select stay_id
, starttime, endtime
, 1 AS dialysis_present
, 1 AS dialysis_active
, 'CRRT' as dialysis_type
from `physionet-data.mimic_icu.inputevents`
where itemid in
(
227536 -- KCl (CRRT) Medications inputevents_mv Solution
, 227525 -- Calcium Gluconate (CRRT) Medications inputevents_mv Solution
)
and amount > 0 -- also ensures it's not null
UNION DISTINCT
select stay_id
, starttime, endtime
, 1 AS dialysis_present
, CASE WHEN itemid NOT IN (224270, 225436) THEN 1 ELSE 0 END AS dialysis_active
, CASE
WHEN itemid = 225441 THEN 'IHD'
WHEN itemid = 225802 THEN 'CRRT' -- CVVH (Continuous venovenous hemofiltration)
WHEN itemid = 225803 THEN 'CVVHD' -- CVVHD (Continuous venovenous hemodialysis)
WHEN itemid = 225805 THEN 'Peritoneal'
WHEN itemid = 225809 THEN 'CVVHDF' -- CVVHDF (Continuous venovenous hemodiafiltration)
WHEN itemid = 225955 THEN 'SCUF' -- SCUF (Slow continuous ultra filtration)
ELSE NULL END as dialysis_type
from `physionet-data.mimic_icu.procedureevents`
where itemid in
(
225441 -- | Hemodialysis | 4-Procedures | procedureevents_mv | Process
, 225802 -- | Dialysis - CRRT | Dialysis | procedureevents_mv | Process
, 225803 -- | Dialysis - CVVHD | Dialysis | procedureevents_mv | Process
, 225805 -- | Peritoneal Dialysis | Dialysis | procedureevents_mv | Process
, 224270 -- | Dialysis Catheter | Access Lines - Invasive | procedureevents_mv | Process
, 225809 -- | Dialysis - CVVHDF | Dialysis | procedureevents_mv | Process
, 225955 -- | Dialysis - SCUF | Dialysis | procedureevents_mv | Process
, 225436 -- | CRRT Filter Change | Dialysis | procedureevents_mv | Process
)
AND value IS NOT NULL
)
-- union together the charttime tables; append times from mv_ranges to guarantee they exist
, stg0 AS
(
SELECT
stay_id, charttime, dialysis_present, dialysis_active, dialysis_type
FROM ce
WHERE dialysis_present = 1
UNION DISTINCT
-- SELECT
-- stay_id, charttime, dialysis_present, dialysis_active, dialysis_type
-- FROM oe
-- WHERE dialysis_present = 1
-- UNION DISTINCT
SELECT
stay_id, starttime AS charttime, dialysis_present, dialysis_active, dialysis_type
FROM mv_ranges
)
SELECT
stg0.stay_id
, charttime
, COALESCE(mv.dialysis_present, stg0.dialysis_present) AS dialysis_present
, COALESCE(mv.dialysis_active, stg0.dialysis_active) AS dialysis_active
, COALESCE(mv.dialysis_type, stg0.dialysis_type) AS dialysis_type
FROM stg0
LEFT JOIN mv_ranges mv
ON stg0.stay_id = mv.stay_id
AND stg0.charttime >= mv.starttime
AND stg0.charttime <= mv.endtime
- 列举不能全面， 遇到没有列举表格，其含义可以查询github上官方源代码中的concept文件夹内的代码和注释。
- 表格名称的简单注释，gcs（Glasgow Coma Scale），icp（Intra Cranial Pressure ），lods（Logistic Organ Dysfunction Score ），apsiii（Acute Physiology Score III ），oasis(Oxford Acute Severity of Illness Score )，sirs（Systemic inflammatory response syndrome ），sofa（Sequential Organ Failure Assessment ）