issues with current data

[alistairewj]

eICU

• eICU BMI is all zeros
• eicu po2 max accidentally coded as min?
• eicu maximum diasbp is very high OR anzics diasbp is very low
• eicu missing pao2:fio2 max ratio

anzics

• anzics minimum diasbp usually lower
• missing d1 glucose for anzics
• hco3 anzics units are wrong
• hct for anzics is missing
• anzics potassium min/max units are wrong
• anzics sodium min/max units are wrong
• temperature source in eicu vs anzics?
• fio2 present in anzics?
• apache glucose missing from anzics
• anzics missing hematocrit_apache
• anzics sodium_apache units wrong

mimic

• inr mimic max/min switched?
• mimic ph_apache is it arterial? has high pHs

MIMIC in general: how to define apache variables if score=0? e.g. messes up temperature

worth comment

• hgb difference in mimic
• hct difference in mimic
• mbp high in anzics

[alistairewj]

Hospital death in eICU needs to be 0/1

[alistairewj]

all above fixed, with caveats below:

eicu maximum diasbp is very high OR anzics diasbp is very low

nothing wrong here.. seems to be a part of the data

apache glucose missing from anzics

seemed to be present, should double check

temperature source in eicu vs anzics?

haven't checked

MIMIC in general: how to define apache variables if score=0? e.g. messes up temperature

hard in general D:

[alistairewj]

eicu

• Eicu map female to F, male to M, other/unknown to null
• Readmission status in eicu is "eventually readmitted" but other data has it as "current admit is readmit"

anzics

• 23 anzics patients survive hospital but die in ICU.. inter hospital transfer?
• Anzics pregnancy - apply dictionary to map 0/1

orchestra

• Orchestra map gender I to null
• Orchestra ICU type numbers instead of words
• Bed size collapse into categories for orchestra

mimic

• Mimic map 0/1/2 for smoker to anzics text categories
• Mimic gcs verbal of 0 needs to be mapped to 5 or something
• Mimic ethnicity combination (use sepsis 3 code)

all

• Hospital admit source and discharge location needs to be merged for all data sources (same for ICU admit and discharge)
• ICU admit type in eicu and mimic are different (ICU type versus elect/emergency, prob incorrect for eicu).. missing anzics and orchestra?
• ICU stay type has no definition and is inconsistent
• ICU type is not well collapsed
• add column for raw bed size number

hospital admit source

eicu
Emergency Department 49735
Operating Room 12102
Floor 10443
Direct Admit 8418
Recovery Room 4162
Other Hospital 2424
Acute Care/Floor 2105
Step-Down Unit (SDU) 1481
PACU 1004
Chest Pain Center 274
Other ICU 265
ICU to SDU 56
ICU 40
Observation 12
Other 7
Name: hospital_admit_source, dtype: int64

anzics
Home 204177
Other Acute Hospital 43118
Other hospital ICU 2134
Chronic Care Hospital (including nursing homes) 1960
Name: hospital_admit_source, dtype: int64

mimic
Emergency Department 16526
Direct Admit 14361
Other Hospital 7246
Other 4
Acute Care/Floor 2
Name: hospital_admit_source, dtype: int64

icu_admit_source

eicu
Emergency Department 64152
Operating Room 17734
Floor 13736
Direct Admit 9925
Recovery Room 5508
Acute Care/Floor 3467
Other Hospital 3389
Step-Down Unit (SDU) 2537
PACU 1315
Other ICU 581
Chest Pain Center 305
ICU 82
ICU to SDU 28
Observation 12
Other 8
Name: icu_admit_source, dtype: int64

anzics
OT/Recovery 141593
Accident & Emergency 71713
Ward 35750
Other Hospital 14292
Other Hospital ICU 2196
Other ICU, same Hospital 440
Name: icu_admit_source, dtype: int64

mimic
Series([], Name: icu_admit_source, dtype: int64)

orchestra
Accident & Emergency 31348
OT/Recovery 17319
Ward 4474
Other Hospital 2401
Intervention room 2129
Other ICU, same Hospital 1105
Intermediate care unit 469
Other unkown 231
Home-care 217
Name: icu_admit_source, dtype: int64

nicst
Series([], Name: icu_admit_source, dtype: int64)

satiq
7.0 259
10.0 104
2.0 104
1.0 65
0.0 26
11.0 11
12.0 3
9.0 2
5.0 2
14.0 1
6.0 1
4.0 1
Name: icu_admit_source, dtype: int64

icu_disch_location

eicu
Floor 60655
Step-Down Unit (SDU) 16615
Acute Care/Floor 13549
Home 11358
Death 6874
Telemetry 6096
Other Hospital 2490
Other External 1779
Skilled Nursing Facility 1206
Other 920
Other ICU 520
Rehabilitation 451
Other Internal 183
Nursing Home 117
ICU 51
Operating Room 7
Other ICU (CABG) 5
Name: icu_disch_location, dtype: int64

anzics
Survived ICU 242400
Died in ICU 13945
Transferred to another hospital 5205
Transferred to another ICU 3997
Name: icu_disch_location, dtype: int64

mimic
Series([], Name: icu_disch_location, dtype: int64)

orchestra
Survived ICU 40952
Transferred to another ICU 12334
Died in ICU 5665
Transferred to another hospital 469
Name: icu_disch_location, dtype: int64

nicst
Series([], Name: icu_disch_location, dtype: int64)

satiq
1.0 490
5.0 54
2.0 30
4.0 5
Name: icu_disch_location, dtype: int64

arf_apache

eicu
0 118544
1 4349
Name: arf_apache, dtype: int64

anzics
0 253476
1 12660
Name: arf_apache, dtype: int64

mimic
Series([], Name: arf_apache, dtype: int64)

orchestra
Series([], Name: arf_apache, dtype: int64)

nicst
Series([], Name: arf_apache, dtype: int64)

satiq
N 505
S 74
Name: arf_apache, dtype: int64

[alistairewj]

• add output of notebooks to GitHub with detail on exclusions (#/percent)
• Why are there non unique patient ID in all databases?
• Why are there non unique encounter ID for anzics?
• Hospital death prob appears to be -1 for readmits, but readmission status is 0. What does readmission status = 0 mean?
• Verify readmissions are excluded for all databases

[alistairewj]

current numbers on duplicate encounters

• 273 in ANZICS
• MIMIC has repeated hospital admissions due to https://github.com/MIT-LCP/gosiss/blob/dc57a49d37ce7ab087791e8bbde654460741c343/mimic-iii/sql/cohort.sql#L68

need to decide with GOSSIS what the inclusion criteria are

• is ventilated_apache == mechvent_24 (particularly for orchestra)? if so we can map orchestra's mechvent_24 to ventilated_apache
• is pao2_apache == min(pao2) for first day? if so we can compare those plots

run notebooks and commit output to github so exclusion criteria are observed

[alistairewj]

• add vitalAperiodic in the has_vit check
• Columns (1,6,8,10,11,17,19,20,24,25,193) have mixed types