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MIT-LCP / eicu-code

Code and website related to the eICU Collaborative Research Database

Home Page:https://eicu-crd.mit.edu

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Identify patients with Cirrhosis

yugangjia opened this issue · comments

commented

Hi, I am trying to identify patients with Cirrhosis before their icu admission.
I searched the "pasthistorypath" in the physionet-data.eicu_crd.pasthistory table and find out the following values are relevant with Cirrhosis

"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/jaundice",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/UGI bleeding",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/encephalopathy",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/ascites",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/varices",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/biopsy proven",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/clinical diagnosis",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/coma"

Any of those should be excluded?
Thanks

commented

Not what you're asking, but have a look at the diagnosis table too.

commented

Thanks. I do find more patients with diagnosis table. My updated query is like this:
select distinct * from (
select distinct patientunitstayid from physionet-data.eicu_crd.pasthistory
where pasthistorypath in (
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/jaundice",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/UGI bleeding",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/encephalopathy",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/ascites",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/varices",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/biopsy proven",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/clinical diagnosis",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/coma")
union all
select distinct patientunitstayid from physionet-data.eicu_crd.apachepredvar
where cirrhosis=1
union all
select distinct patientunitstayid from physionet-data.eicu_crd.diagnosis where icd9code in ("571.2, K70.3",
"571.5, K74.60", "571.6, K74.5", "571.5, K74.69")
)
order by patientunitstayid

commented

select distinct * from (
select distinct patientunitstayid from physionet-data.eicu_crd.pasthistory
where pasthistorypath in (
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/jaundice",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/UGI bleeding",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/encephalopathy",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/ascites",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/varices",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/biopsy proven",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/clinical diagnosis",
"notes/Progress Notes/Past History/Organ Systems/Gastrointestinal (R)/Cirrhosis/coma")
union all
select distinct patientunitstayid from physionet-data.eicu_crd.apachepredvar
where cirrhosis=1
union all
select distinct patientunitstayid from physionet-data.eicu_crd.diagnosis where diagnosisstring in ("gastrointestinal|hepatic disease|hepatic dysfunction|with cirrhosis",
"gastrointestinal|hepatic disease|hepatic dysfunction|with cirrhosis|biliary", "gastrointestinal|hepatic disease|hepatic dysfunction|with cirrhosis|alcoholic", "gastrointestinal|hepatic disease|hepatic dysfunction|with cirrhosis|cryptogenic")
)

commented

I am not at all familiar with eICU, but in your code you are referencing:
icd9code in ("571.2, K70.3", "571.5, K74.60", "571.6, K74.5", "571.5, K74.69")

This also includes icd10 codes, e.g. K74.5. Otherwise the codes seem sensible to me to include.
Would also include these: K74.3 to K74.6

this query sounds reasonable to me
("gastrointestinal|hepatic disease|hepatic dysfunction|with cirrhosis",
"gastrointestinal|hepatic disease|hepatic dysfunction|with cirrhosis|biliary", "gastrointestinal|hepatic disease|hepatic dysfunction|with cirrhosis|alcoholic", "gastrointestinal|hepatic disease|hepatic dysfunction|with cirrhosis|cryptogenic")
)