MIT-LCP / MIT-LCP/mimic-code

Question about how a blood gas sample is defined as arterial

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Description

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Description

Hello,
I get confused about how a blood gas sample is classified as an arterial blood gas sample in mimic iv database.
In mimic_derived, there's a script, bg.sql, that defines mimic_derived.bg table containing specimen field supposed to designate the nature of the blood gas sample, wether it is arterial or not.
This field is actually always null in mimic_derived.bg table.
According to bg.sql, specimen field corresponds to labevents records with itemid equal to 52028.
But strangely, the label associated to itemid in d_labitems is Hematocrit, and actually there's not a single labevents record with itemid equal to 52028.

In bg.sql,
specimen_pred is set to specimen if not null,
else set to 'ART.' if specimen_prob>0,75
else it is null.
As specimen is always null,
finally specimen_pred is only set to 'ART.' if specimen_prob>0,75, else null.

Finally mimic_derived.first_day_bg_art is defined out of mimic_derived.bg table where specimen_pred is equal to 'ART.'
As a consequence, all recordings defined as arterial blood gas in first_day_bg_art actually rely on a probability computation specimen_prob and never on specimen tagged as 'ART.' before being sent to the laboratory for analysis.

If someone has an explanation about that, I'd greatly appreciate it.
Thanks

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reading mimic_derived/bg.sql and tracing the specimen and specimen_pred fields into first_day_bg_art. Compare itemid 52028 across d_labitems and labevents, then consult the MIMIC documentation to determine whether the query or the source data explains the null values and arterial classification.

Written by the indexing model from the issue text.

Assessment

Tech stack
sql
Domain
databases
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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