Negative culture results in microbiologyevents
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Description
Hello,
I believe negative culture results should be “null” in one of the columns, like org_name in microbiologyevents.
https://mimic.mit.edu/docs/iv/modules/hosp/microbiologyevents/
In mySQL
select count( distinct(subject_id)) from mimicIV.microbiologyevents
where org_name is null;
This will return some results but the majority is 'BONE MARROW - CYTOGENETICS' under ‘spec_type_desc’.
This is not microbiology culture, and other types of culture results such as blood culture have a very small number.
My experience as a physician is that negative cultures should be more frequent than positive cultures.
However, this is not the case in the current table.
Please let me know if any other way to find negative culture results or if this is the issue of data extraction.
Thank you for your comments in advance.
Best,
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Research direction
Start with the microbiologyevents documentation and the supplied MySQL query, then inspect how org_name and spec_type_desc are populated for negative and non-culture results. Determine whether the reported distribution reflects extraction or expected data semantics; done means documenting the finding or identifying the specific data or documentation change required.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- mysql, sql
- Domain
- data, databases
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100