Unable to find beta-d-glucan laboratory results in MIMIC-IV despite test being mentioned in notes/radiology reports
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Description
Prerequisites
- Put an X between the brackets on this line if you have done all of the following:
- Checked the online documentation: https://mimic.mit.edu/
- Checked that your issue isn't already addressed: https://github.com/MIT-LCP/mimic-code/issues?utf8=%E2%9C%93&q=
Description
I am unable to find laboratory results for beta-d-glucan despite the test being mentioned in notes/radiology reports. I've tried searching across all dim tables using various case-insensitive representations (e.g. %beta-d-glucan%, %bdg%, %glucan%, etc) with no luck. I've also tried searching using the brand name Fungitell. Searching hosp.d_labitems using where lower(label) like '%beta%' does return the following:
+--------+--------+----------------------+---------------------+------------------+------------------------------------+----------+------------+
| source | itemid | label | fluid | linksto | category | unitname | param_type |
+--------+--------+----------------------+---------------------+------------------+------------------------------------+----------+------------+
| hosp | 50881 | Beta-2 Microglobulin | Blood | | Chemistry | | |
| hosp | 51566 | Beta | Blood | | Chemistry | | |
| hosp | 51567 | Beta Hydroxybutyrate | Blood | | Chemistry | | |
| hosp | 51781 | Beta | Cerebrospinal Fluid | | Chemistry | | |
| hosp | 51810 | Beta | Joint Fluid | | Chemistry | | |
| hosp | 51840 | Beta | Other Body Fluid | | Chemistry | | |
| hosp | 51913 | Beta | Pleural | | Chemistry | | |
| hosp | 51931 | Beta | Stool | | Chemistry | | |
| hosp | 51965 | Beta | Urine | | Chemistry | | |
| hosp | 52184 | TCR Alpha-Beta | Blood | | Hematology | | |
| hosp | 52331 | TCR Alpha-Beta | Bone Marrow | | Hematology | | |
| hosp | 52367 | TCR Alpha-Beta | Other Body Fluid | | Hematology | | |
| hosp | 53119 | Beta | Ascites | | Chemistry | | |
+--------+--------+----------------------+---------------------+------------------+------------------------------------+----------+------------+
which has several results for Beta however I'm unsure if this is referring to Beta Hydroxybutyrate or some other laboratory test.
Any suggestions/explanations would be greatly appreciated!
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First steps
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- Open a pull request that references the issue number.
Research direction
Start with the MIMIC-IV documentation and the reported hosp.d_labitems query, then compare the relevant dim tables and note representations mentioned in the issue. Done means determining whether beta-d-glucan results are present in the released data and explaining where they can be found or why the notes mention a test without corresponding laboratory results.
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