MIT-LCP / MIT-LCP/mimic-code

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
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

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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