docs(mimic-iv): where to find Vitamin C / ascorbic acid (#1962)

.github/workflows/lint_sqlfluff.yml

@@ -1,11 +1,17 @@
 name: SQLFluff
 
+# Lints changed mimic-iv/concepts/*.sql on pull requests and posts GitHub
+# annotations. Fork PRs skip Annotate — GITHUB_TOKEN cannot create check runs
+# from forks (Resource not accessible by integration / 403).
 on:
   - pull_request
 
 jobs:
   lint-mimic-iv:
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      checks: write
     steps:
       - name: checkout
         uses: actions/checkout@v7
@@ -35,8 +41,14 @@ jobs:
         shell: bash
         run: sqlfluff lint --format github-annotation --annotation-level failure --nofail ${{ steps.get_files_to_lint.outputs.lintees }} > annotations.json
       - name: Annotate
+        # Same-repo PRs only: fork tokens get 403 creating check runs, and
+        # ignore-unauthorized-error does not treat that as unauthorized.
+        if: >
+          steps.get_files_to_lint.outputs.lintees != '' &&
+          github.event.pull_request.head.repo.full_name == github.repository
         uses: yuzutech/annotations-action@v0.6.0
         with:
           repo-token: "${{ secrets.GITHUB_TOKEN }}"
           title: "SQLFluff Lint"
-          input: "./annotations.json"
+          input: "./annotations.json"
+          ignore-unauthorized-error: true

README.md

@@ -114,3 +114,7 @@ By committing your code to the [MIMIC Code Repository](https://github.com/mit-lc
 ### Coding style
 
 Please refer to the [style guide](https://github.com/MIT-LCP/mimic-code/blob/main/styleguide.md) for guidelines on formatting your code for the repository.
+
+### MIMIC-IV notes
+
+- [Vitamin C / ascorbic acid](mimic-iv/docs/VITAMIN_C.md)

mimic-iv/README.md

@@ -105,4 +105,8 @@ mimic_utils convert_folder mimic-iv/concepts mimic-iv/concepts_duckdb --destinat
 
 # To PostgreSQL:
 mimic_utils convert_folder mimic-iv/concepts mimic-iv/concepts_postgres --destination_dialect postgres
-```
+```
+
+## Vitamin C / ascorbic acid
+
+No dedicated table — see [docs/VITAMIN_C.md](docs/VITAMIN_C.md).

mimic-iv/concepts/documentation/README.md

@@ -0,0 +1,4 @@
+# Documentation helper queries
+
+Ad-hoc SQL that illustrates known data quirks. Not part of the official derived
+concept build.

mimic-iv/concepts/documentation/vitamin_c_emar.sql

@@ -0,0 +1,10 @@
+-- Candidate Vitamin C administrations in emar (#1962).
+
+SELECT medication, COUNT(*) AS n
+FROM hosp.emar
+WHERE LOWER(medication) LIKE '%ascorbic%'
+   OR LOWER(medication) LIKE '%vitamin c%'
+   OR LOWER(medication) LIKE '%vit c%'
+GROUP BY medication
+ORDER BY n DESC
+LIMIT 50;

mimic-iv/concepts/documentation/vitamin_c_prescriptions.sql

@@ -0,0 +1,11 @@
+-- Candidate Vitamin C / ascorbic acid orders in hosp.prescriptions (#1962).
+-- Review hits manually — multivitamins and abbreviations create false positives.
+
+SELECT drug, COUNT(*) AS n
+FROM hosp.prescriptions
+WHERE LOWER(drug) LIKE '%ascorbic%'
+   OR LOWER(drug) LIKE '%vitamin c%'
+   OR LOWER(drug) LIKE '%vit c%'
+GROUP BY drug
+ORDER BY n DESC
+LIMIT 50;

mimic-iv/docs/VITAMIN_C.md

@@ -0,0 +1,38 @@
+# Finding Vitamin C (ascorbic acid) in MIMIC
+
+There is **no dedicated Vitamin C table** in MIMIC-III or MIMIC-IV.
+
+See [issue #1962](https://github.com/MIT-LCP/mimic-code/issues/1962).
+
+## Where exposure usually lives
+
+| Source | Module | What to search |
+|--------|--------|----------------|
+| `prescriptions` | hosp | drug / drug_name_generic containing `ascorbic`, `vitamin c`, `vit c` |
+| `emar` / `emar_detail` | hosp | administered meds with the same name patterns |
+| `inputevents` (III: `_cv` / `_mv`) | icu | infusions if charted as inputs (rare for vit C) |
+| `labevents` + `d_labitems` | hosp | serum ascorbic acid **levels** (not doses), if ordered |
+
+Retrospective papers that report “Vitamin C exposure” almost always derive a
+cohort from **medication orders / eMAR**, not from a first-class vit-C module.
+
+## Practical guidance
+
+1. Start with `prescriptions` / `emar` string filters; review false positives
+   (multivitamins, “C” abbreviations).
+2. Decide whether you need **orders**, **administrations**, or **serum labs** —
+   they answer different questions.
+3. Do not expect complete capture: OTCs and outside-hospital vitamins are often
+   absent.
+
+## What this repository will not add
+
+A curated “official” Vitamin C concept would need ongoing pharmacy vocabulary
+maintenance. Contribute a versioned derived concept with explicit inclusion
+strings if you build one for a paper.
+
+## Related
+
+- LOINC / terminology: `mimic-iv/docs/LOINC_MAPPING.md` (when present)
+- Lab unit quirks: `mimic-iv/buildmimic/TABLE_NOTES.md` (when present)
+