docs(mimic-iv): Charlson ICD-10-CM notes for C4A / C7A / C7B (#2017)

.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

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
-```
+```
+
+## Charlson ICD-10-CM notes
+
+See [concepts/comorbidity/README.md](concepts/comorbidity/README.md) for Quan (2005) vs ICD-10-CM (`C4A` / `C7A` / `C7B`).

mimic-iv/concepts/comorbidity/README.md

@@ -0,0 +1,24 @@
+# Charlson comorbidity concepts (MIMIC-IV)
+
+SQL in this folder implements the Quan et al. (2005) ICD-9-CM / ICD-10 coding
+algorithms for the Charlson Comorbidity Index against MIMIC-IV `diagnoses_icd`.
+
+## ICD-10 vs ICD-10-CM
+
+Quan et al. published ranges against **WHO ICD-10**. MIMIC-IV stores
+**ICD-10-CM** codes. Most three-character prefixes align; a few CM-only
+categories do not appear in the 2005 tables:
+
+| Code | Meaning | Charlson mapping in this repo |
+|------|---------|--------------------------------|
+| `C4A` | Merkel cell carcinoma | Excluded from `malignant_cancer` (skin malignancy carve-out); see PR discussion on #2017 / #2142 |
+| `C7A` | Malignant neuroendocrine tumors | **Not mapped** — outside Quan’s WHO ICD-10 ranges |
+| `C7B` | Secondary neuroendocrine tumors | **Not mapped** — outside Quan’s WHO ICD-10 ranges |
+
+Leaving `C7A` / `C7B` unmapped is intentional until a published CM-specific
+extension is adopted. Do not widen the `C45`–`C58`-style prefix ranges without
+updating this note and citing a coding reference.
+
+## Related PRs
+
+- [#2142](https://github.com/MIT-LCP/mimic-code/pull/2142) — exclude `C4A` from `malignant_cancer`

mimic-iv/concepts/comorbidity/charlson.sql

@@ -15,6 +15,8 @@
 -- (3) Quan H, Sundararajan V, Halfon P, et al. Coding algorithms for
 -- defining Comorbidities in ICD-9-CM and ICD-10 administrative data.
 -- Med Care. 2005 Nov; 43(11): 1130-9.
+--
+-- ICD-10-CM notes (C4A / C7A / C7B): see comorbidity/README.md
 -- ------------------------------------------------------------------
 
 WITH diag AS (

mimic-iv/concepts_postgres/comorbidity/charlson.sql

@@ -1,6 +1,6 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
 DROP TABLE IF EXISTS mimiciv_derived.charlson; CREATE TABLE mimiciv_derived.charlson AS
-/* ------------------------------------------------------------------ */ /* This query extracts Charlson Comorbidity Index (CCI) based on the */ /* recorded ICD-9 and ICD-10 codes. */ /* Reference for CCI: */ /* (1) Charlson ME, Pompei P, Ales KL, MacKenzie CR. (1987) A new method */ /* of classifying prognostic comorbidity in longitudinal studies: */ /* development and validation.J Chronic Dis; 40(5):373-83. */ /* (2) Charlson M, Szatrowski TP, Peterson J, Gold J. (1994) Validation */ /* of a combined comorbidity index. J Clin Epidemiol; 47(11):1245-51. */ /* */ /* Reference for ICD-9-CM and ICD-10 Coding Algorithms for Charlson */ /* Comorbidities: */ /* (3) Quan H, Sundararajan V, Halfon P, et al. Coding algorithms for */ /* defining Comorbidities in ICD-9-CM and ICD-10 administrative data. */ /* Med Care. 2005 Nov; 43(11): 1130-9. */ /* ------------------------------------------------------------------ */
+/* ------------------------------------------------------------------ */ /* This query extracts Charlson Comorbidity Index (CCI) based on the */ /* recorded ICD-9 and ICD-10 codes. */ /* Reference for CCI: */ /* (1) Charlson ME, Pompei P, Ales KL, MacKenzie CR. (1987) A new method */ /* of classifying prognostic comorbidity in longitudinal studies: */ /* development and validation.J Chronic Dis; 40(5):373-83. */ /* (2) Charlson M, Szatrowski TP, Peterson J, Gold J. (1994) Validation */ /* of a combined comorbidity index. J Clin Epidemiol; 47(11):1245-51. */ /* */ /* Reference for ICD-9-CM and ICD-10 Coding Algorithms for Charlson */ /* Comorbidities: */ /* (3) Quan H, Sundararajan V, Halfon P, et al. Coding algorithms for */ /* defining Comorbidities in ICD-9-CM and ICD-10 administrative data. */ /* Med Care. 2005 Nov; 43(11): 1130-9. */ /* ICD-10-CM notes (C4A / C7A / C7B): see comorbidity/README.md */ /* ------------------------------------------------------------------ */
 WITH diag AS (
   SELECT
     hadm_id,