From 7621f1d3761c9eb5e04623f914e823818ca8f3b9 Mon Sep 17 00:00:00 2001
From: Matthew McDermott <mattmcdermott8@gmail.com>
Date: Tue, 27 Aug 2024 10:41:13 -0400
Subject: [PATCH] Added starter code for datasets information.

---
 src/MEDS-DEV/datasets/MIMIC-IV/README.md        | 10 ++++++++++
 .../datasets/MIMIC-IV/predicates/README.md      |  5 +++++
 .../datasets/MIMIC-IV/predicates/defaults.yaml  | 17 +++++++++++++++++
 src/MEDS-DEV/datasets/README.md                 | 11 +++++++++++
 4 files changed, 43 insertions(+)
 create mode 100644 src/MEDS-DEV/datasets/MIMIC-IV/README.md
 create mode 100644 src/MEDS-DEV/datasets/MIMIC-IV/predicates/README.md
 create mode 100644 src/MEDS-DEV/datasets/MIMIC-IV/predicates/defaults.yaml
 create mode 100644 src/MEDS-DEV/datasets/README.md

diff --git a/src/MEDS-DEV/datasets/MIMIC-IV/README.md b/src/MEDS-DEV/datasets/MIMIC-IV/README.md
new file mode 100644
index 0000000..d5ca188
--- /dev/null
+++ b/src/MEDS-DEV/datasets/MIMIC-IV/README.md
@@ -0,0 +1,10 @@
+# MIMIC-IV
+
+TODO: Summarize MIMIC-IV
+
+TODO: Add citations properly somehow.
+
+## URLs
+
+1. https://physionet.org/content/mimiciv/
+2. https://www.nature.com/articles/s41597-022-01899-x
diff --git a/src/MEDS-DEV/datasets/MIMIC-IV/predicates/README.md b/src/MEDS-DEV/datasets/MIMIC-IV/predicates/README.md
new file mode 100644
index 0000000..cdbd573
--- /dev/null
+++ b/src/MEDS-DEV/datasets/MIMIC-IV/predicates/README.md
@@ -0,0 +1,5 @@
+# Custom MIMIC-IV Predicates
+
+MIMIC-IV uses several coding schemes that are captured in these predicates.
+
+TODO: info
diff --git a/src/MEDS-DEV/datasets/MIMIC-IV/predicates/defaults.yaml b/src/MEDS-DEV/datasets/MIMIC-IV/predicates/defaults.yaml
new file mode 100644
index 0000000..7ef0769
--- /dev/null
+++ b/src/MEDS-DEV/datasets/MIMIC-IV/predicates/defaults.yaml
@@ -0,0 +1,17 @@
+hospital_admission:
+  code: { regex: "^HOSPITAL_ADMISSION//.*" }
+hospital_discharge:
+  code: { regex: "^HOSPITAL_DISCHARGE//.*" }
+
+ED_registration:
+  code: { regex: "^ED_REGISTRATION//.*" }
+ED_discharge:
+  code: { regex: "^ED_OUT//.*" }
+
+icu_admission:
+  code: { regex: "^ICU_ADMISSION//.*" }
+icu_discharge:
+  code: { regex: "^ICU_DISCHARGE//.*" }
+
+death:
+  code: MEDS_DEATH
diff --git a/src/MEDS-DEV/datasets/README.md b/src/MEDS-DEV/datasets/README.md
new file mode 100644
index 0000000..a793c69
--- /dev/null
+++ b/src/MEDS-DEV/datasets/README.md
@@ -0,0 +1,11 @@
+# Datasets
+
+This folder contains details for datasets currently included in the MEDS-DEV effort.
+
+TODO: More details.
+
+## Notes
+
+If you have a version of a task configuration file that is more specialized to a dataset than can be achieved
+with overwriting the predicates alone, then (1) make a GitHub issue explaining why the existing file is not
+used, and (2) add a file here `../tasks/$DATASET_NAME/$TASK_NAME.yaml` with that configuration.