From bf5af2c1fef0ca783aa8c1b9579f0380c60c8538 Mon Sep 17 00:00:00 2001
From: Jakub Dylag <jjd1c23@soton.ac.uk>
Date: Fri, 24 Jan 2025 11:33:42 +0000
Subject: [PATCH] Update README
---
README.md | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/README.md b/README.md
index c267558..aa00cae 100644
--- a/README.md
+++ b/README.md
@@ -24,12 +24,12 @@ This tool automates the verification, translation and organisation of medical co
## Methods
### Workflow Overview
-1. Approved MELD-B concepts are outlined in a CSV spreadsheet (e.g., `PHEN_summary_working.csv`).
+1. Approved concept sets are outlined in a CSV spreadsheet (e.g., `PHEN_summary_working.csv`).
2. Imported code lists in the `/src` directory are validated against NHS TRUD-registered codes.
-3. Mappings from imported code lists to outputted MELD-B concepts are defined in the `PHEN_assign_v3.json` file.
+3. Mappings from imported code lists to outputted concept sets are defined in the `PHEN_assign_v3.json` file.
- See "JSON Phenotype Mapping" section for more details
4. The process is executed via command-line. Refer to the "Usage" section for execution instructions.
-5. Outputted concept code lists are saved to the `/concepts` Git repository, with all changes tracked.
+5. Outputted concept set codes lists are saved to the `/concepts` Git repository, with all changes tracked.
6. The code lists can be exported to SAIL or any other Data Bank.
### Supported Medical Coding Standards
@@ -88,7 +88,7 @@ Processed tables will be saved as `.parquet` files in the `maps/processed/` dire
## Configuration
-The JSON configuration file specifies how input codes are grouped into **concept sets**, which are collections of related codes used for defining phenotypes or other data subsets. The configuration is divided into two main components: the `"concept_sets"` object and the `"codes"` object. The `"codes"` objects specifies the inputted codes; their filepaths, column names and code types, as well as any formatting actions that maybe be neccessary. The `"concept_sets"` object defines the concept groups each of the inputted codes will be assigned to. All files must be formatted as shown below.
+The JSON configuration file specifies how input codes are grouped into **concept sets**, which are collections of related codes used for defining phenotypes or other data subsets. The configuration is divided into two main components: the `"concept_sets"` object and the `"codes"` object. The `"codes"` objects specifies the inputted codes; their filepaths, column names and code types, as well as any formatting actions that maybe be neccessary. The `"concept_sets"` object defines a grouping that each of the inputted codes will be assigned to. All files must be formatted as shown below.
```json
{
"concept_sets": {
--
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