<sup>*</sup>Correspondence to: Jakub J. Dylag, Digital Health and Biomedical Engineering, School of Electronics and Computer Science, Faculty of Engineering and Physical Sciences, University of Southampton, J.J.Dylag@soton.ac.uk
### 🖋 How to cite this work
### How to cite this work
> Dylag JJ, Chiovoloni R, Akbari A, Fraser SD, Boniface MJ. A Tool for Automating the Curation of Medical Concepts derived from Coding Lists. GitLab [Internet]. May 2024. Available from: https://git.soton.ac.uk/meldb/concepts-processing
## 🙌 Introduction
## Introduction
This project generate the medical coding lists that defines cohort phenotypes used for inclusion criteria in MELD-B. The goal is to automatically prepare a code list from an approved clinical specification of inclusion criteria.
The output code list is then used by data providers to select MELD-B cohorts.
## 📃 Method
## Method
### Process
1. Approved MELB-B concepts are defined in a CSV spreadsheet (currently PHEN_summary_working.csv).
2. Imported Code Lists in `/src` are verified against all NHS TRUD registered codes
3. Mappings from Imported Code Lists to Outputted MELD-B Concept's Code list are defined in JSON format within `PHEN_assign_v3.json`.
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@@ -34,6 +37,7 @@ The output code list is then used by data providers to select MELD-B cohorts.
6. Output Concept Code Lists can be exported into SAIL or any other Data Bank
- In certain cases where you wish to sub-divde a code list table or a column features multiple code types additional processing is required. Add a `action` object inside of the `file` object.
- Table with a sub-categorical column:
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@@ -127,15 +136,16 @@ Mappings from Imported Code Lists to Outputted MELD-B Concept's Code list are de
*<b>Large Code lists</b> with numerous phenotypes (e.g. Ho et al), require lots of JSON to be generated. See the "Ho generate JSON" section in process_codes_WP.ipynb for example code to generate
## Usage
## ⚡ Usage
Script preprocess code lists and to map to given concept/phenotype