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<br>
<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`.
......@@ -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
### Medical Coding Standards Supported
| Code Type | Verification | Maps to |
|---------------|--------------|-----------------------------------|
| Readv2 | NHS TRUD | Readv3, SNOMED, ICD10, OPCS4, ATC |
......@@ -55,11 +59,12 @@ MELD-B refers to various diagnostic code formats included in target datasets.
* ICD-10 are codes used in hospital settings and are importnat for the HES linked datasets.
* ATC codes are interntionally accepted for the classification of medicinces and maintained by the WHO.
## ⚙️ Setup
## Setup
- Delete corrupted files that cannot be read with `bash import.sh`
### Code Translation Tables
1. Due to the licencing of NHS TRUD coding tables, the following resources <mark>must be downloaded separately</mark>:
- [nhs_readbrowser_25.0.0_20180401000001](https://isd.digital.nhs.uk/trud/users/guest/filters/2/categories/9/items/8/releases)
- [nhs_datamigration_29.0.0_20200401000001](https://isd.digital.nhs.uk/trud/users/guest/filters/0/categories/9/items/9/releases)
......@@ -76,6 +81,7 @@ MELD-B refers to various diagnostic code formats included in target datasets.
Mappings from Imported Code Lists to Outputted MELD-B Concept's Code list are defined in JSON format within `PHEN_assign_v3.json`.
#### Defining the Strucutre for Folders and Files:
```
"folder":"codes/Medication code source",
"description":"Medication Codes - downloaded 15/12/23",
......@@ -87,6 +93,7 @@ Mappings from Imported Code Lists to Outputted MELD-B Concept's Code list are de
```
#### Define Column Code Types
```
"columns":{
"read2_code":"READCODE",
......@@ -95,11 +102,13 @@ Mappings from Imported Code Lists to Outputted MELD-B Concept's Code list are de
```
#### Define Concepts to be mapped to
```
"meldb_phenotypes": ["ALL_MEDICATIONS"]
```
#### Actions: Additional preprocessing (if required):
- 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:
......@@ -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
### Execution (Bash Script)
`bash ./run.sh`
### Execution (Shell Command)
usage: `python main.py [-h] [-r2] [-r3] [-i] [-s] [-o] [-a] [-m] [-c] [--no-translate] [--no-verify] [--output] [--error-log] mapping_file`
positional arguments:
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> **_EXAMPLE:_** `python main.py PHEN_assign_v3.json -r2 --output output/MELD_concepts_readv2.csv --error-log output/MELD_errors.csv`
## ❤️ Contributing
## Contributing
### Commit to GitLab
```
git add .
git commit -m "my message ..."
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git push
```
## 🏦 Funding
## Funding
This project has received funding from the National Institute of Health Research under grant agreement NIHR203988.
<img src="img/nihr-logo-1200-375.jpg" height="100" />
## ⚖️ License
## License
![apache2](https://img.shields.io/github/license/saltstack/salt)
This work is licensed under a [Apache License, Version 2.0](https://www.apache.org/licenses/LICENSE-2.0).
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