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Commit 319b36cc authored by mjbonifa's avatar mjbonifa
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updated readme

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......@@ -38,9 +38,11 @@ Once installed, you'll be ready to use the `acmc` tool along with the associated
### Install Clinically Assured NHS TRUD Code Mappings
1. **Register at TRUD**: Access clinically assured terminology mappings at [NHS TRUD](https://isd.digital.nhs.uk/trud/user/guest/group/0/account/form).
1. **Register at TRUD**
2. **Subscribe and Accept Licenses**: Subscribe to the following data files:
Registry your account with TRUD at [NHS TRUD](https://isd.digital.nhs.uk/trud/user/guest/group/0/account/form).
3. **Subscribe and Accept Licenses**: Subscribe to the following data files:
- [NHS Read Browser](https://isd.digital.nhs.uk/trud/users/guest/filters/2/categories/9/items/8/releases)
- [NHS Data Migration](https://isd.digital.nhs.uk/trud/users/guest/filters/0/categories/8/items/9/releases)
......@@ -49,9 +51,11 @@ Once installed, you'll be ready to use the `acmc` tool along with the associated
After subscribing, you'll receive an API key once your request is approved (usually within 24 hours).
4. **Get TRUD API KEY**: Copy your API key from [NHS TRUD Account Management](https://isd.digital.nhs.uk/trud/users/authenticated/filters/0/account/manage) and store it securely.
4. **Get TRUD API KEY**
Copy your API key from [NHS TRUD Account Management](https://isd.digital.nhs.uk/trud/users/authenticated/filters/0/account/manage) and store it securely.
5. **Add TRUD API KEY to as an environment variable**
7. **Add TRUD API KEY to as an environment variable**
To set the environment variable temporarily (for the current session), run:
......@@ -74,15 +78,12 @@ Once installed, you'll be ready to use the `acmc` tool along with the associated
```bash
acmc trud install
```
Processed resources will be saved in the `build/maps/processed/` directory.
*Note: NHS TRUD provides one-way mappings. To reverse mappings, duplicate the `.parquet` file and reverse the filename (e.g., `read2_code_to_snomed_code.parquet` to `snomed_code_to_read2_code.parquet`).*
### Install OMOP Vocabularies
1. Register with [Athena](https://athena.ohdsi.org/auth/login)
1. **Register with [OHDSI Athena](https://athena.ohdsi.org/auth/login)**
2. Download vocabularies [Athena OHDSI](https://athena.ohdsi.org/vocabulary/list).
2. **Request download of vocabularies from [OHDSI Athena](https://athena.ohdsi.org/vocabulary/list)**
* Required vocabularies include:
* 1) SNOMED
......@@ -126,11 +127,11 @@ Please execute the following process:
Load the unpacked files into the tables.
```
4. Un-zip the OMOP file
4. **Un-zip the downloaded OMOP files to a directory**
Create a directory where you want the OMOP CSV tables to be stored, the default from the current working directory is `./build/omop`. Unzip the OMOP files into that directory
5. Install OMOP vocabularies
5. **Install OMOP vocabularies**
Run the following acmc command to create a local OMOP database from the download:
......@@ -470,4 +471,8 @@ The tool supports verification and mapping across diagnostic coding formats belo
- [**ICD-10:**](https://icd.who.int/browse10/2019/en) International Classification of Diseases (ICD) is a medical classification list from the World Health Organization (WHO) and widely used in hospital settings, e.g. Hospital Episode Statistics (HES).
- [**ATC Codes:**](https://www.who.int/tools/atc-ddd-toolkit/atc-classification) Anatomical Therapeutic Chemical (ATC) Classification is a drug classification list from the World Health Organization (WHO)
## Notes
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## Notes
Processed resources will be saved in the `build/maps/processed/` directory.
*Note: NHS TRUD provides one-way mappings. To reverse mappings, duplicate the `.parquet` file and reverse the filename (e.g., `read2_code_to_snomed_code.parquet` to `snomed_code_to_read2_code.parquet`).*
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