diff --git a/README.md b/README.md index 9e9dea30d2b13843362913ea7cfc161da6397324..bb03b3d0f9aed673ab7f09355eb269609fdea50e 100644 --- a/README.md +++ b/README.md @@ -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 \ No newline at end of file +## 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`).* \ No newline at end of file