From 4005f707e68c0ca13078fc3b21f313d69a2b8707 Mon Sep 17 00:00:00 2001
From: Michael Boniface <m.j.boniface@soton.ac.uk>
Date: Thu, 20 Feb 2025 17:40:20 +0000
Subject: [PATCH] updated readme

---
 README.md | 134 ++++++++++++++++++++++++++----------------------------
 1 file changed, 65 insertions(+), 69 deletions(-)

diff --git a/README.md b/README.md
index 3b5689f..9e9dea3 100644
--- a/README.md
+++ b/README.md
@@ -20,70 +20,6 @@
 
 This tool automates the verification, translation and organisation of medical coding lists defining  phenotypes for inclusion criteria in cohort analysis. By processing externally sourced clinical inclusion criteria into actionable code lists, this tool ensures consistent and efficient curation of cohort definitions. These code lists can be subsequently used by data providers to construct study cohorts.
 
-## Overview
-
-### Workflow
-
-The high level steps to use the tools are outlined below:
-
-**1. Define concept sets:** A domain expert defines a list of [concept sets](#defining-concept-sets) for each observable characteristic of the phenotype using CSV file format (e.g., `PHEN_concept_sets.csv`).
-
-**2. Define concept code lists for concept sets:** A domain expert defines [code lists](#defining-concept-codes) for each concept set within the phenotype using supported coding list formats and stores them in the `/src` directory.
-
-**3. Define mapping from code lists to concept sets:** A domain expert defines a [phenotype mapping](#mapping-codes-to-concept-sets) that maps code lists to concept sets.
-
-**4. Generate versioned phenotype coding lists and translations:** A domain expert or data engineer processes the phenotype mappings [using the command line tool](#usage) to validate against NHS TRUD-registered codes and mapping and to generate versioned concept set code lists with translations between coding standards. 
-
-### Supported Medical Coding Standards
-
-The tool supports verification and mapping across diagnostic coding formats below:
-
-| Medical Code  | Verification | Translation to                    |
-|---------------|--------------|-----------------------------------|
-| Readv2        | NHS TRUD     | Readv3, SNOMED, ICD10, OPCS4, ATC |
-| Readv3 (CTV3) | NHS TRUD     | Readv3, SNOMED, ICD10, OPCS4      |
-| ICD10         | NHS TRUD     | None                              |
-| SNOMED        | NHS TRUD     | None                              |
-| OPCS4         | NHS TRUD     | None                              |
-| ATC           | None         | None                              |
-
-- [**Read V2:**](https://digital.nhs.uk/services/terminology-and-classifications/read-codes) NHS clinical terminology standard used in primary care and replaced by SNOMED-CT in 2018; Still supported by some data providers as widely used in primary care, e.g. [SAIL Databank](https://saildatabank.com/)
-- [**SNOMED-CT:**](https://icd.who.int/browse10/2019/en) international standard for clinical terminology for Electronic Healthcare Records adopted by the NHS in 2018; Mappings to Read codes are partially provided by [Clinical Research Practice Database (CPRD)](https://www.cprd.com/) and [NHS Technology Reference Update Distribution (TRUD)](https://isd.digital.nhs.uk/trud).
-- [**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
-
-OMOP
-
-Content of your package
-
-Vocabularies release version: v20240830 
-
-Linux/macOS:
-
-```
-export ACMC_TRUD_API_KEY="your_api_key"
-export ACMC_GITLAB_PAT="your_personal_access_token"
-export ACMC_GITHUB_PAT="your_personal_access_token"
-```
-
-Windows (Command prompt):
-
-```
-set ACMC_TRUD_API_KEY=your_api_key
-set ACMC_GITLAB_PAT=your_personal_access_token
-set ACMC_GITHUB_PAT=your_personal_access_token
-```
-
-Windows (Powershell):
-
-```
-$env:ACMC_TRUD_API_KEY="your_api_key"
-$env:ACMC_GITLAB_PAT="your_personal_access_token"
-$env:ACMC_GITHUB_PAT="your_personal_access_token"
-```
-
 ## Requirements
 
 - Python 3.9 or higher
@@ -161,13 +97,38 @@ Once installed, you'll be ready to use the `acmc` tool along with the associated
 	  * 154) NHS Ethnic Category
 	  * 155) NHS Place of Service
 
-	You will be notified by email with a vocabularies version number and link to download a zip file of OMOP database tables in CSV format
+	You will be notified by email with a vocabularies version number and link to download a zip file of OMOP database tables in CSV format. The subject will be `OHDSI Standardized Vocabularies. Your download link` from `pallas@ohdsi.org`
 
-3. Un-zip the OMOP file
+```
+Content of your package
+
+Vocabularies release version: v20240830
+acmc-omop Vocabularies:
+SNOMED	-	Systematic Nomenclature of Medicine - Clinical Terms (IHTSDO)
+ICD9CM	-	International Classification of Diseases, Ninth Revision, Clinical Modification, Volume 1 and 2 (NCHS)
+Read	-	NHS UK Read Codes Version 2 (HSCIC)
+ATC	-	WHO Anatomic Therapeutic Chemical Classification
+OPCS4	-	OPCS Classification of Interventions and Procedures version 4 (NHS)
+HES Specialty	-	Hospital Episode Statistics Specialty (NHS)
+ICD10CM	-	International Classification of Diseases, Tenth Revision, Clinical Modification (NCHS)
+dm+d	-	Dictionary of Medicines and Devices (NHS)
+UK Biobank	-	UK Biobank (UK Biobank)
+NHS Ethnic Category	-	NHS Ethnic Category
+NHS Place of Service	-	NHS Admission Source and Discharge Destination
+Installation of the OHDSI Standardized Vocabularies
+
+Please execute the following process:
+
+    Click on this link to download the zip file. Typical file sizes, depending on the number of vocabularies selected, are between 30 and 1500 MB.
+    Unpack.
+    Reconstitute CPT-4. See below for details.
+    If needed, create the tables.
+    Load the unpacked files into the tables.
+```
 
-	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
+4. Un-zip the OMOP file
+
+	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
 
@@ -475,3 +436,38 @@ This work is licensed under a [Apache License, Version 2.0](https://www.apache.o
 
 ![apache2](https://img.shields.io/github/license/saltstack/salt)
 
+
+
+## Overview
+
+### Workflow
+
+The high level steps to use the tools are outlined below:
+
+**1. Define concept sets:** A domain expert defines a list of [concept sets](#defining-concept-sets) for each observable characteristic of the phenotype using CSV file format (e.g., `PHEN_concept_sets.csv`).
+
+**2. Define concept code lists for concept sets:** A domain expert defines [code lists](#defining-concept-codes) for each concept set within the phenotype using supported coding list formats and stores them in the `/src` directory.
+
+**3. Define mapping from code lists to concept sets:** A domain expert defines a [phenotype mapping](#mapping-codes-to-concept-sets) that maps code lists to concept sets.
+
+**4. Generate versioned phenotype coding lists and translations:** A domain expert or data engineer processes the phenotype mappings [using the command line tool](#usage) to validate against NHS TRUD-registered codes and mapping and to generate versioned concept set code lists with translations between coding standards. 
+
+### Supported Medical Coding Standards
+
+The tool supports verification and mapping across diagnostic coding formats below:
+
+| Medical Code  | Verification | Translation to                    |
+|---------------|--------------|-----------------------------------|
+| Readv2        | NHS TRUD     | Readv3, SNOMED, ICD10, OPCS4, ATC |
+| Readv3 (CTV3) | NHS TRUD     | Readv3, SNOMED, ICD10, OPCS4      |
+| ICD10         | NHS TRUD     | None                              |
+| SNOMED        | NHS TRUD     | None                              |
+| OPCS4         | NHS TRUD     | None                              |
+| ATC           | None         | None                              |
+
+- [**Read V2:**](https://digital.nhs.uk/services/terminology-and-classifications/read-codes) NHS clinical terminology standard used in primary care and replaced by SNOMED-CT in 2018; Still supported by some data providers as widely used in primary care, e.g. [SAIL Databank](https://saildatabank.com/)
+- [**SNOMED-CT:**](https://icd.who.int/browse10/2019/en) international standard for clinical terminology for Electronic Healthcare Records adopted by the NHS in 2018; Mappings to Read codes are partially provided by [Clinical Research Practice Database (CPRD)](https://www.cprd.com/) and [NHS Technology Reference Update Distribution (TRUD)](https://isd.digital.nhs.uk/trud).
+- [**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
-- 
GitLab