Merge pull request #20 from umcu/update-data-flow

Update data flow

README.md

@@ -15,6 +15,8 @@ Data and licenses should be acquired from [UMLS Terminology Services](https://ut
 ## Table of Contents
 - [Download pre-made Dutch MedCAT models](#download-pre-made-dutch-medcat-models)
 - [Folder structure](#folder-structure)
+- [Output format](#output-format)
+- [Data-flow](#data-flow)
 - [Generate UMLS concept table](#generate-umls-concept-table)
 	- [1. Obtain license and download complete UMLS](#1-obtain-license-and-download-complete-umls)
 	- [2. Decompress and install MetamorphoSys](#2-decompress-and-install-metamorphosys)
@@ -39,11 +41,7 @@ dutch-medical-concepts
 └───05_CustomChanges
 ```
 
-## Generate UMLS concept table
-![Data Flow](data-flow.png)
-
-Output CSV format will look like this:
-
+## Output format
 | cui      | name                     | ontologies           | name_status | type_ids |
 |----------|--------------------------|----------------------|-------------|----------|
 | C0000001 | kanker                   | ONTOLOGY1\|ONTOLOGY2 | P           | T001     |
@@ -59,6 +57,10 @@ See https://github.com/CogStack/MedCAT/tree/master/examples for a detailed expla
 
 I'm not sure whether the UMLS license allows for publishing snippets of UMLS data for demonstration purposes, so this repository uses mock data in the examples.
 
+## Data-flow
+![Data-flow](data-flow.jpg)
+
+## Generate UMLS concept table
 ### 1. Obtain license and download complete UMLS 
 To download UMLS, visit the [NIH National Library of Medicine website](https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html). You'll have to apply for a license before you can download the files on https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html. In the following description I downloaded `Full Release (umls-2022AB-full.zip)`. The advantage over `UMLS Metathesaurus Full Subset` is that the Full Release includes MetamorphoSys which makes it possible to create a subset of UMLS prior loading the data in a SQL database. This significantly decreases the required disk space and processing time.