Annotation setup

This document describes how to collect feedback for SemEHR annotations for training machine learning models for improving baseline results.

use eHOST as the annotation tool

Convert SemEHR annotation results to eHOST format. This step uses ann_converter.py at the root folder of this repository.
```
python ann_converter.py text_file semehr_ann_file cui2label_mapping_file output_xml_file
```
- text_file is the full text file
- semehr_ann_file is the SemEHR result json file
- cui2lable_mapping_file is a json file to map UMLS CUI to a label, see below as an example for mapping two CUIs to Ischemic stroke.
```
{
 "C0948008": "Ischemic stroke",
 "C3178801": "Ischemic stroke",
 "C0859253": "Haemorrhage stroke"
}   	
```
Annotation process: use eHOST to load the outputs and ask the annotators to do three things:
- delete not relevant annotations
- add missed annotations using relevant labels from the above mapping file
- correct mislabelled annotations by changing the class to a correct label