Medical oncept Annotation Tool Trainer

MedCATtrainer is a web application for creating, validating, and improving MedCAT concept annotation models on biomedical or clinical text.

It supports both classic active-learning workflows (train on submit) and review-only workflows (collect annotations without changing the model).

What you can do with MedCATtrainer

• Build annotation projects from CSV/XLSX datasets.

• Use either:

  • a Model Pack (recommended), or

  • a Concept DB + Vocabulary pair.

• Optionally use a remote MedCAT model service for document preparation.

• Collect concept-level labels:

  • Correct

  • Incorrect

  • Alternative concept

  • Terminate

  • Irrelevant

• Collect optional meta annotations and relation annotations.

• Use Project Groups for multi-annotator setups.

• Run metrics reports across one or more compatible projects.

• Explore concept hierarchies and export concept filters.

Typical workflow

1. Install and configure MedCATtrainer.

2. Create users and upload model artifacts (Model Pack or CDB/Vocab).

3. Create a project and assign annotators.

4. Annotate and submit documents.

5. Export annotations and evaluate with the metrics tools.

Documentation map

• Installation

• Administrator Setup

• Annotation Project Creation and Management

• Project Groups

• Annotator Guide

• Meta Annotations

• Demo / Try Model

• Advanced Usage

• Maintenance

• Python Client