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). Administrator Setup
3. Create a project and assign annotators. Annotation Project Creation and Management
4. Annotate and submit documents. Annotator Guide
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