NLPSandbox.io is an open platform for benchmarking modular natural language processing (NLP) tools on both public and private datasets. Academics, students, and industry professionals are invited to browse the available tasks and participate by developing and submitting an NLP Sandbox tool.

This repository packages BERT fine-tuned on I2B2 as an NLP Sandbox PHI annotator. The performance of this tool can be viewed and compared to the performance of other PHI annotators on NLPSandbox.io.

Annotation types supported by this annotator:

• Specification
• Requirements
• Usage
  • Running with Docker
  • Running with Python
  • Accessing the user interface
• Development
• Versioning
  • GitHub release tags
  • Docker image tags
• Benchmarking on NLPSandbox.io
• Citation
• Contributing
• License

• NLP Sandbox schemas version: 1.2.0
• Tool version: 1.0.1
• Tool images:
  • docker.synapse.org/syn26486812/bert-i2b2-annotator-bert-ner-i2b2

• Docker Engine >=19.03.0

The command below starts this NLP Sandbox PHI annotator locally.

docker compose up --build

You can stop the container run with Ctrl+C, followed by docker compose down.

Create a Conda environment:

conda create --name phi-annotator python=3.9 -y
conda activate phi-annotator

Install dependencies and download an NER model from HuggingFace (default: David S. Lim's fine-tuned BERT model):

Install and start this NLP Sandbox tool.

cd server && pip install -r requirements.txt
python save_bert.py
python -m openapi_server

This NLP Sandbox tool provides a web interface that you can use to annotate clinical notes. This web client has been automatically generated by openapi-generator. To access the UI, open a new tab in your browser and navigate to one of the following address depending on whether you are running the tool using Docker (production) or Python (development).

• Using Docker: http://localhost/ui
• Using Python: http://localhost:8080/ui

This repository uses semantic versioning to track the releases of this tool. This repository uses "non-moving" GitHub tags, that is, a tag will always point to the same git commit once it has been created.

The artifact published by the CI/CD workflow of this GitHub repository is a Docker image pushed to the Synapse Docker Registry. This table lists the image tags pushed to the registry.

You should avoid using a moving tag like latest when deploying containers in production, because this makes it hard to track which version of the image is running and hard to roll back.

Visit nlpsandbox.io for instructions on how to submit your NLP Sandbox tool and evaluate its performance.

• If you use this NLP Sandbox tool or resources from NLPSandbox.io, please follow these [citation guidelines].

Thinking about contributing to this project? Get started by reading our contribution guide.

Apache License 2.0