b-com / acuitee

Annotation and Curation User Interface for Terms Extraction Engines

ACUITEE (Annotation and Curation User Interface for Terms Extraction Engines)

ACUITEE represents a web application with three main functionalities: visualization, editing and manual curation of the annotation results proposed by automatic parsers. An online demo is availabe here.

Author & Contributors

Author:

Majd SALEH, PhD, Research & Development Engineer, Artificial Intelligence Laboratory, IRT b<>com, France

Contributors:

• Majd SALEH, Stéphane PAQUELET, Cyndie MARTIN, IRT b<>com, France
• Marie DE TAYRAC, Paul ROLLIER, Youenn MEREL, Wilfried CARRE, Chrystele DUBOURG and Sylvie ODENT, CHU de Rennes, France
• Guillaume COLLET and Olivier DAMERON, Univ. Rennes 1, France
• Thomas LABBE and Jean-Michel SANNER, Orange, France

Instructions

1. Clone the source codes to your local machine.
2. Create a virtual environment (python 3.9) with apt install python3.9-venv then python3 -m venv venv
3. Activate you virtual environment with venv\scripts\activate or(source venv/bin/activate)
4. Install the requirements: pip install -r requirements.txt
5. To run the application, you have two options:
   • Development: from the terminal, type flask run. This will run the application with the flask development server and with FLASK_ENV=development. See the file “.flaskenv”.
   • Production: from the terminal, type python main.py. This will run the application with gevent server.

For using ACUITEE as a Docker container, execute the following steps (instead of steps 2 to 5above):

1. Build the Docker image: use your CLI and navigate to the directory of ACUITEE. For example: C:\Users\msaleh\Development\ACUITEE>
2. Execute the following command: docker build --tag acuitee .
3. Run the docker image by executing the following command: docker run -d --publish 5000:5000 --name "acuitee" acuitee where -d is used to make the container (i.e. the running image) working in a detached mode i.e. as a background service in the OS. --publish is used to make the port 5000 on the container visible from the port 5000 of the host (without this, we will not be able to interact with the container).
4. Use your favorite browser, go to the following URL to access the web application ACUITEE: http://localhost:5000/
5. To stop the docker container, use the command docker stop acuitee
6. To start the docker container, use: docker start acuitee

Human Phenotype Ontology (HPO)

This web application, ACUITEE, uses the Human Phenotype Ontology (08/02/2021). Find out more at http://www.human-phenotype-ontology.org