Query Bio2RDF using the Translator Reasoner API (TRAPI)

🔗 https://api.bio2rdf.137.120.31.102.nip.io

Deploy Bio2RDF TRAPI 🛩️

Starts the Translator Reasoner API to query the Bio2RDF SPARQL endpoint

• The TRAPI-SPARQL interface is implemented in Python in the src/ folder
• Uses OpenAPI 3 with Swagger UI, built in Python using zalando/connexion

Requires Python 3.7+ and pip

1. Clone the repository

git clone https://github.com/MaastrichtU-IDS/bio2rdf-trapi.git
cd bio2rdf-trapi

2. Install dependencies

pip3 install -r requirements.txt

If you are facing conflict with already installed packages, then you might want to use a Virtual Environment to isolate the installation in the current folder before installing bio2rdf-trapi:

# Create the virtual environment folder in your workspace
python3 -m venv .venv
# Activate it using a script in the created folder
source .venv/bin/activate

3. Start the API in production mode on http://localhost:8808 with Tornado:

python3 src/api.py

Or start the API in debug mode with Flask (the API will be reloaded automatically at each change to the code):

python3 src/api.py debug

Check CONTRIBUTING.md for more details on how to run the API locally and contribute.

Start with Docker 🐳

Requirements: Docker.

Build and start the container with docker-compose on http://localhost:8808

docker-compose up -d --build

We use nginx-proxy and docker-letsencrypt-nginx-proxy-companion as reverse proxy for HTTP and HTTPS in production. You can change the proxy URL and port via environment variables VIRTUAL_HOST, VIRTUAL_PORT and LETSENCRYPT_HOST in the docker-compose.yml file.

Check the logs:

docker-compose logs

Stop the container:

docker-compose down

Overview of API operations 🧭

Overview of the different operations available in Bio2RDF Translator Reasoner API (supporting kgx)

Query operation

The user sends a ReasonerAPI query to Bio2RDF Nanopublications in the BioLink format (e.g. drug indications). The query is a graph with nodes and edges defined in JSON, and uses classes from the BioLink model.

Predicates operation

The /predicates operation will return the entities and relations provided by this API in a JSON object (following the ReasonerAPI specifications).

Acknowledgments

Service funded by the NIH NCATS Translator project.