The Biolink Model defines a set of common concepts for use in Translator (See here for a Translator glossary). These include semantic types for entities, as well as the relations between them. These concepts are organized into an inheritance hierarchy capturing different granularities of description. Furthermore, each concept contains metadata relating the concept to ontologies.
The Biolink Lookup Service provides a computational interface to the model, including access to previous versions.
Most users will not run their own service, but will make use of the publicly provided service. Several functions are provided, including the ability to look up concepts by name or URI, or to look up ancestors (superclasses) or descendants (subclasses) of concepts.
Examples of use can be found on the live apidocs page, or in the demonstration notebook.
Note: This environment expects Python version 3.8.
Create a virtual environment and activate.
python -m venv venv
source venv/bin/activate
Install dependencies
pip install -r requirements.txt
Run web server.
python main.py --host 0.0.0.0 --port 8144
You may also download and implement the Docker container located in the Docker hub repo: renciorg\bl_lookup.
cd <code base>
docker build -t bl_lookup .docker run -it \
-p <port>:8144 \
bl_lookup
http://"host name or IP":"port"/apidocs
Example helm charts for deploying the container in kubernetes can be found here