Biolink Lookup Service

Introduction

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.

Usage

The Biolink Lookup Service is a convenient wrapper around the Biolink Model Toolkit. It is not a TRAPI service, but instead allows users to find ancestors, descendants, and properties of biolink categories and predicates. For example, the following curl string will look up the ancestors of the chemical substance category in version 1.7.0 of the biolink model:

curl -X GET "https://bl-lookup-sri.renci.org/bl/chemical_substance/ancestors?version=1.7.0" -H "accept: application/json"

Response:

["biolink:MolecularEntity","biolink:BiologicalEntity","biolink:NamedThing","biolink:Entity"]

Many more examples can be seen in the Documentation Notebook

Reporting an Issue

Issues with the Biolink Lookup Service can be reported and viewed at the services github repository here.

Deployment

The service can be built into a docker container, deployable using docker or kubernetes. Details are given in the github README

Links

• Running Instance: https://bl-lookup-sri.renci.org/apidocs/
• Github Repository: https://github.com/TranslatorSRI/bl_lookup
• SmartAPI Registration: http://smart-api.info/registry?q=9df83f691d5fa0d8eb9c9f5f6b6ebb39