Biolink Model Toolkit

The Biolink Model Toolkit (BMT) is a Python library for working with the Biolink Model. It provides convenience methods for querying the Biolink Model in a way that is consistent and in line with the metamodel. It does so by using LinkML, the meta modeling framework that is used for building the Biolink Model. Using BMT, one can query the model for use-cases such as,

• Get me ancestors of a given Biolink Model class
• Get me descendants of a given Biolink Model class
• Get me parent of a given Biolink Model predicate
• Get me parent of a given Biolink Model property
• Given an external class or predicate, find me a Biolink Model class or predicate to which the given class or predicate maps to

The BMT codebase is available at https://github.com/biolink/biolink-model-toolkit and the latest releases are available on https://pypi.org/project/bmt/. BMT is being used across various projects within Translator including KGX, and BL Lookup Service. All teams in Translator are encouraged to make use of BMT for introspecting the Biolink Model, as it takes into account the various semantics of the model and its metamodel. BMT has the simple purpose of “wrapping” the Biolink Model standard (the semantic content of which is specified in a single community curated “master blueprint” data model file in the Biolink Model repository at https://github.com/biolink/biolink-model/blob/master/biolink-model.yaml) in a form which computer programs can directly access in their code. For this reason, all Translator teams are encouraged to use the BMT as te programmatic means to access the Biolink Model in their software systems.