Hetionet was published by Himmelstein et al. in 2017 and was the first public/open biomedical knowledge graph.
Bio2BEL was developed in parallel and was inspired by Hetionet as a more generic mechanism for converting biological knowledge into a common schema, using the Biological Expression Language.
Unfortunately, the associated manuscript spent two years in review, and was ultimately tabled by the original authors. However, in the following pandemic years the construction of biomedical knowledge graphs (albeit, with less principled approaches) became quite popular.
The bio2bel Python package contains shared utilities for converting generic resources
to BEL, and a different repository was created for each resource that can be converted to BEL.
For more context on BEL, see:
- An Incomplete History of Selventa and the Biological Expression Language (BEL)
- A Listing of Publicly Available Content in the Biological Expression Language (BEL)
- A Reading List of Academic Articles using the Biological Expression Language (BEL)
As of update of this page in early Spring 2025, there are not any major public-facing BEL efforts, but the entire PyBEL and Bio2BEL codebases are ripe for revitalization if there's any interest! Please reach out to @cthoyt if you are interested in supporting its maitenance.
