The Biopragmatics Stack is a collection of interlinked software packages that provide the infrastructure for biomedical semantics and pragmatics.

Our docker images can be found on DockerHub.

Bioregistry Logo Bioregistry GitHub logo
An integrative meta-registry of biomedical nomenclatures
Code   PyPI   Website   API   Docs   Docker  
Bioversions Logo Bioversions GitHub logo
A service for tracking the current versions of biomedical ontologies, databases, and semantic spaces.
Code   PyPI   Website   Docs  
Biomappings Logo Biomappings GitHub logo
Community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources.
Code   PyPI   Website   Docs  
PyOBO Logo PyOBO GitHub logo
A software packaging for unified access to biomedical ontologies, databases, and semantic spaces.
Code   PyPI   Website   Docs  
Biolookup Logo Biolookup GitHub logo
A web service for retrieving metadata and ontological information about biomedical entities
Code   PyPI   Website   API   Docs   Docker  

Acknowledgements

The Biopragmatics Stack is developed with ❀️ in πŸ‡©πŸ‡ͺ and πŸ‡ΊπŸ‡Έ by the INDRA Lab in the Laboratory of Systems Pharmacology and the Harvard Program in Therapeutic Science (HiTS) at Harvard Medical School.

Funding

The Biopragmatics Stack has been historically funded by the following awards:

Funding Body Name Grant #
DARPA Automating Scientific Knowledge Extraction HR00111990009
DARPA Young Faculty Award(PI: Benjamin M. Gyori) W911NF2010255