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   Docker  
Bioversions Logo Bioversions GitHub logo
A service for tracking the current versions of biomedical ontologies, databases, and semantic spaces.
Code   PyPI   Website  
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  
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   Docker  

Acknowledgements

The Biopragmatics Stack is developed with ❤️ in 🇩🇪 and 🇺🇸 by the INDRA Lab in the Laboratory of Systems Pharmacology and the Harvard Program in Therapeutic Science (HiTS) at Harvard Medical School.

It’s funded by the DARPA Automating Scientific Knowledge Extraction (ASKE) program under award HR00111990009 and the DARPA Young Faculty Award W911NF2010255 (PI: Benjamin M. Gyori).