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  
Semantic Reasoning Assembler Logo Semantic Reasoning Assembler GitHub logo
Assembles and reasons over semantic mappings at scale with associated provenance and confidence models.
Code   PyPI   Website   Docs  
Biosynonyms Logo Biosynonyms GitHub logo
Community curated synonyms for biogical entities that are not available from primary sources.
Code  
Bioontologies Logo Bioontologies GitHub logo
A wrapper around ROBOT and other low-level functionalities for biomedical ontologies.
Code   PyPI   Website   Docs  
PyOBO Logo PyOBO GitHub logo
A software packaging for unified access to biomedical ontologies, databases, and semantic spaces using the OBO formalism.
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 ❤️ by the Gyori Lab for Computational Biomedicine at Northeastern University and previously at 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 #
Chan Zuckerberg Initiative Advancing Data Integration and Discovery in Biomedicine with the Bioregistry 2023-329850
DARPA Automating Scientific Knowledge Extraction and Modeling HR00112220036
DARPA Young Faculty Award (PI: Benjamin M. Gyori) W911NF2010255