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 
An integrative meta-registry of biomedical nomenclatures
Code   PyPI   Website   API   Docs   Docker  

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

Biomappings 
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 
Assembles and reasons over semantic mappings at scale with associated provenance and confidence models.
Code   PyPI   Website   Docs  

Biosynonyms 
Community curated synonyms for biogical entities that are not available from primary sources.
Code  

Bioontologies 
A wrapper around ROBOT and other low-level functionalities for biomedical ontologies.
Code   PyPI   Website   Docs  

PyOBO 
A software packaging for unified access to biomedical ontologies, databases, and semantic spaces using the OBO formalism.
Code   PyPI   Website   Docs  

Biolookup 
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: