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
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An integrative meta-registry of biomedical nomenclatures
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Bioversions
A service for tracking the current versions of biomedical ontologies, databases, and semantic spaces.
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A service for tracking the current versions of biomedical ontologies, databases, and semantic spaces.
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Biomappings
Community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources.
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Community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources.
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Semantic Reasoning Assembler
Assembles and reasons over semantic mappings at scale with associated provenance and confidence models.
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Assembles and reasons over semantic mappings at scale with associated provenance and confidence models.
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Biosynonyms
Community curated synonyms for biogical entities that are not available from primary sources.
Code
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.
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A wrapper around ROBOT and other low-level functionalities for biomedical ontologies.
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PyOBO
A software packaging for unified access to biomedical ontologies, databases, and semantic spaces using the OBO formalism.
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A software packaging for unified access to biomedical ontologies, databases, and semantic spaces using the OBO formalism.
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Biolookup
A web service for retrieving metadata and ontological information about biomedical entities
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A web service for retrieving metadata and ontological information about biomedical entities
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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 |