Biopragmatics Stack

Software supporting biomedical semantics and pragmatics

Biopragmatics Stack

The Biopragmatics Stack is a set of interconnected software components and curated data artifacts thatsupport standardizing and processing biomedical data and knowledge.

Elements in dashed boxes are planned for future work or exist outside of the Biopragmatics stack.

PURLs

The Biopragmatics Stack useshttps://w3id.org to create persistent uniform resource locators (PURLs)for various rsources. These are configured on GitHub in the.htaccess file inhttps://github.com/perma-id/w3id.org/tree/master/biopragmatics.

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bioregistrybioregistryPublic
📮 An integrative registry of biological databases, ontologies, and nomenclatures.
Python 121 54
biomappingsbiomappingsPublic
🗺️ Community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources.
Jupyter Notebook 51 13
bioversionsbioversionsPublic
🪝 What's the latest version for each database?
Python 27 8
biolookupbiolookupPublic
🔍 The Biolookup Service retrieves metadata and ontological information about biomedical entities.
Python 3

Repositories

Showing 10 of 19 repositories

curies Public
🐸 Idiomatic conversion between URIs and compact URIs (CURIEs) in Python
biopragmatics/curies’s past year of commit activity
Python 22MIT 6 6 4 UpdatedMar 19, 2025
bioversions Public
🪝 What's the latest version for each database?
biopragmatics/bioversions’s past year of commit activity
Python 27MIT 8 14 4 UpdatedMar 18, 2025
bioregistry Public
📮 An integrative registry of biological databases, ontologies, and nomenclatures.
biopragmatics/bioregistry’s past year of commit activity
Python 121MIT 54 138 (3 issues need help) 25 UpdatedMar 18, 2025
semra Public
🛣️ Semantic Mapping Reasoning Assembler (SeMRA): tooling for semantic mappings
biopragmatics/semra’s past year of commit activity
Jupyter Notebook 7MIT 1 5 3 UpdatedMar 15, 2025
obo-db-ingest Public
🗄️ Conversion of biomedical nomenclatures like HGNC to OBO
biopragmatics/obo-db-ingest’s past year of commit activity
Python 7 1 6 2 UpdatedMar 12, 2025
pyobo Public
📛 A Python package for using ontologies, terminologies, and biomedical nomenclatures
biopragmatics/pyobo’s past year of commit activity
Python 62MIT 16 37 (1 issue needs help) 8 UpdatedMar 12, 2025
biolexica Public
📘 Generate and apply coherent biomedical lexical indices for NER and NEN
biopragmatics/biolexica’s past year of commit activity
Jupyter Notebook 2MIT0 4 0 UpdatedMar 10, 2025
biolookup Public
🔍 The Biolookup Service retrieves metadata and ontological information about biomedical entities.
biopragmatics/biolookup’s past year of commit activity
Python 3MIT0 3 1 UpdatedMar 5, 2025
biosynonyms Public
☎️ A decentralized database of synonyms for biomedical concepts
biopragmatics/biosynonyms’s past year of commit activity
Python0CC0-1.00 0 1 UpdatedFeb 10, 2025
bioontologies Public
🏷️ Unified access to biomedical ontologies
biopragmatics/bioontologies’s past year of commit activity
Python 8MIT 1 4 1 UpdatedFeb 10, 2025