Biopragmatics Stack

The Biopragmatics Stack is a set of interconnected software components and curated data artifacts that support 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 uses https://w3id.org to create persistent uniform resource locators (PURLs) for various rsources. These are configured on GitHub in the .htaccess file in https://github.com/perma-id/w3id.org/tree/master/biopragmatics.

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📮 An integrative registry of biological databases, ontologies, and nomenclatures.

HTML 147 70
🗺️ Community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources.

Jupyter Notebook 65 17
🪝 What's the latest version for each database?

Python 31 8
🔍 The Biolookup Service retrieves metadata and ontological information about biomedical entities.

Python 5

Repositories

Showing 10 of 21 repositories

bioregistry Public
📮 An integrative registry of biological databases, ontologies, and nomenclatures.

biopragmatics/bioregistry's past year of commit activity
bioversions Public
🪝 What's the latest version for each database?

biopragmatics/bioversions's past year of commit activity

Python
31
MIT
8 8 0
Updated Aug 17, 2026
biomappings Public
🗺️ Community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources.

biopragmatics/biomappings's past year of commit activity

Jupyter Notebook
65
MIT
17 13 5
Updated Aug 13, 2026
semra Public
🛣️ Semantic Mapping Reasoning Assembler (SeMRA): tooling for semantic mappings

biopragmatics/semra's past year of commit activity

Python
15
MIT
3 8 4
Updated Aug 13, 2026
biopragmatics/bioontologies's past year of commit activity

Python
12
MIT
1 0 0
Updated Aug 13, 2026
pyobo Public
📛 A Python package for using ontologies, terminologies, and biomedical nomenclatures

biopragmatics/pyobo's past year of commit activity
curies Public
🐸 Idiomatic conversion between URIs and compact URIs (CURIEs) in Python

biopragmatics/curies's past year of commit activity

Python
27
MIT
6 8 8
Updated Aug 10, 2026
obo-db-ingest Public
🗄️ Conversion of biomedical nomenclatures like HGNC to OBO

biopragmatics/obo-db-ingest's past year of commit activity

Python
8 1 7 2
Updated Jun 4, 2026
biopragmatics/mapping-registry's past year of commit activity

Just
0 0 0 0
Updated Apr 21, 2026
biolexica Public
📘 Generate and apply coherent biomedical lexical indices for NER and NEN

biopragmatics/biolexica's past year of commit activity

Jupyter Notebook
3
MIT
0 3 0
Updated Feb 4, 2026