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@biopragmatics

Biopragmatics Stack

Software supporting biomedical semantics and pragmatics
README.md

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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  1. bioregistry bioregistry Public

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

    HTML 143 65

  2. biomappings biomappings Public

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

    Jupyter Notebook 61 16

  3. bioversions bioversions Public

    🪝 What's the latest version for each database?

    Python 28 8

  4. biolookup biolookup Public

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

    Python 4

Repositories

Showing 10 of 20 repositories
  • bioversions Public

    🪝 What's the latest version for each database?

    biopragmatics/bioversions’s past year of commit activity
    Python 28 MIT 8 8 24 Updated Apr 3, 2026
  • bioregistry Public

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

    biopragmatics/bioregistry’s past year of commit activity
    HTML 143 MIT 65 163 (2 issues need help) 11 Updated Apr 2, 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 61 MIT 16 14 18 Updated Mar 30, 2026
  • semra Public

    🛣️ Semantic Mapping Reasoning Assembler (SeMRA): tooling for semantic mappings

    biopragmatics/semra’s past year of commit activity
    Python 14 MIT 3 9 7 Updated Mar 26, 2026
  • curies Public

    🐸 Idiomatic conversion between URIs and compact URIs (CURIEs) in Python

    biopragmatics/curies’s past year of commit activity
    Python 25 MIT 7 8 7 Updated Mar 25, 2026
  • pyobo Public

    📛 A Python package for using ontologies, terminologies, and biomedical nomenclatures

    biopragmatics/pyobo’s past year of commit activity
    Python 75 MIT 17 42 (1 issue needs help) 9 Updated Mar 15, 2026
  • 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 7 2 Updated Feb 22, 2026
  • biolexica Public

    📘 Generate and apply coherent biomedical lexical indices for NER and NEN

    biopragmatics/biolexica’s past year of commit activity
    Jupyter Notebook 2 MIT 0 3 0 Updated Feb 4, 2026
  • bioontologies Public

    🏷️ Unified access to biomedical ontologies

    biopragmatics/bioontologies’s past year of commit activity
    Python 11 MIT 1 3 2 Updated Feb 4, 2026
  • biopragmatics.github.io Public

    GitHub site for the Biopragmatics Stack

    biopragmatics/biopragmatics.github.io’s past year of commit activity
    HTML 0 0 0 0 Updated Jan 7, 2026
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