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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 151 70

  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 66 17

  3. bioversions bioversions Public

    🪝 What's the latest version for each database?

    Python 31 8

  4. biolookup biolookup Public

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

    Python 6

Repositories

Showing 10 of 21 repositories
  • semra Public

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

    biopragmatics/semra's past year of commit activity
    Python 16 MIT 3 9 4 Updated Sep 23, 2026
  • pyobo Public

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

    biopragmatics/pyobo's past year of commit activity
    Python 76 MIT 18 38 (1 issue needs help) 11 Updated Sep 23, 2026
  • 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 Sep 23, 2026
  • bioregistry Public

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

    biopragmatics/bioregistry's past year of commit activity
    HTML 151 MIT 70 154 (2 issues need help) 10 Updated Sep 22, 2026
  • curies Public

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

    biopragmatics/curies's past year of commit activity
    Python 28 MIT 7 7 7 Updated Sep 21, 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 66 MIT 17 11 4 Updated Sep 18, 2026
  • mapping-registry Public

    A mapping registry

    biopragmatics/mapping-registry's past year of commit activity
    Just 0 0 0 0 Updated Sep 16, 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 Aug 31, 2026
  • bioontologies Public

    🏷️ Unified access to biomedical ontologies

    biopragmatics/bioontologies's past year of commit activity
    Python 12 MIT 1 0 0 Updated Aug 13, 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
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