Skip to content
@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.

Pinned Loading

  1. bioregistry Public

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

    Python 129 54

  2. biomappings Public

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

    Jupyter Notebook 52 14

  3. bioversions Public

    🪝 What's the latest version for each database?

    Python 27 8

  4. biolookup Public

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

    Python 3

Repositories

Showing 10 of 19 repositories
  • bioversions Public

    🪝 What's the latest version for each database?

    Python 27 MIT 8 11 5 Updated Apr 17, 2025
  • semra Public

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

    Jupyter Notebook 7 MIT 1 5 5 Updated Apr 15, 2025
  • curies Public

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

    Python 23 MIT 6 6 6 Updated Apr 14, 2025
  • bioregistry Public

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

    Python 129 MIT 54 146 (3 issues need help) 21 Updated Apr 14, 2025
  • pyobo Public

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

    Python 65 MIT 16 39 (1 issue needs help) 10 Updated Apr 11, 2025
  • biopragmatics.github.io Public

    GitHub site for the Biopragmatics Stack

    0 0 0 0 Updated Apr 9, 2025
  • bioontologies Public

    🏷️ Unified access to biomedical ontologies

    Python 9 MIT 1 4 2 Updated Apr 8, 2025
  • biomappings Public

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

    Jupyter Notebook 52 CC0-1.0 14 21 16 Updated Mar 24, 2025
  • obo-db-ingest Public

    🗄️ Conversion of biomedical nomenclatures like HGNC to OBO

    Python 7 1 7 2 Updated Mar 12, 2025
  • biolexica Public

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

    Jupyter Notebook 2 MIT 0 4 0 Updated Mar 10, 2025
View all repositories