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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.

    Python 129 56

  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 53 14

  3. bioversions bioversions Public

    🪝 What's the latest version for each database?

    Python 27 8

  4. biolookup biolookup Public

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

    Python 3

Repositories

Showing 10 of 19 repositories
  • bioregistry Public

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

    biopragmatics/bioregistry’s past year of commit activity
    Python 129 MIT 56 148 (3 issues need help) 20 Updated May 21, 2025
  • pyobo Public

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

    biopragmatics/pyobo’s past year of commit activity
    Python 67 MIT 16 38 (1 issue needs help) 10 Updated May 21, 2025
  • bioversions Public

    🪝 What's the latest version for each database?

    biopragmatics/bioversions’s past year of commit activity
    Python 27 MIT 8 9 1 Updated May 21, 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 7 2 Updated May 20, 2025
  • oquat Public

    🎬 Ontology Quality Assesment Toolkit

    biopragmatics/oquat’s past year of commit activity
    Python 5 MIT 1 4 0 Updated May 20, 2025
  • 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 May 16, 2025
  • biolookup Public

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

    biopragmatics/biolookup’s past year of commit activity
    Python 3 MIT 0 3 1 Updated May 16, 2025
  • curies Public

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

    biopragmatics/curies’s past year of commit activity
    Python 23 MIT 6 6 5 Updated May 14, 2025
  • semra Public

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

    biopragmatics/semra’s past year of commit activity
    Jupyter Notebook 9 MIT 1 8 3 Updated May 6, 2025
  • bioontologies Public

    🏷️ Unified access to biomedical ontologies

    biopragmatics/bioontologies’s past year of commit activity
    Python 10 MIT 1 4 3 Updated May 3, 2025
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