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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 Public

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

    Python 122 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
  • bioregistry Public

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

    Python 122 MIT 54 138 (3 issues need help) 22 Updated Apr 1, 2025
  • bioversions Public

    🪝 What's the latest version for each database?

    Python 27 MIT 8 11 4 Updated Apr 1, 2025
  • pyobo Public

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

    Python 62 MIT 16 37 (1 issue needs help) 10 Updated Mar 28, 2025
  • semra Public

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

    Jupyter Notebook 7 MIT 1 5 3 Updated Mar 28, 2025
  • curies Public

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

    Python 22 MIT 6 6 4 Updated Mar 25, 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
  • bioontologies Public

    🏷️ Unified access to biomedical ontologies

    Python 9 MIT 1 4 2 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
  • biolookup Public

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

    Python 3 MIT 0 3 1 Updated Mar 5, 2025
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