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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.

Pinned

  1. bioregistry bioregistry Public

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

    Python 105 47

  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 49 12

  3. bioversions bioversions Public

    🪝 What's the latest version for each database?

    Python 23 6

  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.

    Python 105 MIT 47 105 (2 issues need help) 12 Updated May 9, 2024
  • bioversions Public

    🪝 What's the latest version for each database?

    Python 23 MIT 6 10 3 Updated May 9, 2024
  • biolexica Public

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

    Jupyter Notebook 1 MIT 0 4 1 Updated May 5, 2024
  • pyobo Public

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

    Python 57 MIT 11 37 (1 issue needs help) 3 Updated May 2, 2024
  • curies Public

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

    Python 18 MIT 6 6 4 Updated May 2, 2024
  • biomappings Public

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

    Jupyter Notebook 49 CC0-1.0 12 16 6 Updated May 2, 2024
  • semra Public

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

    Jupyter Notebook 5 MIT 1 3 2 Updated May 2, 2024
  • curies.rs Public

    🦀 Idiomatic conversion between URIs and compact URIs (CURIEs) in Rust

    Rust 4 MIT 1 4 0 Updated Apr 30, 2024
  • .github Public
    0 0 0 0 Updated Apr 22, 2024
  • debio Public

    🥮 Decentralized Biomedical Ontology

    Python 0 MIT 0 1 0 Updated Apr 22, 2024
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