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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 119 52

  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 50 12

  3. bioversions bioversions Public

    🪝 What's the latest version for each database?

    Python 26 7

  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 119 MIT 52 125 (3 issues need help) 15 Updated Oct 31, 2024
  • bioversions Public

    🪝 What's the latest version for each database?

    biopragmatics/bioversions’s past year of commit activity
    Python 26 MIT 7 10 2 Updated Oct 31, 2024
  • curies Public

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

    biopragmatics/curies’s past year of commit activity
    Python 21 MIT 6 6 4 Updated Oct 30, 2024
  • biosynonyms Public

    ☎️ A decentralized database of synonyms for biomedical concepts

    biopragmatics/biosynonyms’s past year of commit activity
    Python 0 CC0-1.0 0 0 0 Updated Oct 28, 2024
  • pyobo Public

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

    biopragmatics/pyobo’s past year of commit activity
    Python 61 MIT 14 40 (1 issue needs help) 3 Updated Oct 22, 2024
  • curies.rs Public

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

    biopragmatics/curies.rs’s past year of commit activity
    Rust 4 MIT 1 5 0 Updated Sep 19, 2024
  • .github Public

    Software and curated data artifacts for standardizing and processing biomedical data and knowledge

    biopragmatics/.github’s past year of commit activity
    0 0 0 0 Updated Sep 3, 2024
  • 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 50 CC0-1.0 12 17 7 Updated Jul 31, 2024
  • 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 4 1 Updated Jul 17, 2024
  • bioontologies Public

    🏷️ Unified access to biomedical ontologies

    biopragmatics/bioontologies’s past year of commit activity
    Python 8 MIT 1 4 0 Updated Jun 28, 2024
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