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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 107 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 7

  4. biolookup 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?

    biopragmatics/bioversions’s past year of commit activity
    Python 23 MIT 7 10 4 Updated Jul 7, 2024
  • bioregistry Public

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

    biopragmatics/bioregistry’s past year of commit activity
    Python 107 MIT 47 108 (2 issues need help) 10 Updated Jul 7, 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 49 CC0-1.0 12 17 7 Updated Jun 30, 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
  • oquat Public

    🎬 Ontology Quality Assesment Toolkit

    biopragmatics/oquat’s past year of commit activity
    Python 5 MIT 1 3 0 Updated Jun 24, 2024
  • pyobo Public

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

    biopragmatics/pyobo’s past year of commit activity
    Python 59 MIT 12 39 (1 issue needs help) 4 Updated Jun 4, 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 May 25, 2024
  • biolexica Public

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

    biopragmatics/biolexica’s past year of commit activity
    Jupyter Notebook 1 MIT 0 4 1 Updated May 5, 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 May 2, 2024
  • semra Public

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

    biopragmatics/semra’s past year of commit activity
    Jupyter Notebook 5 MIT 1 3 2 Updated May 2, 2024
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