Repositories list

• bioregistry

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

  biocurationbioregistrybiopragmatics

  Python

  •

  MIT License

  •52•121•126•19•Updated Dec 12, 2024Dec 12, 2024

• pyobo

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

  bioinformaticsoboontologies+ 3obofoundrybioregistrybiopragmatics

  Python

  •

  MIT License

  •15•61•34•3•Updated Dec 12, 2024Dec 12, 2024

• bioversions

  Public
  🪝 What's the latest version for each database?

  biopragmatics

  Python

  •

  MIT License

  •8•27•13•6•Updated Dec 12, 2024Dec 12, 2024

• obo-db-ingest

  Public
  🗄️ Conversion of biomedical nomenclatures like HGNC to OBO

  rdfowlobo+ 5ontologiesbiocurationobofoundryobographsobographviz

  Python

  •1•7•5•2•Updated Dec 10, 2024Dec 10, 2024

• curies

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

  semantic-webobofoundrycuries+ 1uris

  Python

  •

  MIT License

  •6•21•6•8•Updated Dec 9, 2024Dec 9, 2024

• bioontologies

  Public
  🏷️ Unified access to biomedical ontologies

  Python

  •

  MIT License

  •1•8•4•6•Updated Dec 9, 2024Dec 9, 2024

• biomappings

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

  semanticsontologymappings+ 3biocurationbioregistrybiopragmatics

  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

  •13•51•18•8•Updated Dec 9, 2024Dec 9, 2024

• .github

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

  0•0•0•0•Updated Dec 8, 2024Dec 8, 2024

• biopragmatics.github.io

  Public
  GitHub site for the Biopragmatics Stack

  biopragmatics

  0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

• biosynonyms

  Public
  ☎️ A decentralized database of synonyms for biomedical concepts

  chemistrybiologyontology

  Python

  •

  Creative Commons Zero v1.0 Universal

  •0•0•0•1•Updated Dec 2, 2024Dec 2, 2024

• curies.rs

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

  Rust

  •

  MIT License

  •1•4•5•0•Updated Sep 19, 2024Sep 19, 2024

• biolexica

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

  named-entity-recognitionnamed-entity-linkingbiopragmatics+ 1gilda

  Jupyter Notebook

  •

  MIT License

  •0•2•4•1•Updated Jul 17, 2024Jul 17, 2024

• oquat

  Public
  🎬 Ontology Quality Assesment Toolkit

  obofoundry

  Python

  •

  MIT License

  •1•5•3•0•Updated Jun 24, 2024Jun 24, 2024

• semra

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

  mappingsontology-mergingbiopragmatics+ 1semantic-mappings

  Jupyter Notebook

  •

  MIT License

  •1•7•3•2•Updated May 2, 2024May 2, 2024

• debio

  Public
  🥮 Decentralized Biomedical Ontology

  ontologyobofoundry

  Python

  •

  MIT License

  •1•1•1•0•Updated Apr 22, 2024Apr 22, 2024

• providers

  Public
  🌐 Providers for prefixes that don't have one, but are available in PyOBO

  HTML

  •0•0•0•0•Updated Sep 23, 2023Sep 23, 2023

• biolookup

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

  metadataflaskbioinformatics+ 6chemistrycheminformaticsbiologyontologyobofoundrybiopragmatics

  Python

  •

  MIT License

  •0•3•2•0•Updated Jun 26, 2022Jun 26, 2022

• bioregistry-docker

  Public
  🐋 A dockerfile for the Bioregistry web app

  biopragmaticsdocker

  Shell

  •

  MIT License

  •0•0•0•0•Updated Jan 26, 2022Jan 26, 2022

• biolookup-docker

  Public
  🐋 A dockerfile for the frontend to the Biolookup Service

  dockerbiopragmatics

  Shell

  •

  MIT License

  •0•0•0•0•Updated Nov 9, 2021Nov 9, 2021