Repositories list

• ontology-development-kit

  Public
  Ontology lifecycle management

  robotcontinuous-integrationowl+ 6ontologytravisoboprotegemonarchinitiativeobofoundry

  Dockerfile

  •

  BSD 3-Clause "New" or "Revised" License

  •58•287•86•8•Updated Jan 5, 2026Jan 5, 2026

• odkrunner

  Public
  A binary runner for the Ontology Development Kit

  C

  •

  Other

  •0•4•0•0•Updated Jan 2, 2026Jan 2, 2026

• odkcore

  Public
  Docker-less, core package for the Ontology Development Kit

  Jinja

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•1•1•Updated Jan 1, 2026Jan 1, 2026

• odk-robot-plugin

  Public
  ROBOT plugin for the Ontology Development Kit

  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Dec 19, 2025Dec 19, 2025

• dosdp-tools

  Public
  Utility for working with DOSDP design patterns and OWL ontologies

  design-patternsowlontology+ 4odpmonarchinitiativeobofoundrydosdp-pattern

  Scala

  •

  MIT License

  •5•28•34•20•Updated Dec 10, 2025Dec 10, 2025

• dead_simple_owl_design_patterns

  Public
  A simple system for specifying OWL class design patterns for OBO-ish ontologies.

  templatesontologyodp+ 1obofoundry

  Python

  •

  GNU General Public License v3.0

  •5•46•20•1•Updated Dec 10, 2025Dec 10, 2025

• PandaSaurus

  Public
  Supporting simple queries over ontology annotations in dataframes, using UberGraph queries

  Python

  •

  Apache License 2.0

  •0•2•1•0•Updated Dec 2, 2025Dec 2, 2025

• relation-graph

  Public
  Materialize OWL existential relations

  rdfowlontology+ 1obofoundry

  Scala

  •

  MIT License

  •5•20•8•8•Updated Nov 12, 2025Nov 12, 2025

• semantic-sql

  Public
  SQL and SQLite builds of OWL ontologies

  sqlsparqlowl+ 7ontologiesmonarchinitiativeobofoundrylinkmlrelation-graphoaklibai4curation

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •6•55•14•0•Updated Oct 31, 2025Oct 31, 2025

• ubergraph

  Public
  Integrated OBO ontology store

  rdfowlknowledge-graph+ 2obofoundryncats-translator

  Makefile

  •

  BSD 3-Clause "New" or "Revised" License

  •5•48•33•3•Updated Oct 8, 2025Oct 8, 2025

• pandasaurus_cxg

  Public
  Ontology enrichment tool for CxG standard AnnData files

  Jupyter Notebook

  •

  Apache License 2.0

  •1•3•5•1•Updated Sep 15, 2025Sep 15, 2025

• ontology-access-kit

  Public
  Ontology Access Kit: A python library and command line application for working with ontologies

  pythonrdfsemantic-web+ 8owlontologyapisgeneontologymonarchinitiativeobofoundryontology-api+ 1

  Python

  •

  Apache License 2.0

  •32•156•165•11•Updated Jun 5, 2025Jun 5, 2025

• boomer

  Public
  Bayesian OWL ontology merging

  owlmondoboomer+ 7reasoningowl-ontologygeneontologymonarchinitiativeobofoundryontology-mergingprobabilistic-owl

  Scala

  •

  BSD 3-Clause "New" or "Revised" License

  •2•32•27•15•Updated Jun 4, 2025Jun 4, 2025

• whelk

  Public
  Whelk is an OWL EL reasoner

  Scala

  •

  BSD 3-Clause "New" or "Revised" License

  •6•36•5•9•Updated Mar 5, 2025Mar 5, 2025

• obographviz

  Public
  Customizable translation of OBO graphs to dot for visualization using graphviz and other tools

  javascriptgraphvizjson+ 4nodegraph-visualizationobofoundryobographs

  JavaScript

  •6•26•9•4•Updated Feb 21, 2025Feb 21, 2025

• ontobot-change-agent

  Public
  A GitHub bot for modifying ontology resources.

  botontologychange-language+ 1kgcl

  Python

  •

  MIT License

  •1•9•26•1•Updated Dec 1, 2024Dec 1, 2024

• kgcl-rdflib

  Public
  Tools for working with KGCL

  diffsdiffsemantic-diff+ 8rdfowlontologyknowledge-graphkgobofoundrylinkml+ 1

  Python

  •

  MIT License

  •9•18•15•3•Updated Nov 19, 2024Nov 19, 2024

• kgcl

  Public
  Datamodel for KGCL (Knowledge Graph Change Language)

  rdfsemantic-weblinkml+ 3ontology-diffsontology-changeskgcl

  Python

  •

  MIT License

  •4•20•32•3•Updated Nov 15, 2024Nov 15, 2024

• whelk-paper

  Public
  Code for Whelk performance analyses

  Scala

  •

  MIT License

  •0•1•0•0•Updated Oct 4, 2024Oct 4, 2024

• verificado

  Public
  Python

  •

  Apache License 2.0

  •0•1•0•0•Updated Jun 12, 2024Jun 12, 2024

• biosample-analysis

  Public
  analysis of biosamples in INSDC

  Jupyter Notebook

  •1•3•25•1•Updated Feb 13, 2024Feb 13, 2024

• whelk-rs

  Public
  Whelk is an OWL EL reasoner

  rustsemantic-webowl

  Rust

  •

  MIT License

  •6•15•7•2•Updated Mar 16, 2023Mar 16, 2023

• rdf-sql-bulkloader

  Public
  Python

  •1•1•1•0•Updated Mar 2, 2023Mar 2, 2023

• oakx-grape

  Public
  Experimental OAK plugin for Grape

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •2•5•9•4•Updated Feb 10, 2023Feb 10, 2023

• oakx-plugin-cookiecutter

  Public
  cookiecutter for OAK plugins

  pluginscookiecutteroaklib

  Python

  •0•2•0•0•Updated Jan 11, 2023Jan 11, 2023

• oakx-robot

  Public
  robot plugin for OAK

  Python

  •0•1•0•0•Updated Sep 29, 2022Sep 29, 2022

• obo-shapes

  Public
  SHACL and ShEx shapes for validating OBO ontologies

  Makefile

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Apr 12, 2022Apr 12, 2022

• .github

  Public
  0•0•0•0•Updated Apr 8, 2022Apr 8, 2022

• owl_patternizer

  Public
  generate DOSDP patterns from OWL ontologies

  Prolog

  •

  BSD 3-Clause "New" or "Revised" License

  •2•2•0•0•Updated Feb 28, 2022Feb 28, 2022

• DataHarmonizer

  Public
  A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 sampling data.

  JavaScript

  •

  MIT License

  •33•0•0•0•Updated Dec 9, 2021Dec 9, 2021