Repositories list

• ontology-access-kit

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

  pythonrdfsemantic-web+ 8

  pythonrdfsemantic-webowlontologyapisgeneontologymonarchinitiativeobofoundryontology-api+ 1

  Python

  •

  Apache License 2.0

  •3333 forks•165165 stars•171171 issues•1111 pull requests•Updated Apr 10, 2026Apr 10, 2026

• pandasaurus_cxg

  Public
  Ontology enrichment tool for CxG standard AnnData files

  Jupyter Notebook

  •

  Apache License 2.0

  •11 fork•33 stars•88 issues•11 pull request•Updated Apr 9, 2026Apr 9, 2026

• ontology-development-kit

  Public
  Ontology lifecycle management

  robotcontinuous-integrationowl+ 6

  robotcontinuous-integrationowlontologytravisoboprotegemonarchinitiativeobofoundry

  Dockerfile

  •

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

  •5959 forks•316316 stars•8585 issues•11 pull request•Updated Apr 6, 2026Apr 6, 2026

• semantic-sql

  Public
  SQL and SQLite builds of OWL ontologies

  sqlsparqlowl+ 7

  sqlsparqlowlontologiesmonarchinitiativeobofoundrylinkmlrelation-graphoaklibai4curation

  Python

  •

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

  •66 forks•6060 stars•1616 issues•11 pull request•Updated Mar 30, 2026Mar 30, 2026

• odkcore

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

  semantic-webowlontology+ 2

  semantic-webowlontologyobofoundryontology-development-kit

  Jinja

  •

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

  •22 forks•11 star•11 issue•33 pull requests•Updated Mar 17, 2026Mar 17, 2026

• whelk-rs

  Public
  Whelk is an OWL EL reasoner

  rustsemantic-webowl

  rustsemantic-webowl

  Rust

  •

  MIT License

  •66 forks•1616 stars•55 issues•11 pull request•Updated Mar 14, 2026Mar 14, 2026

• relation-graph

  Public
  Materialize OWL existential relations

  rdfowlontology+ 1

  rdfowlontologyobofoundry

  Scala

  •

  MIT License

  •55 forks•2121 stars•77 issues•1111 pull requests•Updated Mar 13, 2026Mar 13, 2026

• ubergraph

  Public
  Integrated OBO ontology store

  rdfowlknowledge-graph+ 2

  rdfowlknowledge-graphobofoundryncats-translator

  Makefile

  •

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

  •55 forks•4848 stars•3333 issues•33 pull requests•Updated Feb 13, 2026Feb 13, 2026

• kgcl

  Public
  Datamodel for KGCL (Knowledge Graph Change Language)

  rdfsemantic-weblinkml+ 3

  rdfsemantic-weblinkmlontology-diffsontology-changeskgcl

  Python

  •

  MIT License

  •44 forks•2222 stars•3232 issues•33 pull requests•Updated Feb 11, 2026Feb 11, 2026

• odk-robot-plugin

  Public
  ROBOT plugin for the Ontology Development Kit

  Java

  •

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

  •11 fork•00 stars•11 issue•00 pull requests•Updated Jan 28, 2026Jan 28, 2026

• odkrunner

  Public
  A binary runner for the Ontology Development Kit

  semantic-webowlontology+ 2

  semantic-webowlontologyobofoundryontology-development-kit

  C

  •

  Other

  •00 forks•44 stars•00 issues•00 pull requests•Updated Jan 2, 2026Jan 2, 2026

• dosdp-tools

  Public
  Utility for working with DOSDP design patterns and OWL ontologies

  design-patternsowlontology+ 4

  design-patternsowlontologyodpmonarchinitiativeobofoundrydosdp-pattern

  Scala

  •

  MIT License

  •55 forks•3131 stars•3434 issues•2020 pull requests•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+ 1

  templatesontologyodpobofoundry

  Python

  •

  GNU General Public License v3.0

  •55 forks•4747 stars•2020 issues•11 pull request•Updated Dec 10, 2025Dec 10, 2025

• PandaSaurus

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

  Python

  •

  Apache License 2.0

  •00 forks•22 stars•11 issue•00 pull requests•Updated Dec 2, 2025Dec 2, 2025

• boomer

  Public
  Bayesian OWL ontology merging

  owlmondoboomer+ 7

  owlmondoboomerreasoningowl-ontologygeneontologymonarchinitiativeobofoundryontology-mergingprobabilistic-owl

  Scala

  •

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

  •22 forks•3535 stars•2727 issues•1515 pull requests•Updated Jun 4, 2025Jun 4, 2025

• whelk

  Public
  Whelk is an OWL EL reasoner

  Scala

  •

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

  •66 forks•3939 stars•55 issues•99 pull requests•Updated Mar 5, 2025Mar 5, 2025

• obographviz

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

  javascriptgraphvizjson+ 4

  javascriptgraphvizjsonnodegraph-visualizationobofoundryobographs

  JavaScript

  •66 forks•2626 stars•99 issues•44 pull requests•Updated Feb 21, 2025Feb 21, 2025

• ontobot-change-agent

  Public
  A GitHub bot for modifying ontology resources.

  botontologychange-language+ 1

  botontologychange-languagekgcl

  Python

  •

  MIT License

  •11 fork•99 stars•2626 issues•11 pull request•Updated Dec 1, 2024Dec 1, 2024

• kgcl-rdflib

  Public
  Tools for working with KGCL

  diffsdiffsemantic-diff+ 8

  diffsdiffsemantic-diffrdfowlontologyknowledge-graphkgobofoundrylinkml+ 1

  Python

  •

  MIT License

  •99 forks•2020 stars•1515 issues•33 pull requests•Updated Nov 19, 2024Nov 19, 2024

• whelk-paper

  Public
  Code for Whelk performance analyses

  Scala

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Oct 4, 2024Oct 4, 2024

• verificado

  Public
  Python

  •

  Apache License 2.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Jun 12, 2024Jun 12, 2024

• biosample-analysis

  Public
  analysis of biosamples in INSDC

  Jupyter Notebook

  •11 fork•33 stars•33 issues•00 pull requests•Updated Feb 13, 2024Feb 13, 2024

• rdf-sql-bulkloader

  Public
  Python

  •11 fork•11 star•11 issue•00 pull requests•Updated Mar 2, 2023Mar 2, 2023

• oakx-grape

  Public
  Experimental OAK plugin for Grape

  Python

  •

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

  •22 forks•55 stars•99 issues•44 pull requests•Updated Feb 10, 2023Feb 10, 2023

• oakx-plugin-cookiecutter

  Public
  cookiecutter for OAK plugins

  pluginscookiecutteroaklib

  pluginscookiecutteroaklib

  Python

  •00 forks•22 stars•00 issues•00 pull requests•Updated Jan 11, 2023Jan 11, 2023

• oakx-robot

  Public
  robot plugin for OAK

  Python

  •00 forks•11 star•00 issues•00 pull requests•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

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 12, 2022Apr 12, 2022

• .github

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Apr 8, 2022Apr 8, 2022

• owl_patternizer

  Public
  generate DOSDP patterns from OWL ontologies

  Prolog

  •

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

  •22 forks•22 stars•00 issues•00 pull requests•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

  •3636 forks•00 stars•00 issues•00 pull requests•Updated Dec 9, 2021Dec 9, 2021