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

  •3737 forks in INCATools/ontology-access-kit•206206 stars in INCATools/ontology-access-kit•183183 issues in INCATools/ontology-access-kit•88 pull requests in INCATools/ontology-access-kit•Updated Nov 3, 2026Nov 3, 2026

• ontology-development-kit

  Public
  Ontology lifecycle management

  robotcontinuous-integrationowl+ 6

  robotcontinuous-integrationowlontologytravisoboprotegemonarchinitiativeobofoundry

  Dockerfile

  •

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

  •6969 forks in INCATools/ontology-development-kit•388388 stars in INCATools/ontology-development-kit•6969 issues in INCATools/ontology-development-kit•22 pull requests in INCATools/ontology-development-kit•Updated Nov 2, 2026Nov 2, 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

  •44 forks in INCATools/odkcore•44 stars in INCATools/odkcore•33 issues in INCATools/odkcore•11 pull request in INCATools/odkcore•Updated Oct 30, 2026Oct 30, 2026

• relation-graph

  Public
  Materialize OWL existential relations

  rdfowlontology+ 1

  rdfowlontologyobofoundry

  Scala

  •

  MIT License

  •44 forks in INCATools/relation-graph•2424 stars in INCATools/relation-graph•77 issues in INCATools/relation-graph•1717 pull requests in INCATools/relation-graph•Updated Oct 24, 2026Oct 24, 2026

• whelk

  Public
  Whelk is an OWL EL reasoner

  Scala

  •

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

  •55 forks in INCATools/whelk•4747 stars in INCATools/whelk•55 issues in INCATools/whelk•77 pull requests in INCATools/whelk•Updated Oct 24, 2026Oct 24, 2026

• odkrunner

  Public
  A binary runner for the Ontology Development Kit

  semantic-webowlontology+ 2

  semantic-webowlontologyobofoundryontology-development-kit

  C

  •

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

  •00 forks in INCATools/odkrunner•55 stars in INCATools/odkrunner•00 issues in INCATools/odkrunner•00 pull requests in INCATools/odkrunner•Updated Oct 14, 2026Oct 14, 2026

• odk-robot-plugin

  Public
  ROBOT plugin for the Ontology Development Kit

  Java

  •

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

  •00 forks in INCATools/odk-robot-plugin•11 star in INCATools/odk-robot-plugin•11 issue in INCATools/odk-robot-plugin•11 pull request in INCATools/odk-robot-plugin•Updated Oct 14, 2026Oct 14, 2026

• ubergraph

  Public
  Integrated OBO ontology store

  rdfowlknowledge-graph+ 2

  rdfowlknowledge-graphobofoundryncats-translator

  Makefile

  •

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

  •55 forks in INCATools/ubergraph•5353 stars in INCATools/ubergraph•3434 issues in INCATools/ubergraph•33 pull requests in INCATools/ubergraph•Updated Oct 2, 2026Oct 2, 2026

• semantic-sql

  Public
  SQL and SQLite builds of OWL ontologies

  sqlsparqlowl+ 7

  sqlsparqlowlontologiesmonarchinitiativeobofoundrylinkmlrelation-graphoaklibai4curation

  Python

  •

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

  •77 forks in INCATools/semantic-sql•7171 stars in INCATools/semantic-sql•1919 issues in INCATools/semantic-sql•44 pull requests in INCATools/semantic-sql•Updated Sep 22, 2026Sep 22, 2026

• whelk-rs

  Public
  Whelk is an OWL EL reasoner

  rustsemantic-webowl

  rustsemantic-webowl

  Rust

  •

  MIT License

  •1010 forks in INCATools/whelk-rs•2424 stars in INCATools/whelk-rs•44 issues in INCATools/whelk-rs•00 pull requests in INCATools/whelk-rs•Updated Jun 29, 2026Jun 29, 2026

• dosdp-tools

  Public
  Utility for working with DOSDP design patterns and OWL ontologies

  design-patternsowlontology+ 4

  design-patternsowlontologyodpmonarchinitiativeobofoundrydosdp-pattern

  Scala

  •

  MIT License

  •44 forks in INCATools/dosdp-tools•3333 stars in INCATools/dosdp-tools•3232 issues in INCATools/dosdp-tools•1010 pull requests in INCATools/dosdp-tools•Updated May 21, 2026May 21, 2026

• pandasaurus_cxg

  Public
  Ontology enrichment tool for CxG standard AnnData files

  Jupyter Notebook

  •

  Apache License 2.0

  •11 fork in INCATools/pandasaurus_cxg•33 stars in INCATools/pandasaurus_cxg•66 issues in INCATools/pandasaurus_cxg•00 pull requests in INCATools/pandasaurus_cxg•Updated Apr 28, 2026Apr 28, 2026

• kgcl

  Public
  Datamodel for KGCL (Knowledge Graph Change Language)

  rdfsemantic-weblinkml+ 3

  rdfsemantic-weblinkmlontology-diffsontology-changeskgcl

  Python

  •

  MIT License

  •66 forks in INCATools/kgcl•2323 stars in INCATools/kgcl•3232 issues in INCATools/kgcl•33 pull requests in INCATools/kgcl•Updated Feb 11, 2026Feb 11, 2026

• 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 in INCATools/dead_simple_owl_design_patterns•4949 stars in INCATools/dead_simple_owl_design_patterns•2121 issues in INCATools/dead_simple_owl_design_patterns•22 pull requests in INCATools/dead_simple_owl_design_patterns•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 in INCATools/PandaSaurus•22 stars in INCATools/PandaSaurus•11 issue in INCATools/PandaSaurus•00 pull requests in INCATools/PandaSaurus•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 in INCATools/boomer•3737 stars in INCATools/boomer•2727 issues in INCATools/boomer•1717 pull requests in INCATools/boomer•Updated Jun 4, 2025Jun 4, 2025

• obographviz

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

  javascriptgraphvizjson+ 4

  javascriptgraphvizjsonnodegraph-visualizationobofoundryobographs

  JavaScript

  •66 forks in INCATools/obographviz•2727 stars in INCATools/obographviz•99 issues in INCATools/obographviz•44 pull requests in INCATools/obographviz•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 in INCATools/ontobot-change-agent•99 stars in INCATools/ontobot-change-agent•2626 issues in INCATools/ontobot-change-agent•11 pull request in INCATools/ontobot-change-agent•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 in INCATools/kgcl-rdflib•2020 stars in INCATools/kgcl-rdflib•1515 issues in INCATools/kgcl-rdflib•33 pull requests in INCATools/kgcl-rdflib•Updated Nov 19, 2024Nov 19, 2024

• whelk-paper

  Public
  Code for Whelk performance analyses

  Scala

  •

  MIT License

  •00 forks in INCATools/whelk-paper•11 star in INCATools/whelk-paper•00 issues in INCATools/whelk-paper•00 pull requests in INCATools/whelk-paper•Updated Oct 4, 2024Oct 4, 2024

• verificado

  Public
  Python

  •

  Apache License 2.0

  •00 forks in INCATools/verificado•11 star in INCATools/verificado•00 issues in INCATools/verificado•00 pull requests in INCATools/verificado•Updated Jun 12, 2024Jun 12, 2024

• biosample-analysis

  Public
  analysis of biosamples in INSDC

  Jupyter Notebook

  •11 fork in INCATools/biosample-analysis•33 stars in INCATools/biosample-analysis•33 issues in INCATools/biosample-analysis•00 pull requests in INCATools/biosample-analysis•Updated Feb 13, 2024Feb 13, 2024

• rdf-sql-bulkloader

  Public
  Python

  •11 fork in INCATools/rdf-sql-bulkloader•11 star in INCATools/rdf-sql-bulkloader•11 issue in INCATools/rdf-sql-bulkloader•00 pull requests in INCATools/rdf-sql-bulkloader•Updated Mar 2, 2023Mar 2, 2023

• oakx-grape

  Public
  Experimental OAK plugin for Grape

  Python

  •

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

  •22 forks in INCATools/oakx-grape•55 stars in INCATools/oakx-grape•99 issues in INCATools/oakx-grape•44 pull requests in INCATools/oakx-grape•Updated Feb 10, 2023Feb 10, 2023

• oakx-plugin-cookiecutter

  Public
  cookiecutter for OAK plugins

  pluginscookiecutteroaklib

  pluginscookiecutteroaklib

  Python

  •00 forks in INCATools/oakx-plugin-cookiecutter•22 stars in INCATools/oakx-plugin-cookiecutter•00 issues in INCATools/oakx-plugin-cookiecutter•00 pull requests in INCATools/oakx-plugin-cookiecutter•Updated Jan 11, 2023Jan 11, 2023

• oakx-robot

  Public
  robot plugin for OAK

  Python

  •00 forks in INCATools/oakx-robot•11 star in INCATools/oakx-robot•00 issues in INCATools/oakx-robot•00 pull requests in INCATools/oakx-robot•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 in INCATools/obo-shapes•00 stars in INCATools/obo-shapes•00 issues in INCATools/obo-shapes•00 pull requests in INCATools/obo-shapes•Updated Apr 12, 2022Apr 12, 2022

• .github

  Public
  00 forks in INCATools/.github•00 stars in INCATools/.github•00 issues in INCATools/.github•00 pull requests in INCATools/.github•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 in INCATools/owl_patternizer•22 stars in INCATools/owl_patternizer•00 issues in INCATools/owl_patternizer•00 pull requests in INCATools/owl_patternizer•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

  •4141 forks in INCATools/DataHarmonizer•00 stars in INCATools/DataHarmonizer•00 issues in INCATools/DataHarmonizer•00 pull requests in INCATools/DataHarmonizer•Updated Dec 9, 2021Dec 9, 2021