Repositories list

• ontology-development-kit

  Public
  Bootstrap an OBO Library ontology

  robotcontinuous-integrationowl+ 6ontologytravisoboprotegemonarchinitiativeobofoundry

  Jinja

  •

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

  •53•242•86•4•Updated Mar 7, 2025Mar 7, 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

  •29•133•157•9•Updated Mar 7, 2025Mar 7, 2025

• whelk

  Public
  Whelk is an OWL EL reasoner

  Scala

  •

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

  •5•25•3•9•Updated Mar 5, 2025Mar 5, 2025

• semantic-sql

  Public
  SQL and SQLite builds of OWL ontologies

  owlontologiesobofoundry+ 5linkmlrelation-graphoaklibsqlsparql

  Python

  •

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

  •5•43•13•0•Updated Feb 25, 2025Feb 25, 2025

• ubergraph

  Public
  Integrated OBO ontology store

  obofoundryncats-translatorrdf+ 2owlknowledge-graph

  Makefile

  •

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

  •3•44•31•4•Updated Feb 25, 2025Feb 25, 2025

• obographviz

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

  javascriptnodegraph-visualization+ 4obofoundryobographsgraphvizjson

  JavaScript

  •6•24•9•4•Updated Feb 21, 2025Feb 21, 2025

• odk-robot-plugin

  Public
  ROBOT plugin for the Ontology Development Kit

  Java

  •

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

  •0•0•0•0•Updated Feb 12, 2025Feb 12, 2025

• pandasaurus_cxg

  Public
  Ontology enrichment tool for CxG standard AnnData files

  Jupyter Notebook

  •

  Apache License 2.0

  •1•3•3•0•Updated Dec 10, 2024Dec 10, 2024

• 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+ 8owlontologykgobofoundrylinkmlontology-change-languagerdf+ 1

  Python

  •

  MIT License

  •8•17•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

  •3•15•31•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

• relation-graph

  Public
  Materialize OWL existential relations

  rdfowlontology+ 1obofoundry

  Scala

  •

  MIT License

  •4•15•8•14•Updated Sep 26, 2024Sep 26, 2024

• boomer

  Public
  Bayesian OWL ontology merging

  owlmondoboomer+ 7reasoningowl-ontologygeneontologymonarchinitiativeobofoundryontology-mergingprobabilistic-owl

  Scala

  •

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

  •2•28•26•16•Updated Aug 5, 2024Aug 5, 2024

• dosdp-tools

  Public
  Utility for working with DOSDP design patterns and OWL ontologies

  design-patternsowlodp+ 4monarchinitiativeobofoundryontologydosdp-pattern

  Scala

  •

  MIT License

  •5•27•33•18•Updated Jul 22, 2024Jul 22, 2024

• verificado

  Public
  Python

  •

  Apache License 2.0

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

• PandaSaurus

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

  Python

  •

  Apache License 2.0

  •0•2•2•0•Updated Mar 6, 2024Mar 6, 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

  •4•11•7•1•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

• 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•44•27•0•Updated Feb 25, 2022Feb 25, 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

  •28•0•0•0•Updated Dec 9, 2021Dec 9, 2021

• ontology-term-usage

  Public
  determines how an ontology term has been used

  Python

  •

  Creative Commons Zero v1.0 Universal

  •0•4•2•0•Updated Dec 7, 2021Dec 7, 2021

• table-editor

  Public archive
  Lightweight CSV/TSV editor that supports autocomplete and is guided by a DOSDP-aware YAML configuration.

  monarchinitiative

  JavaScript

  •2•4•18•0•Updated Oct 15, 2021Oct 15, 2021