Repositories list

• omim

  Public
  Data ingest pipeline for OMIM.

  biomedical-informaticsmonarchinitiativeontology-engineering

  Jupyter Notebook

  •4•8•71•4•Updated Aug 21, 2025Aug 21, 2025

• mondo-ingest

  Public
  Coordinating the mondo-ingest with external sources

  monarchinitiative

  Jupyter Notebook

  •3•7•250•9•Updated Aug 21, 2025Aug 21, 2025

• mondo

  Public template
  Mondo Disease Ontology

  owlontologydisease+ 4monarchinitiativedisease-classificationobofoundrymondo

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •59•264•352•52•Updated Aug 21, 2025Aug 21, 2025

• monarch-app

  Public
  Monarch Initiative website and API

  monarchinitiative

  Vue

  •

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

  •7•28•249•14•Updated Aug 21, 2025Aug 21, 2025

• closurizer

  Public
  Add closure expansion fields to kgx files following the Golr pattern

  Python

  •0•4•1•1•Updated Aug 21, 2025Aug 21, 2025

• koza

  Public
  Data transformation framework for LinkML data models

  ontologyknowledge-graphmonarchinitiative+ 4obofoundrylinkmlkozaetl

  Python

  •

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

  •5•54•36•7•Updated Aug 21, 2025Aug 21, 2025

• helpdesk

  Public
  The Monarch Initiative Helpdesk

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

  •0•7•6•0•Updated Aug 20, 2025Aug 20, 2025

• namo

  Public
  monarchinitiativeai4curation

  Python

  •

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

  •0•1•0•5•Updated Aug 20, 2025Aug 20, 2025

• monarch-project-copier

  Public
  New template for monarch repos, replaces old cookiecutter

  templatebest-practicescookiecutter+ 2copiermonarchinitiative

  Jinja

  •

  MIT License

  •0•1•1•3•Updated Aug 20, 2025Aug 20, 2025

• cat-merge

  Public
  Tooling for merging individual source KGX files in the Monarch ingest pipeline

  Python

  •1•2•9•1•Updated Aug 20, 2025Aug 20, 2025

• zfin-genotype-to-phenotype-ingest

  Public
  Python

  •

  MIT License

  •0•0•0•1•Updated Aug 20, 2025Aug 20, 2025

• monarch-ingest

  Public
  Data ingest application for Monarch Initiative knowledge graph using Koza

  pythonneo4jsolr+ 7sqlitesemantic-webmonarchinitiativekgxknowledge-graphslinkmllinkml-schema

  Python

  •

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

  •4•19•36•7•Updated Aug 19, 2025Aug 19, 2025

• monarchr

  Public
  R package for easy access, manipulation, and analysis of the Monarch Initiative or other KGX-formatted knowledge graphs.

  knowledge-graphrlangmonarchinitiative

  R

  •

  Other

  •3•15•6•1•Updated Aug 19, 2025Aug 19, 2025

• semsimian-server

  Public
  Rust web server for Semsimian - a semantic similarity implementation

  Rust

  •

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

  •1•0•5•3•Updated Aug 18, 2025Aug 18, 2025

• mic-ingest

  Public
  Ingest for Micronutrient Information Center using OntoGPT

  Python

  •

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

  •0•3•2•1•Updated Aug 18, 2025Aug 18, 2025

• monarch-phenotype-profile-ingest

  Public
  human phenotype related ingests

  Python

  •

  MIT License

  •0•0•0•1•Updated Aug 18, 2025Aug 18, 2025

• clinvar-ingest

  Public
  Python

  •

  MIT License

  •0•3•1•1•Updated Aug 18, 2025Aug 18, 2025

• biogrid-ingest

  Public
  BioGRID ingest

  Python

  •

  MIT License

  •0•0•2•2•Updated Aug 18, 2025Aug 18, 2025

• phenologs-transform

  Public
  Python

  •

  MIT License

  •0•0•0•1•Updated Aug 18, 2025Aug 18, 2025

• alliance-variant-allele-ingest

  Public
  Python

  •

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

  •0•0•0•1•Updated Aug 18, 2025Aug 18, 2025

• go-ingest

  Public
  gene ontology ingest from gene association formatted files

  Python

  •

  MIT License

  •0•0•0•1•Updated Aug 18, 2025Aug 18, 2025

• alliance-phenotype-association-ingest

  Public
  Python

  •

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

  •0•0•0•1•Updated Aug 18, 2025Aug 18, 2025

• gocam_ingest

  Public
  Ingest of GOCAM suitable for inclusion in KG

  Python

  •

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

  •0•2•1•1•Updated Aug 18, 2025Aug 18, 2025

• string_modular

  Public
  Modular ingest of STRING PPIs

  Python

  •

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

  •0•0•1•1•Updated Aug 18, 2025Aug 18, 2025

• maxo-annotations

  Public
  Annotations to terms of the Medical Action Ontology (MAxO)

  monarchinitiativeobofoundryhuman-phenotype-ontology+ 4therapeuticsmaxomedical-actionsmondo-ontology

  Python

  •

  Creative Commons Attribution 4.0 International

  •0•2•72•0•Updated Aug 17, 2025Aug 17, 2025

• upheno-cross-species-ingest

  Public
  Python

  •

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

  •0•0•0•0•Updated Aug 17, 2025Aug 17, 2025

• medgen

  Public
  MedGen ingest.

  monarchinitiative

  Python

  •0•1•9•0•Updated Aug 17, 2025Aug 17, 2025

• ontogpt

  Public
  LLM-based ontological extraction tools, including SPIRES

  nlpaiinformation-extraction+ 13named-entity-recognitionlanguage-modelsnerdata-modelingrelation-extractionmonarchinitiativeobofoundry+ 6

  Jupyter Notebook

  •

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

  •98•720•67•10•Updated Aug 15, 2025Aug 15, 2025

• monarch-robot-plugins

  Public
  Repository to manage monarch specific ROBOT extensions

  Java

  •0•1•0•1•Updated Aug 15, 2025Aug 15, 2025

• pheval.llm

  Public
  Analysis of LLMs for Clinical Observations

  hpomonarchinitiativephenopackets+ 4clinical-diagnosisbiomedical-ontologiesrare-diseaseslarge-language-models

  Python

  •

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

  •1•7•2•2•Updated Aug 15, 2025Aug 15, 2025