Repositories list

• dismech

  Public

  monarch-initiative/dismech’s past year of commit activity
  Disease Mechanisms KB

  monarchinitiativeai4curation

  HTML

  •

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

  •0•8•12•12•Updated Jan 17, 2026Jan 17, 2026

• koza

  Public

  monarch-initiative/koza’s past year of commit activity
  Data transformation framework for LinkML data models

  etlontologyknowledge-graph+ 4monarchinitiativeobofoundrylinkmlkoza

  Python

  •

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

  •5•60•37•9•Updated Jan 17, 2026Jan 17, 2026

• monarch-app

  Public
  Monarch Initiative website and API

  monarchinitiative

  Vue

  •

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

  •7•32•215•17•Updated Jan 17, 2026Jan 17, 2026

• mondo

  Public template
  Mondo Disease Ontology

  owlontologymondo+ 5diseasemonarchinitiativedisease-classificationobofoundryai4curation

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •63•287•401•56•Updated Jan 16, 2026Jan 16, 2026

• MAxO

  Public
  Medical action ontology

  medicineowlontology+ 7medicaldiagnosticsinterventionstreatmentstreatmentmonarchinitiativeobofoundry

  HTML

  •

  Creative Commons Attribution 4.0 International

  •5•61•7•0•Updated Jan 15, 2026Jan 15, 2026

• pheval.exomiser

  Public

  monarch-initiative/pheval.exomiser’s past year of commit activity
  Exomiser plugin for PhEval.

  monarchinitiative

  Python

  •1•4•1•0•Updated Jan 15, 2026Jan 15, 2026

• pheval

  Public
  A framework for empirical evaluation of phenotype matching and prioritisation

  monarchinitiative

  Python

  •

  Apache License 2.0

  •5•13•24•3•Updated Jan 15, 2026Jan 15, 2026

• phenopacket-store

  Public
  Collections of GA4GH phenopackets that represent individuals with Mendelian diseases.

  ga4ghhpomonarchinitiative+ 1phenopackets

  Jupyter Notebook

  •

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

  •5•30•3•0•Updated Jan 15, 2026Jan 15, 2026

• monarch-phenologs

  Public
  monarchinitiative

  Python

  •

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

  •0•3•16•0•Updated Jan 15, 2026Jan 15, 2026

• monarch-ingest

  Public

  monarch-initiative/monarch-ingest’s past year of commit activity
  Data ingest application for Monarch Initiative knowledge graph using Koza

  pythonneo4jsolr+ 7sqlitesemantic-webmonarchinitiativekgxknowledge-graphslinkmllinkml-schema

  Python

  •

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

  •5•20•38•10•Updated Jan 15, 2026Jan 15, 2026

• omim

  Public
  Data ingest pipeline for OMIM.

  biomedical-informaticsmonarchinitiativeontology-engineering

  Jupyter Notebook

  •4•8•73•6•Updated Jan 14, 2026Jan 14, 2026

• zfin-genotype-to-phenotype-ingest

  Public
  Python

  •

  MIT License

  •0•0•0•2•Updated Jan 14, 2026Jan 14, 2026

• mondo-clingen-test

  Public
  Test Repo for some Clingen Gene Tracker - Mondo workflows

  Creative Commons Zero v1.0 Universal

  •0•0•4•0•Updated Jan 13, 2026Jan 13, 2026

• deep-research-client

  Public
  A simple Python wrapper for multiple deep research tools including OpenAI Deep Research, FutureHouse Falcon, and Perplexity AI.

  monarchinitiativeai4curation

  Python

  •1•9•2•7•Updated Jan 12, 2026Jan 12, 2026

• medgen

  Public
  MedGen ingest.

  monarchinitiative

  Python

  •0•1•9•0•Updated Jan 11, 2026Jan 11, 2026

• phenopacket-ingest

  Public
  This is a modular ingest for phenopackets into the Monarch KG

  Python

  •

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

  •0•0•2•2•Updated Jan 10, 2026Jan 10, 2026

• mondo-ingest

  Public
  Coordinating the mondo-ingest with external sources

  monarchinitiative

  Jupyter Notebook

  •4•7•252•6•Updated Jan 9, 2026Jan 9, 2026

• phenopacket-store-toolkit

  Public
  Toolkit for accessing, Q/C, and maintenance of Phenopacket Store

  Python

  •

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

  •0•0•1•0•Updated Jan 8, 2026Jan 8, 2026

• embiggen

  Public
  🍇 Embiggen is the Python Graph Representation learning, Prediction and Evaluation submodule of the GRAPE library.

  machine-learninggraphgraph-representation-learning

  Python

  •

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

  •13•43•4•1•Updated Jan 8, 2026Jan 8, 2026

• pantherdb-orthologs-ingest

  Public
  orthologs ingest from pantherdb

  Python

  •

  MIT License

  •0•0•2•3•Updated Jan 8, 2026Jan 8, 2026

• kghub-downloader

  Public
  Configuration based file caching downloader

  Python

  •0•6•5•4•Updated Jan 7, 2026Jan 7, 2026

• go-ingest

  Public
  gene ontology ingest from gene association formatted files

  Python

  •

  MIT License

  •0•0•0•2•Updated Jan 3, 2026Jan 3, 2026

• alliance-genotype-ingest

  Public
  Python

  •

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

  •0•1•0•2•Updated Jan 3, 2026Jan 3, 2026

• clinvar-ingest

  Public
  Python

  •

  MIT License

  •0•3•1•2•Updated Jan 3, 2026Jan 3, 2026

• alliance-disease-association-ingest

  Public
  Python

  •

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

  •0•0•0•3•Updated Jan 3, 2026Jan 3, 2026

• ncbi-gene

  Public
  Python

  •

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

  •1•0•0•2•Updated Jan 3, 2026Jan 3, 2026

• alliance-phenotype-association-ingest

  Public
  Python

  •

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

  •0•0•0•2•Updated Jan 3, 2026Jan 3, 2026

• alliance-ingest

  Public
  Biolink Model compliant KGX transformation of data from the Alliance of Genome Resources

  Python

  •

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

  •0•0•0•3•Updated Jan 3, 2026Jan 3, 2026

• clingen-ingest

  Public
  Python

  •

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

  •0•3•0•2•Updated Jan 3, 2026Jan 3, 2026

• zfin-orthology-ingest

  Public
  Python

  •

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

  •0•0•0•3•Updated Jan 3, 2026Jan 3, 2026