Repositories list

• mondo

  Public template

  monarch-initiative/mondo’s past year of commit activity
  Mondo Disease Ontology

  owlontologymondo+ 5diseasemonarchinitiativedisease-classificationobofoundryai4curation

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •64•291•397•56•Updated Feb 23, 2026Feb 23, 2026

• 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•17•7•0•Updated Feb 23, 2026Feb 23, 2026

• monarch-app

  Public
  Monarch Initiative website and API

  monarchinitiative

  Vue

  •

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

  •7•34•218•17•Updated Feb 23, 2026Feb 23, 2026

• kozahub

  Public
  Dashboard monitoring KozaHub ingest repository health

  Python

  •0•0•0•0•Updated Feb 23, 2026Feb 23, 2026

• phenopacket-store

  Public

  monarch-initiative/phenopacket-store’s past year of commit activity
  Collections of GA4GH phenopackets that represent individuals with Mendelian diseases.

  ga4ghhpomonarchinitiative+ 1phenopackets

  Jupyter Notebook

  •

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

  •6•33•3•0•Updated Feb 23, 2026Feb 23, 2026

• dismech

  Public

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

  monarchinitiativeobofoundryrare-disease+ 4disease-mechanismslinkmlagentic-aikozahub-ingest

  HTML

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

  •1•11•51•10•Updated Feb 23, 2026Feb 23, 2026

• medgen

  Public

  monarch-initiative/medgen’s past year of commit activity
  MedGen ingest.

  monarchinitiative

  Python

  •0•2•9•0•Updated Feb 22, 2026Feb 22, 2026

• semsimian

  Public
  Simple rust implementation of semantic similarity

  monarchinitiative

  Jupyter Notebook

  •

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

  •5•13•20•3•Updated Feb 20, 2026Feb 20, 2026

• mondo-ingest

  Public
  Coordinating the mondo-ingest with external sources

  monarchinitiative

  Jupyter Notebook

  •4•7•254•6•Updated Feb 20, 2026Feb 20, 2026

• phenio

  Public

  monarch-initiative/phenio’s past year of commit activity
  An integrated ontology for Phenomics

  monarchinitiative

  Makefile

  •

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

  •0•8•19•0•Updated Feb 18, 2026Feb 18, 2026

• pumpkin-py

  Public
  Semantic similarity in python with bitmaps

  Python

  •1•2•1•1•Updated Feb 18, 2026Feb 18, 2026

• omim

  Public
  Data ingest pipeline for OMIM.

  biomedical-informaticsmonarchinitiativeontology-engineering

  Jupyter Notebook

  •4•8•72•6•Updated Feb 18, 2026Feb 18, 2026

• zfin-genotype-to-phenotype-ingest

  Public
  Python

  •

  MIT License

  •0•0•0•3•Updated Feb 18, 2026Feb 18, 2026

• monarch-phenotype-profile-ingest

  Public
  human phenotype related ingests

  kozahub-ingest

  Python

  •

  MIT License

  •0•0•0•4•Updated Feb 17, 2026Feb 17, 2026

• zfin-ingest

  Public
  ZFIN data ingest for the Monarch Knowledge Graph

  kozahub-ingest

  Python

  •

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

  •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

• xenbase-ingest

  Public
  Xenbase data ingest for the Monarch Knowledge Graph

  kozahub-ingest

  Python

  •

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

  •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

• upheno-cross-species-ingest

  Public
  kozahub-ingest

  Python

  •

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

  •0•0•0•4•Updated Feb 17, 2026Feb 17, 2026

• string-ingest

  Public
  kozahub-ingest

  Python

  •

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

  •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

• reactome-ingest

  Public
  Koza transforms for Reactome pathway data

  kozahub-ingest

  Python

  •

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

  •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

• pombase-ingest

  Public
  kozahub-ingest

  Python

  •

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

  •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

• phenopacket-ingest

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

  kozahub-ingest

  Python

  •

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

  •0•0•2•4•Updated Feb 17, 2026Feb 17, 2026

• pantherdb-orthologs-ingest

  Public
  orthologs ingest from pantherdb

  kozahub-ingest

  Python

  •

  MIT License

  •0•0•2•4•Updated Feb 17, 2026Feb 17, 2026

• omim-ingest

  Public
  kozahub-ingest

  Python

  •

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

  •0•0•0•4•Updated Feb 17, 2026Feb 17, 2026

• mmrrc-ingest

  Public
  kozahub-ingest

  Python

  •

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

  •0•0•0•1•Updated Feb 17, 2026Feb 17, 2026

• maxo-annotation-ingest

  Public
  kozahub-ingest

  Python

  •

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

  •0•0•0•4•Updated Feb 17, 2026Feb 17, 2026

• hgnc-ingest

  Public
  Python

  •

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

  •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

• go-ingest

  Public
  gene ontology ingest from gene association formatted files

  kozahub-ingest

  Python

  •

  MIT License

  •0•0•0•4•Updated Feb 17, 2026Feb 17, 2026

• dictybase-ingest

  Public
  Dictybase gene and phenotype ingest for Dictyostelium discoideum

  kozahub-ingest

  Python

  •

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

  •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

• ontotools-docker

  Public
  Configuration to deploy ontotools using docker compose

  monarchinitiative

  TypeScript

  •

  Apache License 2.0

  •10•1•3•0•Updated Feb 17, 2026Feb 17, 2026

• ctd-ingest

  Public
  kozahub-ingest

  Python

  •

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

  •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026