Repositories list

• mondo

  Public template
  Mondo Disease Ontology

  owlontologydisease+ 4monarchinitiativedisease-classificationobofoundrymondo

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •54•239•405•45•Updated Feb 14, 2025Feb 14, 2025

• llm-runner

  Public
  Run multiple AI prompts in batch

  Python

  •

  MIT License

  •0•1•0•0•Updated Feb 14, 2025Feb 14, 2025

• monarchkg-model-organism-gene-transform

  Public
  Python

  •

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

  •0•0•0•0•Updated Feb 14, 2025Feb 14, 2025

• monarch-ingest

  Public
  Data ingest application for Monarch Initiative knowledge graph using Koza

  pythonneo4jsolr+ 7sqlitesemantic-webmonarchinitiativekgxknowledge-graphslinkmllinkml-schema

  Python

  •3•15•35•3•Updated Feb 14, 2025Feb 14, 2025

• monarch-app

  Public
  Monarch Initiative website and API

  monarchinitiative

  Python

  •

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

  •6•20•191•12•Updated Feb 14, 2025Feb 14, 2025

• oak-agent

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 14, 2025Feb 14, 2025

• monarch-documentation

  Public
  Technical documentation for all Monarch applications, packages, services and related projects.

  Python

  •

  GNU General Public License v3.0

  •0•7•21•2•Updated Feb 13, 2025Feb 13, 2025

• vertebrate-breed-ontology

  Public
  monarchinitiativeobofoundry

  Makefile

  •1•12•44•4•Updated Feb 13, 2025Feb 13, 2025

• mic-ingest

  Public
  Ingest for Micronutrient Information Center using OntoGPT

  Python

  •

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

  •0•3•0•1•Updated Feb 13, 2025Feb 13, 2025

• ontotools-docker

  Public
  Configuration to deploy ontotools using docker compose

  monarchinitiative

  Shell

  •

  Apache License 2.0

  •10•1•2•0•Updated Feb 13, 2025Feb 13, 2025

• mondo-ingest

  Public
  Coordinating the mondo-ingest with external sources

  monarchinitiative

  Jupyter Notebook

  •3•6•231•16•Updated Feb 12, 2025Feb 12, 2025

• zfin-genotype-to-phenotype-ingest

  Public
  Python

  •

  MIT License

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

• oncopacket

  Public
  A package to convert cancer data to GA4GH phenopacket

  monarchinitiative

  Jupyter Notebook

  •

  MIT License

  •1•7•20•1•Updated Feb 11, 2025Feb 11, 2025

• gpsea

  Public
  A Python library for discovery of genotype-phenotype associations

  hpomonarchinitiativephenopackets

  Python

  •

  MIT License

  •1•5•12•0•Updated Feb 11, 2025Feb 11, 2025

• phenio

  Public
  An integrated ontology for Phenomics

  monarchinitiative

  Makefile

  •

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

  •0•6•18•0•Updated Feb 10, 2025Feb 10, 2025

• monarch-semantic-similarity-profiles

  Public
  Jupyter Notebook

  •

  MIT License

  •0•2•7•3•Updated Feb 9, 2025Feb 9, 2025

• medgen

  Public
  MedGen ingest.

  monarchinitiative

  Python

  •0•2•9•0•Updated Feb 9, 2025Feb 9, 2025

• omim

  Public
  Data ingest pipeline for OMIM.

  biomedical-informaticsmonarchinitiativeontology-engineering

  Jupyter Notebook

  •3•7•66•5•Updated Feb 9, 2025Feb 9, 2025

• monarch-mapping-commons

  Public
  Building a fully exectuable workflow for boomer

  Python

  •

  Creative Commons Zero v1.0 Universal

  •3•4•13•1•Updated Feb 8, 2025Feb 8, 2025

• cookiecutter-monarch-ingest

  Public
  A Cruft cookiecutter for modular Koza ingests

  Python

  •1•2•6•1•Updated Feb 7, 2025Feb 7, 2025

• setsim

  Public
  A proof of concept of the summing similarity measure.

  Python

  •0•1•4•2•Updated Feb 7, 2025Feb 7, 2025

• curategpt

  Public
  LLM-driven curation assist tool

  aigptontologies+ 7curationbiocurationmonarchinitiativeobofoundryontology-toolsllmontogpt

  Jupyter Notebook

  •

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

  •12•80•30•5•Updated Feb 7, 2025Feb 7, 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

  •2•14•15•0•Updated Feb 6, 2025Feb 6, 2025

• emods

  Public
  Monarch and Linda Crrnic Center project on phenotype identification

  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 5, 2025Feb 5, 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

  •0•5•9•1•Updated Feb 4, 2025Feb 4, 2025

• phenopacket2prompt

  Public
  GA4GH Phenopacket to LLM prompt

  monarchinitiativephenopacketshuman-phenotype-ontology+ 3deep-phenotypinglarge-language-modelsprompt-engineering

  Java

  •

  MIT License

  •2•3•3•1•Updated Feb 4, 2025Feb 4, 2025

• closurizer

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

  Python

  •0•4•1•0•Updated Feb 4, 2025Feb 4, 2025

• monarch-neo4j

  Public
  Dockerized Managed Neo4j Database for Monarch

  Shell

  •

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

  •0•4•1•0•Updated Feb 3, 2025Feb 3, 2025

• phenopacket-store

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

  ga4ghhpomonarchinitiative+ 1phenopackets

  Jupyter Notebook

  •

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

  •4•22•14•0•Updated Feb 3, 2025Feb 3, 2025

• go-ingest

  Public
  gene ontology ingest from gene association formatted files

  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 3, 2025Feb 3, 2025