Repositories list

• mondo-ingest

  Public
  Coordinating the mondo-ingest with external sources

  monarchinitiative

  Jupyter Notebook

  •3•6•231•19•Updated Feb 2, 2025Feb 2, 2025

• medgen

  Public
  MedGen ingest.

  monarchinitiative

  Python

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

• omim

  Public
  Data ingest pipeline for OMIM.

  biomedical-informaticsmonarchinitiativeontology-engineering

  Jupyter Notebook

  •3•7•65•6•Updated Feb 2, 2025Feb 2, 2025

• icd11

  Public
  ICD11 foundation ingest.

  monarchinitiative

  Python

  •1•1•6•1•Updated Feb 1, 2025Feb 1, 2025

• mondo

  Public template
  Mondo Disease Ontology

  owlontologydisease+ 4monarchinitiativedisease-classificationobofoundrymondo

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •54•239•425•40•Updated Feb 1, 2025Feb 1, 2025

• monarch-project-template

  Public
  A Cookiecutter to kickstart Python based projects.

  Python

  •

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

  •2•4•3•0•Updated Jan 31, 2025Jan 31, 2025

• oncopacket

  Public
  A package to convert cancer data to GA4GH phenopacket

  monarchinitiative

  Jupyter Notebook

  •

  MIT License

  •1•7•22•1•Updated Jan 31, 2025Jan 31, 2025

• gpsea

  Public
  A Python library for discovery of genotype-phenotype associations

  hpomonarchinitiativephenopackets

  Python

  •

  MIT License

  •1•5•12•0•Updated Jan 31, 2025Jan 31, 2025

• monarch_pheval

  Public
  monarchinitiative

  Jinja

  •

  MIT License

  •0•1•3•2•Updated Jan 31, 2025Jan 31, 2025

• monarch-semantic-similarity-profiles

  Public
  Jupyter Notebook

  •

  MIT License

  •0•2•8•2•Updated Jan 31, 2025Jan 31, 2025

• phenio

  Public
  An integrated ontology for Phenomics

  monarchinitiative

  Makefile

  •

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

  •0•6•18•0•Updated Jan 30, 2025Jan 30, 2025

• llm-runner

  Public
  Run multiple AI prompts in batch

  Python

  •

  MIT License

  •0•1•0•0•Updated Jan 30, 2025Jan 30, 2025

• monarch-app

  Public
  Monarch Initiative website and API

  monarchinitiative

  Python

  •

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

  •6•19•188•10•Updated Jan 30, 2025Jan 30, 2025

• emods

  Public
  Monarch and Linda Crrnic Center project on phenotype identification

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 30, 2025Jan 30, 2025

• vertebrate-breed-ontology

  Public
  monarchinitiativeobofoundry

  Makefile

  •1•12•44•4•Updated Jan 29, 2025Jan 29, 2025

• zfin-genotype-to-phenotype-ingest

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 29, 2025Jan 29, 2025

• kghub-downloader

  Public
  Configuration based file caching downloader

  Python

  •0•6•4•2•Updated Jan 27, 2025Jan 27, 2025

• monarch-ingest

  Public
  Data ingest application for Monarch Initiative knowledge graph using Koza

  pythonneo4jsolr+ 7sqlitesemantic-webmonarchinitiativekgxknowledge-graphslinkmllinkml-schema

  Python

  •3•15•37•3•Updated Jan 27, 2025Jan 27, 2025

• rppr_stats

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jan 25, 2025Jan 25, 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

  •86•648•62•8•Updated Jan 25, 2025Jan 25, 2025

• hpotools

  Public
  Human Phenotype Ontology tools

  Java

  •

  MIT License

  •0•1•1•0•Updated Jan 25, 2025Jan 25, 2025

• phenopacket2prompt

  Public
  GA4GH Phenopacket to LLM prompt

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

  Java

  •

  MIT License

  •2•3•3•0•Updated Jan 22, 2025Jan 22, 2025

• phenotype2phenopacket

  Public
  Phenotype2Phenopacket is a command-line tool that converts a phenotype annotation into GA4GH Phenopackets, facilitating standardised phenotypic data representation.

  phenotypesmonarchinitiativephenopackets

  Python

  •1•2•0•0•Updated Jan 22, 2025Jan 22, 2025

• pheval-paper

  Public
  Makefile

  •0•0•0•0•Updated Jan 21, 2025Jan 21, 2025

• pheval

  Public
  A framework for empirical evaluation of phenotype matching and prioritisation

  monarchinitiative

  Python

  •

  Apache License 2.0

  •2•12•29•4•Updated Jan 20, 2025Jan 20, 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•21•14•0•Updated Jan 19, 2025Jan 19, 2025

• pyphetools

  Public
  Python Phenopacket Tools

  monarchinitiative

  Python

  •

  MIT License

  •1•14•4•0•Updated Jan 18, 2025Jan 18, 2025

• mondo-curation-analysis

  Public
  monarchinitiative

  Jupyter Notebook

  •0•0•1•0•Updated Jan 18, 2025Jan 18, 2025

• cookiecutter-monarch-ingest

  Public
  A Cruft cookiecutter for modular Koza ingests

  Python

  •1•2•6•1•Updated Jan 17, 2025Jan 17, 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

  •1•11•17•1•Updated Jan 17, 2025Jan 17, 2025