Repositories list

• graph-agent-devops

  Public
  Working directory for reusable "simple" devops for the graph agent

  HCL

  •

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

  •0•0•5•0•Updated Mar 14, 2025Mar 14, 2025

• aurelian

  Public
  A motley crew of agents developed by the Monarch Initiative

  Python

  •

  MIT License

  •0•4•6•2•Updated Mar 14, 2025Mar 14, 2025

• mondo

  Public template
  Mondo Disease Ontology

  owlontologydisease+ 4monarchinitiativedisease-classificationobofoundrymondo

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •56•244•389•48•Updated Mar 14, 2025Mar 14, 2025

• mondo-ingest

  Public
  Coordinating the mondo-ingest with external sources

  monarchinitiative

  Jupyter Notebook

  •3•7•237•6•Updated Mar 14, 2025Mar 14, 2025

• phenopacket2prompt

  Public
  GA4GH Phenopacket to LLM prompt

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

  Java

  •

  MIT License

  •2•4•4•1•Updated Mar 14, 2025Mar 14, 2025

• ontotools-docker

  Public
  Configuration to deploy ontotools using docker compose

  monarchinitiative

  Shell

  •

  Apache License 2.0

  •10•1•2•1•Updated Mar 13, 2025Mar 13, 2025

• upheno-cross-species-ingest

  Public
  Python

  •

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

  •0•0•0•0•Updated Mar 13, 2025Mar 13, 2025

• phenol

  Public
  phenol: Phenotype ontology library

  genomicsontologiesphenotypes+ 5monarchinitiativephenomicshuman-phenotype-ontologymammalian-phenotype-ontologyjava

  Java

  •

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

  •4•23•7•2•Updated Mar 13, 2025Mar 13, 2025

• monarch-phenologs

  Public
  monarchinitiative

  Python

  •

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

  •0•3•14•0•Updated Mar 13, 2025Mar 13, 2025

• omim

  Public
  Data ingest pipeline for OMIM.

  biomedical-informaticsmonarchinitiativeontology-engineering

  Jupyter Notebook

  •3•7•68•4•Updated Mar 12, 2025Mar 12, 2025

• monarchkg-model-organism-phenotype-transform

  Public
  Python

  •

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

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

• ELDER

  Public
  LLM embeddings for rare disease diagnostics

  Python

  •0•4•5•0•Updated Mar 12, 2025Mar 12, 2025

• zfin-genotype-to-phenotype-ingest

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Mar 12, 2025Mar 12, 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•6•9•1•Updated Mar 11, 2025Mar 11, 2025

• clingen-ingest

  Public
  Python

  •

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

  •0•3•0•1•Updated Mar 11, 2025Mar 11, 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

  •89•657•63•10•Updated Mar 11, 2025Mar 11, 2025

• monarch-app

  Public
  Monarch Initiative website and API

  monarchinitiative

  Python

  •

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

  •6•22•212•11•Updated Mar 11, 2025Mar 11, 2025

• llm-matrix

  Public
  Run multiple AI prompts in batch

  Python

  •

  MIT License

  •0•2•0•0•Updated Mar 11, 2025Mar 11, 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

  •5•23•13•2•Updated Mar 10, 2025Mar 10, 2025

• ncbi-gene

  Public
  Python

  •

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

  •1•0•0•0•Updated Mar 10, 2025Mar 10, 2025

• medgen

  Public
  MedGen ingest.

  monarchinitiative

  Python

  •0•1•9•0•Updated Mar 9, 2025Mar 9, 2025

• phenio

  Public
  An integrated ontology for Phenomics

  monarchinitiative

  Makefile

  •

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

  •0•6•18•0•Updated Mar 7, 2025Mar 7, 2025

• pheval

  Public
  A framework for empirical evaluation of phenotype matching and prioritisation

  monarchinitiative

  Python

  •

  Apache License 2.0

  •2•12•29•4•Updated Mar 7, 2025Mar 7, 2025

• phenopacket-store-toolkit

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

  Python

  •

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

  •0•0•0•0•Updated Mar 5, 2025Mar 5, 2025

• biogrid-ingest

  Public
  BioGRID ingest

  Python

  •

  MIT License

  •0•0•2•1•Updated Mar 4, 2025Mar 4, 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•16•0•Updated Mar 3, 2025Mar 3, 2025

• monarch-documentation

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

  Python

  •

  GNU General Public License v3.0

  •0•7•24•1•Updated Mar 3, 2025Mar 3, 2025

• go-ingest

  Public
  gene ontology ingest from gene association formatted files

  Python

  •

  MIT License

  •0•0•0•0•Updated Mar 3, 2025Mar 3, 2025

• clinvar-ingest

  Public
  Python

  •

  MIT License

  •0•3•1•0•Updated Mar 3, 2025Mar 3, 2025

• alliance-genotype-ingest

  Public
  Python

  •

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

  •0•1•0•0•Updated Mar 3, 2025Mar 3, 2025