Repositories list

• aurelian

  Public
  Python

  •

  MIT License

  •0•2•0•1•Updated Mar 1, 2025Mar 1, 2025

• monarch-phenologs

  Public
  monarchinitiative

  Python

  •

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

  •0•3•14•0•Updated Mar 1, 2025Mar 1, 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

  •88•655•63•9•Updated Feb 28, 2025Feb 28, 2025

• monarch-app

  Public
  Monarch Initiative website and API

  monarchinitiative

  Python

  •

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

  •6•21•191•13•Updated Feb 28, 2025Feb 28, 2025

• mondo

  Public template
  Mondo Disease Ontology

  owlontologydisease+ 4monarchinitiativedisease-classificationobofoundrymondo

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •55•241•398•52•Updated Feb 28, 2025Feb 28, 2025

• curategpt

  Public
  LLM-driven curation assist tool

  aigptontologies+ 7curationbiocurationmonarchinitiativeobofoundryontology-toolsllmontogpt

  Jupyter Notebook

  •

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

  •12•81•31•5•Updated Feb 28, 2025Feb 28, 2025

• koza

  Public
  Data transformation framework for LinkML data models

  ontologyknowledge-graphmonarchinitiative+ 4obofoundrylinkmlkozaetl

  Python

  •

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

  •4•48•38•5•Updated Feb 28, 2025Feb 28, 2025

• phenopacket2prompt

  Public
  GA4GH Phenopacket to LLM prompt

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

  Java

  •

  MIT License

  •2•3•4•1•Updated Feb 28, 2025Feb 28, 2025

• mondo-ingest

  Public
  Coordinating the mondo-ingest with external sources

  monarchinitiative

  Jupyter Notebook

  •3•7•237•6•Updated Feb 27, 2025Feb 27, 2025

• phenotype2phenopacket

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

  phenotypesmonarchinitiativephenopackets

  Python

  •2•2•0•0•Updated Feb 27, 2025Feb 27, 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 26, 2025Feb 26, 2025

• mic-ingest

  Public
  Ingest for Micronutrient Information Center using OntoGPT

  Python

  •

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

  •0•3•0•0•Updated Feb 26, 2025Feb 26, 2025

• zfin-genotype-to-phenotype-ingest

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Feb 26, 2025Feb 26, 2025

• pheval

  Public
  A framework for empirical evaluation of phenotype matching and prioritisation

  monarchinitiative

  Python

  •

  Apache License 2.0

  •2•12•30•3•Updated Feb 25, 2025Feb 25, 2025

• pheval.exomiser

  Public
  Exomiser plugin for PhEval.

  monarchinitiative

  Python

  •1•4•3•2•Updated Feb 25, 2025Feb 25, 2025

• omim

  Public
  Data ingest pipeline for OMIM.

  biomedical-informaticsmonarchinitiativeontology-engineering

  Jupyter Notebook

  •3•7•67•4•Updated Feb 24, 2025Feb 24, 2025

• medgen

  Public
  MedGen ingest.

  monarchinitiative

  Python

  •0•1•9•0•Updated Feb 23, 2025Feb 23, 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•1•Updated Feb 21, 2025Feb 21, 2025

• ELDER

  Public
  LLM embeddings for rare disease diagnostics

  Python

  •0•3•5•0•Updated Feb 21, 2025Feb 21, 2025

• llm-matrix

  Public
  Run multiple AI prompts in batch

  Python

  •

  MIT License

  •0•2•0•0•Updated Feb 21, 2025Feb 21, 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•17•1•Updated Feb 20, 2025Feb 20, 2025

• talisman

  Public
  LLM-based gene function enrichment tool

  nlpmonarchinitiativegene-enrichment+ 2llmlarge-language-model

  Jupyter Notebook

  •

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

  •88•10•0•0•Updated Feb 19, 2025Feb 19, 2025

• monarch-ingest

  Public
  Data ingest application for Monarch Initiative knowledge graph using Koza

  pythonneo4jsolr+ 7sqlitesemantic-webmonarchinitiativekgxknowledge-graphslinkmllinkml-schema

  Python

  •3•15•35•4•Updated Feb 19, 2025Feb 19, 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 18, 2025Feb 18, 2025

• monarchkg-model-organism-phenotype-transform

  Public
  Python

  •

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

  •0•0•0•0•Updated Feb 17, 2025Feb 17, 2025

• phenio

  Public
  An integrated ontology for Phenomics

  monarchinitiative

  Makefile

  •

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

  •0•6•18•0•Updated Feb 16, 2025Feb 16, 2025

• monochrom

  Public
  Standardized identifiers and OWL classes for chromosomes and chromosomal parts across species

  genomicsetlowl+ 4chromosomesmonarchinitiativeobofoundrylinkml

  Python

  •2•13•18•0•Updated Feb 15, 2025Feb 15, 2025

• monarch-documentation

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

  Python

  •

  GNU General Public License v3.0

  •0•7•22•1•Updated Feb 15, 2025Feb 15, 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

• vertebrate-breed-ontology

  Public
  monarchinitiativeobofoundry

  Makefile

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