Repositories list

• hpotools

  Public
  Human Phenotype Ontology tools

  Java

  •

  MIT License

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

• omim

  Public
  Data ingest pipeline for OMIM.

  biomedical-informaticsmonarchinitiativeontology-engineering

  Jupyter Notebook

  •3•7•64•3•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•641•62•9•Updated Jan 25, 2025Jan 25, 2025

• mondo

  Public template
  Mondo Disease Ontology

  owlontologydisease+ 4monarchinitiativedisease-classificationobofoundrymondo

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •54•239•425•41•Updated Jan 25, 2025Jan 25, 2025

• phenio

  Public
  An integrated ontology for Phenomics

  monarchinitiative

  Makefile

  •

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

  •0•6•19•1•Updated Jan 24, 2025Jan 24, 2025

• mondo-ingest

  Public
  Coordinating the mondo-ingest with external sources

  monarchinitiative

  Jupyter Notebook

  •3•6•230•17•Updated Jan 23, 2025Jan 23, 2025

• monarch-app

  Public
  Monarch Initiative website and API

  monarchinitiative

  Python

  •

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

  •6•19•188•9•Updated Jan 22, 2025Jan 22, 2025

• gpsea

  Public
  A Python library for discovery of genotype-phenotype associations

  hpomonarchinitiativephenopackets

  Python

  •

  MIT License

  •1•5•14•0•Updated Jan 22, 2025Jan 22, 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

• zfin-genotype-to-phenotype-ingest

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 22, 2025Jan 22, 2025

• pheval-paper

  Public
  Makefile

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

• oncopacket

  Public
  A package to convert cancer data to GA4GH phenopacket

  monarchinitiative

  Jupyter Notebook

  •

  MIT License

  •1•7•22•2•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•19•14•0•Updated Jan 19, 2025Jan 19, 2025

• medgen

  Public
  MedGen ingest.

  monarchinitiative

  Python

  •0•1•9•0•Updated Jan 19, 2025Jan 19, 2025

• pyphetools

  Public
  Python Phenopacket Tools

  monarchinitiative

  Python

  •

  MIT License

  •1•12•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•10•16•1•Updated Jan 17, 2025Jan 17, 2025

• monarch-ingest

  Public
  Data ingest application for Monarch Initiative knowledge graph using Koza

  pythonneo4jsolr+ 7sqlitesemantic-webmonarchinitiativekgxknowledge-graphslinkmllinkml-schema

  Python

  •3•16•33•3•Updated Jan 16, 2025Jan 16, 2025

• closurizer

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

  Python

  •0•4•1•0•Updated Jan 16, 2025Jan 16, 2025

• curategpt

  Public
  LLM-driven curation assist tool

  aigptontologies+ 7curationbiocurationmonarchinitiativeobofoundryontology-toolsllmontogpt

  Jupyter Notebook

  •

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

  •12•75•30•4•Updated Jan 16, 2025Jan 16, 2025

• rppr_stats

  Public
  Makefile

  •0•0•0•0•Updated Jan 16, 2025Jan 16, 2025

• pheval.phen2gene

  Public
  A PhEval plugin for integrating Phen2Gene, enabling gene prioritisation based on phenotypic data in a standardised pipeline.

  monarchinitiative

  Python

  •0•2•0•0•Updated Jan 16, 2025Jan 16, 2025

• monarch-qc

  Public
  WORK IN PROGRESS - new effort at implementing a QC Dashboard for the Monarch KG and Ingest

  TypeScript

  •

  MIT License

  •1•1•18•0•Updated Jan 15, 2025Jan 15, 2025

• QC

  Public
  Makefile

  •1•1•1•12•Updated Jan 15, 2025Jan 15, 2025

• phenomics-assistant

  Public
  LLM retrieval augmented generation agent for the Monarch Knowledge graph.

  knowledge-graphmonarchinitiativelarge-language-models

  Python

  •

  MIT License

  •0•20•3•0•Updated Jan 14, 2025Jan 14, 2025

• koza

  Public
  Data transformation framework for LinkML data models

  ontologyknowledge-graphmonarchinitiative+ 4obofoundrylinkmlkozaetl

  Python

  •

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

  •4•48•37•4•Updated Jan 14, 2025Jan 14, 2025

• maxo-annotation-ingest

  Public
  Python

  •

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

  •0•0•0•0•Updated Jan 13, 2025Jan 13, 2025