Repositories list

• 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•18•14•0•Updated Jan 10, 2025Jan 10, 2025

• pyphetools

  Public
  Python Phenopacket Tools

  monarchinitiative

  Python

  •

  MIT License

  •1•11•3•0•Updated Jan 10, 2025Jan 10, 2025

• maxo-annotation-ingest

  Public
  Python

  •

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

  •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

• mondo-ingest

  Public
  Coordinating the mondo-ingest with external sources

  monarchinitiative

  Jupyter Notebook

  •3•6•229•19•Updated Jan 9, 2025Jan 9, 2025

• monarch-app

  Public
  Monarch Initiative website and API

  monarchinitiative

  Python

  •

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

  •6•19•194•10•Updated Jan 9, 2025Jan 9, 2025

• babelon

  Public
  A format for language profiles for ontologies

  internationalizationlanguage-translationsemantic-web+ 4owlmonarchinitiativeobofoundrylinkml

  Jupyter Notebook

  •

  MIT License

  •0•8•15•0•Updated Jan 9, 2025Jan 9, 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•10•1•Updated Jan 9, 2025Jan 9, 2025

• mondo

  Public template
  Mondo Disease Ontology

  owlontologydisease+ 4monarchinitiativedisease-classificationobofoundrymondo

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •54•238•422•35•Updated Jan 9, 2025Jan 9, 2025

• mic-ingest

  Public
  Ingest for Micronutrient Information Center using OntoGPT

  Python

  •

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

  •0•1•0•0•Updated Jan 8, 2025Jan 8, 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 8, 2025Jan 8, 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 8, 2025Jan 8, 2025

• cookiecutter-monarch-ingest

  Public
  A Cruft cookiecutter for modular Koza ingests

  Python

  •1•2•6•2•Updated Jan 8, 2025Jan 8, 2025

• zfin-genotype-to-phenotype-ingest

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 8, 2025Jan 8, 2025

• mondo-curation-analysis

  Public
  monarchinitiative

  Jupyter Notebook

  •0•0•1•0•Updated Jan 8, 2025Jan 8, 2025

• gpsea

  Public
  A Python library for discovery of genotype-phenotype associations

  hpomonarchinitiativephenopackets

  Python

  •

  MIT License

  •1•5•18•0•Updated Jan 7, 2025Jan 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 Jan 7, 2025Jan 7, 2025

• maxo-annotations

  Public
  Annotations to terms of the Medical Action Ontology (MAxO)

  monarchinitiativeobofoundryhuman-phenotype-ontology+ 4therapeuticsmaxomedical-actionsmondo-ontology

  Python

  •

  Creative Commons Attribution 4.0 International

  •0•2•71•0•Updated Jan 6, 2025Jan 6, 2025

• medgen

  Public
  MedGen ingest.

  monarchinitiative

  Python

  •0•1•9•0•Updated Jan 5, 2025Jan 5, 2025

• omim

  Public
  Data ingest pipeline for OMIM.

  biomedical-informaticsmonarchinitiativeontology-engineering

  Jupyter Notebook

  •3•7•62•2•Updated Jan 5, 2025Jan 5, 2025

• setsim

  Public
  A proof of concept of the summing similarity measure.

  Python

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

• go-ingest

  Public
  gene ontology ingest from gene association formatted files

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 3, 2025Jan 3, 2025

• alliance-genotype-ingest

  Public
  Python

  •

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

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

• clinvar-ingest

  Public
  Python

  •

  MIT License

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

• alliance-disease-association-ingest

  Public
  Python

  •

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

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

• ncbi-gene

  Public
  Python

  •

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

  •0•0•0•0•Updated Jan 3, 2025Jan 3, 2025

• alliance-phenotype-association-ingest

  Public
  Python

  •

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

  •0•0•0•0•Updated Jan 3, 2025Jan 3, 2025

• zfin-orthology-ingest

  Public
  Python

  •

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

  •0•0•0•0•Updated Jan 3, 2025Jan 3, 2025

• clingen-ingest

  Public
  Python

  •

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

  •0•3•0•0•Updated Jan 3, 2025Jan 3, 2025

• monarch-documentation

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

  Python

  •

  GNU General Public License v3.0

  •0•6•19•1•Updated Dec 31, 2024Dec 31, 2024

• monarch-mapping-commons

  Public
  Building a fully exectuable workflow for boomer

  Python

  •

  Creative Commons Zero v1.0 Universal

  •3•4•13•1•Updated Dec 31, 2024Dec 31, 2024