Repositories list

• medgen

  Public
  MedGen ingest.

  monarchinitiative

  Python

  •0•1•9•0•Updated Nov 10, 2024Nov 10, 2024

• omim

  Public
  Data ingest pipeline for OMIM.

  biomedical-informaticsmonarchinitiativeontology-engineering

  Jupyter Notebook

  •3•7•62•5•Updated Nov 10, 2024Nov 10, 2024

• mondo-ingest

  Public
  Coordinating the mondo-ingest with external sources

  monarchinitiative

  Jupyter Notebook

  •3•6•221•19•Updated Nov 9, 2024Nov 9, 2024

• mondo

  Public template
  Mondo Disease Ontology

  owlontologydisease+ 4monarchinitiativedisease-classificationobofoundrymondo

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •53•236•412•37•Updated Nov 9, 2024Nov 9, 2024

• oai-monarch-plugin

  Public
  First pass at a thin wrapper around the Monarch API and ChatGPT plugin

  Python

  •

  MIT License

  •2•13•6•0•Updated Nov 9, 2024Nov 9, 2024

• go-ingest

  Public
  gene ontology ingest from gene association formatted files

  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

• 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

  •76•604•58•8•Updated Nov 8, 2024Nov 8, 2024

• koza

  Public
  Data transformation framework for LinkML data models

  ontologyknowledge-graphmonarchinitiative+ 4obofoundrylinkmlkozaetl

  Python

  •

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

  •4•48•35•3•Updated Nov 8, 2024Nov 8, 2024

• monarch-app

  Public
  Monarch Initiative website and API

  monarchinitiative

  Python

  •

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

  •6•18•175•7•Updated Nov 8, 2024Nov 8, 2024

• pheval

  Public
  A framework for empirical evaluation of phenotype matching and prioritisation

  monarchinitiative

  Python

  •

  Apache License 2.0

  •1•12•27•4•Updated Nov 8, 2024Nov 8, 2024

• 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 Nov 8, 2024Nov 8, 2024

• monarch-mapping-commons

  Public
  Building a fully exectuable workflow for boomer

  Python

  •

  Creative Commons Zero v1.0 Universal

  •3•4•14•2•Updated Nov 8, 2024Nov 8, 2024

• 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•15•16•0•Updated Nov 8, 2024Nov 8, 2024

• monarch-semantic-similarity-profiles

  Public
  Jupyter Notebook

  •

  MIT License

  •0•2•8•2•Updated Nov 7, 2024Nov 7, 2024

• cookiecutter-monarch-ingest

  Public
  A Cruft cookiecutter for modular Koza ingests

  Python

  •1•2•7•0•Updated Nov 6, 2024Nov 6, 2024

• vertebrate-breed-ontology

  Public
  monarchinitiativeobofoundry

  Makefile

  •0•11•50•3•Updated Nov 6, 2024Nov 6, 2024

• pheval.exomiser

  Public
  Exomiser plugin for PhEval.

  monarchinitiative

  Python

  •1•4•3•1•Updated Nov 6, 2024Nov 6, 2024

• automaxo

  Public
  Jupyter Notebook

  •

  MIT License

  •1•1•1•1•Updated Nov 6, 2024Nov 6, 2024

• zfin-genotype-to-phenotype-ingest

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

• kghub-downloader

  Public
  Configuration based file caching downloader

  Python

  •0•6•3•3•Updated Nov 5, 2024Nov 5, 2024

• biogrid-ingest

  Public
  BioGRID ingest

  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

• phenio

  Public
  An integrated ontology for Phenomics

  monarchinitiative

  Makefile

  •

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

  •0•6•25•0•Updated Nov 5, 2024Nov 5, 2024

• monarch_pheval

  Public
  monarchinitiative

  Jinja

  •

  MIT License

  •0•1•2•0•Updated Nov 5, 2024Nov 5, 2024

• 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•9•19•0•Updated Nov 4, 2024Nov 4, 2024

• phenomics-assistant

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

  knowledge-graphmonarchinitiativelarge-language-models

  Python

  •

  MIT License

  •0•19•3•0•Updated Nov 4, 2024Nov 4, 2024

• monarch-phenologs

  Public
  monarchinitiative

  Python

  •

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

  •0•3•14•0•Updated Nov 4, 2024Nov 4, 2024

• curategpt

  Public
  LLM-driven curation assist tool

  aigptontologies+ 7curationbiocurationmonarchinitiativeobofoundryontology-toolsllmontogpt

  Jupyter Notebook

  •

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

  •11•68•23•4•Updated Nov 4, 2024Nov 4, 2024

• pyphetools

  Public
  Python Phenopacket Tools

  monarchinitiative

  Python

  •

  MIT License

  •1•11•3•0•Updated Nov 3, 2024Nov 3, 2024

• alliance-genotype-ingest

  Public
  Python

  •

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

  •0•1•0•0•Updated Nov 3, 2024Nov 3, 2024

• clinvar-ingest

  Public
  Python

  •

  MIT License

  •0•3•1•0•Updated Nov 3, 2024Nov 3, 2024