Repositories list

• mondo-ingest

  Public
  Coordinating the mondo-ingest with external sources

  monarchinitiative

  Jupyter Notebook

  •3•6•223•21•Updated Nov 20, 2024Nov 20, 2024

• monarch-semantic-similarity-profiles

  Public
  Jupyter Notebook

  •

  MIT License

  •0•2•8•2•Updated Nov 20, 2024Nov 20, 2024

• monarch-app

  Public
  Monarch Initiative website and API

  monarchinitiative

  Python

  •

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

  •6•18•182•11•Updated Nov 20, 2024Nov 20, 2024

• monarch-phenologs

  Public
  monarchinitiative

  Python

  •

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

  •0•3•14•0•Updated Nov 20, 2024Nov 20, 2024

• mondo

  Public template
  Mondo Disease Ontology

  owlontologydisease+ 4monarchinitiativedisease-classificationobofoundrymondo

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •53•237•364•40•Updated Nov 20, 2024Nov 20, 2024

• zfin-genotype-to-phenotype-ingest

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 20, 2024Nov 20, 2024

• omim

  Public
  Data ingest pipeline for OMIM.

  biomedical-informaticsmonarchinitiativeontology-engineering

  Jupyter Notebook

  •3•7•61•5•Updated Nov 20, 2024Nov 20, 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 19, 2024Nov 19, 2024

• pheval.llm

  Public
  Analysis of LLMs for Clinical Observations

  monarchinitiative

  Jupyter Notebook

  •

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

  •0•5•7•2•Updated Nov 19, 2024Nov 19, 2024

• phenio

  Public
  An integrated ontology for Phenomics

  monarchinitiative

  Makefile

  •

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

  •0•6•26•1•Updated Nov 19, 2024Nov 19, 2024

• monarch-ingest

  Public
  Data ingest application for Monarch Initiative knowledge graph using Koza

  pythonneo4jsolr+ 7sqlitesemantic-webmonarchinitiativekgxknowledge-graphslinkmllinkml-schema

  Python

  •2•15•31•2•Updated Nov 19, 2024Nov 19, 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

  •77•611•59•9•Updated Nov 18, 2024Nov 18, 2024

• monarch-documentation

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

  Python

  •

  GNU General Public License v3.0

  •0•6•19•2•Updated Nov 18, 2024Nov 18, 2024

• gpsea

  Public
  A Python library for discovery of genotype-phenotype associations

  hpomonarchinitiativephenopackets

  Python

  •

  MIT License

  •1•5•24•5•Updated Nov 18, 2024Nov 18, 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 18, 2024Nov 18, 2024

• medgen

  Public
  MedGen ingest.

  monarchinitiative

  Python

  •0•1•9•0•Updated Nov 17, 2024Nov 17, 2024

• closurizer

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

  Python

  •0•4•1•0•Updated Nov 16, 2024Nov 16, 2024

• curategpt

  Public
  LLM-driven curation assist tool

  aigptontologies+ 7curationbiocurationmonarchinitiativeobofoundryontology-toolsllmontogpt

  Jupyter Notebook

  •

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

  •12•70•24•4•Updated Nov 15, 2024Nov 15, 2024

• maxo-annotation-ingest

  Public
  Python

  •

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

  •0•0•0•0•Updated Nov 15, 2024Nov 15, 2024

• monarch-mapping-commons

  Public
  Building a fully exectuable workflow for boomer

  Python

  •

  Creative Commons Zero v1.0 Universal

  •3•4•14•1•Updated Nov 15, 2024Nov 15, 2024

• go-ingest

  Public
  gene ontology ingest from gene association formatted files

  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 14, 2024Nov 14, 2024

• biogrid-ingest

  Public
  BioGRID ingest

  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 14, 2024Nov 14, 2024

• kghub-downloader

  Public
  Configuration based file caching downloader

  Python

  •0•6•4•3•Updated Nov 14, 2024Nov 14, 2024

• pheval.exomiser

  Public
  Exomiser plugin for PhEval.

  monarchinitiative

  Python

  •1•4•3•1•Updated Nov 14, 2024Nov 14, 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 14, 2024Nov 14, 2024

• phenopacket2prompt

  Public
  GA4GH Phenopacket to LLM prompt

  monarchinitiative

  Java

  •

  MIT License

  •1•3•2•0•Updated Nov 12, 2024Nov 12, 2024

• monarch_pheval

  Public
  monarchinitiative

  Jinja

  •

  MIT License

  •0•1•3•1•Updated Nov 12, 2024Nov 12, 2024

• vertebrate-breed-ontology

  Public
  monarchinitiativeobofoundry

  Makefile

  •1•11•53•5•Updated Nov 11, 2024Nov 11, 2024

• ncbi-gene

  Public
  Python

  •

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

  •0•0•0•0•Updated Nov 11, 2024Nov 11, 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