Repositories list

• mondo

  Public template
  Mondo Disease Ontology

  owlontologydisease+ 4monarchinitiativedisease-classificationobofoundrymondo

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •54•238•417•41•Updated Jan 5, 2025Jan 5, 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

• mondo-ingest

  Public
  Coordinating the mondo-ingest with external sources

  monarchinitiative

  Jupyter Notebook

  •3•6•231•20•Updated Jan 4, 2025Jan 4, 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 3, 2025Jan 3, 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

• maxo-annotation-ingest

  Public
  Python

  •

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

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

• zfin-genotype-to-phenotype-ingest

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 1, 2025Jan 1, 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

• 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•17•14•0•Updated Dec 27, 2024Dec 27, 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•10•19•0•Updated Dec 26, 2024Dec 26, 2024

• hpotools

  Public
  Human Phenotype Ontology tools

  Java

  •

  MIT License

  •0•1•1•0•Updated Dec 23, 2024Dec 23, 2024

• MAxO

  Public
  Medical action ontology

  medicineowlontology+ 7medicaldiagnosticstreatmentmonarchinitiativeobofoundryinterventionstreatments

  HTML

  •

  Creative Commons Attribution 4.0 International

  •4•52•4•0•Updated Dec 23, 2024Dec 23, 2024

• gpsea

  Public
  A Python library for discovery of genotype-phenotype associations

  hpomonarchinitiativephenopackets

  Python

  •

  MIT License

  •1•5•17•1•Updated Dec 21, 2024Dec 21, 2024

• monarch-app

  Public
  Monarch Initiative website and API

  monarchinitiative

  Python

  •

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

  •6•19•193•9•Updated Dec 21, 2024Dec 21, 2024

• pheval

  Public
  A framework for empirical evaluation of phenotype matching and prioritisation

  monarchinitiative

  Python

  •

  Apache License 2.0

  •2•12•28•4•Updated Dec 21, 2024Dec 21, 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

  •84•633•59•8•Updated Dec 20, 2024Dec 20, 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•1•1•Updated Dec 20, 2024Dec 20, 2024

• koza

  Public
  Data transformation framework for LinkML data models

  ontologyknowledge-graphmonarchinitiative+ 4obofoundrylinkmlkozaetl

  Python

  •

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

  •4•48•37•3•Updated Dec 19, 2024Dec 19, 2024

• vertebrate-breed-ontology

  Public
  monarchinitiativeobofoundry

  Makefile

  •1•12•55•4•Updated Dec 19, 2024Dec 19, 2024

• phenio

  Public
  An integrated ontology for Phenomics

  monarchinitiative

  Makefile

  •

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

  •0•6•18•0•Updated Dec 17, 2024Dec 17, 2024