Repositories list

• mondo

  Public template
  Mondo Disease Ontology

  owlontologydisease+ 4monarchinitiativedisease-classificationobofoundrymondo

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •54•239•427•43•Updated Jan 15, 2025Jan 15, 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•17•0•Updated Jan 15, 2025Jan 15, 2025

• QC

  Public
  Makefile

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

• gpsea

  Public
  A Python library for discovery of genotype-phenotype associations

  hpomonarchinitiativephenopackets

  Python

  •

  MIT License

  •1•5•16•0•Updated Jan 15, 2025Jan 15, 2025

• monarch-ingest

  Public
  Data ingest application for Monarch Initiative knowledge graph using Koza

  pythonneo4jsolr+ 7sqlitesemantic-webmonarchinitiativekgxknowledge-graphslinkmllinkml-schema

  Python

  •2•15•32•3•Updated Jan 15, 2025Jan 15, 2025

• closurizer

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

  Python

  •0•4•1•0•Updated Jan 15, 2025Jan 15, 2025

• mondo-ingest

  Public
  Coordinating the mondo-ingest with external sources

  monarchinitiative

  Jupyter Notebook

  •3•6•230•18•Updated Jan 15, 2025Jan 15, 2025

• zfin-genotype-to-phenotype-ingest

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 15, 2025Jan 15, 2025

• monarch-app

  Public
  Monarch Initiative website and API

  monarchinitiative

  Python

  •

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

  •6•19•191•10•Updated Jan 14, 2025Jan 14, 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

• oncoexporter

  Public
  A package to convert cancer data to GA4GH phenopacket

  monarchinitiative

  Jupyter Notebook

  •

  MIT License

  •1•7•22•3•Updated Jan 14, 2025Jan 14, 2025

• pheval-paper

  Public
  Shell

  •0•0•0•0•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

• 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 12, 2025Jan 12, 2025

• medgen

  Public
  MedGen ingest.

  monarchinitiative

  Python

  •0•1•9•0•Updated Jan 12, 2025Jan 12, 2025

• omim

  Public
  Data ingest pipeline for OMIM.

  biomedical-informaticsmonarchinitiativeontology-engineering

  Jupyter Notebook

  •3•7•63•2•Updated Jan 12, 2025Jan 12, 2025

• monarch-neo4j

  Public
  Dockerized Managed Neo4j Database for Monarch

  Shell

  •

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

  •0•2•1•0•Updated Jan 10, 2025Jan 10, 2025

• pyphetools

  Public
  Python Phenopacket Tools

  monarchinitiative

  Python

  •

  MIT License

  •1•12•3•0•Updated Jan 10, 2025Jan 10, 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

• 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

• mondo-curation-analysis

  Public
  monarchinitiative

  Jupyter Notebook

  •0•0•1•0•Updated Jan 8, 2025Jan 8, 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

• 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