Repositories list

• hpotools

  Public
  Human Phenotype Ontology tools

  Java

  •

  MIT License

  •0•1•1•0•Updated Dec 20, 2024Dec 20, 2024

• omim

  Public
  Data ingest pipeline for OMIM.

  biomedical-informaticsmonarchinitiativeontology-engineering

  Jupyter Notebook

  •3•7•62•2•Updated Dec 19, 2024Dec 19, 2024

• mondo-ingest

  Public
  Coordinating the mondo-ingest with external sources

  monarchinitiative

  Jupyter Notebook

  •3•6•230•16•Updated Dec 19, 2024Dec 19, 2024

• mondo

  Public template
  Mondo Disease Ontology

  owlontologydisease+ 4monarchinitiativedisease-classificationobofoundrymondo

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •54•237•401•38•Updated Dec 19, 2024Dec 19, 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 19, 2024Dec 19, 2024

• koza

  Public
  Data transformation framework for LinkML data models

  ontologyknowledge-graphmonarchinitiative+ 4obofoundrylinkmlkozaetl

  Python

  •

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

  •4•49•37•3•Updated Dec 19, 2024Dec 19, 2024

• vertebrate-breed-ontology

  Public
  monarchinitiativeobofoundry

  Makefile

  •1•11•55•4•Updated Dec 19, 2024Dec 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

  •83•628•60•9•Updated Dec 18, 2024Dec 18, 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 Dec 18, 2024Dec 18, 2024

• monarch-app

  Public
  Monarch Initiative website and API

  monarchinitiative

  Python

  •

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

  •6•19•191•9•Updated Dec 18, 2024Dec 18, 2024

• zfin-genotype-to-phenotype-ingest

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

• 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 Dec 17, 2024Dec 17, 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

• zfin-orthology-ingest

  Public
  Python

  •

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

  •0•0•0•0•Updated Dec 16, 2024Dec 16, 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•16•14•0•Updated Dec 15, 2024Dec 15, 2024

• pyphetools

  Public
  Python Phenopacket Tools

  monarchinitiative

  Python

  •

  MIT License

  •1•11•3•0•Updated Dec 15, 2024Dec 15, 2024

• medgen

  Public
  MedGen ingest.

  monarchinitiative

  Python

  •0•1•9•0•Updated Dec 15, 2024Dec 15, 2024

• gpsea

  Public
  A Python library for discovery of genotype-phenotype associations

  hpomonarchinitiativephenopackets

  Python

  •

  MIT License

  •1•5•17•0•Updated Dec 13, 2024Dec 13, 2024

• monarch-ingest

  Public
  Data ingest application for Monarch Initiative knowledge graph using Koza

  pythonneo4jsolr+ 7sqlitesemantic-webmonarchinitiativekgxknowledge-graphslinkmllinkml-schema

  Python

  •2•15•32•2•Updated Dec 13, 2024Dec 13, 2024

• clingen-ingest

  Public
  Python

  •

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

  •0•3•0•0•Updated Dec 12, 2024Dec 12, 2024

• babelon

  Public
  A format for language profiles for ontologies

  internationalizationlanguage-translationsemantic-web+ 4owlmonarchinitiativeobofoundrylinkml

  Jupyter Notebook

  •

  MIT License

  •0•8•15•0•Updated Dec 11, 2024Dec 11, 2024

• curategpt

  Public
  LLM-driven curation assist tool

  aigptontologies+ 7curationbiocurationmonarchinitiativeobofoundryontology-toolsllmontogpt

  Jupyter Notebook

  •

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

  •12•71•29•4•Updated Dec 11, 2024Dec 11, 2024

• pheval.exomiser

  Public
  Exomiser plugin for PhEval.

  monarchinitiative

  Python

  •1•4•3•2•Updated Dec 11, 2024Dec 11, 2024

• pheval.lirical

  Public
  A PhEval plugin integrating LIRICAL for efficient phenotype and variant prioritisation in a standardised pipeline.

  monarchinitiative

  Python

  •0•1•0•0•Updated Dec 11, 2024Dec 11, 2024

• pheval.gado

  Public
  A PhEval plugin for integrating GADO, enabling gene prioritisation based on phenotypic data in a standardised pipeline.

  monarchinitiative

  Python

  •0•0•0•0•Updated Dec 11, 2024Dec 11, 2024

• pheval.svanna

  Public
  A PhEval plugin for integrating SvAnna, enabling structural variant prioritisation in a standardised pipeline.

  monarchinitiative

  Python

  •0•1•0•0•Updated Dec 11, 2024Dec 11, 2024

• cookiecutter-monarch-ingest

  Public
  A Cruft cookiecutter for modular Koza ingests

  Python

  •1•2•7•2•Updated Dec 10, 2024Dec 10, 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•1•Updated Dec 9, 2024Dec 9, 2024

• biogrid-ingest

  Public
  BioGRID ingest

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024

• go-ingest

  Public
  gene ontology ingest from gene association formatted files

  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 3, 2024Dec 3, 2024