Monarch Initiative

All

259 repositories

omim
Public
Data ingest pipeline for OMIM.
biomedical-informatics monarchinitiative ontology-engineering
Jupyter Notebook
•3•8•70•5•Updated Aug 5, 2025Aug 5, 2025
mondo
Public template
Mondo Disease Ontology
owl ontology disease monarchinitiative disease-classification obofoundry mondo
Jupyter Notebook
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Creative Commons Attribution 4.0 International
•59•262•350•60•Updated Aug 5, 2025Aug 5, 2025
semphen
Public
Gene and disease prioritization via semsimian algorithm wrapped around phenio.db + monarch-kg
Python
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MIT License
•0•0•0•0•Updated Aug 4, 2025Aug 4, 2025
kghub-downloader
Public
Configuration based file caching downloader
Python
•0•6•5•0•Updated Aug 4, 2025Aug 4, 2025
phenopacket-store
Public
Collections of GA4GH phenopackets that represent individuals with Mendelian diseases.
ga4gh hpo monarchinitiative phenopackets
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•5•23•16•3•Updated Aug 4, 2025Aug 4, 2025
pheval
Public
A framework for empirical evaluation of phenotype matching and prioritisation
monarchinitiative
Python
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Apache License 2.0
•4•12•24•3•Updated Aug 4, 2025Aug 4, 2025
monarch-app
Public
Monarch Initiative website and API
monarchinitiative
Vue
•
BSD 3-Clause "New" or "Revised" License
•7•28•245•14•Updated Aug 4, 2025Aug 4, 2025
go-ingest
Public
gene ontology ingest from gene association formatted files
Python
•
MIT License
•0•0•0•0•Updated Aug 3, 2025Aug 3, 2025
alliance-genotype-ingest
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•0•1•0•0•Updated Aug 3, 2025Aug 3, 2025
clinvar-ingest
Public
Python
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MIT License
•0•3•1•0•Updated Aug 3, 2025Aug 3, 2025
alliance-disease-association-ingest
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•1•Updated Aug 3, 2025Aug 3, 2025
upheno-cross-species-ingest
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Aug 3, 2025Aug 3, 2025
alliance-phenotype-association-ingest
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Aug 3, 2025Aug 3, 2025
ncbi-gene
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•1•0•0•0•Updated Aug 3, 2025Aug 3, 2025
medgen
Public
MedGen ingest.
monarchinitiative
Python
•0•1•9•0•Updated Aug 3, 2025Aug 3, 2025
clingen-ingest
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•0•3•0•0•Updated Aug 3, 2025Aug 3, 2025
zfin-orthology-ingest
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Aug 3, 2025Aug 3, 2025
maxo-annotation-ingest
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Aug 3, 2025Aug 3, 2025
mondo-ingest
Public
Coordinating the mondo-ingest with external sources
monarchinitiative
Jupyter Notebook
•3•7•248•8•Updated Aug 2, 2025Aug 2, 2025
oncopacket
Public
A package to convert cancer data to GA4GH phenopacket
monarchinitiative
Jupyter Notebook
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MIT License
•1•7•20•2•Updated Aug 2, 2025Aug 2, 2025
pyphetools
Public
Python Phenopacket Tools
monarchinitiative
Python
•
MIT License
•1•15•4•0•Updated Aug 1, 2025Aug 1, 2025
monarch_pheval
Public
monarchinitiative
Makefile
•
MIT License
•1•1•7•2•Updated Jul 31, 2025Jul 31, 2025
koza
Public
Data transformation framework for LinkML data models
ontology knowledge-graph monarchinitiative obofoundry linkml koza etl
Python
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BSD 3-Clause "New" or "Revised" License
•5•54•40•6•Updated Jul 31, 2025Jul 31, 2025
monarch-ingest
Public
Data ingest application for Monarch Initiative knowledge graph using Koza
python neo4j solr sqlite semantic-web monarchinitiative kgx knowledge-graphs linkml linkml-schema
Python
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BSD 3-Clause "New" or "Revised" License
•4•19•36•7•Updated Jul 31, 2025Jul 31, 2025
ontogpt
Public
LLM-based ontological extraction tools, including SPIRES
nlp ai information-extraction named-entity-recognition language-models ner data-modeling relation-extraction monarchinitiative obofoundry
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•97•710•69•10•Updated Jul 30, 2025Jul 30, 2025
zfin-genotype-to-phenotype-ingest
Public
Python
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MIT License
•0•0•0•0•Updated Jul 30, 2025Jul 30, 2025
graph-agent-devops
Public
Working directory for reusable "simple" devops for the graph agent
HCL
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BSD 3-Clause "New" or "Revised" License
•0•0•4•0•Updated Jul 29, 2025Jul 29, 2025
aurelian
Public
A motley crew of agents developed by the Monarch Initiative
Python
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MIT License
•3•18•28•1•Updated Jul 29, 2025Jul 29, 2025
GENO-ontology
Public
Repository for representing genotypes and their association with phenotypes
ontology monarchinitiative obofoundry
Makefile
•6•19•41•0•Updated Jul 28, 2025Jul 28, 2025
phenopacket-store-toolkit
Public
Toolkit for accessing, Q/C, and maintenance of Phenopacket Store
Python
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BSD 3-Clause "New" or "Revised" License
•0•0•2•1•Updated Jul 25, 2025Jul 25, 2025