Monarch Initiative

All

240 repositories

maxo-annotation-ingest
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Jan 11, 2025Jan 11, 2025
mondo-ingest
Public
Coordinating the mondo-ingest with external sources
monarchinitiative
Jupyter Notebook
•3•6•230•13•Updated Jan 11, 2025Jan 11, 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
•54•238•425•36•Updated Jan 11, 2025Jan 11, 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
•2•15•32•3•Updated Jan 10, 2025Jan 10, 2025
monarch-app
Public
Monarch Initiative website and API
monarchinitiative
Python
•
BSD 3-Clause "New" or "Revised" License
•6•19•194•10•Updated Jan 10, 2025Jan 10, 2025
oncoexporter
Public
A package to convert cancer data to GA4GH phenopacket
monarchinitiative
Jupyter Notebook
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MIT License
•1•7•22•3•Updated Jan 10, 2025Jan 10, 2025
koza
Public
Data transformation framework for LinkML data models
ontology knowledge-graph monarchinitiative obofoundry linkml koza etl
Python
•
BSD 3-Clause "New" or "Revised" License
•4•48•37•3•Updated Jan 10, 2025Jan 10, 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
phenopacket-store
Public
Collections of GA4GH phenopackets that represent individuals with Mendelian diseases.
ga4gh hpo monarchinitiative phenopackets
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•4•18•14•0•Updated Jan 10, 2025Jan 10, 2025
pyphetools
Public
Python Phenopacket Tools
monarchinitiative
Python
•
MIT License
•1•11•3•0•Updated Jan 10, 2025Jan 10, 2025
babelon
Public
A format for language profiles for ontologies
internationalization language-translation semantic-web owl monarchinitiative obofoundry linkml
Jupyter Notebook
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MIT License
•0•8•15•0•Updated Jan 9, 2025Jan 9, 2025
pheval.llm
Public
Analysis of LLMs for Clinical Observations
hpo monarchinitiative phenopackets clinical-diagnosis biomedical-ontologies rare-diseases large-language-models
Python
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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.
phenotypes monarchinitiative phenopackets
Python
•1•2•0•0•Updated Jan 8, 2025Jan 8, 2025
phenopacket2prompt
Public
GA4GH Phenopacket to LLM prompt
monarchinitiative phenopackets human-phenotype-ontology deep-phenotyping large-language-models prompt-engineering
Java
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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
zfin-genotype-to-phenotype-ingest
Public
Python
•
MIT License
•0•0•0•0•Updated Jan 8, 2025Jan 8, 2025
mondo-curation-analysis
Public
monarchinitiative
Jupyter Notebook
•0•0•1•0•Updated Jan 8, 2025Jan 8, 2025
gpsea
Public
A Python library for discovery of genotype-phenotype associations
hpo monarchinitiative phenopackets
Python
•
MIT License
•1•5•18•0•Updated Jan 7, 2025Jan 7, 2025
pheval
Public
A framework for empirical evaluation of phenotype matching and prioritisation
monarchinitiative
Python
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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)
monarchinitiative obofoundry human-phenotype-ontology therapeutics maxo medical-actions mondo-ontology
Python
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Creative Commons Attribution 4.0 International
•0•2•71•0•Updated Jan 6, 2025Jan 6, 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-informatics monarchinitiative ontology-engineering
Jupyter Notebook
•3•7•62•2•Updated Jan 5, 2025Jan 5, 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
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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
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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