Monarch Initiative

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238 repositories

gpsea
Public
A Python library for discovery of genotype-phenotype associations
hpo monarchinitiative phenopackets
Python
•
MIT License
•1•5•24•1•Updated Nov 28, 2024Nov 28, 2024
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•2•Updated Nov 28, 2024Nov 28, 2024
mondo
Public template
Mondo Disease Ontology
owl ontology disease monarchinitiative disease-classification obofoundry mondo
Jupyter Notebook
•
Creative Commons Attribution 4.0 International
•54•236•377•35•Updated Nov 27, 2024Nov 27, 2024
mondo-ingest
Public
Coordinating the mondo-ingest with external sources
monarchinitiative
Jupyter Notebook
•3•6•224•14•Updated Nov 27, 2024Nov 27, 2024
monarch-app
Public
Monarch Initiative website and API
monarchinitiative
Python
•
BSD 3-Clause "New" or "Revised" License
•6•18•186•10•Updated Nov 27, 2024Nov 27, 2024
curategpt
Public
LLM-driven curation assist tool
ai gpt ontologies curation biocuration monarchinitiative obofoundry ontology-tools llm ontogpt
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•12•71•27•4•Updated Nov 27, 2024Nov 27, 2024
phenio
Public
An integrated ontology for Phenomics
monarchinitiative
Makefile
•
BSD 3-Clause "New" or "Revised" License
•0•6•17•0•Updated Nov 27, 2024Nov 27, 2024
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•16•16•0•Updated Nov 27, 2024Nov 27, 2024
pheval.kghg
Public
Python
•
MIT License
•0•0•0•0•Updated Nov 27, 2024Nov 27, 2024
go-ingest
Public
gene ontology ingest from gene association formatted files
Python
•
MIT License
•0•0•0•0•Updated Nov 27, 2024Nov 27, 2024
pheval.semphen
Public
Python
•
MIT License
•0•1•0•0•Updated Nov 27, 2024Nov 27, 2024
zfin-genotype-to-phenotype-ingest
Public
Python
•
MIT License
•0•0•0•0•Updated Nov 27, 2024Nov 27, 2024
maxo-annotation-ingest
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Nov 27, 2024Nov 27, 2024
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•9•1•Updated Nov 26, 2024Nov 26, 2024
oncoexporter
Public
A package to convert cancer data to GA4GH phenopacket
monarchinitiative
Jupyter Notebook
•
MIT License
•1•7•22•3•Updated Nov 26, 2024Nov 26, 2024
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 Nov 26, 2024Nov 26, 2024
omim
Public
Data ingest pipeline for OMIM.
biomedical-informatics monarchinitiative ontology-engineering
Jupyter Notebook
•3•7•66•7•Updated Nov 25, 2024Nov 25, 2024
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 Nov 25, 2024Nov 25, 2024
maxo-annotations
Public
Annotations to terms of the Medical Action Ontology (MAxO)
monarchinitiative obofoundry human-phenotype-ontology therapeutics maxo medical-actions mondo-ontology
Creative Commons Attribution 4.0 International
•0•2•70•1•Updated Nov 24, 2024Nov 24, 2024
medgen
Public
MedGen ingest.
monarchinitiative
Python
•0•1•9•0•Updated Nov 24, 2024Nov 24, 2024
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
•
BSD 3-Clause "New" or "Revised" License
•80•615•59•9•Updated Nov 23, 2024Nov 23, 2024
monarch-phenologs
Public
monarchinitiative
Python
•
BSD 3-Clause "New" or "Revised" License
•0•3•14•0•Updated Nov 23, 2024Nov 23, 2024
monarch-documentation
Public
Technical documentation for all Monarch applications, packages, services and related projects.
Python
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GNU General Public License v3.0
•0•6•19•1•Updated Nov 22, 2024Nov 22, 2024
kghub-downloader
Public
Configuration based file caching downloader
Python
•0•6•4•2•Updated Nov 21, 2024Nov 21, 2024
monarch-mapping-commons
Public
Building a fully exectuable workflow for boomer
Python
•
Creative Commons Zero v1.0 Universal
•3•4•14•1•Updated Nov 21, 2024Nov 21, 2024
exomiser.reranking
Public
Jinja
•
MIT License
•0•0•0•0•Updated Nov 20, 2024Nov 20, 2024
vertebrate-breed-ontology
Public
monarchinitiative obofoundry
Makefile
•1•11•54•5•Updated Nov 20, 2024Nov 20, 2024
monarch-semantic-similarity-profiles
Public
Jupyter Notebook
•
MIT License
•0•2•8•2•Updated Nov 20, 2024Nov 20, 2024
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
•4•48•35•3•Updated Nov 19, 2024Nov 19, 2024
closurizer
Public
Add closure expansion fields to kgx files following the Golr pattern
Python
•0•4•1•0•Updated Nov 16, 2024Nov 16, 2024