Monarch Initiative

All

239 repositories

zfin-genotype-to-phenotype-ingest
Public
Python
•
MIT License
•0•0•0•0•Updated Dec 25, 2024Dec 25, 2024
mondo-ingest
Public
Coordinating the mondo-ingest with external sources
monarchinitiative
Jupyter Notebook
•3•6•230•21•Updated Dec 24, 2024Dec 24, 2024
monarchr
Public
R package for easy access, manipulation, and analysis of the Monarch Initiative or other KGX-formatted knowledge graphs.
knowledge-graph rlang monarchinitiative
R
•
Other
•1•11•19•0•Updated Dec 24, 2024Dec 24, 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•17•14•0•Updated Dec 24, 2024Dec 24, 2024
mondo
Public template
Mondo Disease Ontology
owl ontology disease monarchinitiative disease-classification obofoundry mondo
Jupyter Notebook
•
Creative Commons Attribution 4.0 International
•55•237•404•37•Updated Dec 23, 2024Dec 23, 2024
hpotools
Public
Human Phenotype Ontology tools
Java
•
MIT License
•0•1•1•0•Updated Dec 23, 2024Dec 23, 2024
MAxO
Public
Medical action ontology
medicine owl ontology medical diagnostics treatment monarchinitiative obofoundry interventions treatments
HTML
•
Creative Commons Attribution 4.0 International
•4•52•4•0•Updated Dec 23, 2024Dec 23, 2024
medgen
Public
MedGen ingest.
monarchinitiative
Python
•0•1•9•0•Updated Dec 22, 2024Dec 22, 2024
omim
Public
Data ingest pipeline for OMIM.
biomedical-informatics monarchinitiative ontology-engineering
Jupyter Notebook
•3•7•62•2•Updated Dec 22, 2024Dec 22, 2024
gpsea
Public
A Python library for discovery of genotype-phenotype associations
hpo monarchinitiative phenopackets
Python
•
MIT License
•1•5•17•1•Updated Dec 21, 2024Dec 21, 2024
monarch-app
Public
Monarch Initiative website and API
monarchinitiative
Python
•
BSD 3-Clause "New" or "Revised" License
•6•19•193•9•Updated Dec 21, 2024Dec 21, 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 21, 2024Dec 21, 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
•84•629•59•8•Updated Dec 20, 2024Dec 20, 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•1•1•Updated Dec 20, 2024Dec 20, 2024
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•49•37•3•Updated Dec 19, 2024Dec 19, 2024
vertebrate-breed-ontology
Public
monarchinitiative obofoundry
Makefile
•1•11•55•4•Updated Dec 19, 2024Dec 19, 2024
pheval.llm
Public
Analysis of LLMs for Clinical Observations
hpo monarchinitiative phenopackets clinical-diagnosis biomedical-ontologies rare-diseases large-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
pyphetools
Public
Python Phenopacket Tools
monarchinitiative
Python
•
MIT License
•1•11•3•0•Updated Dec 15, 2024Dec 15, 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 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
internationalization language-translation semantic-web owl monarchinitiative obofoundry linkml
Jupyter Notebook
•
MIT License
•0•8•15•0•Updated Dec 11, 2024Dec 11, 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•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