Monarch Initiative

All

236 repositories

mondo-ingest
Public
Coordinating the mondo-ingest with external sources
Jupyter Notebook
•3•6•221•19•Updated Oct 30, 2024Oct 30, 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•47•33•3•Updated Oct 30, 2024Oct 30, 2024
monarch_pheval
Public
Jinja
•
MIT License
•0•1•3•0•Updated Oct 30, 2024Oct 30, 2024
mondo
Public template
Mondo Disease Ontology
owl ontology disease monarchinitiative disease-classification obofoundry mondo
Jupyter Notebook
•
Creative Commons Attribution 4.0 International
•53•234•405•40•Updated Oct 30, 2024Oct 30, 2024
phenopacket-store
Public
Collections of GA4GH phenopackets that represent individuals with Mendelian diseases.
ga4gh hpo phenopackets
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•4•15•16•0•Updated Oct 30, 2024Oct 30, 2024
zfin-genotype-to-phenotype-ingest
Public
Python
•
MIT License
•0•0•0•0•Updated Oct 30, 2024Oct 30, 2024
pheval.llm
Public
Analysis of LLMs for Clinical Observations
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•0•4•7•1•Updated Oct 29, 2024Oct 29, 2024
gpsea
Public
A Python library for discovery of genotype-phenotype associations
Python
•
MIT License
•1•4•23•0•Updated Oct 29, 2024Oct 29, 2024
oai-monarch-plugin
Public
First pass at a thin wrapper around the Monarch API and ChatGPT plugin
Python
•
MIT License
•2•13•6•0•Updated Oct 29, 2024Oct 29, 2024
oncoexporter
Public
Cancer data to GA4GH phenopacket
Jupyter Notebook
•
MIT License
•1•7•22•3•Updated Oct 29, 2024Oct 29, 2024
gocam_modular
Public
Modular ingest of GOCAMs
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Oct 28, 2024Oct 28, 2024
string_modular
Public
Modular ingest of STRING PPIs
Python
•
BSD 3-Clause "New" or "Revised" License
•0•0•1•0•Updated Oct 28, 2024Oct 28, 2024
omim
Public
Data ingest pipeline for OMIM.
biomedical-informatics ontology-engineering
Python
•3•7•60•4•Updated Oct 27, 2024Oct 27, 2024
medgen
Public
MedGen ingest.
Python
•0•1•10•1•Updated Oct 27, 2024Oct 27, 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
•74•601•58•8•Updated Oct 25, 2024Oct 25, 2024
monarch-app
Public
Monarch Initiative website and API
monarchinitiative
Python
•
BSD 3-Clause "New" or "Revised" License
•5•18•166•7•Updated Oct 24, 2024Oct 24, 2024
monarch-phenologs
Public
Python
•
BSD 3-Clause "New" or "Revised" License
•0•3•14•0•Updated Oct 24, 2024Oct 24, 2024
biogrid-ingest
Public
BioGRID ingest
Python
•
MIT License
•0•0•0•0•Updated Oct 24, 2024Oct 24, 2024
phenomics-assistant
Public
LLM retrieval augmented generation agent for Monarch.
Python
•
MIT License
•0•18•3•0•Updated Oct 24, 2024Oct 24, 2024
curategpt
Public
LLM-driven curation assist tool (pre-alpha)
ai gpt ontologies curation biocuration monarchinitiative obofoundry ontology-tools llm ontogpt
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•11•63•23•5•Updated Oct 23, 2024Oct 23, 2024
automaxo
Public
Jupyter Notebook
•
MIT License
•1•1•1•1•Updated Oct 23, 2024Oct 23, 2024
pheval
Public
A framework for empirical evaluation of phenotype matching and prioritisation
monarchinitiative
Python
•
Apache License 2.0
•1•12•26•3•Updated Oct 23, 2024Oct 23, 2024
vertebrate-breed-ontology
Public
Makefile
•0•10•50•3•Updated Oct 23, 2024Oct 23, 2024
monarchr
Public
R package for easy access, manipulation, and analysis of Monarch KG data
R
•
Other
•1•9•20•0•Updated Oct 22, 2024Oct 22, 2024
monarch-mapping-commons
Public
Building a fully exectuable workflow for boomer
Python
•
Creative Commons Zero v1.0 Universal
•3•4•14•2•Updated Oct 22, 2024Oct 22, 2024
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 Oct 21, 2024Oct 21, 2024
pyphetools
Public
Python Phenopacket Tools
Python
•
MIT License
•1•11•4•0•Updated Oct 18, 2024Oct 18, 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
•1•14•31•1•Updated Oct 16, 2024Oct 16, 2024
monarch-phenotype-profile-ingest
Public
human phenotype related ingests
Python
•
MIT License
•0•0•0•0•Updated Oct 15, 2024Oct 15, 2024
phenopacket2prompt
Public
GA4GH Phenopacket to LLM prompt
Java
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MIT License
•1•2•3•2•Updated Oct 11, 2024Oct 11, 2024