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ontogpt
LLM-based ontological extraction tools, including SPIRESmondo
Mondo Disease Ontologybiolink-api
API for linked biological knowledgedipper
Data Ingestion Pipeline for Monarchcurate-gpt
LLM-driven curation assist tool (pre-alpha)MAxO
Medical action ontologykoza
Data transformation framework for LinkML data modelsSEPIO-ontology
Ontology for representing scientific evidence and provenance informationmonarch-legacy
Monarch web application and APIembiggen
๐ Embiggen is the Python Graph Representation learning, Prediction and Evaluation submodule of the GRAPE library.SvAnna
Efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencingloinc2hpo
Java library to map LOINC-encoded test results to Human Phenotype Ontologyphenol
phenol: Phenotype ontology librarykboom
Bayes OWL Ontology MergingGENO-ontology
Repository for representing genotypes and their association with phenotypesphenomics-assistant
LLM retrieval augmented generation agent for Monarch.monarch-ui
The previous version of the Monarch Initiative websitemonarch-disease-ontology-RETIRED
THIS IS THE OLD REPO: Use this one instead: https://github.com/monarch-initiative/mondo-buildowlsim-v3
Ontology Based Profile MatchingSquirls
Interpretable prioritization of splice variants in diagnostic next-generation sequencingmonarch-ingest
Data ingest application for Monarch Initiative knowledge graph using Kozaphenopacket-store
Collections of GA4GH phenopackets that represent individuals with Mendelian diseases.phenogrid
The phenogrid widgetoai-monarch-plugin
First pass at a thin wrapper around the Monarch API and ChatGPT pluginmonochrom
Standardized identifiers and OWL classes for chromosomes and chromosomal parts across speciesdragon-ai-results
hpoannotqc
HPO Annotation QContorunner
pyphetools
Python Phenopacket Toolsfenominal
Phenomenal text mining for disease and phenotype conceptssemsimian
Simple rust implementation of semantic similarityHpoCaseAnnotator
Next-generation Biocuration App for annotating cases and PhenoPacketsbabelon
A format for language profiles for ontologiesvertebrate-breed-ontology
gpt-mapping-manuscript
helpdesk
The Monarch Initiative Helpdeskpheval
There is currently no empirical framework to evaluate the performance of phenotype matching and prioritization tools, much needed to guide tuning for cross species inference. Many algorithms are evaluated using simulations, which may fail to capture real-world scenarios. This gap presents a number of problems: it is difficult to optimize algorithms if we do not know which choices lead to better results; performance may be sensitive to factors that are subject to change, such as ontology structure or annotation completeness. We will develop a modular Phenotypic Inference Evaluation Framework, PhEval and use it to optimize our own algorithms, as well as deliver it as a community resource.oncoexporter
Cancer data to GA4GH phenopacketmonarch-ui-new
DO NOT USESLDBGen
mapping-walker
walks mapping graphs running boomerkghub-downloader
Configuration based file caching downloaderdisease-miner
mining and merging disease resourcesmonarchr
R package for easy access, manipulation, and analysis of Monarch KG dataphenio
An integrated ontology for Phenomicsomim
Data ingest pipeline for OMIM.agent-smith-ai
PhenoteFX
PhenoteFXmonarch-cypher-queries
mondo-ingest
Coordinating the mondo-ingest with external sourcesgpsea
A Python library for discovery of genotype-phenotype associationsmonarch-project-template
A Cookiecutter to kickstart Python based projects.monarch-phenote
stub for monarch phenoteoai-monarch-wrapper
Alpha test for a Monarch-backed plugin for ChatGPT.pyrophen
Pyrophen generates a FHIR Code system representing the Human Phenotype Ontologymonarch-ontology
Top level monarch importer ontologymonarch-mapping-commons
Building a fully exectuable workflow for boomermondolib
Python library for mondo QCnegativeExampleSelection
Demonstration of bias in graph machine learning owing to negative example selectionhpo-plain-index
Generates a solr index of plain language terms in the HPO and their grouping classesmonarch-owlsim-data
monarch-neo4j
Dockerized Managed Neo4j Database for Monarchont-review
ols_monarch
A dockerised version of the OLS for Monarch Ontologiespheval.exomiser
This is the Exomiser plugin for PhEval. Highly experimental.monarch-mme
Matchmaker Exchange for Monarchphenopacket2prompt
GA4GH Phenopacket to LLM promptmonarch-semantic-similarity-profiles
talisman-paper
SciGraph-docker-monarch-ontology
phenotype2phenopacket
malco
Multilingual Analysis of LLMs for Clinical Observationsclosurizer
Add closure expansion fields to kgx files following the Golr patternglyco-phenotype-ontology
An ontology module describing molecular glyco-phenotypescat-merge
Tooling for merging individual source KGX files in the Monarch ingest pipelinemonarch-phenologs
maxo-annotations
Annotations to terms of the Medical Action Ontology (MAxO)ontogpt-experiments
Experiments and analysis related to OntoGPT methods.release-utils
Utilities for generating tsv downloads, release diffs, and other reports from scigraph and solrsleep-apnea-clustering
R library and scripts to process sleep data for clusteringbiolink-model-pydantic
Pydantic dataclasses for the Biolink modelQC
monarch-ontology-dashboard
The Monarch Initiative Ontology dashboard focuses on increasing quality of all Monarch related ontologiesga4gh-server
Implementation of the ga4gh/schemasphenoCompare
Phenotype Comparehpo-survey-analysis
Toolkit for analyzing surveys utilizing the HPOexomiser-phenotype-data-revised
Repo for generating monarch data dependencies like the one used by exomisermonarch-file-server
Terraform, scripts, and documentation for the monarch public file serveryactp
Yet Another Clinical Trials Parsermonarch-plater-docker
analysis-sandbox
Scripts to analyze monarch data sets and scigraphclingen-ingest
phenotypr-body
monarch-py
Monarch Python APIomia-ontology
Source files for axiomatizing the ontology of OMIAmckb
Monarch Cancer Knowledge BaseSciGraph-docker-monarch-data
Build two Docker images with the monarch configs. Uses master HEAD from the SciGraph github repo.setsim
A proof of concept of the summing similarity measure.automaxo
web-hippo
The Monarch HIPPO: Deriving insight from the medical literature by fuzzy semantic searches over diseases and phenotypes.Love Open Source and this site? Check out how you can help us