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Monarch Initiative (@monarch-initiative)

monarch-initiative

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Registered over 11 years ago
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Python
34.0 %

Jupyter Notebook
22.6 %

Java
13.2 %

Makefile 11.3 %

JavaScript
4.7 %

HTML
2.8 %

Vue 1.9 %

R
1.9 %

Web Ontology Language 1.9 %

Scala
1.9 %

Others 3.6 %

ontogpt

LLM-based ontological extraction tools, including SPIRES

Jupyter Notebook

mondo

Mondo Disease Ontology

Jupyter Notebook

biolink-api

API for linked biological knowledge

dipper

Data Ingestion Pipeline for Monarch

MAxO

Medical action ontology

curate-gpt

LLM-driven curation assist tool (pre-alpha)

Jupyter Notebook

koza

Data transformation framework for LinkML data models

SEPIO-ontology

Ontology for representing scientific evidence and provenance information

monarch-legacy

Monarch web application and API

embiggen

🍇 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 sequencing

loinc2hpo

Java library to map LOINC-encoded test results to Human Phenotype Ontology

phenol

phenol: Phenotype ontology library

kboom

Bayes OWL Ontology Merging

GENO-ontology

Repository for representing genotypes and their association with phenotypes

phenomics-assistant

LLM retrieval augmented generation agent for Monarch.

monarch-ui

The previous version of the Monarch Initiative website

monarch-disease-ontology-RETIRED

THIS IS THE OLD REPO: Use this one instead: https://github.com/monarch-initiative/mondo-build

owlsim-v3

Ontology Based Profile Matching

Squirls

Interpretable prioritization of splice variants in diagnostic next-generation sequencing

monarch-ingest

Data ingest application for Monarch Initiative knowledge graph using Koza

phenopacket-store

Collections of GA4GH phenopackets that represent individuals with Mendelian diseases.

Jupyter Notebook

phenogrid

The phenogrid widget

oai-monarch-plugin

First pass at a thin wrapper around the Monarch API and ChatGPT plugin

monochrom

Standardized identifiers and OWL classes for chromosomes and chromosomal parts across species

dragon-ai-results

Jupyter Notebook

pyphetools

Python Phenopacket Tools

hpoannotqc

HPO Annotation QC

ontorunner

Jupyter Notebook

HpoTextMining

Perform text mining for identification of HPO terms in free text from scientific publication.

vertebrate-breed-ontology

fenominal

Phenomenal text mining for disease and phenotype concepts

semsimian

Simple rust implementation of semantic similarity

Jupyter Notebook

HpoCaseAnnotator

Next-generation Biocuration App for annotating cases and PhenoPackets

babelon

A format for language profiles for ontologies

gpt-mapping-manuscript

Jupyter Notebook

helpdesk

The Monarch Initiative Helpdesk

pheval

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.

phenio

An integrated ontology for Phenomics

oncoexporter

Cancer data to GA4GH phenopacket

Jupyter Notebook

monarch-ui-new

SLDBGen

mapping-walker

walks mapping graphs running boomer

kghub-downloader

Configuration based file caching downloader

disease-miner

mining and merging disease resources

Web Ontology Language

monarchr

R package for easy access, manipulation, and analysis of Monarch KG data

omim

Data ingest pipeline for OMIM.

agent-smith-ai

PhenoteFX

monarch-mapping-commons

Building a fully exectuable workflow for boomer

monarch-cypher-queries

mondo-ingest

Coordinating the mondo-ingest with external sources

Jupyter Notebook

gpsea

A Python library for discovery of genotype-phenotype associations

Jupyter Notebook

monarch-project-template

A Cookiecutter to kickstart Python based projects.

monarch-phenote

stub for monarch phenote

oai-monarch-wrapper

Alpha test for a Monarch-backed plugin for ChatGPT.

pyrophen

Pyrophen generates a FHIR Code system representing the Human Phenotype Ontology

monarch-ontology

Top level monarch importer ontology

mondolib

Python library for mondo QC

malco

Multilingual Analysis of LLMs for Clinical Observations

Jupyter Notebook

negativeExampleSelection

Demonstration of bias in graph machine learning owing to negative example selection

Jupyter Notebook

hpo-plain-index

Generates a solr index of plain language terms in the HPO and their grouping classes

monarch-owlsim-data

monarch-neo4j

Dockerized Managed Neo4j Database for Monarch

ont-review

Jupyter Notebook

ols_monarch

A dockerised version of the OLS for Monarch Ontologies

pheval.exomiser

This is the Exomiser plugin for PhEval. Highly experimental.

monarch-mme

Matchmaker Exchange for Monarch

phenopacket2prompt

GA4GH Phenopacket to LLM prompt

monarch-semantic-similarity-profiles

Jupyter Notebook

talisman-paper

Jupyter Notebook

SciGraph-docker-monarch-ontology

phenotype2phenopacket

closurizer

Add closure expansion fields to kgx files following the Golr pattern

glyco-phenotype-ontology

An ontology module describing molecular glyco-phenotypes

cat-merge

Tooling for merging individual source KGX files in the Monarch ingest pipeline

monarch-phenologs

maxo-annotations

Annotations to terms of the Medical Action Ontology (MAxO)

ontogpt-experiments

Experiments and analysis related to OntoGPT methods.

Jupyter Notebook

release-utils

Utilities for generating tsv downloads, release diffs, and other reports from scigraph and solr

sleep-apnea-clustering

R library and scripts to process sleep data for clustering

biolink-model-pydantic

Pydantic dataclasses for the Biolink model

QC

monarch-ontology-dashboard

The Monarch Initiative Ontology dashboard focuses on increasing quality of all Monarch related ontologies

ga4gh-server

Implementation of the ga4gh/schemas

phenoCompare

Phenotype Compare

hpo-survey-analysis

Toolkit for analyzing surveys utilizing the HPO

Jupyter Notebook

exomiser-phenotype-data-revised

Repo for generating monarch data dependencies like the one used by exomiser

monarch-file-server

Terraform, scripts, and documentation for the monarch public file server

monarch-plater-docker

analysis-sandbox

Scripts to analyze monarch data sets and scigraph

Jupyter Notebook

clingen-ingest

phenotypr-body

monarch-py

Monarch Python API

omia-ontology

Source files for axiomatizing the ontology of OMIA

mckb

Monarch Cancer Knowledge Base

Web Ontology Language

SciGraph-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

Jupyter Notebook

web-hippo

The Monarch HIPPO: Deriving insight from the medical literature by fuzzy semantic searches over diseases and phenotypes.