Discover monarch-initiative/analysis-sandbox Open Source project

576

mondo

Mondo Disease Ontology

API for linked biological knowledge

224

biolink-api

Data Ingestion Pipeline for Monarch

dipper

LLM-driven curation assist tool (pre-alpha)

curate-gpt

Data transformation framework for LinkML data models

MAxO

Medical action ontology

HTML

koza

Ontology for representing scientific evidence and provenance information

SEPIO-ontology

Monarch web application and API

monarch-legacy

🍇 Embiggen is the Python Graph Representation learning, Prediction and Evaluation submodule of the GRAPE library.

embiggen

Efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing

SvAnna

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

loinc2hpo

phenol: Phenotype ontology library

phenol

Bayes OWL Ontology Merging

kboom

Repository for representing genotypes and their association with phenotypes

GENO-ontology

LLM retrieval augmented generation agent for Monarch.

phenomics-assistant

The previous version of the Monarch Initiative website

monarch-ui

Vue

monarch-disease-ontology-RETIRED

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

Prolog

owlsim-v3

Ontology Based Profile Matching

Interpretable prioritization of splice variants in diagnostic next-generation sequencing

Squirls

Data ingest application for Monarch Initiative knowledge graph using Koza

monarch-ingest

Collections of GA4GH phenopackets that represent individuals with Mendelian diseases.

phenopacket-store

phenogrid

The phenogrid widget

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

oai-monarch-plugin

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

monochrom

dragon-ai-results

hpoannotqc

ontorunner

HpoTextMining

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

pyphetools

Python Phenopacket Tools

Phenomenal text mining for disease and phenotype concepts

fenominal

Simple rust implementation of semantic similarity

semsimian

Next-generation Biocuration App for annotating cases and PhenoPackets

HpoCaseAnnotator

A format for language profiles for ontologies

babelon

vertebrate-breed-ontology

gpt-mapping-manuscript

The Monarch Initiative Helpdesk

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.

Cancer data to GA4GH phenopacket

oncoexporter

monarch-ui-new

DO NOT USE

SLDBGen

walks mapping graphs running boomer

mapping-walker

Configuration based file caching downloader

kghub-downloader

mining and merging disease resources

disease-miner

Web Ontology Language

monarchr

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

phenio

An integrated ontology for Phenomics

Data ingest pipeline for OMIM.

omim

agent-smith-ai

PhenoteFX

monarch-cypher-queries

Coordinating the mondo-ingest with external sources

mondo-ingest

A Python library for discovery of genotype-phenotype associations

gpsea

A Cookiecutter to kickstart Python based projects.

monarch-project-template

monarch-phenote

stub for monarch phenote

Alpha test for a Monarch-backed plugin for ChatGPT.

oai-monarch-wrapper

Pyrophen generates a FHIR Code system representing the Human Phenotype Ontology

pyrophen

Top level monarch importer ontology

monarch-ontology

Building a fully exectuable workflow for boomer

monarch-mapping-commons

Python library for mondo QC

mondolib

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

negativeExampleSelection

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

hpo-plain-index

monarch-owlsim-data

Dockerized Managed Neo4j Database for Monarch

monarch-neo4j

Shell

ont-review

A dockerised version of the OLS for Monarch Ontologies

ols_monarch

This is the Exomiser plugin for PhEval. Highly experimental.

pheval.exomiser

Matchmaker Exchange for Monarch

monarch-mme

Scala

phenopacket2prompt

GA4GH Phenopacket to LLM prompt

monarch-semantic-similarity-profiles

talisman-paper

SciGraph-docker-monarch-ontology

phenotype2phenopacket

Multilingual Analysis of LLMs for Clinical Observations

malco

Add closure expansion fields to kgx files following the Golr pattern

closurizer

An ontology module describing molecular glyco-phenotypes

glyco-phenotype-ontology

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

cat-merge

monarch-phenologs

Annotations to terms of the Medical Action Ontology (MAxO)

maxo-annotations

ontogpt-experiments

Experiments and analysis related to OntoGPT methods.

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

release-utils

R library and scripts to process sleep data for clustering

sleep-apnea-clustering

biolink-model-pydantic

Pydantic dataclasses for the Biolink model

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

monarch-ontology-dashboard

HTML

ga4gh-server

Implementation of the ga4gh/schemas

Scala

phenoCompare

Phenotype Compare

HTML

hpo-survey-analysis

Toolkit for analyzing surveys utilizing the HPO

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

exomiser-phenotype-data-revised

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

monarch-file-server

Yet Another Clinical Trials Parser

yactp

Source files for axiomatizing the ontology of OMIA

monarch-plater-docker

clingen-ingest

phenotypr-body

monarch-py

omia-ontology

Monarch Cancer Knowledge Base

mckb

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

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

100

web-hippo