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Monarch Documentation

The Monarch Initiative and our collaborators develop a wide range of tools and ontologies to tackle global challenges such as Rare Disease. Here we document the software and data infrastructure across the entire Monarch ecosystem. If you would like any specific documentation to be added please use our Monarch-wide issue tracker.

Standards documentation

Repository	Description	Tracker
Phenopackets	An ISO-endorsed open standard for sharing disease and phenotype information.	Issue Tracker
Simple Standard for Ontology Mappings (SSSOM)	A simple metadata standard for describing semantic mappings.	Issue Tracker
Human Phenotype Ontology	Provides a standardized vocabulary of phenotypic abnormalities in human disease.	Issue Tracker
obographs	The obographs ontology format aims and providing a simple graph-oriented JSON format for ontologies.	Issue Tracker
Mondo Disease Ontology	Aims to harmonize disease definitions across the world.	Issue Tracker
Genotype Ontology	An ontology that represents the levels of genetic variation specified in genotypes.	Issue Tracker
Scientific Evidence and Provenance Information Ontology	An ontology that supports the description of evidence and provenance information for scientific claims.	Issue Tracker
Vertebrate Breed Ontology	An ontology created to serve as a single computable resource for vertebrate breed names.	Issue Tracker
The Unified Phenotype Ontology (uPheno)	Aims to unify the annotation of phenotypes across species.	Issue Tracker
Medical Action Ontology		Issue Tracker
Ontology of Biological Attributes		Issue Tracker
Uberon Anatomy Ontology	An integrated cross-species anatomy ontology.	Issue Tracker
Environmental Exposure Ontology		Issue Tracker
Dead simple owl design pattern (DOS-DP) exchange format		Issue Tracker
Knowledge Graph Change Language		Issue Tracker
Babelon - A simple standard for managing ontology translations and language profiles		Issue Tracker

Tools documentation

Repository	Description	Tracker
Exomiser	A tool for finding potential disease-causing variants in whole-exome or whole-genome sequencing data.	Issue Tracker
Monarch Knowledge Graph & Services	Integrates gene, disease, and phenotype data across species.	Issue Tracker
Monarch App	A web application for exploring the Monarch Knowledge Graph.	Issue Tracker
Monarch API	The Monarch API is used to access information from the Monarch Knowledge Graph programmatically.	Issue Tracker
Ontology Development Kit (ODK)	A toolkit and workflow system for managing the ontology life-cycle.	Issue Tracker
Ontology Access Kit (OAK)	A python toolkit for accessing and visualising ontologies.	Issue Tracker
SSSOM Toolkit	A python toolkit for processing SSSOM mapping files.	Issue Tracker
LIkelihood Ratio Interpretation of Clinical AbnormaLities (LIRICAL)	LIkelihood Ratio Interpretation of Clinical AbnormaLities performs phenotype-driven prioritization of candidate diseases and genes in the setting of genomic diagnostics.	Issue Tracker
PhEval	PhEval is a Python package for evaluating phenotype-powered variant prioritisation systems such as Exomiser.	Issue Tracker
obographviz		Issue Tracker
robot		Issue Tracker
OntoGPT	OntoGPT is a Python package for extracting structured information from text with large language models (LLMs), instruction prompts, and ontology-based grounding.	Issue Tracker
TALISMAN	TALISMAN is a Python package for summarizing gene set functions using large language models (LLMs).	Issue Tracker
CurateGPT	AI Assisted Ontology Curation.	Issue Tracker
Monarch Python Toolkit		Issue Tracker
Babelon Toolkit		Issue Tracker
Fenominal		Issue Tracker
Koza		Issue Tracker
LinkML	The Linked Data Modeling Language (LinkML) is a flexible modeling language that allows you to author schemas (models) in YAML that describe the structure of your data.	Issue Tracker
Monarch Ingest	The Monarch Ingest pulls in data from a wide variety of biomedical data sources and generates Biolink-compliant KGX files that are used to build the Monarch KG.	Issue Tracker
Monarch Mapping Commons	SSSOM Mappings collected and curated by the Monarch Initiative.	Issue Tracker
HPO Language Translations	Infrastructure to collect and coordinate HPO language translations.	Issue Tracker
Phenomizer	A web application for clinical diagnostics in human genetics using semantic similarity searches in ontologies.	Issue Tracker
Phenogrid	Phenogrid is a web component that visualizes semantic similarity calculations provided by OWLSim, as provided through APIs from the Monarch Initiative.	Issue Tracker
Monarch Assistant	An LLM retrieval augmented generation (RAG) agent for Monarch Initiative.	Issue Tracker
pheval.llm	LLM Benchmarking in differential diagnostics.	Issue Tracker
phenopacket2prompt	Creation of prompts from phenopackets, in multiple languages, intended for prompting LLMs.	Issue Tracker
AutoMAxO	Streamline the creation of ontology annotations of MAxO via LLMs.	Issue Tracker

Data documentation

Repository	Description	Tracker
HPOA - Disease Annotations		Issue Tracker
HPOA - Phenotype to Gene Associations		Issue Tracker
HPOA - Gene to Phenotype Associations		Issue Tracker
HPOA Knowledge Graph Ingestible		Issue Tracker
Alliance Knowledge Graph Ingestible		Issue Tracker

Other documentation and training materials

Repository	Description	Tracker
OBO Academy	A resource for self-paced training of Semantic Engineers.	Issue Tracker
Best practices for collaborative open source coding	The best practice / house style guide maintained by Monarch's LBNL team members.	Issue Tracker