monarch-database

# monarch-database ## Overview The Monarch Initiative integrates disease-phenotype-gene relationships from 30+ biomedical databases (OMIM, Orphanet, ClinVar, MGI, ZFIN, Reactome) into a unified knowledge graph. The REST API at `https://api.monarchinitiative.org/v3/api` provides access to associations between genes, diseases, and phenotypes using MONDO disease IDs, Human Phenotype Ontology (HPO) terms, and standard gene identifiers. No authentication is required; the service is free for academic use. ## When to Use - Mapping a disease (MONDO ID) to all associated causal genes and their evidence sources - Retrieving phenotype profiles (HP terms) for a disease to build phenotypic similarity models - Ranking candidate genes by phenotypic similarity to a patient's HPO symptom list - Querying cross-species gene-phenotype associations (mouse, zebrafish, fly) for model organism comparisons - Exploring rare disease gene-phenotype networks for diagnostic candidate generation - Resolving entity metadata (gene symbol, disease name, phenotype label) from a MONDO/HP/HGNC ID - Use `opentargets-database` instead when you need drug-target evidence scores or tractability data alongside disease associations - Use `clinvar-database` when you need clinical pathogenicity classifications with submitter review status ## Prerequisites - **Python packages**: `requests`, `pandas`, `matplotlib` - **Data requirements**: MONDO IDs (e.g., `MONDO:0007374`), HP term IDs (e.g., `HP:0001250`), or gene sy...