Monarch Initiative API

Free Monarch Initiative API with no key: integrated disease, gene and phenotype records with cross-references to OMIM, Orphanet, ICD-10, MeSH, SNOMED and UMLS.

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Endpoint tested and returned HTTP 200 on 2026-08-21

What is the Monarch Initiative API?

The Monarch Initiative API is a free, key-free interface to an integrated biomedical knowledge graph. Entity lookups return a disease, gene or phenotype with its name, description, synonyms and a dense set of cross-references to OMIM, Orphanet, ICD-10-CM, MeSH, MedGen, NCIT, SNOMED and UMLS.

Monarch's purpose is translation between vocabularies. Rare disease information is fragmented across registries that each mint their own identifiers, and the `xref` array on a Monarch record is the map between them — the Marfan syndrome entry links DOID, GARD, ICD-10-CM Q87.4, MedGen, MeSH, MedDRA, NCIT, OMIM 154700, two Orphanet codes, a SNOMED concept and a UMLS CUI in one response. If you need to join two health datasets that disagree about identifiers, this is the shortest path.

The graph is built on Biolink Model semantics, so every node carries a `category` such as `biolink:Disease` and edges are typed — which is what makes phenotype-driven queries across species possible. Provenance is stated rather than implied: `provided_by` and `file_source` name the ingest that supplied each record, so `phenio_nodes` tells you the entry came from the merged phenotype ontology build. Descriptions are aggregated from upstream sources and written for a general audience; they summarise published knowledge and are not clinical guidance.

Quick facts

Base URL: https://api-v3.monarchinitiative.org/v3/api
Authentication: No API key or account. Monarch is an open-science project and its integrated data is openly licensed, but individual ingested sources carry their own terms — OMIM in particular restricts redistribution, so check before bulk reuse.
Rate limit: No published limit. Monarch also publishes the whole knowledge graph for download, which is the right route for systematic work.
Pricing: Free. Aggregated content inherits the licences of its upstream sources.
CORS: Enabled — callable directly from browser JavaScript
Official docs: Read the docs

How to use the Monarch Initiative API

Every request below was executed against the live API on 2026-08-21, and the response shown is the real body it returned — not an illustration.

1. Fetch the disease record for Marfan syndrome

GET https://api-v3.monarchinitiative.org/v3/api/entity/MONDO:0007947

curl

curl 'https://api-v3.monarchinitiative.org/v3/api/entity/MONDO:0007947' \
  -H 'Accept: application/json'

JavaScript (fetch)

const res = await fetch("https://api-v3.monarchinitiative.org/v3/api/entity/MONDO:0007947", {
  headers: {
    "Accept": "application/json",
  },
});
if (!res.ok) throw new Error(`Request failed: ${res.status}`);
const data = await res.json();
console.log(data);

Python (requests)

import requests

headers = {
    "Accept": "application/json",
}

res = requests.get("https://api-v3.monarchinitiative.org/v3/api/entity/MONDO:0007947", headers=headers, timeout=20)
res.raise_for_status()
print(res.json())

Response — HTTP 200 (truncated)

{
  "id": "MONDO:0007947",
  "category": "biolink:Disease",
  "name": "Marfan syndrome",
  "xref": [
    "DOID:14323",
    "GARD:0016535",
    "ICD10CM:Q87.4",
    "ICD9:759.82",
    "MEDGEN:44287",
    "MESH:D008382",
    "MedDRA:10026829",
    "NANDO:1200644",
    "NANDO:2200968",
    "NCIT:C34807",
    "NORD:1403",
    "OMIM:154700",
    "Orphanet:284963",
    "Orphanet:558",
    "SCTID:19346006",
    "UMLS:C0024796",
    "icd11.foundation:236564145"
  ],
  "synonym": [
    "MFS",
    "MFS1",
    "Marfan syndrome",
    "Marfan syndrome type 1",
    "Marfan syndrome, type 1",
    "Marfan's syndrome"
  ],
  "full_name": null,
  "in_taxon": null,
  "in_taxon_label": null,
  "symbol": null,
  "file_source": "phenio_nodes",
  "provided_by": "phenio_nodes",
  "type": null,
  "description": "A disorder of the connective tissue. Connective tissue provides strength and flexibility to structures throughout the body such as bones, ligaments, muscles, walls of blood vessels, and heart valves. Marfan syndrome affects most organs and tissues, especially the skeleton, lungs, eyes, heart, and the large blood vessel that distributes blood from the heart to the rest of the body (the aorta). It is caused by mutations in the FBN1 gene, which provides instructions for making a protein called fibrillin-1. Marfan syndrome is inherited in an autosomal dominant pattern. At least 25% of cases are due to a new (de novo) mutation. Treatment is based on the signs and symptoms in each person.",
  "iri": null,
  "has_attribute": null,
  "has_biological_sex": null,
  "exact_synonym": [
    "MFS",
    "

Parameters

Parameter	Type	Required	Description
`id`	path segment	Required	A CURIE identifying the entity — MONDO, HGNC, HP, OMIM and others resolve. `MONDO:0007947`
`(endpoint) /search`	path	Optional	Free-text search across the graph, filterable by category. `/v3/api/search?q=marfan`
`(endpoint) /entity/{id}/{category}`	path	Optional	Associations from an entity, such as its phenotypes or causal genes. `/entity/MONDO:0007947/biolink:DiseaseToPhenotypicFeatureAssociation`
`category`	query	Optional	Restrict search results to a Biolink category such as `biolink:Disease`. `biolink:Disease`
`limit / offset`	query	Optional	Paging controls on search and association endpoints. `20`

Response fields

idstring: The CURIE for the entity, normally a MONDO identifier for diseases.
categorystring: Biolink Model class, such as `biolink:Disease`. Determines which other fields are populated.
namestring: Preferred label for the entity.
xref[]array: Cross-references to other vocabularies, each prefixed — `OMIM:`, `Orphanet:`, `ICD10CM:`, `SCTID:`, `UMLS:` and more. The most valuable field for data integration.
synonym[]array: All known alternative names, with `exact_synonym` separating the strictly equivalent ones.
descriptionstring: Plain-language summary aggregated from upstream sources. Descriptive, not clinical advice.
provided_by / file_sourcestring: Which Monarch ingest supplied the record — the provenance trail for any value you use.
in_taxon / symbol / full_namevaries: Populated for gene entities and null for diseases. Check `category` before reading them.

What you can build with the Monarch Initiative API

Translate a disease identifier between OMIM, Orphanet, ICD-10 and MONDO
Look up the phenotypes associated with a rare disease
Find candidate genes for a set of observed phenotypes
Reconcile disease names across two health datasets
Build a rare disease reference page with sourced cross-references

Common errors and how to fix them

404

The CURIE prefix is wrong or unsupported.

Fix: Prefixes are case-sensitive and specific — `MONDO:0007947`, not `mondo:0007947` or a bare number. Search first if you only have a name.

Null fields on a disease record

Gene-specific fields are present but empty.

Fix: The response schema is shared across entity types. Read `category` and ignore the fields that do not apply.

Missing expected cross-reference

Not every disease maps to every vocabulary.

Fix: Rare diseases frequently have no ICD-10 code at all, which is a real gap in the source terminologies rather than a Monarch omission.

Slow association queries

Some entities have very large association sets.

Fix: Page with `limit` and `offset`, or download the knowledge graph for bulk analysis.

Monarch Initiative API — frequently asked questions

Is the Monarch Initiative API free?

Yes, free with no key or registration. Monarch is an open-science project; its integration is openly licensed, though individual ingested sources such as OMIM impose their own redistribution terms.

What is a MONDO identifier?

MONDO is a merged disease ontology that unifies definitions from OMIM, Orphanet, DOID, NCIT and others into one identifier per disease concept. It exists precisely because those sources disagree, and it is the hub Monarch's cross-references radiate from.

Can I use this to diagnose a patient from their symptoms?

No. The API returns published associations between phenotypes, genes and diseases, which is research and reference information. Diagnosis requires clinical assessment; these associations are inputs to expert judgement, not a substitute for it.

How do I find a disease when I only have its name?

Use the `/search` endpoint with `q` set to the name and `category=biolink:Disease` to filter. It returns candidate entities with their CURIEs, which you then pass to the entity endpoint.

Tools that pair with this API

JSON Formatter

Format, beautify and minify JSON online with 2-space, 4-space or tab indentation. Sort keys alphabetically and catch syntax errors instantly — free and private.

JSON Path Finder

Evaluate a dot/bracket path against your JSON and list every leaf path for discovery. Free online JSON path finder that runs 100% in your browser.

JSON to CSV Converter

Convert a JSON array of objects to CSV online. Automatic column headers from the union of all keys, delimiter choice and proper quoting — all in-browser.

Monarch Initiative is an independent third-party service and is not affiliated with ByteTools or ByteVancer. Details on this page were verified on 2026-08-21; always check the official documentation before relying on this API in production, as terms and limits can change.