Mondo Disease Ontology Scraper

Mondo Disease Ontology Scraper

Scrape disease definitions, synonyms, and ontology relationships from the Mondo Disease Ontology, up to a million terms per run. Every term comes with its ID, label, definition, and cross-references to other ontologies. Export to CSV, JSON, Excel, or XML.

Biomedical researchers and bioinformaticians need structured disease data, but querying the Mondo Disease Ontology manually or through its SPARQL endpoint is slow and requires technical setup. This Actor reads the public Mondo API directly, letting you pull disease terms by keyword or fetch the full ontology in order. Each term arrives in one flat, analysis-ready row.

Who uses it	What they scrape Mondo Disease Ontology for
Bioinformaticians	Building a local disease knowledge graph for variant interpretation pipelines.
Clinical data curators	Standardizing disease names across electronic health records with Mondo IDs.
Pharma researchers	Mapping internal disease lists to a public ontology for target discovery.
Health-tech developers	Populating a symptom checker or diagnostic tool with canonical disease definitions.

What it does

This Actor collects disease terms from the Mondo Disease Ontology by keyword search or sequential fetch, and returns each term as a flat row with its ontology ID, label, definition, and cross-references.

• 🔍 Keyword search: pass a disease name or partial term and get back the matching Mondo entries.
• 📋 Bulk fetch: leave the query empty to pull terms sequentially from the ontology, up to your maxItems limit.
• 🔗 Cross-reference mapping: each row includes links to equivalent terms in OMIM, Orphanet, DOID, and other ontologies.

Results export to CSV, JSON, Excel, or XML, or straight from the API.

What you can do with Mondo Disease Ontology data

🧬 Standardize disease names in a biobank.

A clinical data curator fetches Mondo terms matching free-text diagnoses from a biobank cohort, then maps each patient record to a stable Mondo ID for downstream GWAS analysis.

📊 Build a disease knowledge graph.

A bioinformatician pulls the full Mondo ontology with cross-references to OMIM and Orphanet, then loads the flat file into Neo4j to power a variant interpretation tool.

💊 Map internal disease lists for drug repurposing.

A pharma researcher searches Mondo for each disease in an internal pipeline list, retrieves the canonical definition and synonyms, and aligns the company's targets with public ontology terms.

🩺 Populate a diagnostic decision-support tool.

A health-tech developer fetches disease definitions and synonyms from Mondo, then seeds a symptom-checker UI with clinician-reviewed, ontology-backed disease descriptions.

Why choose this scraper

	What you get
No SPARQL needed	Query the ontology through a simple text field, no query language required.
Flat, analysis-ready output	Every disease term arrives as one row in CSV, JSON, Excel, or XML, ready for pandas, R, or a database.
Cross-references included	Each term carries its mappings to OMIM, Orphanet, DOID, and other major biomedical ontologies.
Up to a million terms	Pull a handful of diseases for a pilot study or the entire ontology for a production pipeline.

How it compares

No other Store actor targets Mondo Disease Ontology the same way, so the honest comparison is with the alternatives teams actually weigh.

	Mondo Disease Ontology Scraper	Build it in-house	By hand
Setup	Run it now, zero config	Days of engineering	None, but hours per pull
When Mondo Disease Ontology changes	Maintained for you	You fix it	You re-learn the page
Proxies, retries, anti-bot	Built in	Your problem	Browser only
Output	Fixed JSON schema, CSV/Excel export	Whatever you build	Copy-paste
Cost	Pay per result	Engineering time	Analyst hours

Configure the run

Drive the Actor with an optional disease name or keyword, or leave the query empty to fetch terms in ontology order. Set a maximum number of diseases to cap the run. The Input tab lists every parameter.

A first run with the defaults:

{
 "maxItems": 10
}

A larger pull:

{
 "maxItems": 200
}

Pricing

Pay-per-result: $0.0085 per result collected. You pay only for the results written to your dataset.

Results collected	Approximate cost
100 results	$0.85
1,000 results	$8.50
10,000 results	$85.00

New Apify accounts start with $5 in free credit.

Free users

Free-plan runs return up to 10 results as a preview. Upgrade your Apify plan to collect up to 1,000,000 results per run.

Run it

1. Create a free Apify account with $5 in credit.
2. Open the Mondo Disease Ontology Scraper.
3. Set your inputs and any filters, then click Start.
4. Export the results as CSV, Excel, JSON, or XML from the Dataset tab.

Run it programmatically through the Apify API (run-sync-get-dataset-items) or the ApifyClient for JavaScript and Python.

Use with AI agents (MCP)

Give an AI agent live access to Mondo Disease Ontology through the Model Context Protocol. Add the Actor to Claude, Cursor, or any MCP client:

$claude mcp add --transport http apify "https://mcp.apify.com?tools=parseforge/mondo-disease-scraper"

Then prompt it in plain language to run the scraper and read back the results.

Troubleshooting

Why am I getting no results for my query?

Check the spelling of your disease name or keyword. Mondo uses canonical labels and synonyms. Try a shorter substring or a different synonym. You can also leave the query empty to browse terms and find the exact label.

The run stopped before reaching my maxItems limit.

The Actor stops when it has fetched all available terms matching your query, or when it reaches the end of the ontology if no query was given. This is expected behavior. Try a broader query or leave the query empty to pull more terms.

Some cross-reference fields are empty in my output.

Not every Mondo term has mappings to every external ontology. Empty cross-reference fields mean no mapping exists for that term in that specific ontology. This is normal and reflects the source data.

The export file is too large to open in Excel.

Reduce the maxItems value and split your fetch into multiple smaller runs. Alternatively, export to CSV and load the file into a database or a dataframe library like pandas, which handles large files efficiently.

I need a field that is not in the output.

The Actor returns the fields provided by the Mondo API. If you need additional ontology properties, check the Mondo documentation to see if they are available through the public endpoints, and contact the Actor maintainer with your request.

FAQ

Question	Answer
What is the Mondo Disease Ontology?	Mondo is a community-driven ontology that harmonizes disease definitions across multiple biomedical resources, including OMIM, Orphanet, and the Disease Ontology. It provides a single, unified identifier for each disease concept.
Do I need an API key or authentication?	No. This Actor reads the public Mondo API endpoints. You do not need to register an application or manage credentials.
What fields does each disease row contain?	Each row includes the Mondo ID, primary label, definition, synonyms, and cross-reference mappings to other ontologies such as OMIM, Orphanet, and DOID. The exact field list is visible in the sample output on the Actor's page.
Can I search for a disease by its common name?	Yes. Pass a disease name or partial keyword in the query field, and the Actor returns matching Mondo terms with their canonical labels and synonyms.
How do I fetch the entire ontology?	Leave the query field empty and set maxItems to a high number. The Actor will pull terms in ontology order until it reaches your limit.
What export formats are supported?	You can export your dataset to CSV, JSON, Excel, or XML from the Apify platform.
Are cross-references to OMIM and Orphanet included?	Yes. Each disease row carries its mappings to equivalent terms in OMIM, Orphanet, DOID, and other ontologies when those mappings exist in Mondo.
Can I limit how many diseases are collected?	Yes. Set the maxItems field to any number between 1 and 1,000,000. The run stops after collecting that many terms.
Is this Actor suitable for production bioinformatics pipelines?	Yes. The flat, consistent schema and bulk-fetch capability make it straightforward to integrate into automated ETL workflows that feed databases or analysis notebooks.
How often is the Mondo data updated?	The Actor queries the live Mondo API on each run, so you always receive the latest disease terms and mappings available from the ontology.

Related actors

Browse the full ParseForge collection for more scrapers.

🆘 Need help? Email parseforge@protonmail.com with your run ID, your input, and what you expected.

⚠️ Disclaimer. This Actor is unofficial and is not affiliated with, endorsed by, or sponsored by Monarch Initiative. It collects only publicly available data. You are responsible for using the collected data in compliance with the source's terms of service and applicable data-protection laws, including GDPR, CCPA, and PIPL. Do not use it to collect personal data unlawfully.