🧬 Orphanet Rare Diseases Scraper

🚀 Pull structured rare-disease records in seconds. Turn Orphanet ORPHAcodes into clean rows with names, synonyms, definitions, and cross-references to ICD-10, ICD-11, OMIM, UMLS, MeSH, MedDRA, and MONDO.

🕒 Last updated: 2026-06-05 · 📊 18 fields per record · 11,400+ ORPHAcodes available · 9 languages

Orphanet is the reference portal for rare diseases and orphan drugs, and Orphadata is its open data service. This Actor reads the keyless Orphadata cross-referencing API and returns one tidy record per rare disease, including every terminology mapping that Orphanet publishes for that code.

Coverage spans the full Orphanet nomenclature: more than 11,400 ORPHAcodes covering disorders, groups of disorders, and subtypes. Each record carries the preferred term, known synonyms, a clinical definition where available, the disorder group and typology, the last update date, and the cross-references that let you join Orphanet data to ICD-10, ICD-11, OMIM, UMLS, MeSH, MedDRA, and MONDO.

🎯 Target Audience	💡 Primary Use Cases
Bioinformaticians and data scientists	Building rare-disease terminology maps
Health-tech and EHR teams	Enriching patient records with standard codes
Pharma and clinical research groups	Orphan-drug and indication research
Medical ontology and knowledge-graph builders	Linking ORPHAcodes across vocabularies

📋 What the Orphanet Rare Diseases Scraper does

• Reads single ORPHAcodes you supply, or pulls the latest codes straight from the Orphadata list endpoint.
• Returns the preferred term, synonyms, disorder group, typology, and clinical definition.
• Extracts cross-references to ICD-10, ICD-11, OMIM, UMLS, MeSH, MedDRA, and MONDO.
• Keeps the full raw cross-reference list with mapping relations and ICD browser links.
• Works in nine languages for preferred terms, synonyms, and definitions.

🎬 Full Demo (🚧 Coming soon)

⚙️ Input

Field	Type	Description
orphaCodes	array	Optional list of ORPHAcodes (for example 558). Leave empty to pull codes automatically from the Orphadata list endpoint.
language	string	Language for terms, synonyms, and definitions. One of en, fr, de, es, it, nl, pl, pt, cs.
maxItems	integer	Maximum number of records to collect. Free plan is capped at 10.

Scrape specific diseases by code:

{
    "orphaCodes": ["558", "61", "141"],
    "language": "en",
    "maxItems": 3
}

Pull a batch of records automatically:

{
    "language": "en",
    "maxItems": 25
}

⚠️ Good to Know: Orphadata publishes data under the Creative Commons Attribution 4.0 licence. Fields such as mesh or medDRA are present only when Orphanet has a validated mapping for that disease, so they may be empty on some records.

📊 Output

Field	Description
🔢 orphaCode	Orphanet identifier for the disease
📌 preferredTerm	Official preferred name
🧬 disorderGroup	Disorder, group of disorders, or subtype
🧩 typology	Typology label (for example Disease)
📖 definition	Clinical definition when available
🔗 url	Orphanet record page
📅 lastUpdated	Last update timestamp from Orphanet
🏷 synonyms	Alternative names
🩺 icd10	ICD-10 codes
🩺 icd11	ICD-11 codes
🧬 omim	OMIM references
🔬 umls	UMLS concept IDs
📚 mesh	MeSH descriptors
⚠️ medDRA	MedDRA codes
🔗 mondo	MONDO references
🗂 crossReferences	Full mapping list with relation and ICD links
🕒 scrapedAt	Collection timestamp
❌ error	Null on success

Real sample records:

{
    "orphaCode": "166024",
    "preferredTerm": "Multiple epiphyseal dysplasia-macrocephaly-facial dysmorphism syndrome",
    "disorderGroup": "Disorder",
    "synonyms": ["Multiple epiphyseal dysplasia, Al-Gazali type"],
    "icd10": ["Q77.3"],
    "icd11": ["LD24.61"],
    "omim": ["607131"],
    "umls": ["C4304500"],
    "url": "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=166024"
}

{
    "orphaCode": "58",
    "preferredTerm": "Alexander disease",
    "disorderGroup": "Disorder",
    "synonyms": ["AxD"],
    "icd10": ["G93.8"],
    "icd11": ["8A44.2"],
    "omim": ["203450"],
    "umls": ["C0270726"],
    "url": "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=58"
}

{
    "orphaCode": "166032",
    "preferredTerm": "Multiple epiphyseal dysplasia-miniepiphyses syndrome",
    "disorderGroup": "Disorder",
    "synonyms": [],
    "icd10": ["Q77.3"],
    "icd11": ["LD24.61"],
    "omim": ["609325"],
    "umls": ["C5924992"],
    "url": "http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=166032"
}

✨ Why choose this Actor

• Authoritative source. Data comes straight from the official Orphadata cross-referencing API.
• Vocabulary mappings included. Join Orphanet to ICD, OMIM, UMLS, MeSH, MedDRA, and MONDO out of the box.
• Multilingual. Nine language options for names and definitions.
• Clean shape. One flat record per disease, ready for analysis and knowledge graphs.

📈 How it compares to alternatives

Approach	Cross-references	Multilingual	Maintenance
This Actor	All Orphanet mappings	9 languages	None on your side
Manual portal lookups	One disease at a time	Limited	High
Raw XML downloads	Yes, but heavy parsing	Yes	You parse and maintain

🚀 How to use

1. Sign up for a free Apify account with our referral link.
2. Open the Orphanet Rare Diseases Scraper.
3. Enter ORPHAcodes, or leave the list empty to pull records automatically.
4. Pick a language and set how many records you want.
5. Run the Actor and collect your dataset.

💼 Business use cases

Health-tech and EHR enrichment

Need	Outcome
Standard codes on patient records	Map ORPHAcodes to ICD and OMIM
Consistent disease naming	Use preferred terms and synonyms

Pharma and clinical research

Need	Outcome
Orphan-drug indication research	Browse disorders by group and typology
Cohort definition	Link diseases across vocabularies

Knowledge graphs and ontologies

Need	Outcome
Cross-vocabulary linking	Use MONDO, UMLS, and MeSH references
Entity resolution	Match synonyms to a single ORPHAcode

Academic and epidemiology work

Need	Outcome
Rare-disease prevalence studies	Start from a clean code list
Multilingual datasets	Pull terms in nine languages

🔌 Automating Orphanet Rare Diseases Scraper

Connect the Actor to Make, Zapier, Slack, Airbyte, GitHub, and Google Drive through the Apify API and integrations. Trigger runs on a schedule and push records into your warehouse, sheet, or messaging channel automatically.

🌟 Beyond business use cases

• Research: build reproducible rare-disease datasets for papers and reviews.
• Personal: explore the terminology behind a specific diagnosis.
• Non-profit: support patient-advocacy resources with standard codes.
• Experimentation: prototype medical chatbots and ontology tools.

🤖 Ask an AI assistant

Paste a record into ChatGPT, Claude, Perplexity, or Microsoft Copilot and ask it to summarize the disease, explain a mapping relation, or group records by disorder type.

❓ Frequently Asked Questions

What is an ORPHAcode? A unique identifier assigned by Orphanet to each rare disease, group, or subtype.

Where does the data come from? The official Orphadata cross-referencing API at api.orphadata.com.

Do I need an API key? No. The Orphadata endpoints used here are keyless.

Which vocabularies are covered? ICD-10, ICD-11, OMIM, UMLS, MeSH, MedDRA, and MONDO, when Orphanet provides a mapping.

Why are some code fields empty? Orphanet only publishes validated mappings, so a disease may lack a MeSH or MedDRA code.

Can I scrape specific diseases? Yes. Provide their ORPHAcodes in the input.

What if I leave the code list empty? The Actor pulls codes from the Orphadata list endpoint up to your item limit.

Which languages are supported? English, French, German, Spanish, Italian, Dutch, Polish, Portuguese, and Czech.

How many records can I get? Free plans return up to 10. Paid plans go up to 1,000,000.

Is the data licensed for reuse? Orphadata uses Creative Commons Attribution 4.0. Credit Orphanet when you publish.

Does it return clinical definitions? Yes, when Orphanet provides one for the disease.

🔌 Integrate with any app

Use the Apify API to run the Actor and fetch results from your own code, or wire it into low-code platforms through the standard Apify integrations.

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💡 Pro Tip: browse the complete ParseForge collection.

🆘 Need Help? Open our contact form

⚠️ Disclaimer: independent tool, not affiliated with Orphanet or Orphadata. Only publicly available data collected.