🔬 ChEMBL Assays Scraper

🚀 Export ChEMBL bioactivity assay records in seconds. Description, type, organism, target, document, confidence score, and cell line.

🕒 Last updated: 2026-06-05 · 📊 19 fields per record · 1.7 million+ assays · EBI ChEMBL public API

The ChEMBL Assays Scraper turns the public ebi.ac.uk/chembl/api/data/assay endpoint into a structured dataset. It supports list, target-scoped, search, and exact-ID modes, and exposes every assay filter the API accepts.

🎯 Target Audience	💡 Primary Use Cases
💊 Drug discovery teams	Snapshot assays for a target
🧪 Bioinformaticians	Mirror ChEMBL assays into a warehouse
📊 Computational chemists	Filter by confidence score and assay type
🛡️ Pharma BD	Cross-reference assays with documents
👩‍🔬 Academic researchers	Build assay-to-target matrices
👩‍💻 Developers	Drive an assay browser UI

📋 What the ChEMBL Assays Scraper does

• Calls the public /data/assay endpoint with the filters you provide.
• Supports list, target-scoped, free-text, and exact-ID modes.
• Filters by assay type, organism, and minimum confidence score.
• Pushes a clean diagnostic record on upstream errors.
• Exports to every Apify dataset format.

💡 Why it matters: Assays are the bridge between targets and compounds. Mirroring them lets you build the full target-assay-activity graph in your own warehouse.

🎬 Full Demo

🚧 Coming soon.

⚙️ Input

Field	Type	Required	Description
maxItems	integer	No	Free 10. Paid up to 1,000,000.
assayChemblId	string	No	Exact lookup such as `CHEMBL1217643`.
targetChemblId	string	No	Filter assays for a specific target.
search	string	No	Free-text search across descriptions.
assayType	enum	No	B, F, A, P, T, U.
organism	string	No	Exact assay organism.
minConfidenceScore	integer	No	0 to 9. Drop assays below this.

Example 1. EGFR binding assays.

{ "targetChemblId": "CHEMBL203", "assayType": "B", "maxItems": 50 }

Example 2. Exact assay lookup.

{ "assayChemblId": "CHEMBL1217643" }

⚠️ Good to Know: ChEMBL paginates 200 records per page. The actor walks pagination until maxItems is hit.

📊 Output

Field	Type	Description
🆔 assayChemblId	string	ChEMBL assay id.
📝 description	string	Assay description.
🔬 assayType	string	One-letter assay type code.
📝 assayTypeDescription	string	Human-readable type.
🧬 organism	string	Assay organism.
🧫 assayTissue	string	Tissue source.
🧬 assayStrain	string	Strain.
🧬 assaySubcellularFraction	string	Subcellular fraction.
🎯 targetChemblId	string	Linked target id.
📄 documentChemblId	string	Linked publication.
🏅 confidenceScore	number	0 to 9 confidence.
📝 confidenceDescription	string	Confidence description.
🧫 cellChemblId	string	Cell-line id.
🔢 bao_format	string	BAO format id.
🔗 relationshipType	string	Target relationship type.
📝 relationshipDescription	string	Relationship description.
🗂️ assayCategory	string	Category.
🕒 scrapedAt	string	When this row was fetched.
❌ error	string	Set on upstream error.

{
  "assayChemblId": "CHEMBL1217643",
  "description": "Inhibition of EGFR",
  "assayType": "B",
  "organism": "Homo sapiens",
  "targetChemblId": "CHEMBL203",
  "confidenceScore": 8,
  "scrapedAt": "2026-06-05T12:00:00.000Z",
  "error": null
}

✨ Why choose this Actor

| 🆓 | Public EBI ChEMBL endpoint, no key required. | | 🎯 | Target-scoped pagination in one call. | | 🏅 | Confidence-score filter at scrape time. | | 🛟 | Clean diagnostic records on errors. | | 💾 | Push to dataset for instant export. |

📈 How it compares to alternatives

Approach	Setup	Target filter	Auto export
chembl_webresource_client Python	install + script	manual	manual
Raw fetch on the REST endpoint	30 min +	manual	manual
This Actor	5 sec	✅	✅

🚀 How to use

1. Click Try for free.
2. Provide a target id, assay id, or other filters.
3. Click Start and download the dataset.

💼 Business use cases

💊 Assay shortlists. Build per-target assay catalogs for screening teams.

🧪 Confidence-aware pipelines. Only ingest assays with confidence score >= 7.

🛡️ Competitive landscape. Cross-reference assay documents against literature trackers.

📊 Pipeline analytics. Track new ChEMBL releases.

🔌 Automating ChEMBL Assays Scraper

• Make and Zapier trigger this actor on a schedule.
• Cron keeps your mirror fresh.
• Webhooks notify on completion.
• Pipe to BigQuery, Snowflake, or Postgres with native integrations.

🌟 Beyond business use cases

🎓 Education. Teach drug-discovery with live assay data.

🧪 Personal research. Explore assays for your favorite target.

🤝 Non-profit and open data. Publish an assay dashboard.

🧰 Tinkering. Quick assay lookups.

🤖 Ask an AI assistant about this scraper

Pop this README into ChatGPT, Claude, or any AI assistant and ask it to map your specific workflow to the actor's inputs.

❓ Frequently Asked Questions

❓ Need an API key? No.

❓ Source? Official EBI ChEMBL REST API.

❓ Schedule runs? Yes.

❓ Rate limits? Light per-IP throttle.

❓ API or scraping? API.

❓ Schema stability? Stable.

❓ Maximum run? 1,000,000 records on paid plans.

❓ Confidence filter? Server-side or client-side via minConfidenceScore.

❓ Target-scoped? Yes, via targetChemblId.

❓ Download formats? Any Apify dataset format.

🔌 Integrate with any app

Apify ships native integrations with Make, Zapier, Slack, Discord, Google Drive, Google Sheets, Gmail, Airbyte, Keboola, Telegram, GitHub, and any REST API or webhook endpoint.

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