🎯 Open Targets Platform Scraper

🚀 Export drug-target-disease associations in seconds. Query the Open Targets Platform GraphQL API across targets, diseases, drugs, and free-text search. No API key, no registration, no manual GraphQL stitching.

🕒 Last updated: 2026-05-13 · 📊 4 entity modes · 🧬 60,000+ targets · 🦠 26,000+ diseases · 💊 13,000+ drugs · 🌐 EBI GraphQL API

The Open Targets Platform Scraper queries the Open Targets v4 GraphQL API and returns rich, joined records for targets (genes), diseases, drugs, and free-text search. Open Targets is a public-private partnership between EMBL-EBI, GSK, Sanofi, Bristol Myers Squibb, Pfizer, Genentech, MSD, and the Wellcome Sanger Institute that integrates genetics, genomics, transcriptomics, drug, and literature evidence into target-disease association scores used across drug discovery.

This Actor exposes four query modes in one input form: pull a target by Ensembl ID (or HGNC symbol), a disease by EFO / MONDO ID, a drug by ChEMBL ID, or a free-text search across all three. Each record returns the canonical ID, name, descriptive metadata, and the relevant association table (associated diseases, associated targets, mechanisms of action, indications, drug warnings).

🎯 Target Audience	💡 Primary Use Cases
Drug discovery teams, target ID scientists, computational biologists, bioinformaticians, regulatory analysts, journal editors, ML researchers	Target prioritization, drug repurposing, disease-target maps, ChEMBL-to-EFO joins, indication discovery, mechanism-of-action audits, ML feature engineering

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📋 What the Open Targets Scraper does

Four query modes in a single Actor:

• 🧬 Target mode. Fetch by Ensembl gene ID (e.g. ENSG00000146648 for EGFR), or by HGNC symbol that the Actor resolves via the GraphQL search hit. Returns approvedSymbol, approvedName, biotype, function descriptions, hallmarks, tractability modalities, pathways, the top associated diseases (scored), and the drug + clinical-candidate table.
• 🦠 Disease mode. Fetch by EFO or MONDO ID (e.g. EFO_0000222 for Acute Myeloid Leukemia). Returns description, therapeutic areas, synonyms, parents, children, the top associated targets (scored), and the drug + clinical-candidate table.
• 💊 Drug mode. Fetch by ChEMBL ID (e.g. CHEMBL1201583). Returns description, drug type, maximum clinical stage, synonyms, trade names, cross-references, mechanisms of action with target objects, indications with diseases, drug warnings, and parent molecule.
• 🔎 Search mode. Free-text search across target + disease + drug. Returns one row per hit with entity type, ID, name, description, and relevance score.

💡 Why it matters: Open Targets is the canonical public source for evidence-based target prioritization in pharma. Building your own GraphQL queries means schema introspection, pagination plumbing, and constant rewrites. This Actor returns ready-joined records on every run.

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🎬 Full Demo

🚧 Coming soon: a 3-minute walkthrough showing how to go from sign-up to a downloaded target-disease dataset.

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⚙️ Input

Input	Type	Default	Behavior
mode	enum	"target"	One of target, disease, drug, search.
maxItems	integer	10	Records to return. Free plan caps at 10, paid plan at 1,000,000.
ensemblId	string	"ENSG00000146648"	For target mode. EGFR by default.
symbol	string	""	For target mode. HGNC symbol fallback resolved via search.
efoId	string	"EFO_0000222"	For disease mode. EFO or MONDO ID.
chemblId	string	"CHEMBL1201583"	For drug mode. ChEMBL drug ID.
searchQuery	string	""	For search mode. Free-text query string.
searchEntities	string[]	[]	For search mode. Restrict to target, disease, or drug. Empty = all three.

Example: target mode for EGFR with associated diseases.

{
    "mode": "target",
    "ensemblId": "ENSG00000146648",
    "maxItems": 50
}

Example: free-text search across targets and diseases for "cancer".

{
    "mode": "search",
    "searchQuery": "cancer",
    "searchEntities": ["target", "disease"],
    "maxItems": 25
}

⚠️ Good to Know: target mode accepts either ensemblId or symbol. When you provide a symbol like BRAF, the Actor first calls the GraphQL search query to resolve the canonical Ensembl ID, then fetches the target object. Disease IDs follow EFO / MONDO / Orphanet conventions (EFO_*, MONDO_*, Orphanet_*). Drug IDs follow the ChEMBL CHEMBL* convention. Search hits include a relevance score that you can sort downstream.

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📊 Output

The output shape varies by mode. Each record always carries an entity field, an id, a url, and a scrapedAt timestamp.

🧾 Search-mode schema

Field	Type	Example
🏷️ entity	enum	"target", "disease", or "drug"
🆔 id	string	"ENSG00000139618"
🔗 url	string	"https://platform.opentargets.org/target/ENSG00000139618"
📛 name	string	"BRCA2"
📝 description	string	"BRCA2 DNA repair associated"
🎯 score	number	471.1691
🕒 scrapedAt	ISO 8601	"2026-05-13T22:26:22.091Z"

🧾 Target-mode schema (selected fields)

Field	Type	Notes
🏷️ entity	string	"target"
🆔 id	string	Ensembl gene ID
🔬 approvedSymbol	string	HGNC symbol
📛 approvedName	string	Full gene name
🧬 biotype	string	e.g. protein_coding
📜 functionDescriptions	string[]	UniProt descriptions
🎯 hallmarks	object	Cancer hallmarks block
💊 tractability	object[]	Modality / value / label tuples
🔁 pathways	object[]	Reactome pathways
🦠 associatedDiseases	object	Top diseases with scores
💊 drugAndClinicalCandidates	object	Drugs in development

📦 Sample record (search mode)

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✨ Why choose this Actor

	Capability
🎯	Four query modes. Target, disease, drug, and free-text search in one Actor.
🧬	Joined records. Target rows carry associated diseases, drugs, hallmarks, pathways, and tractability in a single document.
🔁	Symbol fallback. Pass BRCA1 or EGFR and the Actor resolves the Ensembl ID via the search hit before fetching the full object.
🦠	EFO + MONDO + Orphanet. Standard biomedical ontologies, ready for joins.
💊	ChEMBL cross-reference. Drug mode joins ChEMBL IDs to mechanisms of action, indications, and warnings.
⚡	Fast. GraphQL queries with retry and pagination size 250.
🚫	No authentication. Works on the public GraphQL endpoint. No login or API key.

📊 Open Targets is the de facto reference dataset for target prioritization in modern drug discovery.

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📈 How it compares to alternatives

Approach	Cost	Coverage	Refresh	Modes	Setup
⭐ Open Targets Scraper (this Actor)	$5 free credit, then pay-per-use	Full Open Targets	Live per run	target, disease, drug, search	⚡ 2 min
Hand-rolled GraphQL	Free	Full	Manual	Manual	🐢 Days
OmicsDB / commercial target-ID platforms	$$$/year	Curated subset	Quarterly	Many	⏳ Weeks
Static EBI dataset dumps	Free	Snapshot	Stale	None	🕒 Variable

Pick this Actor when you want broad target-disease-drug coverage, four ready-built query modes, and no pipeline maintenance.

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🚀 How to use

1. 📝 Sign up. Create a free account with $5 credit (takes 2 minutes).
2. 🌐 Open the Actor. Go to the Open Targets Platform Scraper page on the Apify Store.
3. 🎯 Set input. Pick a mode, enter an ID (or a search query), and set maxItems.
4. 🚀 Run it. Click Start and let the Actor collect your data.
5. 📥 Download. Grab your results in the Dataset tab as CSV, Excel, JSON, or XML.

⏱️ Total time from signup to downloaded dataset: 3-5 minutes. No coding required.

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💼 Business use cases

💊 Pharma R&D & Target ID Target prioritization scored by disease association Tractability dashboards across portfolios Drug repurposing audits against new indications Mechanism-of-action joins with ChEMBL	🧬 Computational Biology ML feature tables joining ENSG, EFO, and ChEMBL IDs Pathway enrichment with Reactome IDs Genetic-constraint annotation of candidate genes Cross-disease target overlap analyses
📰 Scientometrics & Competitive Intelligence Tracking competitor pipelines by ChEMBL drug ID Indication-creep mapping across portfolios Clinical-stage distribution by mechanism Drug-warning surveillance for safety teams	🤖 ML & AI for Drug Discovery Knowledge graphs joining target, disease, and drug Embedding generation for drug-target prediction Benchmark suites for biomedical NLP Retrieval-augmented LLM applications

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🔌 Automating Open Targets Scraper

Control the scraper programmatically for scheduled runs and pipeline integrations:

• 🟢 Node.js. Install the apify-client NPM package.
• 🐍 Python. Use the apify-client PyPI package.
• 📚 See the Apify API documentation for full details.

The Apify Schedules feature lets you trigger this Actor on any cron interval. Quarterly refreshes catch every Open Targets release.

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🌟 Beyond business use cases

Data like this powers more than commercial workflows. The same structured records support research, education, civic projects, and personal initiatives.

🎓 Research and academia Reproducible target prioritization with versioned dataset pulls Teaching datasets for bioinformatics and pharmacology Open-source benchmark publications Cross-database joins with ChEMBL, UniProt, and PDB	🎨 Personal and creative Indie biomedical-search apps for curious users Visualizations for science communication Educational drug-target dashboards Portfolio projects on biomedical NLP
🤝 Non-profit and civic Neglected-disease target prioritization Open-science pandemic preparedness Public-domain biomedical-data outreach Civic transparency on pharma pipelines	🧪 Experimentation Train target-disease association models Prototype agentic tools that resolve gene symbols Benchmark biomedical knowledge graphs Generate target embeddings at scale

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🤖 Ask an AI assistant about this scraper

Open a ready-to-send prompt about this ParseForge actor in the AI of your choice:

• 💬 ChatGPT
• 🧠 Claude
• 🔍 Perplexity
• 🅒 Copilot

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❓ Frequently Asked Questions

🧩 How does it work?

Pick a mode (target / disease / drug / search), enter the ID or query, click Start, and the Actor posts a GraphQL document to api.platform.opentargets.org/api/v4/graphql. Records are emitted as clean JSON ready for download. No browser automation, no captchas, no setup.

🧬 Where does the data come from?

Directly from the Open Targets Platform GraphQL API. Open Targets is a public-private partnership coordinated by EMBL-EBI.

🔬 Why are there four modes instead of one?

Each entity (target, disease, drug) has a different shape and a different set of association tables. Modelling them as one mode would force a lowest-common-denominator schema. The four modes return the right joined data for each entity, plus a flat-list search mode for discovery.

🆔 How do I resolve a gene symbol to an Ensembl ID?

Use target mode and pass the symbol in the symbol field while leaving ensemblId empty. The Actor runs the GraphQL search query, takes the top hit with entity = target, and uses its Ensembl ID to fetch the full target object.

🦠 Which disease ontologies are supported?

Open Targets uses EFO, MONDO, and Orphanet identifiers. The efoId input accepts all three (e.g. EFO_0000222, MONDO_0003582, Orphanet_145).

💊 Which drug ontology is supported?

ChEMBL drug IDs (CHEMBL*). Drug records cross-reference DrugBank, PubChem, and other sources via the crossReferences block.

🔁 How often is the dataset refreshed?

Open Targets ships quarterly platform releases. Every run of this Actor hits the live GraphQL endpoint, so your dataset reflects the current release at run time.

⏰ Can I schedule regular runs?

Yes. Use Apify Schedules to run this Actor on any cron interval (weekly, monthly, quarterly) and keep a downstream target-disease database in sync.

⚖️ Is this data legal to use?

Open Targets data is released under a CC0 dedication. The raw association data is publicly accessible. Review Open Targets licensing for your specific use case, especially for redistribution.

💳 Do I need a paid Apify plan to use this Actor?

No. The free Apify plan is enough for testing and small runs (10 records per run). A paid plan lifts the limit and unlocks scheduling, higher concurrency, and larger datasets.

🎯 What if I need evidence-level detail?

This Actor returns target-level, disease-level, drug-level, and search-result records. For row-level evidence (single GWAS hits, single literature citations), reach out via the contact form below to request a companion evidence scraper.

🆘 What if I need help?

Our support team is here to help. Contact us through the Apify platform or use the Tally form linked below.

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🔌 Integrate with any app

Open Targets Scraper connects to any cloud service via Apify integrations:

• Make - Automate multi-step workflows
• Zapier - Connect with 5,000+ apps
• Slack - Get run notifications in your channels
• Airbyte - Pipe target-disease data into your warehouse
• GitHub - Trigger runs from commits and releases
• Google Drive - Export datasets straight to Sheets

You can also use webhooks to trigger downstream actions when a run finishes. Push fresh association data into your drug-discovery backend, or alert your team in Slack when a watched target updates.

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💡 Pro Tip: browse the complete ParseForge collection for more reference-data scrapers.

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🆘 Need Help? Open our contact form to request a new scraper, propose a custom data project, or report an issue.

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⚠️ Disclaimer: this Actor is an independent tool and is not affiliated with, endorsed by, or sponsored by Open Targets, EMBL-EBI, or any of its partner organizations. All trademarks mentioned are the property of their respective owners. Only publicly available open biomedical data is collected.