🧫 NCBI Gene Scraper

🚀 Export NCBI Gene records in seconds. Gene IDs, symbols, descriptions, organisms, chromosomes, aliases, and summaries — direct from the public NCBI E-utilities API.

🕒 Last updated. 2026-06-05 · 📊 12 fields per record · tens of millions of curated gene records across all species in Entrez Gene · Public API · No login required

The NCBI Gene Scraper turns the NCBI Entrez E-utilities public endpoint into a clean, structured dataset. It queries the source live, normalizes the response into one row per record, and pushes the result into an Apify dataset you can download or pipe to your warehouse.

Tens of millions of curated gene records across all species in Entrez Gene are covered in a single run, with stable field names and null-safe parsing.

🎯 Target Audience	💡 Primary Use Cases
🧬 Geneticists	Build gene panels from a phenotype query
💊 Pharma	Map drug targets to gene records
🎓 Educators	Generate gene fact sheets
🤖 ML teams	Train biomedical entity linkers

📋 What the NCBI Gene Scraper does

• Calls the public NCBI Entrez E-utilities endpoint with the parameters you supply.
• Parses the response and flattens each record into a single dataset row.
• Casts numeric fields to numbers where applicable for clean spreadsheet imports.
• Surfaces rate-limit or upstream errors as a single-row error record instead of crashing.
• Exports to every Apify dataset format supported in the UI.

💡 Why it matters. The raw NCBI Entrez E-utilities response is great for API consumers but awkward for spreadsheets and BI tools. This actor normalizes the shape so the data drops straight into pandas, BigQuery, or a Google Sheet.

🎬 Full Demo

🚧 Coming soon.

⚙️ Input

Field	Type	Required	Description
query	string	No	NCBI Gene Entrez query. Example. BRCA1[gene] AND human[orgn].
maxItems	integer	No	Free users. 10. Paid users. up to 1,000,000. Prefill. 10.

Example 1.

{
  "query": "example",
  "maxItems": 10
}

Example 2.

{
  "query": "example",
  "maxItems": 50
}

⚠️ Good to Know. This actor calls the public NCBI Entrez E-utilities endpoint with no authentication required. Upstream rate limits apply; if the source returns a limit notice, you will see it as a single error record in your dataset.

📊 Output

Each record is a flat object. error is always last.

Field	Type	Description
🔹 gene_id	string	Field from the NCBI Entrez E-utilities response.
🔹 symbol	string	Field from the NCBI Entrez E-utilities response.
🔹 description	string	Field from the NCBI Entrez E-utilities response.
🔹 organism	string	Field from the NCBI Entrez E-utilities response.
🔹 chromosome	string	Field from the NCBI Entrez E-utilities response.
🔹 maptype	string	Field from the NCBI Entrez E-utilities response.
🔹 summary	string	Field from the NCBI Entrez E-utilities response.
🔹 aliases	string	Field from the NCBI Entrez E-utilities response.
🔹 synonyms	string	Field from the NCBI Entrez E-utilities response.
🔹 ncbi_url	string	Field from the NCBI Entrez E-utilities response.
🔹 scrapedAt	string	Field from the NCBI Entrez E-utilities response.
🔹 error	string	Set if the upstream response was an error or rate-limit.

Sample record.

{
  "gene_id": "sample_gene_id",
  "symbol": "sample_symbol",
  "description": "sample_description",
  "organism": "sample_organism",
  "chromosome": "sample_chromosome",
  "maptype": "sample_maptype",
  "summary": "sample_summary",
  "aliases": "sample_aliases",
  "synonyms": "sample_synonyms",
  "ncbi_url": "sample_ncbi_url",
  "scrapedAt": "sample_scrapedAt",
  "error": null
}

✨ Why choose this Actor

| 🆓 | Works with the public NCBI Entrez E-utilities endpoint. No API key, no signup. | | 🧹 | Clean field names, ready for BI tools. | | 🔢 | Numeric strings cast to real numbers where it makes sense. | | 🛟 | Upstream errors and rate limits surface as a clean error record. | | 🔌 | One-click export to every Apify dataset format. | | 💾 | Push to dataset, then pipe to BigQuery, Snowflake, Postgres, or Google Sheets. |

📈 How it compares to alternatives

Approach	Setup time	Clean shape	Pagination	Error handling
Roll your own fetch	30 min +	❌	manual	manual
Copy-paste from the browser	5 min, fragile	❌	❌	❌
This Actor	5 sec, no install	✅	✅	✅

🚀 How to use

1. Click Try for free.
2. Fill in the input (or leave defaults).
3. Click Start.
4. Within seconds, the dataset is ready for download or integration.

💼 Business use cases

📊 Analytics. Pipe records into your warehouse and join against internal data for cross-source dashboards.

🤖 Automation. Trigger this actor on a schedule, then push results to Slack, Airtable, or Google Sheets.

🧪 Research. Snapshot the public state of NCBI Entrez E-utilities on a date and archive it for reproducible studies.

📰 Editorial. Verify quotes, numbers, or records cited in stories with a one-click fresh pull.

🔌 Automating NCBI Gene Scraper

• Make / Zapier. Trigger this actor on a schedule, push results to Slack, Airtable, Google Sheets, or anywhere else.
• Cron schedule. Use the native Apify scheduler to run on any cadence.
• Webhooks. Get a POST to your endpoint the moment a run finishes.
• Pipe to BigQuery / Snowflake / Postgres. Native Apify integrations move datasets straight into your warehouse.

🌟 Beyond business use cases

🎓 Education. Build classroom datasets without paying for a commercial feed.

🧪 Personal research. Track changes in the source over time on your own schedule.

🤝 Non-profit and open data. Build public dashboards without writing client code.

🧰 Tinkering and prototyping. Wire up a fresh data feed in seconds to test a new chart or model.

🤖 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. The schema, examples, and field list above contain everything an LLM needs to design a working pipeline.

❓ Frequently Asked Questions

❓ Do I need an API key? No. This actor calls the public NCBI Entrez E-utilities endpoint with no authentication required.

❓ Is there a rate limit? The upstream source may rate-limit aggressive use. If you hit a limit, the actor pushes a single error record rather than crashing.

❓ Which formats can I download? Every format Apify's dataset UI supports.

❓ Are values cast to numbers? Where the source returns numeric strings for numeric fields, yes.

❓ How do you handle upstream errors? A single record with a populated error field is pushed, then the actor exits cleanly.

❓ Can I schedule runs? Yes. Use Apify's native scheduler, Make, Zapier, or cron.

❓ Is this scraping or API? API. The NCBI Entrez E-utilities endpoint is fully public; this actor only normalizes the response.

❓ Will the schema change? Core fields are stable. Optional fields surface as null when the source omits them.

❓ How fresh is the data? Each run hits the live endpoint, so the data is as fresh as the source allows.

❓ Can I filter the output? Yes. The input fields above let you narrow the result set before it lands in your dataset.

🔌 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. Trigger runs from a calendar event, a form submission, a cron job, or pipe results straight into BigQuery, Snowflake, or a Postgres warehouse.

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