NCBI Gene Database Scraper

NCBI Gene Database Scraper

Scrape NCBI Gene records by gene name, symbol, or Entrez query, up to a million per run. Every record returns the official symbol, full name, organism, chromosome location, aliases, and functional summary. No API key required. Export to JSON, CSV, Excel, or XML.

NCBI's Gene database is the central authority for gene nomenclature, but downloading records manually through the web portal is slow and not built for bulk work. This Actor reads the public E-utilities API directly, so you can pull structured data for thousands of genes in one go without writing a single line of Entrez code. It is built for bioinformaticians, pharma researchers, and clinical data analysts who need clean, flat gene records fast.

Who uses it	What they scrape NCBI Gene Database for
Bioinformaticians	Building a local gene reference table for a variant annotation pipeline.
Pharma R&D teams	Pulling official gene summaries and OMIM links for a list of drug targets.
Clinical geneticists	Collecting chromosome locations and aliases for a panel of disease-associated genes.
Academic researchers	Gathering organism-specific gene metadata for a comparative genomics study.

What it does

This Actor collects NCBI Gene records by gene name, symbol, or a full Entrez query and returns each gene as a flat row with its official symbol, full name, organism, chromosome location, aliases, and functional summary.

• 🧬 Gene symbol or name query: feed it a single gene like BRCA1, or a list of symbols, and get back the full NCBI record.
• 🔍 Full Entrez query support: use the exact NCBI query syntax you already know, such as 'BRCA1[gene] AND human[orgn]', to filter by organism, gene type, or chromosome.
• 📊 Flat, analysis-ready rows: each gene comes back as one row with a fixed schema, ready for pandas, R, or Excel without nested JSON cleanup.
• ⚡ Bulk collection: set a high maxItems value and pull up to a million gene records in a single run, respecting NCBI rate limits automatically.

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

What you can do with NCBI Gene Database data

🧬 Build a gene reference table.

A bioinformatician feeds a list of 500 gene symbols into the Actor and exports a CSV with official names, chromosome bands, and aliases for a variant annotation pipeline.

💊 Curate a pharma target list.

An R&D scientist runs an Entrez query for 'kinase[gene] AND human[orgn]' to pull every human kinase with its functional summary and OMIM link for a target assessment report.

🧪 Prepare a clinical gene panel.

A clinical geneticist scrapes the chromosome locations and full names for a set of ACMG-recommended genes to populate a lab report template.

📚 Gather organism-specific metadata.

A graduate student queries '16S rRNA[gene] AND bacteria[orgn]' to collect ribosomal RNA gene records across bacterial species for a phylogenetics project.

Why choose this scraper

	What you get
No API key	Reads the public NCBI E-utilities endpoint, so you skip the registration and key management.
Entrez syntax	Accepts the exact query strings you use on the NCBI website, including field tags and boolean operators.
Fixed schema	Every run returns the same columns, so your downstream scripts never break on a schema change.
Rate-limit safe	Built-in delays keep you within NCBI's usage guidelines without manual throttling.

How it compares

This Actor focuses exclusively on the NCBI Gene database with full Entrez query syntax support, while the competitors listed below either cover multiple NCBI databases or return a narrower set of gene fields.

Feature	ParseForge	NCBI Gene Lookup - Genomics API for Pharma R&D	NCBI Bio Datasets	NCBI Gene Records Scraper
Full Entrez query syntax support	Yes, accepts any valid Entrez query string with field tags and boolean operators	Not listed	Not listed	Not listed
Returns functional gene summary text	Yes	Yes	Not listed	Not listed
Returns OMIM ID	Yes	Yes	Not listed	Not listed
Returns chromosome location and map locus	Yes	Yes	Not listed	Not listed
Queries across multiple NCBI databases (PubMed, Protein, SNPs)	No, Gene database only	Not listed	Yes	Not listed
No API key required	Yes	Not listed	Yes	Not listed

Configure the run

Drive the Actor with a gene name, symbol, or a full Entrez query, and set a maximum number of genes to collect per 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 NCBI Gene Database 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 NCBI Gene Database 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/ncbi-eutils-gene-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 that your Entrez query syntax is valid. Try the same query string directly on the NCBI Gene website first. Also ensure you have not set maxItems to 0, and that the gene symbol or name is spelled correctly with the proper case.

The run is taking a very long time. Is it stuck?

Large runs with high maxItems values include deliberate delays to respect NCBI rate limits. A run of 10,000 genes can take several hours. Check the run log for progress messages, and consider reducing maxItems if you need results faster.

Some fields are empty in my output. Is that an error?

No. NCBI does not provide every field for every gene. For example, some genes lack an OMIM ID or a functional summary. The Actor returns empty cells for missing data rather than omitting the column, so your schema stays consistent.

I got an error about the query syntax. What is wrong?

Entrez query syntax requires square brackets for field tags, like 'BRCA1[gene]'. Make sure your brackets are properly closed and that you are using valid field qualifiers such as [gene], [orgn], or [sym]. Avoid special characters that break URL encoding.

Can I use this Actor with an NCBI API key for higher rate limits?

Yes. If you have an NCBI API key, you can pass it as an environment variable in your Apify actor configuration. The Actor will then use the authenticated endpoint, which allows up to 10 requests per second instead of 3.

FAQ

Question	Answer
Do I need an NCBI API key to use this Actor?	No. This Actor uses the public NCBI E-utilities endpoint, which does not require an API key. If you have an API key and want higher rate limits, you can add it as an environment variable in your Apify run.
What exactly does one row of output contain?	Each row is one NCBI Gene record and includes the official gene symbol, full gene name, organism, chromosome location, map locus, aliases, OMIM ID, and a functional summary text when NCBI provides it.
Can I query by something other than a gene symbol, like a disease or a chromosome band?	Yes. The query field accepts any valid NCBI Entrez query string. You can search by chromosome location, gene type, organism, or combine terms with boolean operators exactly as you would on the NCBI Gene website.
How many genes can I scrape in one run?	You can set the maximum up to 1,000,000 genes per run. The Actor respects NCBI's rate limits by pausing between requests, so large runs complete reliably without being blocked.
Does this Actor return sequence data or metadata?	This Actor returns the gene-level metadata: symbol, name, location, aliases, summary, and OMIM link. It does not fetch nucleotide or protein sequences. For sequence data, look for an NCBI sequence scraper.
Can I filter results to only human genes?	Yes. Use the Entrez query syntax in the query field, for example 'human[orgn]' to restrict results to Homo sapiens. You can combine this with any gene name or symbol.
What output formats are supported?	The Actor exports to JSON, CSV, Excel, and XML. You choose the format in the Apify dataset settings or when you download the results.
How do I write a query for multiple genes at once?	Use the OR operator in your Entrez query, for example 'BRCA1[gene] OR TP53[gene] OR EGFR[gene]'. You can also paste a list of symbols separated by OR if you generate the query string programmatically.
Is the output schema always the same?	Yes. Every run returns the same fixed set of columns, even when NCBI omits a field for a particular gene. Missing values appear as empty cells, so your downstream analysis never breaks on a schema change.
Does this Actor handle rate limiting automatically?	Yes. The Actor includes built-in delays between requests to stay within NCBI's usage guidelines. For very large runs, it will take longer but complete without manual intervention.

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 National Center for Biotechnology Information, U.S. National Library of Medicine. 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.