NCBI Gene Summary Scraper

NCBI Gene Summary Scraper

Scrape official NCBI Gene summaries in bulk from a list of Gene IDs, up to a million per run. Every record returns the gene name, description, synonyms, organism, and full Entrez Gene summary text. No API key required. Export to CSV, JSON, Excel, or XML.

NCBI's EUtilities API requires building HTTP requests, handling XML responses, and managing rate limits which slows down any large-scale genomics project. This Actor reads the official gene summaries directly from the NCBI database for any list of Gene UIDs and returns each one in a clean, flat row. No API key, no XML parsing, and no manual request throttling.

Keep your gene research moving by getting plain-text summaries for thousands of genes at once.

Who uses it	What they scrape NCBI Gene for
Bioinformaticians	Building up-to-date gene reference tables for analysis pipelines
Genomics researchers	Annotating a gene list of interest with official NCBI functional summaries
Pharma R&D teams	Reviewing curated gene function data for target identification and prioritization
Clinical data curators	Cross-checking gene-disease associations against the authoritative NCBI Gene resource

What it does

This Actor collects NCBI Gene summary records from a user-provided list of Gene UIDs and returns each one as a flat row with its name, description, synonyms, organism, and full summary text.

• 🧬 Batch gene retrieval: Provide any list of NCBI Gene UIDs and fetch every summary in one run.
• 📋 Structured flat output: Each gene becomes one row with the name, full description, synonyms, organism, and summary text as separate columns.
• ⏸️ Built-in rate limiting: Requests are automatically throttled to comply with NCBI usage policies without configuration.
• 📦 Multiple export formats: Save your dataset as CSV, JSON, Excel, XML, or RSS feed.

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

What you can do with NCBI Gene data

📊 Annotate a gene panel for clinical reporting.

A bioinformatician runs a list of 500 cancer panel Gene IDs through the Actor to pull the official full-text summaries, ensuring the lab report annotations are sourced from NCBI.

🧪 Update a target database for drug discovery.

A computational biologist feeds an internal pipeline with fresh Gene summaries for thousands of potential drug targets to monitor functional annotation changes between NCBI releases.

📚 Reconcile gene nomenclature and synonyms.

A data curator scrapes synonyms and the official full name for a set of genes to de-duplicate conflicting identifiers across multiple datasets.

🎓 Build a teaching dataset for a bioinformatics course.

A lecturer generates a spreadsheet of gene summaries for model organisms by providing the relevant Gene IDs, giving students a curated foundation for function prediction exercises.

Why choose this scraper

	What you get
No API key	Skip the NCBI API key registration and supply the Gene IDs you need.
Plain text, not XML	Receive human-readable summary text instead of having to parse nested XML.
One row per gene	Every gene comes back in a fixed schema so you can join it directly to your own data.

How it compares

This Actor focuses on fetching curated gene summaries, while the PubMed Scraper retrieves journal article abstracts from a different NCBI database.

Feature	ParseForge	PubMed Scraper
Scrapes NCBI Gene summaries	Yes	Not listed
Scrapes PubMed abstracts	No	Yes
Input by PMIDs or keywords	Not listed	Yes
Returns gene name and synonyms	Yes	Not listed
Returns MeSH terms	Not listed	Yes

Configure the run

Drive the Actor from a list of NCBI Gene UIDs and set a cap on how many records are returned. The Input tab lists every parameter.

A first run with the defaults:

{
 "geneIds": [
 "672",
 "7157",
 "1956",
 "4609",
 "3845"
 ],
 "maxItems": 10
}

A larger pull:

{
 "geneIds": [
 "672",
 "7157",
 "1956",
 "4609",
 "3845"
 ],
 "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 Summary 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 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-summary-scraper"

Then prompt it in plain language to run the scraper and read back the results.

Troubleshooting

Why am I getting no results?

Check that your Gene IDs are valid NCBI UIDs. An incorrect or discontinued UID will return no summary text. Try looking up one of your IDs directly on the NCBI Gene website to confirm it exists.

Why did my run fail or give a time-out error?

This usually means NCBI's servers temporarily rejected a request. The built-in rate limiting prevents most issues, but very large runs can be affected by NCBI maintenance. Retrying the run with the same list typically resolves this.

The 'Maximum genes' field is set, but I still only got a few results.

The 'Maximum genes' field acts as a cap on how many records to collect from your input list. If your list contains fewer IDs than this cap, the Actor will only return results for the supplied IDs.

Why are some synonym fields empty?

Some genes in NCBI have no listed synonyms. An empty field means NCBI's record for that gene does not include any alternative symbols or names.

Is it possible to get data for genes from multiple organisms in one run?

Absolutely. include the Gene UIDs for all your organisms of interest in the Gene IDs list. The output will contain the correct organism scientific and common name for each row.

FAQ

Question	Answer
Do I need an NCBI API key to use this Actor?	No. The Actor is designed to work without an NCBI API key, though it adheres to EUtilities usage guidelines by automatically spacing out requests.
What is an NCBI Gene UID?	It is the unique numeric identifier NCBI assigns to each gene record. You can find it at the end of a Gene database URL, such as the '7157' in ncbi.nlm.nih.gov/gene/7157 for the human TP53 gene.
How many genes can I scrape in one run?	The input schema accepts up to one million Gene IDs. The 'Maximum genes' field lets you limit the number of records collected per run.
What organism data is returned?	The record includes both the scientific name and the common name of the organism associated with the gene, as provided by NCBI.
Does this Actor return gene sequences or variant data?	No. This Actor retrieves only the gene summary information, which includes the official name, description, synonyms, organism, and the curated summary text. For sequences, you would need a different NCBI tool.
Is the summary text returned as a single field?	Yes. The complete Entrez Gene summary paragraph is returned in a single 'Summary' field, ready for text mining or direct display.
How does the Actor avoid getting blocked by NCBI?	It includes built-in request throttling that respects NCBI's rate limit guidelines, making it safe for large batch runs without manual timing.
Can I resume a run if it gets interrupted?	Yes. The Actor processes Gene IDs from your provided list. If a run is interrupted, you can initiate a new run with the remaining IDs.
What is the difference between this Actor and scraping PubMed?	PubMed returns journal article abstracts and metadata. This Actor returns the NCBI Gene database summary, which is a curated description of a gene's function, not a research paper.

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.