Ensembl Gene Lookup Scraper

Ensembl Gene Lookup Scraper

Look up human gene symbols on Ensembl and get stable IDs, biotype, and genomic coordinates in one flat table. Feed it a list of symbols like BRCA1 or TP53 and receive structured data ready for bioinformatics pipelines, exported to CSV, JSON, Excel, or XML.

Ensembl's REST API requires you to query genes one by one, which slows down any analysis that starts from a list of gene symbols. This actor reads the public Ensembl lookup endpoint in parallel, takes your list of human gene symbols, and returns each match with its stable Ensembl ID, biotype, chromosome location, and description. No API key, no rate-limit headaches, a clean dataset from your symbols.

Who uses it	What they scrape Ensembl for
Bioinformaticians	Converting a list of gene symbols from differential expression analysis into Ensembl IDs for pathway enrichment tools.
Genomics researchers	Fetching the latest gene metadata for a panel of candidate genes before running variant annotation.
Data engineers in biotech	Building an automated ETL pipeline that keeps internal gene databases synchronized with Ensembl reference data.
Clinical geneticists	Looking up the cytogenetic band and biotype for a set of genes flagged in a patient report.

What it does

This Actor accepts a list of human gene symbols and returns each matched gene as a flat row with its Ensembl stable ID, biotype, genomic coordinates, and description.

• 🧬 Batch gene symbol lookup: Paste a list of human gene symbols and the actor resolves them all in one run.
• 📊 Structured output: Every row includes the Ensembl stable ID, gene biotype, chromosome, start and end positions, and description.
• ⚡ Parallel requests: Symbols are queried concurrently so a panel of hundreds of genes completes in seconds.
• 🔢 Configurable limit: Set a maximum number of genes to collect per run, from a single symbol up to one million.

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

What you can do with Ensembl data

🧪 Prepare a gene list for enrichment analysis.

A bioinformatician pastes the significant genes from an RNA-seq experiment and gets back Ensembl IDs and biotypes to feed into DAVID or g:Profiler.

🗺️ Map clinical variants to gene locations.

A clinical geneticist looks up the cytogenetic band and genomic coordinates for a panel of genes mentioned in a variant report to cross-reference with CNV calls.

🔄 Sync an internal gene database with Ensembl.

A data engineer runs the actor weekly on a list of tracked gene symbols to update any changed IDs or biotype classifications in the company data warehouse.

🔎 Filter a gene list to protein-coding genes only.

A researcher supplies a mixed list of symbols and uses the biotype field in the output to discard pseudogenes and non-coding RNAs before designing a CRISPR screen.

Why choose this scraper

	What you get
Batch resolution	Convert dozens or thousands of gene symbols to Ensembl IDs in one operation instead of querying the REST API one by one.
Stable identifiers	Get the current Ensembl stable ID for each symbol, avoiding the drift that happens when symbols are retired or renamed.
Genomic context	Each row delivers the chromosome name, start position, end position, and biotype so you can filter protein-coding genes from pseudogenes.
Pipeline-ready formats	Export to CSV, JSON, Excel, or XML and feed the output directly into nextflow, snakemake, or custom analysis scripts.

How it compares

This actor focuses on batch gene symbol lookup with configurable limits, while the other Ensembl scraper targets cross-species gene ID and biotype retrieval.

Feature	ParseForge	Ensembl Gene Scraper - Gene IDs, Biotype & Location
Batch gene symbol lookup	Yes, accepts a list of human gene symbols and resolves them in parallel	Not listed
Configurable maximum genes per run	Yes, set from 1 to 1,000,000	Not listed
Cross-species support	Human only	Yes
Gene description in output	Yes	Not listed
Genomic coordinates (start and end positions)	Yes	Yes

Configure the run

Drive the Actor with a list of human gene symbols, and set a maximum number of genes to collect per run so only the first N matches reach your dataset. The Input tab lists every parameter.

A first run with the defaults:

{
 "symbols": [
 "BRCA1",
 "TP53",
 "EGFR",
 "MYC",
 "KRAS"
 ],
 "maxItems": 10
}

A larger pull:

{
 "symbols": [
 "BRCA1",
 "TP53",
 "EGFR",
 "MYC",
 "KRAS"
 ],
 "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 Ensembl Gene Lookup 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 Ensembl 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/ensembl-gene-lookup-scraper"

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

Troubleshooting

Why am I getting fewer results than the number of symbols I submitted?

Some gene symbols may be outdated or not recognized by Ensembl. Check that your symbols are current HGNC-approved names. Retired symbols or those from other species will not return a match.

The actor is timing out on a large list of symbols.

Try increasing the timeout in your run settings or split your symbol list into smaller batches. The actor queries symbols in parallel, but very large lists can still take time depending on Ensembl's response speed.

I got an error about the input format.

Make sure you are providing a valid JSON array of strings in the symbols field. Each symbol should be a plain text string like ["BRCA1", "TP53"], not a comma-separated list.

The output is missing the chromosome location for some genes.

Some Ensembl gene entries, particularly those on alternate haplotypes or patches, may not have a primary chromosome location. These genes will still appear with their ID and biotype but with empty coordinate fields.

Can I resume a run that was interrupted?

The actor does not currently support resuming from a checkpoint. If a run is interrupted, restart it with the same symbol list. Already collected genes will be fetched again.

FAQ

Question	Answer
What is the difference between a gene symbol and an Ensembl stable ID?	A gene symbol like BRCA1 is a human-readable name that can change over time. An Ensembl stable ID like ENSG00000012048 is a permanent identifier that stays the same even if the symbol is updated.
Can I look up genes from species other than human?	This actor is configured for human gene symbols. The Ensembl lookup endpoint supports other species, but the current input schema expects human symbols.
How many gene symbols can I look up in one run?	You can set the maximum genes parameter anywhere from 1 to 1,000,000. The actor will process symbols in parallel and stop once it reaches your limit.
What happens if a gene symbol is not found on Ensembl?	Symbols that do not match any Ensembl gene are skipped. The actor returns only the successfully resolved genes in your dataset.
Does this actor require an Ensembl API key?	No. It reads the public Ensembl REST API lookup endpoint, which does not require authentication or an API key.
What biotypes can appear in the output?	The biotype field returns the Ensembl classification such as protein_coding, lncRNA, miRNA, pseudogene, or processed_transcript, depending on what Ensembl annotates for each gene.
Can I use this to get gene sequences?	No, this actor returns gene metadata like IDs, biotype, and coordinates. For sequences, you would need a different tool that queries the sequence endpoint.
How do I export the results for use in R or Python?	You can export your dataset as CSV or JSON directly from the Apify platform, then read it with read.csv in R or pandas.read_csv in Python.
Is the output sorted in any particular order?	The output rows appear in the same order as the symbols you provided, so you can match results back to your input list by position.
What is the cytogenetic band and when would I use it?	The cytogenetic band is a position on a chromosome like 17q21.31. It is useful for correlating gene locations with karyotype results or FISH probe targets.

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 EMBL-EBI. 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.