Ensembl Genomics Scraper

Ensembl Genomics Scraper

Scrape Ensembl genomics data for genes, variants, and sequences across 20 species, up to a million records per run. Every result returns stable IDs, chromosomal coordinates, biotype, and computed annotations. No API key or login. Export to CSV, JSON, Excel, or XML.

Ensembl's REST API requires you to paginate, handle rate limits, and parse nested JSON for each species endpoint. This Actor reads the public Ensembl REST API directly, letting you query by gene symbol, stable ID, genomic region, sequence ID, or human variant rsID, and returns each match in one flat row. It covers human, mouse, zebrafish, fruit fly, and 16 other reference genomes.

Who uses it	What they scrape Ensembl for
Bioinformaticians	Fetch gene coordinates and biotypes for a list of symbols to annotate a differential expression table.
Clinical geneticists	Look up variant consequences and population frequencies for a set of dbSNP rsIDs.
Genomics researchers	Retrieve all genes overlapping a chromosomal region to build a locus map.
Data engineers	Pull DNA sequences by Ensembl stable ID for downstream alignment or primer design.

What it does

This Actor collects Ensembl gene annotations, variant consequences, and DNA sequences by symbol, stable ID, region, or rsID, and returns each record as a flat row.

• 🔍 Lookup by gene symbol: submit a list of gene symbols like BRCA2 or TP53 and get back stable IDs, biotype, and location.
• 🆔 Lookup by stable ID: query directly with Ensembl IDs (ENSG, ENST, ENSP) for precise record retrieval.
• 🧬 Overlap region: provide a chromosomal region in format chromosome:start-end and receive every gene feature in that interval.
• 🧵 Sequence by ID: fetch raw DNA sequence for any Ensembl stable ID across supported species.
• ⚡ Variation by rsID: retrieve human variant annotations, consequences, and allele frequencies from a list of dbSNP rsIDs.

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

What you can do with Ensembl data

📋 Annotate a gene list from a differential expression study.

A bioinformatician pastes 200 gene symbols into the Actor, selects human, and gets back Ensembl stable IDs, biotypes, and chromosomal coordinates to merge with their expression results.

🧬 Map all genes in a GWAS locus.

A researcher supplies a chromosomal region like 7:140424943-140624564 in overlapRegion mode and receives every gene feature in that interval for candidate prioritization.

🩺 Retrieve variant consequences for a clinical report.

A clinical geneticist submits a list of rsIDs in variation mode and obtains allele frequencies, consequence predictions, and genomic context for each variant.

🧪 Fetch DNA sequences for primer design.

A lab scientist provides Ensembl transcript IDs in sequence mode and downloads the raw DNA sequence to design PCR primers.

Why choose this scraper

	What you get
20 reference species	Human, mouse, rat, zebrafish, fruit fly, worm, yeast, and 13 more plants and vertebrates.
Five query modes	Lookup by symbol, stable ID, region, sequence ID, or human variant rsID in a single Actor.
Flat row output	Nested Ensembl REST responses are flattened into one row per record for direct analysis.
No API key	Reads the public Ensembl REST endpoints with no registration or authentication.

How it compares

This Actor offers five query modes and 20 species, while the alternative focuses on gene ID and biotype lookup.

Feature	ParseForge	Ensembl Gene Scraper - Gene IDs, Biotype & Location
Lookup by gene symbol	Yes	Yes
Lookup by stable ID	Yes	Not listed
Overlap region query	Yes	Not listed
DNA sequence retrieval	Yes	Not listed
Variant rsID lookup	Yes	Not listed
Species supported	20	Not listed

Configure the run

Drive the Actor from gene symbols, stable IDs, genomic regions, sequence IDs, or variant rsIDs, one mode per run, and filters apply as each record is fetched so only matches reach your dataset. The Input tab lists every parameter.

A first run with the defaults:

{
  "maxItems": 10,
  "mode": "lookupSymbol",
  "species": "homo_sapiens",
  "symbols": [
    "BRCA2",
    "TP53",
    "EGFR",
    "MYC",
    "KRAS"
  ]
}

A larger pull:

{
  "maxItems": 200,
  "mode": "lookupSymbol",
  "species": "homo_sapiens",
  "symbols": [
    "BRCA2",
    "TP53",
    "EGFR",
    "MYC",
    "KRAS"
  ]
}

Pricing

Pay-per-result: $0.024 per result collected. You pay only for the results written to your dataset.

Results collected	Approximate cost
100 results	$2.40
1,000 results	$24.00
10,000 results	$240.00

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 Genomics 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-genomics-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 gene symbols?

Check that the species selection matches your gene symbols. A mouse symbol queried against human will return no match. Also verify the symbol is current Ensembl nomenclature.

Why does my region query return an error?

Ensure the region format is exactly chromosome:start-end with no spaces, and that the chromosome name matches Ensembl convention for your species, such as 7 not chr7 for human.

Why is variation mode ignoring my species setting?

Variation mode is human-only and ignores the species field. For non-human variants, use the Ensembl website directly or a VEP tool.

Why did I hit the maximum records limit?

Free users are capped at 10 records for preview. Upgrade to a paid Apify plan to increase the limit up to 1,000,000 records per run.

FAQ

Question	Answer
Do I need an Ensembl API key?	No. This Actor uses the public Ensembl REST API endpoints, which are open and require no registration or authentication.
Which species are supported?	Twenty reference genomes are available, including human, mouse, rat, zebrafish, fruit fly, roundworm, baker's yeast, thale cress, chicken, pig, cow, dog, cat, horse, sheep, rhesus macaque, chimpanzee, western clawed frog, medaka, and mosquito.
Can I query multiple gene symbols in one run?	Yes. In lookupSymbol mode you can provide a list of gene symbols, and the Actor will fetch each one and return a combined dataset.
What format is the genomic region input?	Use the format chromosome:start-end, for example 7:140424943-140624564 or X:1000000-2000000. The Actor returns all gene features overlapping that interval.
Does variation mode work for non-human species?	Variation mode currently supports only human dbSNP rsIDs. For other species, use the lookup or sequence modes.
What is a stable ID?	An Ensembl stable ID is a unique identifier for a gene, transcript, or protein, such as ENSG00000139618 for a gene or ENST00000380152 for a transcript.
Can I get raw DNA sequence?	Yes. Use the sequence mode with an Ensembl stable ID to retrieve the raw DNA sequence for that feature.
How many records can I scrape?	Free users are limited to 10 records for preview. Paid users can fetch up to 1,000,000 records per run.
What export formats are available?	You can export your dataset to CSV, JSON, Excel, or XML from the Apify platform.

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.