🧬 Ensembl Genomics Scraper

🚀 Export genes, variants, and DNA sequences in seconds. Look up by gene symbol, stable ID, chromosomal region, or human rsID across 20+ species. Returns biotype, coordinates, transcript IDs, sequence, allele frequencies, and assembly metadata.

🕒 Last updated: 2026-05-23 · 📊 30 fields per record · 🧬 20+ species · 🔁 5 modes · 🧫 Ensembl genome reference

The Ensembl Genomics Scraper queries the public Ensembl genome reference, the de facto open browser for vertebrate, model-organism, and select non-vertebrate genomes. It returns up to 30 structured fields per record, including stable ID, display name, object type, biotype, species, chromosome, start, end, strand, assembly, description, canonical transcript, source, logic name, molecule type, sequence length and sequence, variant name, variant class, minor allele and frequency, ancestral allele, allele string, most-severe consequence, mappings, evidence, synonyms, mode, query, and the scrape timestamp.

The catalog spans 20+ reference species 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. This Actor returns gene lookups, region overlaps, sequence fetches, and human variant resolutions in one run.

🎯 Target Audience	💡 Primary Use Cases
Bioinformaticians, pharma research, genetics labs, academic researchers, computational biology students, biotech startups, precision-medicine teams	Gene annotation pipelines, variant impact analysis, comparative genomics, target identification, rsID resolution for GWAS, sequence retrieval for primer design

---

📋 What the Ensembl Genomics Scraper does

Five query workflows in a single Actor:

• 🧬 Lookup by gene symbol. Resolve BRCA2, TP53, EGFR, etc. to Ensembl stable IDs, coordinates, biotype, and canonical transcript.
• 🆔 Lookup by stable ID. Pass ENSG00000139618 or ENST00000380152 for any Ensembl-supported species.
• 🗺️ Overlap region. Return all gene features inside chromosome:start-end (e.g. 7:140424943-140624564).
• 🧪 Sequence by ID. Fetch the raw DNA, cDNA, or protein sequence for any Ensembl stable ID.
• 🧬 Variation by rsID. Resolve human dbSNP rsIDs (e.g. rs56116432, rs1042522) to allele frequencies, consequences, and ancestral alleles.

Each record bundles the relevant Ensembl-native fields, the species, the mode used, the original query string, and a collection timestamp.

💡 Why it matters: the Ensembl genome browser is the most widely cited open genome reference in life sciences. Hand-coding a REST client means handling rate limits, schema-per-endpoint quirks, and pagination. This Actor delivers consistent records you can pipe straight into BI tools, notebooks, or pipelines.

---

🎬 Full Demo

🚧 Coming soon: a 3-minute walkthrough showing how to go from sign-up to a downloaded dataset.

---

⚙️ Input

Input	Type	Default	Behavior
maxItems	integer	10	Records to return. Free plan caps at 10, paid plan at 1,000,000.
mode	string	"lookupSymbol"	One of lookupSymbol, lookupId, overlapRegion, sequence, variation.
species	string	"homo_sapiens"	Ensembl species slug. Used by symbol, region, sequence modes.
symbols	array	["BRCA2","TP53","EGFR","MYC","KRAS"]	Gene symbols for lookupSymbol mode.
stableIds	array	[]	Ensembl stable IDs for lookupId or sequence.
region	string	""	Genomic region chr:start-end for overlapRegion.
rsids	array	[]	dbSNP rsIDs for variation mode (human-only).

Example: human cancer-gene panel.

{
    "maxItems": 5,
    "mode": "lookupSymbol",
    "species": "homo_sapiens",
    "symbols": ["BRCA1", "BRCA2", "TP53", "EGFR", "KRAS"]
}

Example: all genes overlapping the BRCA2 locus.

{
    "maxItems": 100,
    "mode": "overlapRegion",
    "species": "homo_sapiens",
    "region": "13:32315086-32400266"
}

Example: resolve TP53 missense variant rsIDs.

{
    "maxItems": 10,
    "mode": "variation",
    "rsids": ["rs1042522", "rs56116432", "rs17878362"]
}

⚠️ Good to Know: the Ensembl species slug follows the genus_species convention (e.g. homo_sapiens, mus_musculus). The variation mode is human-only (dbSNP). For coordinate-based queries, regions must follow chr:start-end with assembly coordinates matching the current Ensembl release for that species.

---

📊 Output

Each record contains up to 30 fields depending on the mode. Download the dataset as CSV, Excel, JSON, or XML.

🧾 Schema

Field	Type	Example
🆔 stableId	string	"ENSG00000139618"
🏷️ displayName	string	"BRCA2"
🔧 objectType	string	"Gene"
🧬 biotype	string	"protein_coding"
🐾 species	string	"homo_sapiens"
🧭 chromosome	string	"13"
▶️ start	number	32315086
⏹️ end	number	32400266
↔️ strand	number	1
📐 assemblyName	string	"GRCh38"
📝 description	string | null	"BRCA2 DNA repair associated"
🧾 canonicalTranscript	string	"ENST00000380152.8"
🏛️ source	string	"ensembl_havana"
🧠 logicName	string	"ensembl_havana_gene_homo_sapiens"
🧪 molecule	string	"dna"
📏 sequenceLength	number	84981
🧬 sequence	string	"ATG..."
🆔 variantName	string	"rs1042522"
🏷️ varClass	string	"SNP"
🔡 minorAllele	string	"C"
📊 minorAlleleFreq	number	0.3401
🌳 ancestralAllele	string	"G"
🧬 alleleString	string	"C/G"
⚠️ mostSevereConsequence	string	"missense_variant"
🗺️ mappings	array	[ ... ]
🔬 evidence	array	["Frequency","1000Genomes"]
🔗 synonyms	array	["NM_000546.6:c.215C>G"]
🔧 mode	string	"lookupSymbol"
🔎 query	string	"BRCA2"
🕒 scrapedAt	ISO 8601	"2026-05-23T10:00:00.000Z"

📦 Sample records

---

✨ Why choose this Actor

	Capability
🧬	20+ reference species. Human, mouse, rat, zebrafish, fly, worm, yeast, arabidopsis, and more.
🔁	Five modes in one Actor. Symbol lookup, ID lookup, region overlap, sequence fetch, and variant resolution.
🆔	dbSNP rsID resolution. Human variants returned with MAF, ancestral allele, consequence, evidence.
🗺️	Region-based queries. Pull all gene features inside any chromosomal interval.
🧪	Raw sequence retrieval. DNA, cDNA, or protein, by Ensembl stable ID.
🚫	No authentication. Works against the public Ensembl reference. No login or API key needed.
🔁	Always fresh. Each run pulls the live reference, reflecting the latest Ensembl release.

📊 The Ensembl reference underpins thousands of life-science publications and GWAS pipelines worldwide.

---

📈 How it compares to alternatives

Approach	Cost	Coverage	Refresh	Setup
⭐ Ensembl Genomics Scraper (this Actor)	$5 free credit, then pay-per-use	20+ species, 5 modes	Live per run	⚡ 2 min
Hand-written Ensembl REST client	Free + engineering	Same	Build it yourself	🛠️ Hours
Commercial bio-databases	$$$$	Same + curation	Real-time	⏳ Procurement
Hard-coded gene tables	Free	One snapshot	Manual	🐢 Tech debt

Pick this Actor when you want consistent Ensembl records without writing and maintaining a REST client.

---

🚀 How to use

1. 📝 Sign up. Create a free account with $5 credit (takes 2 minutes).
2. 🌐 Open the Actor. Go to the Ensembl Genomics Scraper page on the Apify Store.
3. 🎯 Set input. Pick a mode, a species, and a query payload (symbols, stable IDs, region, or rsIDs). Set maxItems.
4. 🚀 Run it. Click Start and let the Actor collect your data.
5. 📥 Download. Grab your results in the Dataset tab as CSV, Excel, JSON, or XML.

⏱️ Total time from signup to downloaded dataset: 3-5 minutes. No coding required.

---

💼 Business use cases

💊 Pharma & Drug Discovery Target identification by gene panel Variant impact triage in pipelines Comparative genomics across model organisms Pre-clinical species selection workflows	🧪 Clinical Genomics & Diagnostics rsID-to-consequence lookups for GWAS Variant interpretation pipelines Reference gene annotation for sequencing reports Coordinate liftover validation
🌱 Agricultural Genomics Crop and livestock breeding gene catalogs Trait-associated marker discovery Comparative analysis (cow, pig, chicken, sheep) Genome-assembly QC	🧫 Biotech R&D Primer design from raw DNA sequence CRISPR guide design pipelines Synthetic biology target sourcing Orthology mapping across model species

---

🔌 Automating Ensembl Genomics Scraper

Control the scraper programmatically for scheduled runs and pipeline integrations:

• 🟢 Node.js. Install the apify-client NPM package.
• 🐍 Python. Use the apify-client PyPI package.
• 📚 See the Apify API documentation for full details.

The Apify Schedules feature lets you trigger this Actor on any cron interval. Hook a webhook to a Slack channel for alerting when a panel of variants flips consequence in a new Ensembl release.

---

🌟 Beyond business use cases

Open genome data powers more than commercial R&D. The same structured records support research, education, civic projects, and personal initiatives.

🎓 Research and academia Reproducible variant interpretation datasets Comparative genomics coursework Open-data thesis projects Cross-species ortholog studies	🎨 Personal and creative Personal-genome interpretation hobby projects Citizen-science genealogy and ancestry tools Educational visualizations of gene structure Bioinformatics learning portfolios
🤝 Non-profit and civic Rare-disease research collectives Patient-advocacy variant dashboards Open biomedical-data initiatives Public-health surveillance pipelines	🧪 Experimentation Train variant-effect prediction models Prototype gene-annotation AI agents Build genomics-aware chatbots Test bioinformatics pipelines on real records

---

🤖 Ask an AI assistant about this scraper

Open a ready-to-send prompt about this ParseForge actor in the AI of your choice:

• 💬 ChatGPT
• 🧠 Claude
• 🔍 Perplexity
• 🅒 Copilot

---

❓ Frequently Asked Questions

🧩 How does it work?

Pick a mode, a species, and a query payload. The Actor reads the public Ensembl reference and emits a clean structured record per gene, region, sequence, or variant.

📏 How accurate is the data?

Ensembl is the de facto open genome browser, curated by EMBL-EBI and the Wellcome Sanger Institute. The reference is updated several times per year. For clinical reporting always cross-check against the latest release notes.

🔁 How often is the dataset refreshed?

Ensembl publishes major releases roughly every two months and patch updates more frequently. Every run of this Actor pulls the live reference.

🐾 Which species are supported?

20+ reference species 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.

🧬 Which variant set is supported?

dbSNP rsIDs for human. Other species are supported for gene lookups, region overlaps, and sequence retrieval.

⏰ Can I schedule regular runs?

Yes. Use Apify Schedules to run this Actor on any cron interval. A weekly run is enough to track inter-release annotation drift.

⚖️ Is this data legal to use?

Ensembl is published as open data under standard academic licenses. Commercial use is permitted; check the source for any attribution preferences.

💼 Can I use this data commercially?

Yes. The Ensembl reference is openly licensed for commercial reuse with attribution to EMBL-EBI.

💳 Do I need a paid Apify plan to use this Actor?

No. The free Apify plan is enough for testing and small queries (10 records per run). A paid plan lifts the limit and unlocks scheduling and higher concurrency.

🔧 What if a stable ID is from an older Ensembl release?

The Actor uses the current Ensembl reference. Deprecated stable IDs return an error record with a clear message; use the Ensembl ID history view to resolve to the current ID.

🆘 What if I need help?

Our support team is here to help. Contact us through the Apify platform or use the Tally form linked below.

---

🔌 Integrate with any app

Ensembl Genomics Scraper connects to any cloud service via Apify integrations:

• Make - Automate multi-step workflows
• Zapier - Connect with 5,000+ apps
• Slack - Get run notifications in your channels
• Airbyte - Pipe gene and variant records into your warehouse
• GitHub - Trigger runs from commits and releases
• Google Drive - Export datasets straight to Sheets

You can also use webhooks to push fresh variant annotations into a Notion knowledge base or alert on gene-panel changes.

---

🔗 Recommended Actors

• 🧪 KEGG Pathways Scraper - Biochemical pathways and orthologies
• 📚 ArXiv Scraper - Pre-print research papers
• 🔬 Figshare Scraper - Open scientific datasets and supplementary files
• 🧬 ClinicalTrials.gov Scraper - U.S. clinical trial registry
• 📊 GBIF Biodiversity Scraper - Global biodiversity occurrence records

💡 Pro Tip: browse the complete ParseForge collection for more open-science scrapers.

---

🆘 Need Help? Open our contact form to request a new scraper, propose a custom data project, or report an issue.

---

⚠️ Disclaimer: this Actor is an independent tool and is not affiliated with, endorsed by, or sponsored by Ensembl, EMBL-EBI, the Wellcome Sanger Institute, or NCBI/dbSNP. All trademarks mentioned are the property of their respective owners. Only publicly available open genome reference data is collected.