🧬 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.

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.

📊 Data fields

Each record includes: alleleString, ancestralAllele, assemblyName, biotype, canonicalTranscript, chromosome, description, displayName, end, evidence, logicName, mappings, minorAllele, minorAlleleFreq, mode, molecule, mostSevereConsequence, objectType, query, scrapedAt, sequence, sequenceLength, source, species, stableId, start, strand, synonyms, varClass, variantName. These field names come straight from the actor's dataset schema, so what you see here is what lands in your dataset.

🚀 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.

🔗 Recommended Actors

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• 📚 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.

⚠️ 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.

🆘 Need Help?

If you hit a bug, have questions about setup, or need a scraper we haven't built yet, open our contact form or write to parseforge@protonmail.com. We also take on paid custom data projects.

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