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NCBI Gene Database Scraper

Query NCBI Gene through Entrez syntax such as BRCA1[gene] AND human[orgn]. Returns gene symbol, description, organism, chromosome, map location, summary, aliases, and designations. Useful for genomics pipelines, target discovery, and clinical research across model organisms.

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from $7.50 / 1,000 results

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🧫 NCBI Gene Scraper

🚀 Export NCBI Gene records in seconds. Gene IDs, symbols, descriptions, organisms, chromosomes, aliases, and summaries — direct from the public NCBI E-utilities API.

The NCBI Gene Scraper turns the NCBI Entrez E-utilities public endpoint into a clean, structured dataset. It queries the source live, normalizes the response into one row per record, and pushes the result into an Apify dataset you can download or pipe to your warehouse.

Tens of millions of curated gene records across all species in Entrez Gene are covered in a single run, with stable field names and null-safe parsing.

🎯 Target Audience	💡 Primary Use Cases
🧬 Geneticists	Build gene panels from a phenotype query
💊 Pharma	Map drug targets to gene records
🎓 Educators	Generate gene fact sheets
🤖 ML teams	Train biomedical entity linkers

📋 What the NCBI Gene Scraper does

Calls the public NCBI Entrez E-utilities endpoint with the parameters you supply.
Parses the response and flattens each record into a single dataset row.
Casts numeric fields to numbers where applicable for clean spreadsheet imports.
Surfaces rate-limit or upstream errors as a single-row error record instead of crashing.
Exports to every Apify dataset format supported in the UI.

💡 Why it matters. The raw NCBI Entrez E-utilities response is great for API consumers but awkward for spreadsheets and BI tools. This actor normalizes the shape so the data drops straight into pandas, BigQuery, or a Google Sheet.

📊 Data fields

Each record includes: aliases, chromosome, description, gene_id, maptype, ncbi_url, organism, results, scrapedAt, summary, symbol, synonyms. These field names come straight from the actor's dataset schema, so what you see here is what lands in your dataset.

⚠️ Good to Know. This actor calls the public NCBI Entrez E-utilities endpoint with no authentication required. Upstream rate limits apply; if the source returns a limit notice, you will see it as a single error record in your dataset.

🚀 How to use

Click Try for free.
Fill in the input (or leave defaults).
Click Start.
Within seconds, the dataset is ready for download or integration.

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Disclaimer. This actor scrapes only publicly available data. ParseForge is not affiliated with, endorsed by, or sponsored by any of the third-party services referenced. Users are responsible for complying with the target site's terms of service and applicable law. Create a free account w/ $5 credit.

🆘 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.

For faster answers, join our Discord. It's the best place to get support and suggest new actors.

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Query the HUGO Gene Nomenclature Committee database for approved human gene symbols, names, aliases, chromosomal location, gene family, RefSeq, Ensembl, OMIM, UniProt, and external links. Export to JSON, CSV, or Excel for bioinformatics, genomics research, and pharmaceutical pipelines.

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Ensembl Gene Lookup Scraper

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NCBI ClinVar Variant Scraper

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Query NCBI ClinVar for human genetic variants tied to disease. Search by gene symbol, variant ID, or clinical significance and pull variation IDs, gene info, molecular consequence, clinical assertions, and review status. Useful for clinical genomics, variant curation, and research.

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NCBI Bio Datasets

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Query NCBI databases (PubMed, Gene, Protein, SNPs) via the E-utilities API. Search biomedical literature, gene sequences, protein data, and genetic variants — no API key required.

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NCBI dbSNP Variant Scraper

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Search NCBI dbSNP for short genetic variants by gene symbol or rs ID. Returns rs accession, chromosome position, allele info, gene context, and global minor allele frequencies. Useful for GWAS pipelines, variant annotation, population genetics, and pharmacogenomics work.

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ChEMBL Targets Scraper

parseforge/chembl-targets-scraper

Query the ChEMBL target catalog by ID, keyword, organism, or target type. Records include target ChEMBL ID, preferred name, organism, target type, gene symbol, tax ID, components with accession and description, and cross references. Useful for drug discovery research and target review.

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GTEx Gene Expression Scraper

parseforge/gtex-gene-expression-scraper

Profile any gene across human tissues with the GTEx Portal. Resolve a symbol like BRCA1, TP53, or EGFR to its gencode ID, then pull median expression for all 54 tissues with tissue name, median TPM, UBERON ontology ID, and dataset release. Great for target research and expression analysis.

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UniProt Proteins Scraper

parseforge/uniprot-proteins-scraper

Query UniProt with its native syntax such as reviewed=true or organism_id 9606. Returns accession, protein name, organism, gene names, sequence, length, function, keywords, EC numbers, and reference count. Restrict to Swiss-Prot reviewed entries. Useful for proteomics and drug discovery.

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