UniProt Proteins Scraper

UniProt Proteins Scraper

Scrape UniProt protein entries by any query, up to a million per run. Each protein comes with its accession, name, gene, organism, sequence, and functional annotations. No API key. Export to JSON, CSV, Excel, or XML.

UniProt's official API needs a key, has rate limits, and returns deeply nested JSON that you have to flatten yourself. This reads the public UniProtKB search directly, accepts the full UniProt query syntax, and returns each protein as one flat row. Filter to reviewed Swiss-Prot entries only, or pull the whole result set.

Who uses it	What they scrape UniProt for
Bioinformaticians	Building local protein databases for sequence analysis pipelines
Drug discovery researchers	Pulling target protein metadata and sequences for screening
Academic labs	Collecting reviewed Swiss-Prot entries for a specific gene family
Data engineers	Feeding protein data into a warehouse or graph database

What it does

This Actor collects UniProt protein entries by search query and returns each one as a flat row with accession, protein and gene names, organism, sequence, and functional annotations.

• 🔍 Full UniProt query syntax: use reviewed:true, organism_id:9606, gene:insulin, and any other UniProtKB field.
• ✅ Reviewed-only switch: restrict results to Swiss-Prot entries with one checkbox.
• 📊 Flat output: every protein is one row, no nested JSON to parse.
• 📦 Bulk export: collect up to 1,000,000 proteins per run to JSON, CSV, Excel, or XML.

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

What you can do with UniProt data

🧬 Build a protein database.

A bioinformatician runs a query like organism_id:9606 AND reviewed:true to collect all reviewed human proteins into a local database for sequence analysis.

💊 Screen drug targets.

A drug discovery researcher pulls metadata and sequences for a list of target genes to prioritize candidates for screening.

📚 Curate a gene family.

An academic lab collects all Swiss-Prot entries for a specific gene family to compare annotations across species.

🔗 Feed a knowledge graph.

A data engineer exports protein entries with cross-references and keywords to load into a graph database for relationship mining.

Why choose this scraper

	What you get
No API key	The official UniProt API requires registration and rate limits; this reads the public search directly.
Flat schema	Every protein is one row, so you can load it straight into a spreadsheet or database.
Full query syntax	Use any UniProtKB field, from organism_id to reviewed:true, exactly as you would on the website.
Reviewed-only filter	One checkbox restricts results to Swiss-Prot entries, the manually curated gold standard.

How it compares

All three competitors scrape the same UniProt source, but this Actor focuses on a flat, query-driven export with a reviewed-only switch and no per-result pricing.

Feature	ParseForge	UniProt Protein Scraper - Sequences, Genes & Function	UniProt Proteins Scraper - Protein Metadata	Uniprot Scraper
Full UniProt query syntax	Yes	Not listed	Not listed	Not listed
Reviewed-only (Swiss-Prot) filter	Yes	Not listed	Not listed	Yes
Protein sequence in output	Yes	Yes	Not listed	Not listed
Flat row per protein	Yes	Not listed	Not listed	Not listed
No API key required	Yes	Yes	Not listed	Yes
Bulk export up to 1M proteins	Yes	Not listed	Not listed	Not listed

Configure the run

Drive the Actor with a UniProt search query, optionally restrict to reviewed Swiss-Prot entries, and cap the number of proteins per run. The Input tab lists every parameter.

A first run with the defaults:

{
  "maxItems": 10
}

A larger pull:

{
  "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 UniProt Proteins 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 UniProt 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/uniprot-proteins-scraper"

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

Troubleshooting

Why am I getting no results?

Check your query syntax. UniProt queries are case-sensitive for field names. Try a simpler query first, like insulin, then add filters one at a time.

Why did the run stop before reaching my maximum?

The Actor stops when there are no more results matching your query. If you expected more, broaden the query or remove the Reviewed Only restriction.

Why is the run slow?

Large result sets take time to paginate. Reduce the maximum number of proteins, or narrow your query with additional filters.

Why are some fields empty?

Not all UniProt entries have every annotation. Reviewed Swiss-Prot entries are more complete than unreviewed TrEMBL entries. Use the Reviewed Only switch for richer data.

Can I use this for commercial purposes?

UniProt data is freely available under a Creative Commons license. Check the UniProt website for the current license terms.

FAQ

Question	Answer
Do I need a UniProt API key?	No. This Actor reads the public UniProtKB search interface directly, so no registration or key is required.
What query syntax can I use?	The full UniProt query syntax is supported. You can use fields like reviewed:true, organism_id:9606, gene:insulin, and combine them with AND, OR, and NOT.
How do I get only reviewed Swiss-Prot entries?	Set the Reviewed Only checkbox to true, or include reviewed:true in your query. Both produce the same result.
What is the maximum number of proteins I can collect?	You can collect up to 1,000,000 proteins per run. Set the Maximum proteins field to your desired cap.
What output formats are supported?	The Actor exports to JSON, CSV, Excel, and XML. Choose the format when you run it.
Does the Actor return protein sequences?	Yes, the full amino acid sequence is included for each protein, along with accession, names, gene, organism, and functional annotations.
Can I search by gene name?	Yes. Use the gene field in your query, for example gene:insulin, to find proteins associated with that gene.
Can I search by organism?	Yes. Use organism_id with a taxonomy ID, for example organism_id:9606 for human, or organism_name for a text search.
Is the data from UniProtKB or Swiss-Prot?	By default the Actor searches all of UniProtKB, which includes both Swiss-Prot (reviewed) and TrEMBL (unreviewed) entries. Use the Reviewed Only switch to restrict to Swiss-Prot.
How is the data structured?	Each protein is returned as one flat row with fields like accession, protein name, gene, organism, sequence, and annotations. No nested JSON.

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 UniProt Consortium. 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.