EBI Proteins API Scraper

EBI Proteins API Scraper

Scrape protein data from the EBI Proteins API by protein name or organism, up to a million records per run. Each protein comes with its sequence, function, taxonomy, and cross-references. No API key. Export to CSV, JSON, Excel, or XML.

The EBI Proteins API provides detailed protein records, but querying it manually means writing code, handling pagination, and parsing nested JSON. This Actor reads the public API directly, filters by protein name or organism, and returns each match in one flat, consistent schema. No registration, no rate-limit headaches, the protein data you need.

Who uses it	What they scrape EBI Proteins API for
Bioinformaticians	Building local protein databases for sequence analysis
Drug discovery researchers	Gathering protein targets and their functional annotations
Academic labs	Compiling protein datasets for publications or teaching
Data engineers	Feeding protein data into pipelines or knowledge graphs

What it does

This Actor collects protein records from the EBI Proteins API by protein name or organism, and returns each one as a flat row.

• 🔍 Protein name filter: search for proteins by name, e.g. 'insulin' or 'p53'.
• 🧬 Organism filter: restrict results to a specific organism, e.g. 'Homo sapiens'.
• 📊 Flat output: every protein is returned as a single row with all fields, ready for spreadsheets or databases.
• ⚡ High volume: collect up to 1,000,000 proteins in a single run.

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

What you can do with EBI Proteins API data

🧬 Build a protein reference set.

A bioinformatician runs the Actor with an organism filter like 'Escherichia coli' to collect all proteins for a local BLAST database.

💊 Gather drug targets.

A researcher searches for a protein name like 'kinase' to compile a list of potential targets with their sequences and functions.

📚 Support a publication.

An academic lab collects proteins for a specific organism and exports the dataset as CSV for supplementary material.

🔗 Feed a knowledge graph.

A data engineer schedules the Actor to pull protein records and load them into a graph database for relationship mining.

Why choose this scraper

	What you get
No API key	The EBI Proteins API is public; this Actor handles the requests for you.
Flat schema	Nested API responses are flattened into one row per protein, no JSON wrangling.
Scalable	From a single protein to a million, the Actor paginates automatically.
Export ready	Download as CSV, JSON, Excel, or XML for downstream tools.

How it compares

No other Store actor targets EBI Proteins API the same way, so the honest comparison is with the alternatives teams actually weigh.

	EBI Proteins API Scraper	Build it in-house	By hand
Setup	Run it now, zero config	Days of engineering	None, but hours per pull
When EBI Proteins API changes	Maintained for you	You fix it	You re-learn the page
Proxies, retries, anti-bot	Built in	Your problem	Browser only
Output	Fixed JSON schema, CSV/Excel export	Whatever you build	Copy-paste
Cost	Pay per result	Engineering time	Analyst hours

Configure the run

Drive the Actor with a protein name, an organism, or both, and set a maximum number of proteins to collect. Filters are applied by the API as it reads, so only matching records reach your dataset. 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 EBI Proteins API 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 EBI Proteins API 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/ebi-proteins-api-scraper"

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

Troubleshooting

Why am I getting no results?

Verify your protein name or organism. The API may require exact matches or specific formatting. Try a simpler query first, like a common protein name.

The run stops before reaching maxItems.

The API may have returned all available results for your query. Check the run log for the total count, or broaden your filters.

I get an error about invalid input.

Ensure maxItems is an integer between 1 and 1,000,000. Protein and organism should be strings without special characters unless supported by the API.

The output has missing fields for some proteins.

Not all proteins have every annotation. The EBI API returns only available data, so some fields may be null or absent.

The run is slow for large maxItems.

The API paginates, and each request takes time. Reduce maxItems or run the Actor with a higher timeout setting.

FAQ

Question	Answer
Do I need an API key for the EBI Proteins API?	No. The EBI Proteins API is publicly accessible, and this Actor makes the requests without any authentication.
Can I filter by both protein name and organism?	Yes. Provide both fields in the input, and the Actor will return only proteins that match both criteria.
What is the maximum number of proteins I can collect?	You can set maxItems up to 1,000,000. The Actor will paginate through the API until it reaches that number or no more results exist.
What format is the output?	Each protein is returned as a flat JSON object. You can export the dataset as CSV, JSON, Excel, or XML from the Apify platform.
Does this Actor include protein sequences?	Yes, the EBI Proteins API returns the amino acid sequence for each protein, and it is included in the output.
Can I run this on a schedule?	Yes, you can set up a recurring schedule in Apify to collect updated protein data automatically.
Is there a rate limit?	The EBI Proteins API has usage guidelines, but this Actor handles retries and backoff to stay within limits.
What if I get no results?	Check your protein name or organism spelling. The API is case-sensitive for some fields, so try variations.
Can I search for a partial protein name?	The API supports exact and wildcard searches depending on the endpoint. Try using a broader term or check the EBI documentation.
Is this Actor affiliated with EBI?	No, this is an independent tool that uses the public EBI Proteins API. It is not endorsed by the European Bioinformatics Institute.

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🆘 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 European Bioinformatics Institute. 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.