EBI Proteins API Scraper
Pricing
from $7.50 / 1,000 results
EBI Proteins API Scraper
Collects protein metadata from the EBI Proteins API by protein name, organism, or both. Returns each protein as a flat row with accession, function annotations, and cross-references.
Pricing
from $7.50 / 1,000 results
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ParseForge
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11 days ago
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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.
- ๐ Protein name filter: search for proteins by name, e.g. 'insulin' or 'p53'.
- ๐งฌ Organism filter: restrict results to a specific organism, e.g. 'Homo sapiens'.
- ๐ Flat output: every protein is returned as a single row with all fields, ready for spreadsheets or databases.
- โก 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
๐งฌ 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.
๐ Gather drug targets.
A researcher searches for a protein name like 'kinase' to compile a list of potential targets with their sequences and functions.
๐ Support a publication.
An academic lab collects proteins for a specific organism and exports the dataset as CSV for supplementary material.
๐ 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:
A larger pull:
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
- Create a free Apify account with $5 in credit.
- Open the EBI Proteins API Scraper.
- Set your inputs and any filters, then click Start.
- 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:
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. |
Related actors
Browse the full ParseForge collection for more scrapers.
๐ Need help? Email parseforge@protonmail.com with your run ID, your input, and what you expected.
โ ๏ธ 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.
