UniProt Scraper - Proteins, Genes & Sequences

Scrape the UniProt protein knowledgebase in bulk. Extract accession, protein and gene names, organism, taxonomy, function, PDB cross-references and the full amino-acid sequence to CSV/JSON. No API key, no login.

---

What does the UniProt Scraper do?

This Actor turns UniProt data into a structured dataset. You point it at one organism or metadata only, several queries, it walks the result pages one after another, and it writes one clean row per protein entrie into your dataset — ready to export as JSON, CSV or Excel, or to pull straight from the Apify API.

UniProt publishes UniProtKB through a keyless REST API, and the Actor queries it directly with an explicit field list so each response stays small and predictable. Paging uses the cursor UniProt returns in the Link header rather than an offset, which is the only method that stays consistent across millions of matches. Pagination is followed automatically until it runs out of results, hits your page limit or hits your Max items cap, whichever comes first. Every row is de-duplicated across the whole run, so you are never billed twice for the same protein entrie.

There is no API key, no login and no browser involved. That keeps runs fast and cheap, and it means you can schedule the Actor without worrying about credentials expiring.

Who is it for?

• Bioinformatics and computational-biology teams assembling reference sets.
• Drug-discovery groups pulling target proteins with structures and function.
• AI and ML teams building protein sequence corpora.
• Academic researchers exporting an organism's proteome for analysis.
• Developers adding protein lookup to a research product.

Use cases

• Export every reviewed protein for one organism as a proteome table.
• Pull all kinases with their sequences for a modelling pipeline.
• Collect PDB cross-references to find which targets have solved structures.
• Build a labelled sequence corpus for machine learning.
• Map gene names to canonical accessions for data cleanup.

Why use this UniProt Scraper?

• 🔑 Keyless — no account, no API token, no cookies to paste.
• 📦 22 fields per protein entrie — everything the source exposes, already typed.
• 📄 Real pagination — it walks page after page instead of returning the first screen.
• 🎯 Precise caps — Max items stops the run exactly where you want it, so the bill is predictable.
• 📊 Export anywhere — JSON, CSV, Excel or HTML, plus the Apify API and integrations.
• 💸 Pay per result — you pay for rows you actually receive, with no platform fees to calculate.

What data can you extract?

Every run produces one row per protein entrie, with these fields:

Field	Type	Description
accession	string	Primary UniProt accession
entryName	string	UniProtKB entry name
proteinName	string	Recommended protein name
alternativeNames	string	Alternative names, separated by a pipe
ecNumbers	string	EC numbers, separated by a pipe
geneNames	string	Gene names, separated by a pipe
geneSynonyms	string	Gene synonyms, separated by a pipe
organism	string	Scientific name of the source organism
commonName	string	Common name of the organism when published
taxonId	number	NCBI taxonomy identifier
lineage	string	Taxonomic lineage, separated by a pipe
isReviewed	boolean	True for manually reviewed Swiss-Prot entries
functionText	string	Curated function description when published
sequenceLength	number	Number of amino acids
molecularWeight	number	Molecular weight in daltons
sequence	string	Full amino-acid sequence
pdbIds	string	PDB structure IDs, separated by a pipe
entryUrl	string	UniProt entry page
fastaUrl	string	Direct FASTA download URL
query	string	Search query this row came from
page	number	Result page the entry appeared on
scrapedAt	string	ISO timestamp of extraction

Output example

{
  "accession": "P24941",
  "alternativeNames": "Cell division protein kinase 2 | p33 protein kinase",
  "commonName": "Human",
  "ecNumbers": "2.7.11.22",
  "entryName": "CDK2_HUMAN",
  "entryUrl": "https://www.uniprot.org/uniprotkb/P24941",
  "fastaUrl": "https://rest.uniprot.org/uniprotkb/P24941.fasta",
  "functionText": "Serine/threonine-protein kinase involved in the control of the cell cycle\u2026",
  "geneNames": "CDK2",
  "geneSynonyms": "CDKN2",
  "isReviewed": true,
  "lineage": "Eukaryota | Metazoa | Chordata | Craniata | Vertebrata | Mammalia | Primates | Hominidae | Homo",
  "molecularWeight": 33930,
  "organism": "Homo sapiens",
  "page": 1,
  "pdbIds": "1AQ1 | 1B38 | 1B39 | 1BUH | 1CKP | 1DI8 | 1DM2 | 1E1V | 1E1X | 1E9H \u2026",
  "proteinName": "Cyclin-dependent kinase 2",
  "query": "kinase",
  "scrapedAt": "2026-09-18T09:15:33.902Z",
  "sequence": "MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKEL\u2026",
  "sequenceLength": 298,
  "taxonId": 9606
}

How to use

Option A — one organism

{
  "maxItems": 1000,
  "maxPagesPerSearch": 4,
  "organismId": "9606",
  "reviewedOnly": true,
  "searchQueries": [
    "kinase"
  ]
}

1. Open the Actor and fill in the first field.
2. Set the page limit and Max items to bound the run.
3. Click Start, then export from the Output tab.

Option B — metadata only, several queries

{
  "includeSequence": false,
  "maxItems": 2000,
  "maxPagesPerSearch": 10,
  "reviewedOnly": true,
  "searchQueries": [
    "gene:TP53",
    "insulin"
  ]
}

Everything in the first field is processed independently, so you can batch several targets into one run and split them apart afterwards.

Input parameters

Parameter	Type	Default	Description
searchQueries	array	–	UniProt queries to run, e.
reviewedOnly	boolean	true	Restrict to manually curated Swiss-Prot entries.
organismId	string	–	NCBI taxonomy ID to restrict the search, e.
includeSequence	boolean	true	Include the full sequence string.
maxPagesPerSearch	integer	4	How many result pages to walk for each search.
maxItems	integer	500	Stop after this many entries.
maxConcurrency	integer	2	Parallel requests.
proxyConfiguration	object	{"useApifyProxy": true}	Proxy used to fetch pages.

Tips for best results

• UniProt query syntax works as-is: kinase, gene:TP53, organism_id:9606 all run.
• Reviewed only restricts to Swiss-Prot, the manually curated subset — far smaller and far cleaner.
• Set Organism ID to a taxonomy ID such as 9606 for human or 10090 for mouse.
• The API returns up to 500 entries per request, so large exports need few calls.
• sequence holds the full amino-acid string, so exports get large — cap results if you only need metadata.
• pdbIds tells you at a glance which proteins have solved structures.
• functionText is curated prose and is empty for most unreviewed entries.
• fastaUrl is a direct download link, ready for a bulk fetch step.
• Keep concurrency low — UniProt is a free public service shared by the whole field.
• Pair with the ChEMBL scraper to connect targets to bioactive compounds.

Integrations

Send results straight into the tools you already use: Google Sheets, Slack, Zapier, Make, Airtable or any Webhook. You can also schedule the Actor to run hourly, daily or weekly and have each run append to the same dataset, which is how you build a price or availability history rather than a one-off snapshot.

API usage

Run the Actor and collect results from any language. Replace <YOUR_TOKEN> with your Apify API token.

cURL

curl -X POST "https://api.apify.com/v2/acts/logiover~uniprot-protein-scraper/run-sync-get-dataset-items?token=<YOUR_TOKEN>" \
  -H "Content-Type: application/json" \
  -d '{"maxItems": 1000, "maxPagesPerSearch": 4, "organismId": "9606", "reviewedOnly": true, "searchQueries": ["kinase"]}'

Node.js

import { ApifyClient } from 'apify-client';

const client = new ApifyClient({ token: '<YOUR_TOKEN>' });
const run = await client.actor('logiover/uniprot-protein-scraper').call({"maxItems": 1000, "maxPagesPerSearch": 4, "organismId": "9606", "reviewedOnly": true, "searchQueries": ["kinase"]});
const { items } = await client.dataset(run.defaultDatasetId).listItems();
console.log(items);

Python

from apify_client import ApifyClient

client = ApifyClient('<YOUR_TOKEN>')
run = client.actor('logiover/uniprot-protein-scraper').call(run_input={"maxItems": 1000, "maxPagesPerSearch": 4, "organismId": "9606", "reviewedOnly": true, "searchQueries": ["kinase"]})
for item in client.dataset(run['defaultDatasetId']).iterate_items():
    print(item)

Use with AI agents (MCP)

This Actor is available through the Apify MCP server, so an AI agent can call it as a tool. Point your agent at https://mcp.apify.com and it can run the UniProt Scraper on demand — for example: "Pull the first 500 protein entries from UniProt and summarise what you find." The agent receives the same structured rows you would get from the UI.

FAQ

Do I need a UniProt account or API key?

No. The Actor reads publicly available data only. There is nothing to authenticate and no credentials to rotate.

How many protein entries can I get in one run?

As many as the source exposes. Raise the page limit and Max items together; the run stops at whichever limit it reaches first.

Why did I get fewer rows than I asked for?

The source ran out of protein entries. That is normal for narrow searches — broaden the query or add more targets to one run.

Are results de-duplicated?

Yes. Each protein entrie is emitted once per run, even when it appears on several pages, so you are never billed twice for the same record.

Why are some fields empty?

UniProt does not publish every attribute for every protein entrie. Empty means the source did not supply it, not that extraction failed.

What export formats are supported?

JSON, CSV, Excel, HTML and RSS from the Output tab, plus the Apify API and any integration you connect.

How fast is it?

It is pure HTTP with no browser, so a page of results typically takes a second or two. Raise Max concurrency carefully — the source rate-limits aggressive crawling.

Can I schedule it?

Yes. Use the Apify scheduler to run it on any interval and append each run to the same dataset for time-series analysis.

Does it work behind a proxy?

It uses Apify Proxy automatically. You can switch groups or supply your own proxies in Proxy configuration.

How often does the data change?

UniProt updates continuously. Re-run whenever you need current data; the Actor always reads the live source, never a cache.

Is the output schema stable?

Yes. Field names and types are fixed, so downstream pipelines will not break between runs.

What if the source changes its format?

Open an issue on the Issues tab and it gets fixed. The Actor is actively maintained.

Is it legal?

This Actor reads only publicly available data from UniProt — the same content any visitor or client sees without logging in. It does not bypass authentication, does not collect private data and does not attempt to defeat access controls. You are responsible for how you use the output: respect the source's terms of service, applicable copyright, and data-protection law such as GDPR where personal data is involved. Scraping public data is generally lawful in the EU and the US, but the responsibility for the downstream use of that data sits with you.

Related scrapers

• ChEMBL Scraper — Bioactive compounds and drugs
• PubMed Scraper — Biomedical literature
• Europe PMC Scraper — Abstracts and citations
• PubChem Scraper — Chemical substance data