uniprot-query

name	uniprot-query
description	Query UniProt database for protein sequences, metadata, and search by criteria. Use this skill when: (1) Looking up protein information by UniProt accession ID, (2) Searching proteins by gene name, organism, function, or disease, (3) Retrieving comprehensive protein metadata including domains, PTMs, and annotations.
license	MIT
category	knowledge-retrieval
tags	["uniprot","protein","database","metadata","sequence"]

UniProt Query

Query the UniProt knowledgebase for comprehensive protein information.

When to Use

• Look up protein by UniProt accession (e.g., P00533 for EGFR)
• Search proteins by gene name, organism, or keywords
• Retrieve protein metadata: function, domains, diseases, PTMs
• Get protein sequences and structural annotations

Workflow

Use Case 1: Protein Lookup by ID

Fetch complete protein information including metadata.

from open_biomed.tools.tool_registry import TOOLS
import requests
import json

# Get protein sequence (existing tool)
tool = TOOLS["protein_uniprot_request"]
proteins, _ = tool.run(accession="P0DTC2")  # SARS-CoV-2 Spike
protein = proteins[0]

# Fetch full metadata from UniProt API
url = f"https://rest.uniprot.org/uniprotkb/P0DTC2?format=json"
response = requests.get(url)
metadata = parse_uniprot_entry(response.json())

See examples/lookup_by_id.py for complete implementation.

Use Case 2: Search by Criteria

Search UniProt by gene name, organism, keywords, or disease.

import requests

base_url = "https://rest.uniprot.org/uniprotkb/search"

# Example queries:
queries = {
    "gene_exact:EGFR AND organism_id:9606": "Human EGFR",
    "gene_exact:S AND organism_id:2697049": "SARS-CoV-2 Spike",
    "keyword:Kinase AND organism_id:9606": "Human kinases",
    "diabetes AND organism_id:9606": "Diabetes-related proteins",
}

params = {
    "query": "gene_exact:EGFR AND organism_id:9606 AND reviewed:true",
    "fields": "accession,gene_primary,protein_name,organism_name,length",
    "format": "json",
    "size": 10
}
response = requests.get(base_url, params=params)

See examples/search_by_criteria.py for complete implementation.

Query Syntax Reference

Field	Example	Description
gene_exact	gene_exact:EGFR	Exact gene name match
gene	gene:BRCA	Gene name (partial match)
organism_id	organism_id:9606	Organism by TaxID
organism	organism:"Homo sapiens"	Organism by name
protein_name	protein_name:kinase	Protein name search
keyword	keyword:Kinase	UniProt keyword
cc_disease	cc_disease:diabetes	Disease association
reviewed	reviewed:true	Swiss-Prot only (curated)

Common Organism IDs: Human (9606), Mouse (10090), SARS-CoV-2 (2697049), E. coli (83333)

Combine queries: Use AND, OR to combine criteria:

• gene_exact:EGFR AND organism_id:9606 AND reviewed:true

Expected Outputs

Metadata JSON (lookup_by_id)

{
  "accession": "P0DTC2",
  "uniProtId": "SPIKE_SARS2",
  "protein": {"name": "Spike glycoprotein"},
  "gene": {"primary": "S", "synonyms": []},
  "organism": {"scientific_name": "...", "taxon_id": 2697049},
  "sequence": {"length": 1273, "mass": 141178},
  "function": ["Attaches the virion to host receptor..."],
  "domains": [{"type": "Domain", "description": "RBD", "location": "319-541"}],
  "keywords": ["Glycoprotein", "Transmembrane", "Viral attachment"],
  "subcellular_location": ["Virion membrane"]
}

Text Report

======================================================================
UNIPROT PROTEIN REPORT
======================================================================
Accession:     P0DTC2
Protein:       Spike glycoprotein
Gene:          S
Organism:      Severe acute respiratory syndrome coronavirus 2
Length:        1273 aa

FUNCTION
Attaches the virion to the cell membrane by interacting with
host receptor ACE2...

DOMAINS
• Domain: BetaCoV S1-NTD (14-303)
• Region: Receptor-binding domain (319-541)

Search Results JSON

{
  "query": "gene_exact:S AND organism_id:2697049",
  "total_results": 10,
  "results": [
    {"accession": "P0DTC2", "gene": "S", "protein_name": "Spike glycoprotein", ...}
  ]
}

Error Handling

Error	Solution
Accession not found	Verify UniProt ID format (e.g., P00533, not EGFR)
No search results	Broaden query, remove reviewed:true, check organism ID
Timeout	Reduce size parameter, simplify query
Rate limited	Wait and retry; UniProt allows 10 requests/second

Available Tools

Tool	Purpose
protein_uniprot_request	Fetch protein sequence by accession (existing)

The workflows in this skill extend the basic tool with full metadata retrieval via UniProt REST API.

References

• references/query_fields.md - Complete query field reference
• references/metadata_fields.md - Available metadata fields
• UniProt API Docs: https://www.uniprot.org/api-documentation