uniprot-query

Research

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.

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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