Skills uniprot-database
🧬

uniprot-database

Safe 🌐 Network access📁 Filesystem access

Query UniProt protein database via REST API

Also available from: davila7

Search protein databases, retrieve sequences, and map identifiers across biological databases. This skill provides direct access to UniProt, the comprehensive protein sequence and functional information resource.

Supports: Claude Codex Code(CC)
🥈 77 Silver
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Test it

Using "uniprot-database". Search for human hemoglobin proteins

Expected outcome:

  • Found 3 reviewed human hemoglobin entries:
  • - P69905 - Hemoglobin subunit alpha (HBA1) - 142 aa
  • - P68871 - Hemoglobin subunit beta (HBB) - 147 aa
  • - P02100 - Hemoglobin subunit epsilon (HBE1) - 147 aa

Using "uniprot-database". Get BRCA1 protein sequence

Expected outcome:

  • P38398 - Breast cancer type 1 susceptibility protein (BRCA1)
  • Organism: Homo sapiens (Human)
  • Length: 1863 amino acids
  • Retrieved in FASTA format for downstream analysis

Using "uniprot-database". Map UniProt to RefSeq

Expected outcome:

  • Mapped 2 UniProt accessions to RefSeq protein IDs:
  • P01308 -> NP_000198.1
  • P04637 -> NP_000537.3

Security Audit

Safe
v4 • 1/17/2026

Legitimate bioinformatics skill providing access to UniProt, the trusted public protein database. All 616 static findings are false positives. The scanner misinterpreted markdown code block delimiters as shell commands and flagged standard HTTP requests to rest.uniprot.org as network activity. No malicious patterns, data exfiltration, or security threats exist in the codebase.

8
Files scanned
7,974
Lines analyzed
2
findings
4
Total audits

Risk Factors

🌐 Network access (6)
scripts/uniprot_client.py:31 scripts/uniprot_client.py:61 scripts/uniprot_client.py:83 references/api_examples.md:12 references/api_examples.md:32 SKILL.md:54
📁 Filesystem access (2)
references/api_examples.md:105 references/api_examples.md:395
Audited by: claude View Audit History →

Quality Score

68
Architecture
100
Maintainability
85
Content
21
Community
100
Security
91
Spec Compliance

What You Can Build

Retrieve protein sequences

Look up protein sequences by gene name or accession number for downstream analysis

Map database identifiers

Convert protein identifiers between UniProt, PDB, RefSeq, and Ensembl formats

Explore protein annotations

Access GO terms, functional descriptions, and domain information for teaching

Try These Prompts

Basic protein search 
Find human insulin proteins in UniProt and return their accessions and sequences in FASTA format
Gene-specific query 
Search for reviewed human BRCA1 proteins and show gene names, organism, and length
ID mapping 
Map these UniProt accessions P01308 and P04637 to their corresponding PDB entries
Complex query 
Find all reviewed human membrane proteins with kinase activity that have PDB structures

Best Practices

  • Use reviewed:true filter for Swiss-Prot entries to ensure data quality
  • Request only needed fields to reduce bandwidth and processing time
  • Implement delays between batch requests to respect API rate limits

Avoid

  • Avoid requesting all fields for large queries; specify needed fields only
  • Do not ignore rate limits; implement proper delays for batch operations
  • Avoid mixing Swiss-Prot and TrEMBL without understanding curation differences

Frequently Asked Questions

What is UniProt?
UniProt is the leading comprehensive protein sequence and functional information database maintained by the European Bioinformatics Institute.
What formats are supported?
FASTA, JSON, TSV, XML, Excel, RDF, TXT, and GFF formats are available for different use cases.
What is the difference between Swiss-Prot and TrEMBL?
Swiss-Prot entries are manually curated and reviewed; TrEMBL entries are computationally predicted annotations.
How many proteins can I retrieve at once?
Search queries return up to 500 results per request; use streaming for larger datasets or pagination.
How long are ID mapping results available?
ID mapping job results are stored for 7 days before being automatically deleted.
Is an API key required?
No API key is required for basic UniProt API usage; the service is free for academic and commercial use.

Developer Details

Author

K-Dense-AI

License

MIT

Repository

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/uniprot-database

Ref

main

File structure

📁 references/

📄 api_examples.md

📄 api_fields.md

📄 id_mapping_databases.md

📄 query_syntax.md

📁 scripts/

📄 uniprot_client.py

📄 EVALUATION_OUTPUT.json

📄 SKILL.md